Patent Publication Number: US-9850539-B2

Title: Biomarkers for the molecular classification of bacterial infection

Description:
CROSS REFERENCE TO RELATED APPLICATION 
     This application is a divisional of U.S. patent application Ser. No. 14/214,853 filed Mar. 15, 2014, which claims priority to U.S. Provisional Application No. 61/788,266, filed Mar. 15, 2013, each of which are incorporated herein by reference in their entireties. 
    
    
     STATEMENT OF GOVERNMENT INTEREST 
     This invention was made with government support under federal grant numbers R01-A1068804, K24-AI093969, 5U01AI066569-05, 3U01AI066569-05S1 awarded by the National Institutes of Health and N66001-09-C-2082 awarded by Defense Advanced Research Projects Agency of the Department of Defense. The U.S. Government has certain rights to this invention. 
    
    
     TECHNICAL FIELD 
     The present invention relates to methods of identifying and treating subjects suffering from bacterial infection. 
     BACKGROUND 
     Septicemia causes substantial morbidity and mortality among patients in the United States, with a rising burden of  Staphylococcus aureus  infection. Although blood cultures are the diagnostic gold standard for blood stream infection (BSI), sensitivity is limited and results are not rapidly available. Such diagnostic delays can extend the time to administration of effective antibiotics, which is an independent risk factor for mortality. Conversely, diagnostic uncertainty also leads to high rates of empiric overtreatment, fueling the burden of antimicrobial resistance. Thus, novel approaches that are faster and more accurate are needed to differentiate between the major pathogens causing sepsis and BSI. 
     Whereas conventional diagnostic approaches have focused on identifying the infecting pathogen, a growing body of evidence suggests that the host&#39;s inflammatory response to the pathogen also represents a potential diagnostic tool. In vitro and In vivo experiments have revealed fundamental differences in host response to Gram-positive and Gram-negative bacterial infection, including significant differences in Toll-like receptor (TLR) signaling and cytokine production. Distinctive gene expression profiles exist for viral, bacterial, and fungal infections in both animal model systems and ex vivo stimulation of human peripheral blood leukocytes. Peripheral blood mononuclear cell (PBMC) gene expression signatures have also been evaluated in humans for a variety of conditions including severe infection, bacterial vs. viral illness, systemic lupus erythematosus, atherosclerosis, and radiation exposure. Taken together, these studies provide strong evidence that global changes in host blood gene expression patterns can be used to differentiate disease states. 
       Staphylococcus aureus  causes a spectrum of human infection. Diagnostic delays and uncertainty lead to treatment delays and inappropriate antibiotic use. Early diagnostic strategies for  S. aureus  BSI could improve patient care by reducing the time required to establish the diagnosis and provide appropriate treatment while avoiding unnecessary anti-MRSA antibiotics. There is a need in the art to have alternative methods for diagnosing and treating patients with bacterial infection, such as sepsis. 
     SUMMARY 
     The present invention is directed to a method of developing a diagnostic assay for identifying and/or classifying a bacterial infection in a subject. The method comprising determining the gene expression levels of at least two biomarkers in a subject infected with bacterial infection, wherein the biomarkers are selected from one or more of Tables 3-17; comparing the gene expression levels of the biomarkers in the subject with the gene expression levels of the biomarkers in a control; identifying factors, wherein each factor comprises differentially expressed biomarkers that have the greatest ability to differentiate between gene expression in the subject and the control; providing a weighted value for the differentially expressed biomarkers within the factor; and determining a relationship between the factor and the bacterial infection using the weighted values of the differentially expressed biomarkers with an algorithm, wherein a relationship between the factor and the bacterial infection is used to develop the diagnostic assay. The method may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a healthy subject. The biomarkers may be selected from Table 8 and Table 10. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.9898. The method may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a subject that has an  Escherichia coli  blood stream infection. The biomarkers may be selected from Table 8 and Table 10. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.8372. The method may distinguish a subject that has an  Escherichia coli  blood stream infection from a healthy subject. The biomarkers may be selected from Table 8 and Table 10. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.9229. The method may distinguish a subject that has a gram positive blood stream infection from a subject that has a gram negative blood stream infection. The biomarkers may be selected from Table 9. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.8503. The method may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a healthy subject. The biomarkers may be selected from Table 7. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.9217. The method may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a healthy subject. The biomarkers may be selected from Tables 3, 4, and 6. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.9522. The method may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a healthy subject. The biomarkers may be selected from Tables 3, 4, 5 and 6. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.9964. The method may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a subject that has an  Escherichia coli  blood stream infection. The biomarkers may be selected from Tables 3, 4, 5 and 6. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.9935. The method may distinguish a subject that has an  Escherichia coli  blood stream infection from a healthy subject. The biomarkers may be selected from Tables 3, 4, 5 and 6. The factor may comprise about 5 to about 250 biomarkers. The relationship may have an AUC value of 0.9484. At least one of the differentially expressed biomarkers may have an increased expression level compared to the control. At least one of the differentially expressed biomarkers may have a decreased expression level compared to the control. At least one of the differentially expressed biomarkers may have an increased expression level compared to the control and at least one of the differentially expressed biomarkers may have a decreased expression level compared to the control. The factor may comprise about 10 biomarkers. The method of any one of the preceding claims, wherein the factor may comprise about 20 biomarkers. The factor may comprise about 50 biomarkers. The factor may comprise about 100 biomarkers. The factor may comprise about 150 biomarkers. The factor may comprise about 200 biomarkers. The factor may comprise about 250 biomarkers. The subject may be a mammal. The subject may be a human. The subject may be a mouse. The biological sample may be selected from the group consisting of tissues, cells, biopsies, blood, lymph, serum, plasma, urine, saliva, mucus, and tears. The sample may comprise plasma. The RNA gene expression levels may be determined. 
     The present invention is directed to method of identifying and treating a bacterial infection in a subject. The method comprises performing the diagnostic assay as developed by the methods, as described above, and administrating an antibacterial therapy to the subject diagnosed with a bacterial infection. The method further comprising quantifying the amount of at least one biomarker present in a biological sample derived from the subject, wherein the biomarker may be associated with a factor. At least one of the differentially expressed biomarkers may have an increased expression level compared to the control. At least one of the differentially expressed biomarkers may have a decreased expression level compared to the control. At least one of the differentially expressed biomarkers may have an increased expression level compared to the control and at least one of the differentially expressed biomarkers may have a decreased expression level compared to the control. The factor may comprise about 10 biomarkers. The method of any one of the preceding claims, wherein the factor may comprise about 20 biomarkers. The factor may comprise about 50 biomarkers. The factor may comprise about 100 biomarkers. The factor may comprise about 150 biomarkers. The factor may comprise about 200 biomarkers. The factor may comprise about 250 biomarkers. The subject may be a mammal. The subject may be a human. The subject may be a mouse. The biological sample may be selected from the group consisting of tissues, cells, biopsies, blood, lymph, serum, plasma, urine, saliva, mucus, and tears. The sample may comprise plasma. The RNA gene expression levels may be determined. 
     The present invention is also directed towards a method of identifying and treating a subject suspected of having a bacterial blood stream infection (BSI). The method comprises determining gene expression levels of at least two biomarkers in a peripheral blood cell sample of the subject, wherein the biomarkers are selected from any one of Tables 3-17; comparing the gene expression levels of the at least two biomarkers to standard gene expression levels wherein the standard gene expression levels correspond to the gene expression levels for the biomarkers in a control; identifying the subject as having a bacterial BSI if the gene expression levels of the biomarkers are different than the standard gene expression levels; and administering an effective amount of antibiotic therapy to treat the subject identified as having a bacterial BSI. The bacterial BSI may be  Staphylococcus aureus  BSI or  Escherichia coli  BSI. The bacterial blood stream infection may be  S. aureus  BSI and the biomarkers may be selected from one of Tables 3-8 or 10. At least about 2 to about 250 biomarkers may be selected from one of Tables 3-8 or 10. The bacterial blood stream infection may be  E. coli  BSI and the biomarkers may be selected from one of Tables 3-6, 8 or 10. At least about 2 to about 250 biomarkers may be selected from one of Tables 3-6, 8 or 10. The control may be a healthy subject. At least one of the biomarkers may have an increased gene expression level compared to the control. At least one of the biomarkers may have a decreased gene expression level compared to the control. At least one of the biomarkers may have an increased gene expression level compared to the control and at least one of the biomarkers has a decreased gene expression level compared to the control. The gene expression levels of about 10 biomarkers may be determined. The gene expression levels of about 20 biomarkers may be determined. The gene expression levels of about 50 biomarkers may be determined. The gene expression levels of about 100 biomarkers may be determined. The gene expression levels of about 150 biomarkers may be determined. The gene expression levels of about 200 biomarkers may be determined. The gene expression levels of about 250 biomarkers may be determined. The subject may be a mammal. The subject may be a human. The subject may be a mouse. The biological sample may be selected from the group consisting of tissues, cells, biopsies, blood, lymph, serum, plasma, urine, saliva, mucus, and tears. The sample may comprise plasma. The RNA gene expression levels may be determined. 
     The present invention is directed to method of distinguishing and treating  Staphylococcus aureus  blood stream infection (BSI) from  Escherichia coli  BSI in a subject suspected of having a bacterial infection. The method comprises determining gene expression levels of at least two biomarkers in a peripheral blood cell sample of the subject, wherein the biomarkers are selected from any one of Tables 8 and 10 or Tables 3-6; comparing the gene expression levels of the at least two biomarkers to standard gene expression levels wherein the standard gene expression levels correspond to the gene expression levels for the biomarkers in a control; identifying the subject as having a  S. aureus  BSI if the gene expression levels of the biomarkers are different than the standard gene expression levels and identifying the subject as having an  E. coli  BSI if the gene expression levels of the biomarkers are the same as the standard gene expression levels; and administering an effective amount of appropriate antibacterial therapy to treat the subject identified as having a  S. aureus  BSI or  E. coli . The control may be a subject having an  E. coli  BSI. At least one of the biomarkers may have an increased gene expression level compared to the control. At least one of the biomarkers may have a decreased gene expression level compared to the control. At least one of the biomarkers may have an increased gene expression level compared to the control and at least one of the biomarkers has a decreased gene expression level compared to the control. The gene expression levels of about 10 biomarkers may be determined. The gene expression levels of about 20 biomarkers may be determined. The gene expression levels of about 50 biomarkers may be determined. The gene expression levels of about 100 biomarkers may be determined. The gene expression levels of about 150 biomarkers may be determined. The gene expression levels of about 200 biomarkers may be determined. The gene expression levels of about 250 biomarkers may be determined. The subject may be a mammal. The subject may be a human. The subject may be a mouse. The biological sample may be selected from the group consisting of tissues, cells, biopsies, blood, lymph, serum, plasma, urine, saliva, mucus, and tears. The sample may comprise plasma. The RNA gene expression levels may be determined. 
     The present invention is directed to method of distinguishing and treating a gram positive bacterial infection from a gram negative bacterial infection in a subject suspected of having a bacterial infection. The method comprises determining gene expression levels of at least two biomarkers in a peripheral blood cell sample of the subject, wherein the biomarkers are selected from Table 9; comparing the gene expression levels of the at least two biomarkers to standard gene expression levels wherein the standard gene expression levels correspond to the gene expression levels for the biomarkers in a control; identifying the subject as having a gram positive bacterial infection if the gene expression levels of the biomarkers are different than the standard gene expression levels in a control; and administering an effective amount of appropriate antibacterial therapy to treat the subject identified as a gram positive bacterial infection. The gram positive bacterial infection may be  Staphylococcus aureus . The control may be a subject having a gram negative bacterial infection. The gram negative bacterial infection may be  Escherichia coli . At least one of the biomarkers may have an increased gene expression level compared to the control. At least one of the biomarkers may have a decreased gene expression level compared to the control. At least one of the biomarkers may have an increased gene expression level compared to the control and at least one of the biomarkers has a decreased gene expression level compared to the control. The gene expression levels of about 10 biomarkers may be determined. The gene expression levels of about 20 biomarkers may be determined. The gene expression levels of about 50 biomarkers may be determined. The gene expression levels of about 100 biomarkers may be determined. The gene expression levels of about 150 biomarkers may be determined. The gene expression levels of about 200 biomarkers may be determined. The gene expression levels of about 250 biomarkers may be determined. The subject may be a mammal. The subject may be a human. The subject may be a mouse. The biological sample may be selected from the group consisting of tissues, cells, biopsies, blood, lymph, serum, plasma, urine, saliva, mucus, and tears. The sample may comprise plasma. The RNA gene expression levels may be determined. 
     The present invention is directed method of identifying and treating a subject suspected of having a methicillin-resistant  Staphylococcus aureus  (MRSA) infection. The method comprises determining gene expression levels of at least one biomarker in a peripheral blood cell sample of the subject wherein the biomarker is selected from Table 11; comparing the gene expression levels of the biomarker to a standard gene expression level of the biomarker, wherein the standard gene expression level corresponds to the gene expression level of the biomarker in a subject that has a methicillin-sensitive  Staphylococcus aureus  (MSSA) infection; identifying the subject as having MRSA if the gene expression levels of the biomarkers are different than the standard gene expression levels; and administering an effective amount of an antibiotic therapy to treat the subject identified as having MRSA. The antibiotic therapy may be mupirocine or vancomycin. At least one of the biomarkers may have an increased gene expression level compared to the control. At least one of the biomarkers may have a decreased gene expression level compared to the control. At least one of the biomarkers may have an increased gene expression level compared to the control and at least one of the biomarkers has a decreased gene expression level compared to the control. The gene expression levels of about 10 biomarkers may be determined. The gene expression levels of about 20 biomarkers may be determined. The gene expression levels of about 50 biomarkers may be determined. The gene expression levels of about 100 biomarkers may be determined. The gene expression levels of about 150 biomarkers may be determined. The gene expression levels of about 200 biomarkers may be determined. The gene expression levels of about 250 biomarkers may be determined. The subject may be a mammal. The subject may be a human. The subject may be a mouse. The biological sample may be selected from the group consisting of tissues, cells, biopsies, blood, lymph, serum, plasma, urine, saliva, mucus, and tears. The sample may comprise plasma. The RNA gene expression levels may be determined. 
     The present invention is also directed to a method for determining the efficacy of an anti-bacterial treatment regime in a subject. The method comprises determining a baseline gene expression level for at least one biomarker selected from Tables 3-17; administering to the subject a therapeutic regimen; and redetermining the gene expression level of the at least one biomarker in the subject. A difference in the gene expression level of the at least one biomarker indicates the efficacy of the therapeutic regimen. At least one of the biomarkers may have an increased gene expression level compared to the control. At least one of the biomarkers may have a decreased gene expression level compared to the control. At least one of the biomarkers may have an increased gene expression level compared to the control and at least one of the biomarkers has a decreased gene expression level compared to the control. The gene expression levels of about 10 biomarkers may be determined. The gene expression levels of about 20 biomarkers may be determined. The gene expression levels of about 50 biomarkers may be determined. The gene expression levels of about 100 biomarkers may be determined. The gene expression levels of about 150 biomarkers may be determined. The gene expression levels of about 200 biomarkers may be determined. The gene expression levels of about 250 biomarkers may be determined. The subject may be a mammal. The subject may be a human. The subject may be a mouse. The biological sample may be selected from the group consisting of tissues, cells, biopsies, blood, lymph, serum, plasma, urine, saliva, mucus, and tears. The sample may comprise plasma. The RNA gene expression levels may be determined. 
     The present invention is also directed to a composition of matter comprising (a) a probe array for determining a biomarker level in a sample, the array comprising of a plurality of probes that hybridizes to one or more biomarkers selected from Tables 3-17; or (b) a kit for determining a biomarker level in a sample, comprising the probe array of (a) and instructions for carrying out the determination of biomarker expression level in the sample. The composition may further comprise a solid support with the plurality of probes attached thereto. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  shows a schematic of derivation and validation cohorts. 
         FIG. 2  shows that murine  S. aureus  classifier accurately identifies  S. aureus  infection under a variety of conditions. Conditions represented include different murine hosts (A), bacterial genetic backgrounds (B), and time from inoculation (C). Animals with  S. aureus  infection are depicted by a red “x”. Uninfected control mice are depicted by black circles. 
         FIG. 3  shows that the murine  S. aureus  classifier differentiates  S. aureus  from  E. coli  infection. (A) Inbred mice were tested under three conditions: uninfected controls (black circles),  S. aureus  infected (red “x”), and  E. coli  infected (blue triangles). The y-axis represents the predicted probability that a given animal was infected with  S. aureus . (B) The murine  S. aureus  classifier is validated in outbred CD-1 mice where it differentiates  S. aureus  infection from  E. coli  infection and uninfected controls. 
         FIG. 4  shows the performance of the human  S. aureus  classifier. (A) The human  S. aureus  classifier differentiates  S. aureus  BSI from both uninfected controls and  E. coli  BSI. (B) A separate classifier was generated using only  S. aureus  and  E. coli -infected human subjects and tested using leave-one-out cross-validation. 
         FIG. 5  shows the projection of the mouse  S. aureus  classifier onto human subjects. The murine  S. aureus  classifier identifies humans with  S. aureus  BSI, but does not differentiate  S. aureus  from  E. coli  BSI. 
         FIG. 6  shows validation in an independent human cohort. (A) The murine  S. aureus  classifier differentiates between  S. aureus  infection and healthy. (B) The human  S. aureus  classifier differentiates between  S. aureus  infection and healthy. 
         FIG. 7  shows bacterial challenge experiments. (A) Survival curves for A/J and C57BL/6J mice following an intra-peritoneal infection with  S. aureus  (16107 CFU/g) or  E. coli  (66104 CFU/g). Principal Components Analysis plots of the samples in the dataset. Samples are colored by infection status and pathogen. (B)  S. aureus  infection by time after inoculation (n=10 animals/time point). (C)  E. coli  infection by time after inoculation (n=10 animals/time point). (D) PCA differentiated by pathogen. 
         FIG. 8  shows heat maps of genes contributing to the murine  S. aureus  classifier. (A) Genes within the top five factors contributing to the murine  S. aureus  classifier were identified and ranked by p-value after Bonferroni correction. A subset of genes (393 after removing duplicates) is depicted here, stratified by pathogen. (B) The same genes depicted in part (A) are categorized first pathogen and then by time since infection. 
         FIG. 9  shows a Venn diagram demonstrating the number of overlapping probes in each murine experimental group pairwise comparison. Probes were included that had significantly different levels of expression after Bonferroni correction. 
         FIGS. 10A-10P  show that sixteen murine factors independently associated with  S. aureus  infection projected onto healthy controls (left panel, black circles), animals with  E. coli  infection (middle panel, blue triangles), and animals with  S. aureus  infection (right panel, red “x”). The y-axis represents the factor score. 
         FIG. 11  shows that a factor-based classifier distinguishes MRSA from MSSA infection in mice. An ROC curve is shown for this classification. 
         FIG. 12  shows Venn diagram demonstrating the number of overlapping probes in each human experimental group pairwise comparison. Probes were included that had significantly different levels of expression after Bonferroni correction. No probes met this cutoff for the  S. aureus  vs.  E. coli  comparison. 
         FIGS. 13A-13S  show seventeen human factors independently associated with  S. aureus  BSI projected onto healthy controls (left panel, black circles), subjects with  E. coli  BSI (middle panel, blue triangles), and subjects with  S. aureus  BSI (right panel, red “x”). The y-axis represents the factor score. 
         FIG. 14  shows heat map of genes contributing to the human  S. aureus  classifier. Genes within the top two factors contributing to the human  S. aureus  classifier were identified and ranked by p-value after Bonferroni correction. A subset of genes (86 after removing duplicates) is depicted here, stratified by pathogen. 
     
    
    
     DETAILED DESCRIPTION 
     The present disclosure provides biomarkers useful for identifying and/or classifying a bacterial infection a subject.  S. aureus  and  Escherichia coli  were used as prototypical Gram-positive and Gram-negative bacteria due to their prevalence and clinical relevance. Host gene expression was measured in mice with bacterial infection across multiple conditions. From these data, a molecular classifier was derived for  S. aureus  infection in inbred mice and validated in a cohort of outbred mice. Host gene expression data from a well-characterized cohort of septic human subjects was used to identify a molecular classifier that accurately distinguished  S. aureus  BSI from  E. coli  BSI or uninfected controls. Murine and human  S. aureus  classifiers exhibited significant similarity particularly in comparing  S. aureus  infection to the healthy state. Furthermore, both murine and human classifiers were validated in an independent human cohort. The present disclosure demonstrates that the in vivo host response to Gram-positive infections is conserved from mouse to human and can be harnessed as a novel diagnostic strategy in patients with bacterial sepsis. 
     This study takes significant steps forward on multiple levels in the ongoing effort to understand this pathogen; the host response to it; and identify new diagnostic and therapeutic avenues. A diagnostic modality capable of differentiating infection from health across species is described. Host gene expression classifiers can differentiate infection due to  S. aureus  from that of  E. coli  but this effect is less pronounced in the complex human host. The approach described here also affords great insight into the conserved and disparate pathways utilized by mice and humans in response to these infections. Evidence to support the paradigm shift in how diagnostics are thought about is provided as well as new areas for research into the pathways that subserve sepsis pathophysiology have been identified. 
     For the purposes of promoting an understanding of the principles of the present disclosure, reference will now be made to preferred embodiments and specific language will be used to describe the same. It will nevertheless be understood that no limitation of the scope of the disclosure is thereby intended, such alteration and further modifications of the disclosure as illustrated herein, being contemplated as would normally occur to one skilled in the art to which the disclosure relates. 
     Articles “a” and “an” are used herein to refer to one or to more than one (i.e. at least one) of the grammatical object of the article. By way of example, “an element” means at least one element and can include more than one element. 
     Unless otherwise defined, all technical terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. 
     1. Definitions 
     The terms “comprise(s),” “include(s),” “having,” “has,” “can,” “contain(s),” and variants thereof, as used herein, are intended to be open-ended transitional phrases, terms, or words that do not preclude the possibility of additional acts or structures. The singular forms “a,” “and” and “the” include plural references unless the context clearly dictates otherwise. The present disclosure also contemplates other embodiments “comprising,” “consisting of” and “consisting essentially of,” the embodiments or elements presented herein, whether explicitly set forth or not. 
     For the recitation of numeric ranges herein, each intervening number there between with the same degree of precision is explicitly contemplated. For example, for the range of 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the number 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 are explicitly contemplated. 
     Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. In case of conflict, the present document, including definitions, will control. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the present invention. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting. 
     “About” is used to provide flexibility to a numerical range endpoint by providing that a given value may be “slightly above” or “slightly below” the endpoint without affecting the desired result. 
     The term “antibiotic” as used herein refers to an agent that either kills or inhibits the growth of a microorganism. Antibiotics may include beta-lactam antibiotics, such as penicillin, which are produced by fungi in the genus  Penicillium , cephalosporins, carbapenems, aminoglycosides, sulfonamides, quinolones, oxazolidinones, fluoroquinolone, marcolide, ketolide, rifampin, chloramphenicol, glycopeptide, and trimethoprim. The antibiotics may be ciproflaxacin, levofloxacin, gatifloxacin, moxifloxacin, ofloxacin, norflaxacin, erythromycin, azithromycin, clarithromycin, telithromycin, rifamipin, tetracycline, minocycline, chloramphenicol, gentamicin, linezolid, penicillin, amoxicillin, ceftriaxone, imipenem, vancomycin, teicoplainin, sulfamethoxazole, isoniazid, ethambutol, para-aminosalicylic acid, mupicorin, or cycloserine. 
     The “area under curve” or “AUC” refers to area under a ROC curve. AUC under a ROC curve is a measure of accuracy. An area of 1 represents a perfect test, whereas an area of 0.5 represents an insignificant test. A preferred AUC may be at least approximately 0.700, at least approximately 0.750, at least approximately 0.800, at least approximately 0.850, at least approximately 0.900, at least approximately 0.910, at least approximately 0.920, at least approximately 0.930, at least approximately 0.940, at least approximately 0.950, at least approximately 0.960, at least approximately 0.970, at least approximately 0.980, at least approximately 0.990, or at least approximately 0.995. 
     As used herein, the term “biomarker” refers to a naturally occurring biological molecule present in a subject at varying concentrations useful in identifying and/or classifying a disease or a condition, such as a bacterial infection. For example, the biomarker can be a gene that is upregulated or downregulated in a subject that has a disease, such as a bacterial infection. The biomarker can include genes, proteins, nucleic acids, ribonucleic acids, or a polypeptide used as an indicator or marker for bacterial infection. In some embodiments, the biomarker is a gene. In one embodiment where the bacterial infection comprises  S. aureus , the biomarker is selected from the group consisting of the biomarkers provided in Tables 3-17, and combinations thereof. In another embodiment where the bacterial infection comprises  E. coli , the biomarker is selected from the group consisting of the biomarkers provided in Tables 3-17, and combinations thereof. 
     As used herein, the term “bacterial infection” refers to those disease states characterized by the presence of a pathogenic bacteria. Such bacteria may be gram-positive or gram-negative. Examples of gram-positive bacteria include, but are not limited to,  S. aureus . Examples of gram-negative bacteria include, but are not limited to,  E. coli . A bacterial infection may be sepsis. 
     As used herein, the term “factor” refers to a group of co-expressed genes. A factor becomes a term in binary regression model to distinguish or predict subjects with and without infection, or distinguish the type of infection 
     “Sample,” “test sample,” “specimen,” “sample from a subject,” and “patient sample” as used herein may be used interchangeable and may be a sample of blood, tissue, urine, serum, plasma, amniotic fluid, cerebrospinal fluid, placental cells or tissue, endothelial cells, leukocytes, or monocytes. The sample can be used directly as obtained from a patient or can be pre-treated, such as by filtration, distillation, extraction, concentration, centrifugation, inactivation of interfering components, addition of reagents, and the like, to modify the character of the sample in some manner as discussed herein or otherwise as is known in the art. 
     As used herein, the term “subject” and “patient” are used interchangeably herein and refer to both human and nonhuman animals. The term “nonhuman animals” of the disclosure includes all vertebrates, e.g., mammals and non-mammals, such as nonhuman primates, sheep, dog, cat, horse, cow, chickens, amphibians, reptiles, and the like. Preferably, the subject is a human patient that has a bacterial infection. 
     The term “biological sample” as used herein includes, but is not limited to, a sample containing tissues, cells, and/or biological fluids isolated from a subject. Examples of biological samples include, but are not limited to, tissues, cells, biopsies, blood, lymph, serum, plasma, urine, saliva, mucus and tears. In one embodiment, the biological sample is a blood sample (such as a plasma sample). A biological sample may be obtained directly from a subject (e.g., by blood or tissue sampling) or from a third party (e.g., received from an intermediary, such as a healthcare provider or lab technician). 
     Any cell type, tissue, or bodily fluid may be utilized to obtain a sample. Such cell types, tissues, and fluid may include sections of tissues such as biopsy and autopsy samples, frozen sections taken for histologic purposes, blood (such as whole blood), plasma, serum, sputum, stool, tears, mucus, saliva, bronchoalveolar lavage (BAL) fluid, hair, skin, red blood cells, platelets, interstitial fluid, ocular lens fluid, cerebral spinal fluid, sweat, nasal fluid, synovial fluid, menses, amniotic fluid, semen, etc. Cell types and tissues may also include lymph fluid, ascetic fluid, gynecological fluid, urine, peritoneal fluid, cerebrospinal fluid, a fluid collected by vaginal rinsing, or a fluid collected by vaginal flushing. A tissue or cell type may be provided by removing a sample of cells from an animal, but can also be accomplished by using previously isolated cells (e.g., isolated by another person, at another time, and/or for another purpose). Archival tissues, such as those having treatment or outcome history, may also be used. Protein or nucleotide isolation and/or purification may not be necessary. 
     “Sepsis” as used herein is a condition characterized by a whole-body inflammatory state that is triggered by either a proven (on the basis of sampling or radiology) or probable (considering the patient&#39;s clinical presentation, white cell count, CRP, radiology) infection. The infection may be caused by bacteria, virus or fungi. Triggers of sepsis include pneumonia, such as ventilator-associated pneumonia, abdominal infection, kidney infection, and bloodstream infection. The body may develop this inflammatory response by the immune system to microbes in the blood, urine, lungs, skin, or other tissues. A lay term for sepsis is blood poisoning, also used to describe septicaemia. Septicaemia is a related medical term referring to the presence of pathogenic organisms in the bloodstream, leading to sepsis. 
     Symptoms related to the provoking infection, sepsis is characterized by presence of acute inflammation present throughout the entire body, and is, therefore, frequently associated with fever and elevated white blood cell count (leukocytosis) or low white blood cell count (leukopenia) and lower-than-average temperature, and vomiting. The modern concept of sepsis is that the host&#39;s immune response to the infection causes most of the symptoms of sepsis, resulting in hemodynamic consequences and damage to organs. This immunological response causes widespread activation of acute-phase proteins, affecting the complement system and the coagulation pathways, which then cause damage to the vasculature as well as to the organs. Various neuroendocrine counter-regulatory systems are then activated as well, often compounding the problem. Even with immediate and aggressive treatment, this may progress to multiple organ dysfunction syndrome and eventually death. 
     “Subject” and “patient” as used herein interchangeably refers to any vertebrate, including, but not limited to, a mammal (e.g., cow, pig, camel, llama, horse, goat, rabbit, sheep, hamsters, guinea pig, cat, dog, rat, and mouse, a non-human primate (for example, a monkey, such as a cynomolgous or rhesus monkey, chimpanzee, etc.) and a human). In some embodiments, the subject may be a human or a non-human. The subject or patient may be undergoing other forms of treatment. 
     As used herein, “treatment,” “therapy” and/or “therapy regimen” refer to the clinical intervention made in response to a disease, disorder or physiological condition manifested by a patient or to which a patient may be susceptible. The aim of treatment includes the alleviation or prevention of symptoms, slowing or stopping the progression or worsening of a disease, disorder, or condition and/or the remission of the disease, disorder or condition. In certain embodiments, the treatment comprises anti-bacterial therapy, such as the administration of antibiotics. 
     The term “effective amount” or “therapeutically effective amount” refers to an amount sufficient to effect beneficial or desirable biological and/or clinical results. 
     2. Factors and Biomarkers for Bacterial Infection 
     One aspect of the present disclosure provides biomarkers useful for the identification and/or classification of a bacterial infection. In one embodiment, the present disclosure provides biomarkers that are differentially expressed, such as upregulated, down-regulated, or disregulated in a bacterial infection, as compared to normal populations who do not have the condition, such a bacterial infection. 
     In some embodiments, the bacterial infection comprises a gram-positive bacteria, such as  S. aureus . In those embodiments where the bacterial infection comprises  S. aureus , the biomarker is selected from the group consisting of the biomarkers provided in Tables 3-17, and combinations thereof. In other embodiments, the bacterial infection comprises a gram-negative bacteria, such as  E. coli . In those embodiments where the bacterial infection comprises  E. coli , the biomarker is selected from the group consisting of the biomarkers provided in Tables 3-17, and combinations thereof. 
     In some embodiments, the biomarkers are selected from one or more biomarkers that are up-regulated, down-regulated or over-expressed in a subject suffering from a bacterial infection. 
     In some specific embodiments, the biomarkers are selected from one or more biomarkers up-regulated, down-regulated or over-expressed more than 50-fold, 40-fold, 30-fold, 20-fold, 15-fold, 10-fold, 9-fold, 8-fold, 7-fold, 6-fold, 5-fold, 4-fold, 3-fold, 2-fold, or 1-fold in a subject suffering from a bacterial infection, when compared to a control. In some embodiments, the biomarker comprises one or more biomarkers found in Tables 3-17, wherein the up-regulation, down-regulating or over-expression of one or more of the biomarker in the subject&#39;s biological sample, when compared to a control, indicates that the subject is suffering from a bacterial infection comprising  S. aureus . In other embodiments, the biomarker comprises one or more biomarkers found in Tables 3-17, wherein the up-regulation, down-regulation, or over-expression of one or more of the biomarkers indicates the subject is suffering from a bacterial infection comprising  E. coli.    
     In some embodiments, at least about one of the differentially expressed biomarkers may have an increased expression level compared to the control. In some embodiments, at least about one of the differentially expressed biomarkers may have a decreased expression level compared to the control. In some embodiments, at least about one of the differentially expressed biomarkers may have an increased expression level compared to the control and at least about one of the differentially expressed biomarkers may have a decreased expression level compared to the control. 
     3. Methods Using Biomarkers of the Present Disclosure 
     The present disclosure describes how different hosts respond differently to  S. aureus  than to  E. coli  infection in a quantifiable way, providing a new diagnostic avenue. Bayesian sparse factor modeling and penalized binary regression were used to define peripheral blood gene-expression classifiers of murine and human  S. aureus  infection. The murine-derived classifier distinguished  S. aureus  infection from healthy controls and  Escherichia coli -infected mice across a range of conditions (mouse and bacterial strain, time post infection) and was validated in outbred mice (AUC&gt;0.97). A  S. aureus  classifier derived from a cohort of 94 human subjects distinguished  S. aureus  blood stream infection (BSI) from healthy subjects (AUC 0.99) and  E. coli  BSI (AUC 0.84). Murine and human responses to  S. aureus  infection share common biological pathways, allowing the murine model to classify  S. aureus  BSI in humans (AUC 0.84). Both murine and human  S. aureus  classifiers were validated in an independent human cohort (AUC 0.95 and 0.92, respectively). The approach described here lends insight into the conserved and disparate pathways utilized by mice and humans in response to these infections. Furthermore, this study advances the understanding of  S. aureus  infection; the host response to it; and identifies new diagnostic and therapeutic avenues. 
     A series of genes or biomarkers may be selected from Tables 3-17 and optimized for diagnosis. The number of genes may be at least 1 gene, at least 5 genes, at least 10 genes, at least 25 genes, at least 30 genes, at least 35 genes, at least 40 genes, at least 45 genes, at least 50 genes, at least 55 genes, at least 60 genes, at least 65 genes, at least 70 genes, at least 75 genes, at least 80 genes, at least 85 genes, at least 90 genes, at least 95 genes, at least 100 genes, at least 125 genes, at least 150 genes, at least 175 genes, at least 200 gene, or at least 250 genes selected from Tables 3-17. RNA probes may be developed for the selected genes. A patient sample may be obtained and examined. For example, RNA may be examined after extraction from the sample or directed from the sample without extraction. The RNA may be measured by PCR or another RNA detection platform. The RNA expression may be measure and compared to control level for these selected genes. An algorithm may be used to produce a probability or score. Cut-off values or scores may be established and used to make a definitive diagnosis. For example, if the patient&#39;s gene expression levels are above the cut-off value or score, the patient is diagnosed as having infection. After the diagnosis is made, the subject may be treated for the infection. 
     In one embodiment, the present disclosure provides a method for identifying and/or classifying a bacterial infection in a subject comprising, consisting of, or consisting essentially of: 
     (a) determining a biomarker expression profile (expression level) in a biological sample from the subject; 
     (b) characterizing the subject&#39;s biomarker profile; and 
     (c) comparing the subject&#39;s biomarker profile with the biomarker profile of a control from subjects not suffering from a bacterial infection (e.g., a healthy subject); and 
     (d) administering an appropriate ant-bacterial therapy if one or more of the biomarkers are upregulated, down-regulated or overexpressed. 
     In one embodiment, the method further includes obtaining the biological sample from the subject. In one embodiment, the identification and/or classification of a condition such as a bacterial infection can be determined by comparing the subjects biomarker profile to a reference biomarker profile, such as one that corresponds to biological samples obtained from a normal population (e.g., healthy population) that do not have a condition such as a bacterial infection, or that corresponds to biological samples obtained from a population that have a condition such as a bacterial infection. Optionally, the reference profile comprises multiple biomarker expression profiles, with each corresponding to a type of a condition such as a bacterial infection with a gram-negative or gram-positive bacteria. 
     In some embodiments, the present disclosure provides methods for identifying and/or classifying a condition such as bacterial infection by characterizing a biomarker found in Tables 3-17. 
     4. Methods of Developing a Diagnostic Assay 
     The present invention is directed to a method of developing a diagnostic assay for identifying and/or classifying a bacterial infection in a subject. The method comprising determining the gene expression levels of at least about two biomarkers in a subject infected with bacterial infection, wherein the biomarkers are selected from one or more of the top 200 genes of mouse factors 7, 15, 23, and 26, human factors 4, 20, 40, and 74, as shown in Tables 3-10; genes discriminating infection due to MRSA or MSSA, as shown in Table 11, a gene from the 50 most significant biological pathways arising from the pairwise comparisons, as shown in Tables 12-16, or one of the genes in common between mice and humans, as shown in Table 17. The method comprises comparing the gene expression levels of the biomarkers in the subject with the gene expression levels of the biomarkers in a control; identifying factors, wherein each factor comprises differentially expressed biomarkers that have the greatest ability to differentiate between gene expression in the subject and the control; providing a weighted value for the differentially expressed biomarkers within the factor; and determining a relationship between the factor and the bacterial infection using the weighted values of the differentially expressed biomarkers with an algorithm, wherein a relationship between the factor and the bacterial infection is used to develop the diagnostic assay. 
     The diagnostic assay may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a healthy subject. The biomarkers may be selected from human factor 20 (56 genes) and/or human factor 74 (137 genes), which are shown in Tables 8 and 10, respectively. The factor may comprise about 1 to about 193 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, or at least about 193 of the biomarkers listed in Tables 8 and 10. The relationship may have an AUC value of about 0.9500 to about 0.9999. For example, the AUC value may be at least about 0.9500, at least about 0.9550, at least about 0.9600, at least about 0.9650, at least about 0.9750, at least about 0.9800, at least about 0.9850, at least about 0.9860, at least about 0.9870, at least about 0.9880, at least about 0.9885, at least about 0.9890, at least about 0.9898, at least about 0.9900, or at least about 0.9999. The relationship may have an AUC value of at least about 0.9898. 
     The diagnostic assay may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a subject that has an  Escherichia coli  blood stream infection. The biomarkers may be selected from human factor 20 (56 genes) and/or human factor 74 (137 genes), which are shown in Tables 8 and 10, respectively. The factor may comprise about 1 to about 193 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, or at least about 193 of the biomarkers listed in Tables 8 and 10. The relationship may have an AUC value of about 0.8100 to about 0.9999. For example, the AUC value may be at least about 0.8100, at least about 0.8150, at least about 0.8200, at least about 0.8250, at least about 0.8300, at least about 0.8350, at least about 0.8360, at least about 0.8370, at least about 0.8380, at least about 0.8400, at least about 0.8500, at least about 0.8550, at least about 0.8600, at least about 0.8650, at least about 0.8700, at least about 0.8750, at least about 0.8800, at least about 0.8850, at least about 0.8900, at least about 0.8950, at least about 0.9000, at least about 0.9100, at least about 0.9200, at least about 0.9300, at least about 0.9400, at least about 0.9500, at least about 0.9600, at least about 0.9700, at least about 0.9800, at least about 0.9900, or at least about 0.9999. The relationship may have an AUC value of at least 0.8372. 
     The diagnostic assay may distinguish a subject that has an  Escherichia coli  blood stream infection from a healthy subject. The biomarkers may be selected from human factor 20 (56 genes) and/or human factor 74 (137 genes), which are shown in Tables 8 and 10, respectively. The factor may comprise about 1 to about 193 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least bout 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, or at least about 193 of the biomarkers listed in Tables 8 and 10. The relationship may have an AUC value of about 0.9000 to about 0.9999. For example, the AUC value may be at least about 0.9000, at least about 0.9050, at least about 0.9100, at least about 0.9150, at least about 0.9200, at least about 0.9210, at least about 0.9220, at least about 0.9230, at least about 0.9240, at least about 0.9250, at least about 0.9260, at least about 0.9270, at least about 0.9280, at least about 0.9300, at least about 0.9350, at least about 0.9400, at least about 0.9500, at least about 0.9600, at least about 0.9700, at least about 0.9800, at least about 0.9900, or at least about 0.9999. The relationship may have an AUC value of at least about 0.9229. 
     The diagnostic assay may distinguish a subject that has a gram positive blood stream infection from a subject that has a gram negative blood stream infection. The biomarkers may be selected from human factor 40 (26 genes), as shown in Table 9. The factor may comprise about 1 to about 26 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, or at least about 26 of the biomarkers listed in Table 9. The relationship may have an AUC value of about 0.8100 to about 0.9999. For example, the AUC value may be 0.8100, at least about 0.8150, at least about 0.8200, at least about 0.8250, at least about 0.8300, at least about 0.8350, at least about 0.8400, at least about 0.8450, at least about 0.8480, at least about 0.8490, at least about 0.8500, at least about 0.8510, at least about 0.8520, at least about 0.8550, at least about 0.8600, at least about 0.8650, at least about 0.8700, at least about 0.8750, at least about 0.8800, at least about 0.8850, at least about 0.8900, at least about 0.8950, at least about 0.9000, at least about 0.9100, at least about 0.9200, at least about 0.9300, at least about 0.9400, at least about 0.9500, at least about 0.9600, at least about 0.9700, at least about 0.9800, at least about 0.9900, or at least about 0.9999. The relationship may have an AUC value of at least about 0.8503. 
     The diagnostic assay may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a healthy subject. The biomarkers may be selected from human factor 4 (349 genes), as shown in Table 7. The factor may comprise about 1 to about 349 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, at least about 195, at least about 200, at least about 205, at least about 210, at least about 215, at least about 220, at least about 225, at least about 230, at least about 235, at least about 240, at least about 245, at least about 250, at least about 255, at least about 260, at least about 265, at least about 270, at least about 275, at least about 280, at least about 285, at least about 290, at least about 295, at least about 300, at least about 305, at least about 310, at least about 315, at least about 320, at least about 325, at least about 330, at least about 335, at least about 340, at least about 345, at least about 349 of the biomarkers listed in Table 7. The relationship may have an AUC value of about 0.9000 to about 0.9999. For example, the AUC value may be at least about 0.9000, at least about 0.9050, at least about 0.9100, at least about 0.9150, at least about 0.9200, at least about 0.9210, at least about 0.9215, at least about 0.9220, at least about 0.9230, at least about 0.9240, at least about 0.9250, at least about 0.9260, at least about 0.9270, at least about 0.9280, at least about 0.9300, at least about 0.9350, at least about 0.9400, at least about 0.9500, at least about 0.9600, at least about 0.9700, at least about 0.9800, at least about 0.9900, or at least about 0.9999. The relationship may have an AUC value of at least about 0.9217. 
     The diagnostic assay may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a healthy subject. The biomarkers may be selected from mouse factors 7, 15, and/or 26, of which the top 200 of each factor are shown in Tables 3, 4, and 6. The factor may comprise about 1 to about 250 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, at least about 195, at least about 200, at least about 205, at least about 210, at least about 215, at least about 220, at least about 225, at least about 230, at least about 235, at least about 240, at least about 245, or at least about 250 of the biomarkers listed in Tables 3, 4, and 6. The relationship may have an AUC value of about 0.9200 to about 0.9999. For example, the AUC value may be at least about 0.9200, at least about 0.9250, at least about 0.9300, at least about 0.9350, at least about 0.9400, at least about 0.9450, at least about 0.9500, at least about 0.9510, at least about 0.9520, at least about 0.9530, at least about 0.9540, at least about 0.9550, at least about 0.9600, at least about 0.9650, at least about 0.9700, at least about 0.9750, at least about 0.9800, at least about 0.9850, at least about 0.9900, at least about 0.9950, or at least about 0.9999. The relationship may have an AUC value of at least about 0.9522. 
     The diagnostic assay may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a healthy subject. The biomarkers may be selected from mouse factors 7, 15, 23, and/or 26, of which the top 200 of each factor are shown in Tables 3, 4, 5, and 6. The factor may comprise about 1 to about 250 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, at least about 195, at least about 200, at least about 205, at least about 210, at least about 215, at least about 220, at least about 225, at least about 230, at least about 235, at least about 240, at least about 245, or at least about 250 of the biomarkers listed in Tables 3, 4, 5, and 6. The relationship may have an AUC value of about 0.9500 to about 0.9999. For example, the AUC value may be at least about 0.9500, at least about 0.9550, at least about 0.9600, at least about 0.9650, at least about 0.9700, at least about 0.9750, at least about 0.9800, at least about 0.9850, at least about 0.9900, at least about 0.9910, at least about 0.9920, at least about 0.9930, at least about 0.9940, at least about 0.9950, at least about 0.9960, at least about 0.9970, at least about 0.9980, at least about 0.9990, or at least about 0.9999. The relationship may have an AUC value of at least about 0.9964. 
     The diagnostic assay may distinguish a subject that has a  Staphylococcus aureus  blood stream infection from a subject that has an  Escherichia coli  blood stream infection. The biomarkers may be selected from mouse factors 7, 15, 23, and/or 26, of which the top 200 of each factor are shown in Tables 3, 4, 5, and 6. The factor may comprise about 1 to about 250 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, at least about 195, at least about 200, at least about 205, at least about 210, at least about 215, at least about 220, at least about 225, at least about 230, at least about 235, at least about 240, at least about 245, or at least about 250 of the biomarkers listed in Tables 3, 4, 5, and 6. The relationship may have an AUC value of about 0.9500 to about 0.9999. For example, the AUC value may be at least about 0.9500, at least about 0.9550, at least about 0.9600, at least about 0.9650, 0.9700, at least about 0.9750, at least about 0.9800, at least about 0.9850, at least about 0.9900, at least about 0.9910, at least about 0.9920, at least about 0.9930, at least about 0.9940, at least about 0.9950, at least about 0.9960, at least about 0.9970, at least about 0.9980, at least about 0.9990, or at least about 0.9999. The relationship may have an AUC value of at least about 0.9935. 
     The diagnostic assay may distinguish a subject that has an  Escherichia coli  blood stream infection from a healthy subject. The biomarkers may be selected from mouse factors 7, 15, 23, and/or 26, of which the top 200 of each factor are shown in Tables 3, 4, 5, and 6. The factor may comprise about 1 to about 250 biomarkers. For example, the factor may comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 105, at least about 110, at least about 115, at least about 120, at least about 125, at least about 130, at least about 135, at least about 140, at least about 145, at least about 150, at least about 155, at least about 160, at least about 165, at least about 170, at least about 175, at least about 180, at least about 185, at least about 190, at least about 195, at least about 200, at least about 205, at least about 210, at least about 215, at least about 220, at least about 225, at least about 230, at least about 235, at least about 240, at least about 245, or at least about 250 of the biomarkers listed in Tables 3, 4, 5, and 6. The relationship may have an AUC value of about 0.9200 to about 0.9999. For example, the AUC value may be at least about 0.9200, at least about 0.9250, at least about 0.9300, at least about 0.9350, at least about 0.9400, at least about 0.9440, at least about 0.9450, at least about 0.9460, at least about 0.9470, at least about 0.9480, at least about 0.9490, at least about 0.9500, at least about 0.9510, at least about 0.9520, at least about 0.9530, at least about 0.9540, at least about 0.9550, at least about 0.9600, at least about 0.9650, at least about 0.9700, at least about 0.9750, at least about 0.9800, at least about 0.9850, at least about 0.9900, at least about 0.9950, or at least about 0.9999. The relationship may have an AUC value of at least about 0.9484. 
     5. Methods of Identifying and Treating a Bacterial Infection 
     The present invention is directed to method of identifying and treating a bacterial infection in a subject. The method comprises performing the diagnostic assay as developed by the methods, as described above, and administrating an antibacterial therapy to the subject diagnosed with a bacterial infection. The method further comprising quantifying the amount of at least about one biomarker present in a biological sample derived from the subject, wherein the biomarker may be associated with a factor. 
     The present invention is also directed towards a method of identifying and treating a subject suspected of having a bacterial blood stream infection (BSI). The method comprises determining gene expression levels of at least about two biomarkers in a peripheral blood cell sample of the subject, wherein the biomarkers are selected from any one of Tables 3-17; comparing the gene expression levels of the at least about two biomarkers to standard gene expression levels wherein the standard gene expression levels correspond to the gene expression levels for the biomarkers in a control; identifying the subject as having a bacterial BSI if the gene expression levels of the biomarkers are different than the standard gene expression levels; and administering an effective amount of antibiotic therapy to treat the subject identified as having a bacterial BSI. The bacterial BSI may be  Staphylococcus aureus  BSI or  Escherichia coli  BSI. The bacterial blood stream infection may be  S. aureus  BSI and the biomarkers may be selected from one of Tables 3-8 or 10. 
     The present invention is directed to method of distinguishing and treating  Staphylococcus aureus  blood stream infection (BSI) from  Escherichia coli  BSI in a subject suspected of having a bacterial infection. The method comprises determining gene expression levels of at least about two biomarkers in a peripheral blood cell sample of the subject, wherein the biomarkers are selected from any one of Tables 8 and 10 or Tables 3-6; comparing the gene expression levels of the at least about two biomarkers to standard gene expression levels wherein the standard gene expression levels correspond to the gene expression levels for the biomarkers in a control; identifying the subject as having a  S. aureus  BSI if the gene expression levels of the biomarkers are different than the standard gene expression levels and identifying the subject as having an  E. coli  BSI if the gene expression levels of the biomarkers are the same as the standard gene expression levels; and administering an effective amount of appropriate antibacterial therapy to treat the subject identified as having a  S. aureus  BSI or  E. coli . The control may be a subject having an  E. coli  BSI. The present invention is directed to method of distinguishing and treating a gram positive bacterial infection from a gram negative bacterial infection in a subject suspected of having a bacterial infection. The method comprises determining gene expression levels of at least about two biomarkers in a peripheral blood cell sample of the subject, wherein the biomarkers are selected from Table 9; comparing the gene expression levels of the at least about two biomarkers to standard gene expression levels wherein the standard gene expression levels correspond to the gene expression levels for the biomarkers in a control; identifying the subject as having a gram positive bacterial infection if the gene expression levels of the biomarkers are different than the standard gene expression levels in a control; and administering an effective amount of appropriate antibacterial therapy to treat the subject identified as a gram positive bacterial infection. The gram positive bacterial infection may be  Staphylococcus aureus . The control may be a subject having a gram negative bacterial infection. The gram negative bacterial infection may be  Escherichia coli.    
     The present invention is directed method of identifying and treating a subject suspected of having a methicillin-resistant  Staphylococcus aureus  (MRSA) infection. The method comprises determining gene expression levels of at least about one biomarker in a peripheral blood cell sample of the subject wherein the biomarker is selected from Table 11; comparing the gene expression levels of the biomarker to a standard gene expression level of the biomarker, wherein the standard gene expression level corresponds to the gene expression level of the biomarker in a subject that has a methicillin-sensitive  Staphylococcus aureus  (MSSA) infection; identifying the subject as having MRSA if the gene expression levels of the biomarkers are different than the standard gene expression levels; and administering an effective amount of an antibiotic therapy to treat the subject identified as having MRSA. The antibiotic therapy may be mupirocine or vancomycin. 
     6. Methods of Determining Efficacy of Treatment Using Biomarkers 
     Another aspect of the present disclosure provides for methods for monitoring the treatment of conditions such as a bacterial infection. In one embodiment, the method comprises a method of determining the efficacy of treatment regime (e.g., anti-bacterial therapy) in a subject comprising, consisting of, or consisting essentially of: (a) determining a baseline value for the expression of one or more biomarkers associated with bacterial infection; (b) administering to the subject an anti-bacterial therapy regime; and (c) redetermining the expression levels of one or more biomarkers in the subject, wherein observed changes in one or more or the biomarker expression levels as compared to a control is correlated with the efficacy of the therapeutic regimen. 
     In instances where a change in the biomarker expression is not seen, a change in treatment may be warranted. Such a determination, and the different type of treatment to employ, can be made readily determined by one skilled in the art. 
     7. Probabilitya And Threshold 
     A probability score could be produced using various methods, such as those methods using a ENet score as described in Chen et al., IEEE Transactions on Biomedical Engineering 58: 468-479 (2011). For example, one method of determining the probability score is the following: Let X be a p×n matrix of observed data in the real number domain, where each column corresponds to one of n samples, quantifying the associated gene-expression values for all p genes under investigation. To address the “large p, small n” problem in an unsupervised setting the data are assumed to satisfy X=AS+E, where A is a p×r matrix, S is r×n and E is p×n. The columns of A represent the factor “loadings” and each column of S represents factor “scores” for the associated sample (column of X); the rows of S are called factors. E is the usual error matrix. 
     Thresholds may be defined based on how the classifier performs using the final testing platform that would be implemented clinically. This will require a balance of sensitivity, specificity, and input from end-users. An alternative to a threshold is determining the probability that the patient in question has a  S. aureus  infection. 
     8. Treatment 
     Treatment may include being administered oxygen, either by a tube that is placed near the nose or through a clear plastic mask. Depending on the results of the tests, the physician may order medications. These medications may include antibiotics given intravenously (given directly into the vein). Initially, the antibiotics may be those that kill many different bacteria because the exact kind of infection the patient has is not known. Once the blood culture results show the identity of the bacteria, the doctor may select a different antibiotic that kills the specific organism responsible for the infection. The doctor may also order IV salt solution saline and medications to increase the blood pressure it is too low. The patient may be admitted to the hospital at least until the blood culture results are known. If the patient is very ill and with low blood pressure, the doctor may admit the patient to the intensive care unit (ICU) and may consult specialist doctors to help in the management of the illness. If results show an infection in the abdomen, either drainage of the infection by the placement of tubes or surgery may be necessary. The physician will administer anti-autoimmune drugs or biologics as well to modify the body&#39;s aggressive immune response to microbes, which leads to sepsis. 
     Treatment for sepsis or severe sepsis/septic shock may further include early goal directed therapy, antibiotic, a vasopressor, such as norepinephrine and dopamine, a steroid, such as corticosteroids, insulin, painkillers, sedatives, oxygen, cerebrospinal fluid, and intravenous fluid to the subject. For application of these therapies, a central venous catheter and an arterial catheter may be used. Other hemodynamic variables (such as cardiac output, mixed venous oxygen saturation, or stroke volume variation) may also be used. 
     Treatment of organ dysfunction may include hemodialysis in kidney failure, mechanical ventilation in pulmonary dysfunction, transfusion of blood products, and drug and fluid therapy for circulatory failure. Ensuring adequate nutrition may further be required by enteral feeding, but if necessary by parenteral nutrition during a prolonged illness. 
     a.  S. aureus    
       S. aureus  bacterial infection may be treated with an antibiotic, such as penicillin and penicillinase-resistant β-lactam antibiotics, such as methicillin, dicloxacillin, nafcillin, oxacillin, and flucloxacillin, cephalosporin, gentamicin, or combinations thereof.  S. aureus  infection may also be treated with a combination therapy of a penicillinase-resistant penicillin or cephalosporin (in case the organism is MSSA) and clindamycin or a quinolone. Other therapies include clindamycin, trimethoprim-sulfamethoxazole (TMP-SMX), rifampin, doxycycline, or a quinolone. Combination of TMP-SMX and rifampin may also be used 
     i. MRSA 
     In some embodiments, the subject has MRSA and is resistant to β-lactam antibiotic, such as methicillin. MRSA is also called oxacillin-resistant  S. aureus . MRSA may be treated with mupirocine or vancomycin. 
     b.  E. coli    
       E. coli  bacterial infection may be treated with antibiotics. 
     9. Composition of Matter 
     Another aspect of the present disclosure provides a composition of matter comprising, consisting of, or consisting essentially of: (a) a probe array for determining a biomarker level in a sample, the array comprising of a plurality of probes that hybridizes to one or more biomarkers that are associated with bacterial infection; or (b) a kit for determining a biomarker level in a sample, comprising the probe array of (a) and instructions for carrying out the determination of biomarker expression level in the sample. In certain embodiments the probe array of (a) further comprises a solid support with the plurality of probes attached thereto. 
     10. Sample 
     The present disclosure provides a method of determining the identification and/or classification of a bacterial infection on at least one sample obtained from an individual. The individual may be any mammal, but is preferably a human. 
     The present disclosure may involve obtaining more than one sample, such as two samples, such as three samples, four samples or more from individuals, and preferably the same individual. This allows the relative comparison of expression both as in the presence or absence of at least one biomarker between the two samples. Alternatively, a single sample may be compared against a “standardized” sample, such a sample comprising material or data from several samples, preferably also from several individuals. 
     11. Sample Preparation 
     Before analyzing the sample, it will often be desirable to perform one or more sample preparation operations upon the sample. Typically, these sample preparation operations will include such manipulations as concentration, suspension, extraction of intracellular material, e.g., nucleic acids from tissue/whole cell samples and the like, amplification of nucleic acids, fragmentation, transcription, labeling and/or extension reactions. 
     Any method required for the processing of a sample prior to detection by any of the methods noted herein falls within the scope of the present disclosure. These methods are typically well known by a person skilled in the art. 
     12. Detection 
     It is within the general scope of the present disclosure to provide methods for the detection of gene expression as a biomarker. An aspect of the present disclosure relates to the detection of the gene expression as described in the plots and graphs of the figures contained herein. As used herein, the term “detect” or “determine the presence of” refers to the qualitative measurement of undetectable, low, normal, or high concentrations of one or more biomarkers such as, for example, nucleic acids, ribonucleic acids, or polypeptides and other biological molecules. Detection may include 1) detection in the sense of presence versus absence of one or more biomarkers as well as 2) the registration/quantification of the level or degree of expression of one or more biomarkers, depending on the method of detection employed. The term “quantify” or “quantification” may be used interchangeable, and refer to a process of determining the quantity or abundance of a substance in a sample (e., a biomarker), whether relative or absolute. For example, quantification may be determined by methods including but not limited to, micro-array analysis, qRT-PCR, band intensity on a Northern or Western blot, or by various other methods known in the art. 
     The detection of one or more biomarker molecules allows for the identification and/or classification of a condition such as a bacterial infection. The classification of such conditions is of relevance both medically and scientifically and may provide important information useful for the diagnosis, prognosis and treatment of the condition. The diagnosis of a condition such as a bacterial infection is the affirmation of the presence of the condition, as is the object of the present disclosure, on the expression of at least one biomarker herein. Prognosis is the estimate or prediction of the probable outcome of a condition such as a bacterial infection and the prognosis of such is greatly facilitated by increasing the amount of information on the particular condition. The method of detection is thus a central aspect of the present disclosure. 
     Any method of detection falls within the general scope of the present disclosure. The detection methods may be generic for the detection of gene expression, nucleic acids, polypeptides and the like. The detection methods may be directed towards the scoring of a presence or absence of one or more biomarker molecules or may be useful in the detection of expression levels. 
     The detection methods can be divided into two categories herein referred to as in situ methods or screening methods. The term in situ method refers to the detection of nucleic acid and/or protein molecules in a sample wherein the structure of the sample has been preserved. This may thus be a biopsy wherein the structure of the tissue is preserved. In situ methods are generally histological i.e. microscopic in nature and include but are not limited to methods such as: in situ hybridization techniques and in situ PCR methods. 
     Screening methods generally employ techniques of molecular biology and most often require the preparation of the sample material in order to access the nucleic acid and/or polypeptide molecules to be detected. Screening methods include, but are not limited to methods such as: Array systems, affinity matrices, Northern blotting and PCR techniques, such as real-time quantitative RT-PCR. 
     13. Probe 
     One aspect of the present disclosure is to provide a probe which can be used for the detection of a gene, a nucleic acid and/or polypeptide molecule as defined herein. A probe as defined herein is a specific sequence of a nucleic acid and/or polypeptide used to detect nucleic acids and/or polypeptides by hybridization. For example, a nucleic acid is also here any nucleic acid, natural or synthetic such as DNA, RNA, LNA or PNA. A probe may be labeled, tagged or immobilized or otherwise modified according to the requirements of the detection method chosen. A label or a tag is an entity making it possible to identify a compound to which it is associated. It is within the scope of the present disclosure to employ probes that are labeled or tagged by any means known in the art such as but not limited to: radioactive labeling, fluorescent labeling and enzymatic labeling. Furthermore the probe, labeled or not, may be immobilized to facilitate detection according to the detection method of choice and this may be accomplished according to the preferred method of the particular detection method. 
     14. Detection Methods 
     Another aspect of the present disclosure regards the detection of nucleic acid and/or polypeptide molecules by any method known in the art. In the following are given examples of various detection methods that can be employed for this purpose, and the present disclosure includes all the mentioned methods, but is not limited to any of these. In some embodiments, the RNA gene expression levels may be determined. 
     c. In Situ Hybridization 
     In situ hybridization (ISH) applies and extrapolates the technology of nucleic acid and/or polypeptide hybridization to the single cell level, and, in combination with the art of cytochemistry, immunocytochemistry and immunohistochemistry, permits the maintenance of morphology and the identification of cellular markers to be maintained and identified, allows the localization of sequences to specific cells within populations, such as tissues and blood samples. ISH is a type of hybridization that uses a complementary nucleic acid to localize one or more specific nucleic acid sequences in a portion or section of tissue (in situ), or, if the tissue is small enough, in the entire tissue (whole mount ISH). DNA ISH can be used to determine the structure of chromosomes and the localization of individual genes and optionally their copy numbers. Fluorescent DNA ISH (FISH) can for example be used in medical diagnostics to assess chromosomal integrity. RNA ISH is used to assay expression and gene expression patterns in a tissue/across cells, such as the expression of miRNAs/nucleic acid molecules. Sample cells are treated to increase their permeability to allow the probe to enter the cells, the probe is added to the treated cells, allowed to hybridize at pertinent temperature, and then excess probe is washed away. A complementary probe is labeled with a radioactive, fluorescent or antigenic tag, so that the probe&#39;s location and quantity in the tissue can be determined using autoradiography, fluorescence microscopy or immunoassay, respectively. The sample may be any sample as herein described. The probe is likewise a probe according to any probe based upon the biomarkers mentioned herein. 
     An aspect of the present disclosure includes the method of detection by in situ hybridization as described herein. 
     d. In Situ PCR 
     In situ PCR is the PCR based amplification of the target nucleic acid sequences prior to ISH. For detection of RNA, an intracellular reverse transcription (RT) step is introduced to generate complementary DNA from RNA templates prior to in situ PCR. This enables detection of low copy RNA sequences. 
     Prior to in situ PCR, cells or tissue samples are fixed and permeabilized to preserve morphology and permit access of the PCR reagents to the intracellular sequences to be amplified. PCR amplification of target sequences is next performed either in intact cells held in suspension or directly in cytocentrifuge preparations or tissue sections on glass slides. In the former approach, fixed cells suspended in the PCR reaction mixture are thermally cycled using conventional thermal cyclers. After PCR the cells are cytocentrifugated onto glass slides with visualization of intracellular PCR products by ISH or immunohistochemistry. In situ PCR on glass slides is performed by overlaying the samples with the PCR mixture under a coverslip which is then sealed to prevent evaporation of the reaction mixture. Thermal cycling is achieved by placing the glass slides either directly on top of the heating block of a conventional or specially designed thermal cycler or by using thermal cycling ovens. Detection of intracellular PCR-products is achieved by one of two entirely different techniques. In indirect in situ PCR by ISH with PCR-product specific probes, or in direct in situ PCR without ISH through direct detection of labeled nucleotides (e.g. digoxigenin-11-dUTP, fluorescein-dUTP, 3H-CTP or biotin-16-dUTP) which have been incorporated into the PCR products during thermal cycling. 
     An embodiment of the present disclosure concerns the method of in situ PCR as mentioned herein above for the detection of nucleic acid molecules as detailed herein. 
     e. Microarray 
     A microarray is a microscopic, ordered array of nucleic acids, proteins, small molecules, cells or other substances that enables parallel analysis of complex biochemical samples. A DNA microarray consists of different nucleic acid probes, known as capture probes that are chemically attached to a solid substrate, which can be a microchip, a glass slide or a microsphere-sized bead. Microarrays can be used e.g. to measure the expression levels of large numbers of polypeptides/proteins/nucleic acids simultaneously. 
     Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing, or electrochemistry on microelectrode arrays. 
     An aspect of the present disclosure regards the use of microarrays for the expression profiling of biomarkers in conditions such as bacterial infection. For this purpose, and by way of example, RNA is extracted from a cell or tissue sample, the small RNAs (18-26-nucleotide RNAs) are size-selected from total RNA using denaturing polyacrylamide gel electrophoresis (PAGE). Then oligonucleotide linkers are attached to the 5′ and 3′ ends of the small RNAs and the resulting ligation products are used as templates for an RT-PCR reaction with 10 cycles of amplification. The sense strand PCR primer has a Cy3 fluorophore attached to its 5′ end, thereby fluorescently labeling the sense strand of the PCR product. The PCR product is denatured and then hybridized to the microarray. A PCR product, referred to as the target nucleic acid that is complementary to the corresponding RNA capture probe sequence on the array will hybridize, via base pairing, to the spot at which the capture probes are affixed. The spot will then fluoresce when excited using a microarray laser scanner. The fluorescence intensity of each spot is then evaluated in terms of the number of copies of a particular biomarker, using a number of positive and negative controls and array data normalization methods, which will result in assessment of the level of expression of a particular biomarker. 
     Several types of microarrays can be employed such as spotted oligonucleotide microarrays, pre-fabricated oligonucleotide microarrays or spotted long oligonucleotide arrays. 
     In spotted oligonucleotide microarrays the capture probes are oligonucleotides complementary to nucleic acid sequences. This type of array is typically hybridized with amplified. 
     PCR products of size-selected small RNAs from two samples to be compared that are labeled with two different fluorophores. Alternatively, total RNA containing the small RNA fraction is extracted from the abovementioned two samples and used directly without size-selection of small RNAs, and 3′ end labeled using T4 RNA ligase and short RNA linkers labeled with two different fluorophores. The samples can be mixed and hybridized to one single microarray that is then scanned, allowing the visualization of up-regulated and down-regulated biomarker genes in one go. The downside of this is that the absolute levels of gene expression cannot be observed, but the cost of the experiment is reduced by half. Alternatively, a universal reference can be used, comprising of a large set of fluorophore-labelled oligonucleotides, complementary to the array capture probes. 
     In pre-fabricated oligonucleotide microarrays or single-channel microarrays, the probes are designed to match the sequences of known or predicted biomarkers. There are commercially available designs that cover complete genomes from companies such as Affymetrix, or Agilent. These microarrays give estimations of the absolute value of gene expression and therefore the comparison of two conditions requires the use of two separate microarrays. 
     Spotted long oligonucleotide arrays are composed of 50 to 70-mer oligonucleotide capture probes, and are produced by either ink-jet or robotic printing. Short Oligonucleotide Arrays are composed of 20-25-mer oligonucleotide probes, and are produced by photolithographic synthesis (Affymetrix) or by robotic printing. More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes. Arrays can contain up to 390,000 spots, from a custom array design. 
     An embodiment of the present disclosure concerns the method of microarray use and analysis as described herein. 
     f. PCR 
     The terms “PCR reaction”, “PCR amplification”, “PCR”, “pre-PCR”, “Q-PCR”, “real-time quantitative PCR” and “real-time quantitative RT-PCR” are interchangeable terms used to signify use of a nucleic acid amplification system, which multiplies the target nucleic acids being detected. Examples of such systems include the polymerase chain reaction (PCR) system and the ligase chain reaction (LCR) system. Other methods recently described and known to the person of skill in the art are the nucleic acid sequence based amplification and Q Beta Replicase systems. The products formed by said amplification reaction may or may not be monitored in real time or only after the reaction as an end-point measurement. 
     g. Real-Time Quantitative RT-PCR 
     Real-time quantitative RT-PCR is a modification of polymerase chain reaction used to rapidly measure the quantity of a product of polymerase chain reaction. It is preferably done in real-time, thus it is an indirect method for quantitatively measuring starting amounts of DNA, complementary DNA or ribonucleic acid (RNA). This is commonly used for the purpose of determining whether a genetic sequence is present or not, and if it is present the number of copies in the sample. There are 3 methods which vary in difficulty and detail. Like other forms of polymerase chain reaction, the process is used to amplify DNA samples, using thermal cycling and a thermostable DNA polymerase. 
     The three commonly used methods of quantitative polymerase chain reaction are through agarose gel electrophoresis, the use of SYBR Green, a double stranded DNA dye, and the fluorescent reporter probe. The latter two of these three can be analysed in real-time, constituting real-time polymerase chain reaction method. 
     Agarose gel electrophoresis is the simplest method, but also often slow and less accurate then other methods, depending on the running of an agarose gel via electrophoresis. It cannot give results in real time. The unknown sample and a known sample are prepared with a known concentration of a similarly sized section of target DNA for amplification. Both reactions are run for the same length of time in identical conditions (preferably using the same primers, or at least primers of similar annealing temperatures). Agarose gel electrophoresis is used to separate the products of the reaction from their original DNA and spare primers. The relative quantities of the known and unknown samples are measured to determine the quantity of the unknown. This method is generally used as a simple measure of whether the probe target sequences are present or not, and rarely as ‘true’ Q-PCR. 
     Using SYBR Green dye is more accurate than the gel method, and gives results in real time. A DNA binding dye binds all newly synthesized double stranded (ds)DNA and an increase in fluorescence intensity is measured, thus allowing initial concentrations to be determined. However, SYBR Green will label all dsDNA including any unexpected PCR products as well as primer dimers, leading to potential complications and artifacts. The reaction is prepared as usual, with the addition of fluorescent dsDNA dye. The reaction is run, and the levels of fluorescence are monitored; the dye only fluoresces when bound to the dsDNA. With reference to a standard sample or a standard curve, the dsDNA concentration in the PCR can be determined. 
     The fluorescent reporter probe method is the most accurate and most reliable of the methods. It uses a sequence-specific nucleic acid based probe so as to only quantify the probe sequence and not all double stranded DNA. It is commonly carried out with DNA based probes with a fluorescent reporter and a quencher held in adjacent positions, so-called dual-labeled probes. The close proximity of the reporter to the quencher prevents its fluorescence; it is only on the breakdown of the probe that the fluorescence is detected. This process depends on the 5′ to 3′ exonuclease activity of the polymerase involved. The real-time quantitative PCR reaction is prepared with the addition of the dual-labeled probe. On denaturation of the double-stranded DNA template, the probe is able to bind to its complementary sequence in the region of interest of the template DNA (as the primers will too). When the PCR reaction mixture is heated to activate the polymerase, the polymerase starts synthesizing the complementary strand to the primed single stranded template DNA. As the polymerization continues it reaches the probe bound to its complementary sequence, which is then hydrolyzed due to the 5′-3′ exonuclease activity of the polymerase thereby separating the fluorescent reporter and the quencher molecules. This results in an increase in fluorescence, which is detected. During thermal cycling of the real-time PCR reaction, the increase in fluorescence, as released from the hydrolyzed dual-labeled probe in each PCR cycle is monitored, which allows accurate determination of the final, and so initial, quantities of DNA. 
     Any method of PCR that can determine the expression of a nucleic acid molecule as defined herein falls within the scope of the present disclosure. A preferred embodiment of the present disclosure includes the real-time quantitative RT-PCR method, based on the use of either SYBR Green dye or a dual-labeled probe for the detection and quantification of nucleic acids according to the herein described. 
     h. Northern Blot Analysis 
     An aspect of the present disclosure includes the detection of the nucleic acid molecules herein disclosed by techniques such as Northern blot analysis. Many variations of the protocol exist. 
     The following examples are offered by way of illustration and not by way of limitation. 
     The present invention has multiple aspects, illustrated by the following non-limiting examples. 
     15. Examples 
     The foregoing may be better understood by reference to the following examples, which are presented for purposes of illustration and are not intended to limit the scope of the invention. 
     EXAMPLE 1 
     Materials and Methods 
     Preparation of Bacterial Cells. One methicillin-susceptible  S. aureus  (Sanger 476) and three methicillin-resistant  S. aureus  genetic backgrounds (USA100, USA300, and MW2) were used. Overnight  S. aureus  cultures were inoculated into fresh tryptic soy broth and incubated aerobically at 30° C. to log-phase growth (optical density 600 nm of ˜1.0). Cells were harvested by centrifugation, rinsed, and resuspended in phosphate-buffered saline (PBS).  E. coli O 18:K1:H7 was grown at 30° C. overnight in Luria-Bertani broth. Cultures were then diluted with fresh medium and grown for an additional 1 to 2 hours. Upon reaching log phase, cells were treated as described for  S. aureus.    
     Human Subjects. Subjects were enrolled at Duke University Medical Center (DUMC; Durham, N.C.), Durham VAMC (Durham, N.C.), UNC Hospitals (Chapel Hill, N.C.), and Henry Ford Hospital (Detroit, Mich.) as part of a prospective, NIH-sponsored study to develop novel diagnostic tests for severe sepsis and community acquired pneumonia (ClinicalTrials.gov NCT00258869). Enrolled patients had a known or suspected infection and exhibited two or more Systemic Inflammatory Response Syndrome criteria. Patients were excluded if they had an imminently terminal co-morbid condition, advanced AIDS (CD4 count, 50), were being appropriately treated with an antibiotic pre-enrollment, or were enrolled in another clinical trial. Blood was drawn for microarray analysis on the day of hospital presentation with the exception of two subjects (S19 and S29). In these latter two cases, blood was not available for microarray preparation from that time point. However, blood drawn 24 hours into the hospitalization was available and so was used. Subjects in the current report had culture-confirmed monomicrobial BSI due to  S. aureus  (n=32; median age 58 years; range 24-91) or  E. coli  (n=19; median age 58; range 25-91). Uninfected controls (n=43; median age 30 years; range 23-59) were enrolled at DUMC as part of a study on the effect of aspirin on platelet function among healthy volunteers. Subjects were recruited through advertisements posted on the Duke campus. Blood used to derive gene expression data in these healthy controls was drawn prior to aspirin challenge. 
     Murine Sepsis Experiments. Except where noted, mice were purchased from The Jackson Laboratory (Bar Harbor, Me.) and allowed to acclimate for 7 days. All experiments were performed on 6-8 week old mice. For the murine  S. aureus  classifier, seven inbred mouse strains (3 mice/strain: 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, C57BL/6J, C3H/HeJ, and NOD/LtJ) were IP inoculated with 10 7  CFU/g of  S. aureus  Sanger476, euthanized at 2 h after injection, and bled. This was repeated using the four different  S. aureus  genetic backgrounds (USA100, USA300, MW2, and Sanger476) in A/J mice (n=3 per  S. aureus  background). For time series experiments, both A/J and C57BL/6J mouse strains were IP inoculated with  S. aureus  Sanger476 as above, and sacrificed at 2, 4, 6, and 12 h after injection (n=5 per mouse strain at each time point). For survival experiments, mice were monitored twice daily after injection and culled upon reaching a moribund state. Animal sacrifice was carried out by carbon dioxide inhalation. Blood was collected by intracardiac puncture and stored in RNAlater at −70° C. for microarray experiments. 
     The murine  E. coli  infection model was carried out as described above except a smaller inoculum (6×10 4  CFU/g) was used. Furthermore, the time at which animals were sickest but still alive was 24 hours for  E. coli  inoculation, which is later than for  S. aureus . Consequently, A/J and C57BL/6J mice inoculated with  E. coli  were sacrificed 24 h after challenge (n=5 per mouse strain). Control mice were not injected. 
     Outbred CD-1 mice were purchased from Charles River Laboratories (Wilmington, Mass.) to validate the murine  S. aureus  classifier. CD-1 mice were IP inoculated with 10 7  CFU/g of  S. aureus  (USA300 and Sanger 476) and 6×10 4  CFU/g of  E. coli . Animals including controls were sacrificed at 2 and 24 h postinfection (n=10 mice per pathogen at each time point). Blood was collected and stored as described for the derivation cohort. 
     EXAMPLE 2 
     Microarray Preparation 
     Total RNA was extracted from mouse blood using the Mouse RiboPure Blood RNA kit (Ambion, Austin, Tex.) according to the manufacturer&#39;s instructions. Globin mRNA was removed from whole blood RNA using the Globinclear kit (Ambion, Austin, Tex.). All samples passed the quality criteria of the Agilent Bioanalyzer and were used for microarray analysis. Since the total RNA yield of many samples was low, one round of linear amplification was performed for all samples using the MessageAmp Premier kit (Ambion, Austin, Tex.). RNA integrity numbers were calculated for all samples and found to be within tolerance limits. Microarrays were normalized using Robust Multichip Average (RMA). Affymetrix GeneChip Mouse Genome 430 2.0 Arrays were used (Santa Clara, Calif.). Biotin-labeled cDNA was hybridized to the arrays for 16 hours at 45° C. according to the manufacturer&#39;s instructions. Arrays were then washed and labeled with streptavidin-phycoerythrin (strep-PE), and the signal was amplified using biotinylated antistreptavidin followed by another round of staining with strep-PE. These steps were performed on the Affymetrix fluidics station according to the recommended protocol. Amplification and microarray hybridization were performed at the Duke University Microarray Core. Labeled gene chips were scanned using an Affymetrix Genechip Scanner 7G (Santa Clara, Calif.). This array contains 45,101 probe sets to analyze the expression level of over 39,000 transcripts and variants from over 34,000 mouse genes. 
     Human microarrays were prepared by first extracting total RNA from human blood using the PAXgene Blood RNA Kit (Qiagen, Valencia, Calif.) according to the manufacturer&#39;s recommended protocol including DNase treatment. Following isolation, RNA quantity was determined via a Nanodrop UV-Vis Spectrophotometer (Thermo Fisher Scientific, Pittsburgh, Pa.) and quality via capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, Calif.). RNA quantity and quality was assessed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, Calif.). RNA integrity numbers were calculated for all samples and found to be within tolerance limits. Microarrays were normalized using RMA. Hybridization and microarray data collection was then performed at Expression Analysis (Durham, N.C.) using the GeneChip® Human Genome U133A 2.0 Array (Affymetrix, Santa Clara, Calif.) according to the “Affymetrix Technical Manual.” 
     Target was prepared and hybridized according to the “Affymetrix Technical Manual”. A set of four peptide nucleic acid (PNA) oligomers (Applied Biosystems, Foster City, Calif.) with sequences complimentary to globin mRNA were added to 2.5 ug of total RNA to reduce globin RNA transcription, then converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet). After first strand synthesis, residual RNA was degraded by the addition of RNaseH and a double-stranded cDNA molecule was generated using DNA Polymerase I and DNA Ligase. The cDNA was then purified and concentrated using a phenol:chloroform extraction followed by ethanol precipitation. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In vitroTranscription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20 ug) was incubated at 94° C. for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99° C. for 5 minutes, incubated at 45° C. for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42° C. for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25° C.) and stringent (50° C.) solutions variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution. Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500. 
     Fluorescent images were detected in a GeneChip Scanner 3000 and expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All Gene-Chips were scaled to a median intensity setting of 500. Murine and human microarray data have been deposited in the NCBI GEO (accession # GSE33341). 
     EXAMPLE 3 
     Deriving the Murine and Human  S. aureus  Classifiers 
     Microarray data was analyzed in two steps following the analysis strategy previously outlined and utilized. First, a Bayesian sparse factor model was fit to the expression data without regard to phenotype. Second, factors were then used as independent variables to build a penalized binary regression with variable selection model trained to identify  S. aureus  infection. In order to minimize issues with overfitting, batch was not included in the regression models. A Bayesian penalized regression technique was used for variable selection which allows for weighted model averaging of the resultant models, such that weights are computed from model fit on the training data. The model averaging approach incorporates uncertainty in choice of model as well as regression coefficient. This has been shown to lead to out of sample predictive accuracies that are superior to penalized maximum likelihood approaches. Assumptions for this approach are typical of probit regression including a linear response surface between predictors and the transformed latent probability variable. Genes were filtered for analysis using nonspecific filtering for genes with high mean expression and high variance across samples. Samples with a high number of outlying genes were removed during the factor analysis. Mice were batched into discrete experiments with each experiment containing the relevant controls to avoid confounding. The development and application of this methodological approach has been previously described. Using the same murine experimental data, another classifier was derived to classify methicillin resistant vs. methicillin-sensitive  S. aureus  infection. The methodology was otherwise the same as that described above. 
     A factor model was fitted on the human data independently from the mouse data. The factor model was fit to 9,109 genes after nonspecific filtering to remove unexpressed and uniformly expressed genes. Z-scores were computed independently for each gene without regard to experimental design. Subjects with absolute zscores greater than 3 in more than 5% of the genes on the array were identified as outliers and were not used to fit the factor model. The factor model was trained on the 91 samples (after removal of three outliers) from three batches of expression data, and this resulted in 79 factors. These 79 factors were then projected onto the full data set (including the three subjects removed for validation) with the goal of distinguishing  S. aureus  BSI from healthy controls or  E. coli  BSI. Leave-one-out cross-validation was utilized in order to control for overfitting of the penalized binary regression model. In order to minimize issues with overfitting, batch was not included in the regression models. Matlab (Natick, Mass., USA) scripts to perform these operations are available. Nonparametric testing was used to evaluate model performance (Wilcoxon rank sum for 2-group comparisons or Kruskal-Wallis for 3 or more-group comparisons) unless otherwise indicated. 
     One limitation of this approach is that the marginal significance of genes within the factor-based classifier cannot be defined. Instead, gene lists were created to identify genes with differential expression between specified groups with respect to gene-level and factor-level analyses. For 3-group comparisons ( S. aureus  vs.  E. coli  vs. Healthy controls) one-way analysis of variance (ANOVA) was used. For pairwise comparisons, Student&#39;s t-test was used. Results were statistically significant at p&lt;0.05 after Bonferroni correction for multiple testing. Spreadsheets of gene/factor lists are provided as supplemental material. 
     EXAMPLE 4 
     Creating a Human Ortholog of the Murine  S. aureus  Classifier 
     Chip Comparer (available from URL:chipcomparer.genome.duke.edu/) was used to identify human orthologs for all possible mouse genes. When there were multiple orthologs, the anti-sense target probes that shared the fewest probes with other genes as identified by the probe label. Chip Comparer identified 17,600 probe sets on the Affymetrix GeneChip Human Genome U133A 2.0 Array that have orthologs in the Affymetrix GeneChip Mouse Genome 430 2.0 Array. Factor scores from the mouse factor model were estimated using this set of 17,600 genes as follows: Given a matrix of expression values, X, and a factor model X=BF+e, missing values were first replaced by mean expression levels for those genes. Step 2: Inverse regression was utilized to compute F*, to estimate the factor scores. Step 3: X was estimated by computing BF* and replaced missing values with the corresponding values from this matrix. Steps 2 and 3 were then repeated until the estimates for the missing values converged. 
     EXAMPLE 5 
     External Validation in an Independent Cohort 
     To externally validate the murine and human  S. aureus  classifiers, publically available expression data from a pediatric cohort with  S. aureus  infection and healthy controls were used. Hospitalized children with invasive  S. aureus  infection were enrolled with sample collection occurring after microbiological confirmation. Healthy controls included children undergoing elective surgical procedures and at healthy outpatient clinic visits. This dataset includes multiple expression platforms. For the purposes of consistency, subjects with Affymetrix U133A data yielding 46  S. aureus -infected patients and 10 healthy controls were included. Given the absence of subjects with  E. coli  infection in the validation cohort, new murine and human  S. aureus  classifiers were derived that excluded animals or subjects with  E. coli  infection. These classifiers were derived and then projected onto the 56-sample validation cohort as described heretofore. 
     EXAMPLE 6 
     Heat Map Generation 
     In order to generate heat maps of gene expression, the factors from the murine and human  S. aureus  classifiers were used. Probes from each factor were identified and tested for differential expression in a one-way ANOVA. Probes with significantly different levels of expression after Bonferroni correction were retained. For the murine data, there were thousands of probes (˜1000-3000, typically) meeting these criteria. Consequently, the p-values were sorted in ascending order and the 100 most significant probes from each factor were retained. Duplicate probes across the factors were removed. The human expression heat map was created in the same manner except all significant probes are presented considering there were fewer factors and genes in the human  S. aureus  classifier as compared to the murine classifier. Heat maps were generated using Matlab (Natick, Mass., USA). 
     EXAMPLE 7 
     Pathway Analysis 
     Pathway analysis for functional annotation of genes was performed with the MetaCore tool of the GeneGO package (GeneGo, Inc., St. Joseph, Mich., USA) (available from URL:www/genego.com). P-values were assigned to pathways based on the number of genes mapping to a particular pathway relative to the total number of genes in that pathway. Statistically significant pathways were defined as a p-value &lt;0.05 (False Discovery Rate [FDR]-adjusted) based on hypergeometric distributions. 
     EXAMPLE 8 
     Murine Sepsis Due to  S. aureus  and  E. coli    
     Clinically relevant  S. aureus  infections in humans typically arise from a primary focus with secondary dissemination. To mimic this process, mice were inoculated via the intraperitoneal (IP) route. Infection-susceptible and infection-resistant inbred mouse strains (A/J and C57BL/6J, respectively) were inoculated with  S. aureus  (Sanger476) or  E. coli  (018:K1:H7) (n=5 per mouse strain and bacterial species). A survival analysis was carried out to determine the optimal duration of infection for subsequent experiments ( FIG. 7A ). Based on this data, A/J and C57BL/6J mice were infected with  S. aureus  (sacrificed at t=0, 2, 4, 6, and 12 hours post-infection; n=10 animals/time point) or  E. coli  (t=0, 2, 6, 12, and 24 hours post-infection; n=10 animals/time point). The effect of infection status, bacterial pathogen, and duration of infection on global patterns of gene expression was assessed using principal component analysis (PCA) (Partek Genomics Suite) ( FIG. 7B-D ). Gene expression patterns clustered by infection status and by pathogen ( S. aureus  vs.  E. coli ). Animals infected with  S. aureus  demonstrated a time-dependent change in gene expression that first manifested at two hours, by which time bacteremia has occurred. This pattern remained stable through 12 hours, when most animals have succumbed to sepsis.  E. coli -infected animals did not reveal this time-dependent progression based on the time points sampled, but had a distinctly different pattern of gene expression that was evident at 2 hours and persisted through 24 hours following infection. A heat map depicting the time-dependent nature of these gene expression changes is presented in  FIG. 8 . 
     EXAMPLE 9 
     Peripheral Blood Gene Expression Signatures Classify  S. aureus -Infected from Uninfected Mice 
     To create a host gene expression-based classifier for  S. aureus  infection, mice from a variety of experimental conditions were utilized (n=187 total). Seven strains of inbred mice were challenged with 4  S. aureus  genetic backgrounds via IP inoculation and sacrificed at various time points as described in Experimental Procedures. The comparator group for model derivation included 50 A/J or C57BL/6J mice inoculated with  E. coli  (O18:K1:H7) as well as 54 non-inoculated mice. Whole blood mRNA was used to generate microarray expression data. A list of differentially expressed genes is presented in Tables 3-17.  FIG. 9  presents the number of overlapping genes in each pairwise comparison. Patterns of co-expressing genes were defined using sparse latent factor regression in an unsupervised manner (i.e. without knowledge of the source animal&#39;s infection status). Factor models are a well-known technique for describing correlation structure in high dimension, low sample size data sets. The sparse latent factor model works by collecting genes that are highly correlated into groups. Predictive models are then built from the latent factors—vectors that describe the aggregate behavior of the group. Subsequently, these factors served as independent variables in a variable selection, binary regression model to distinguish animals with and without  S. aureus  infection. This approach was taken in lieu of using individual gene expression changes for several reasons. A given gene with biological relevance may be differentially expressed in response to  S. aureus  infection but not to the degree that would meet statistical significance. Considering this altered gene expression exists amid a network of other such changes, the collective perturbations in that particular pathway would be more easily detected using factor analysis. Furthermore, changes across multiple biological pathways will be reflected across multiple factors. These can then be collectively harnessed for their diagnostic potential using a binary regression model. 
     Thirty factors were identified, of which 16 demonstrated a pattern of expression significantly associated with infection status (mFactors 15, 7, 23, 13, 9, 29, 28, 2, 17, 16, 21, 1, 5, 4, 26, and 19 in order of greatest significance; ANOVA; p&lt;0.0017 for  S. aureus  vs. control vs.  E. coli  after Bonferroni correction;  FIG. 10 ). These 30 factors were fitted into a penalized binary regression model, termed the “murine  S. aureus  classifier”. The best performing model, as defined by the model with the largest log likelihood value, included four factors (mFactors 7, 15, 23, and 26). Other models may be just as adequate, but this “top” model is referred to. Leave-one-out cross-validation was used to control overfitting and to estimate the model&#39;s performance in subgroups of experimental conditions as described below (mouse strain,  S. aureus  genetic background, duration of infection, and bacterial species [ S. aureus  vs.  E. coli ]). A schematic of the derivation and validation experiments is depicted in  FIG. 1 . 
     The Murine Derivation Cohort includes  S. aureus  infection (n=83), healthy control mice (n=54), and  E. coli  infection (n=50). It served as a validation cohort to assess Mouse Strain Effect,  S. aureus  Genetic Background Effect, Time Course, and to compare  S. aureus  vs.  E. coli  and  E. coli  vs. Healthy. The murine  S. aureus  classifier was externally validated in Outbred Mice (n=30) and the CAPSOD Human Cohort. The CAPSOD Human Cohort includes  S. aureus  BSI (n=32), healthy volunteers (n=43), and  E. coli  BSI (n=19). It served as a validation cohort to compare  S. aureus  vs. Healthy,  S. aureus  vs.  E. coli , and  E. coli  vs. Healthy. Model derivation and validation using the entire cohort of animals or humans is depicted by the blue outline and arrows. An independent classifier was generated using only subjects with  S. aureus  or  E. coli  BSI (green outline). This classifier was validated using leave one out cross validation (green arrow). The Human Pediatric Cohort (n=46  S. aureus,  10 Healthy) used for external validation does not include patients with  E. coli  infection. Therefore,  S. aureus  classifiers were generated from the murine and CAPSOD cohorts that excluded  E. coli  data (red outline and thick red arrow). The Human Pediatric Cohort was used to derive a Human  S. aureus  vs. Healthy classifier which was validated in the  S. aureus -infected and Healthy populations within the murine and CAPSOD human cohorts (thin red arrow). 
     The ability of the murine-derived host gene expression classifier to identify  S. aureus  infection was tested in 7 inbred mouse strains of varying infection susceptibilities. In all 7 strains, the murine  S. aureus  classifier accurately differentiated  S. aureus -infected from control mice (p=4.89×10 −16 ; AUC=0.9964) ( FIG. 2A ). The ability to characterize  S. aureus  infection persisted when A/J mice (infection-susceptible) were challenged with four different  S. aureus  backgrounds: USA100 (the predominant US nosocomial methicillin resistant  S. aureus  [MRSA] genetic background); USA300 (the predominant US community-acquired MRSA genetic background); USA400 (MW2); and Sanger 476 (a methicillin susceptible genetic background) (p=1.92×10 −10  vs. control mice; AUC=1.00) ( FIG. 2B ). Furthermore, the murine  S. aureus  classifier consistently discriminated  S. aureus  infected mice from controls at 2, 4, 6, and 12 hours post-inoculation (p=4.41×10 −16  vs. uninfected mice; AUC 1.00) ( FIG. 2C ). This time interval was selected because two hours is the earliest time point at which  S. aureus  can be cultured from blood; while 12 hours was the point at which animals began to die of  S. aureus  sepsis ( FIG. 7A ). In summary, a classifier based on murine-derived host gene expression accurately identified the presence of  S. aureus  infection in mice under a variety of host, pathogen, and temporal conditions. 
     EXAMPLE 10 
     Murine  S. aureus  Classifier Distinguishes  S. aureus  Infected from  E. coli -Infected Mice 
     Next, it was determined whether the murine  S. aureus  classifier could differentiate  S. aureus  from  E. coli  infection. Both the infection-susceptible A/J and infection-resistant C57BL/6J strains were infected with either  S. aureus  (Sanger 476) or  E. coli  (O18:K1:H7). Animals were sacrificed at 2, 6, and 12 hours after inoculation. The murine  S. aureus  classifier correctly identified 50 of 53 (94.3%) animals as either infected with  S. aureus  or not at 2 hours (50/53), 100% of animals at 6 hours (n=20), and 96.7% of animals at 12 hours (29/30) ( FIG. 3A ). This corresponded to an overall p-value of 7.94×10 −26  by Kruskal-Wallis test (comparing  S. aureus  vs.  E. coli  vs. Healthy controls) with an AUC of 0.9935 across all time points. Next, the murine  S. aureus  classifier was independently validated in outbred CD-1 mice with  S. aureus  infection (Sanger 476 or USA300),  E. coli  infection (018:K1:H7), or uninfected controls (10 animals per condition). The murine derived  S. aureus  model accurately classified 95% of all animals where the reference standard was the known experimental condition (38/40; p=1.47×10 −6 ; 90% sensitivity and 100% specificity; AUC=0.9775) ( FIG. 3B ). 
     The murine  S. aureus  classifier was generated to identify  S. aureus  infection within a population including both healthy and  E. coli  infected animals. However, it is possible this classifier is primarily distinguishing “sick” from “not-sick” phenotypes. In such a case, it would be expected that the classifier would still differentiate animals with  E. coli  infection from uninfected controls. However, this was not observed (AUC 0.5089; p=0.8785) demonstrating the specificity of this classifier for  S. aureus  infection. Thus, a murine derived host gene expression classifier accurately distinguished  S. aureus -infected from  E. coli -infected or uninfected mice across multiple host strains, pathogens, post-infection time points, and was validated in outbred mice. 
     Given this ability to discriminate infection due to different bacterial species, the potential for a factor based classifier was further explored to distinguish infection due to methicillin-resistant (MRSA) or methicillin-sensitive  S. aureus  (MSSA), which have been shown to differ in their pathogenicity and virulence. The same 30 factors described above were fitted into a penalized binary regression model with the specific aim of differentiating MRSA from MSSA infection. Leave-one-out cross-validation was used to control overfitting and to estimate the model&#39;s performance in a population of 19 MRSA-infected and 84 MSSA-infected mice ( FIG. 11 ). Despite some overlap, this classifier accurately differentiated infection due to MRSA or MSSA (AUC 0.8396; p=4.14×10 −6 ). Genes discriminating infection due to MRSA or MSSA that remained significant after adjusting for multiple tests are presented in Table 11. Table 11 shows the probes and corresponding genes that were differentially expressed (after Bonferroni correction) in mice with MRSA vs. MSSA infection. 
     EXAMPLE 11 
     Human  S. aureus  Classifier 
     It was determined whether peripheral blood gene expression in humans could yield a classifier for  S. aureus  BSI. Peripheral whole blood mRNA from 32 patients with  S. aureus  BSI, 19 patients with  E. coli  BSI, and 43 healthy control subjects were used to generate microarray data (Table 1). Also presented is the average probe expression in each comparator group and the fold-change within the pairwise comparison. A list of differentially expressed genes is presented in Tables 7-10.  FIG. 12  presents the number of overlapping genes in each pairwise comparison. Seventy-nine factors were defined and fitted into a linear regression model trained to identify the presence of  S. aureus  BSI. Although 17 factors were independently associated with  S. aureus  BSI ( FIG. 13 ), only two factors remained in the best performing model (hFactors 20 and 74). Similar to the murine  S. aureus  classifier, the human  S. aureus  classifier was generated blind to microbiological diagnosis in an unsupervised manner. Gender was controlled for in the model&#39;s derivation considering the predilection for female sex in  E. coli  BSI (Table 2). The model&#39;s performance in phenotypic subgroups was estimated using leave-one-out cross-validation. The classifier accurately differentiated those with  S. aureus  BSI from healthy controls (72/75 correctly classified; AUC=0.9898; p=5.41×10 −13 ) ( FIG. 4A ). The human  S. aureus  classifier also correctly distinguished  S. aureus  from  E. coli  BSI in 82% (42/51) of cases (AUC=0.8372; p=6.77×10 −4 ). When the human  S. aureus  classifier was applied to subjects with  E. coli  BSI vs. healthy controls, an intermediate level of discrimination (56/62 correctly classified; AUC 0.9229; p=1.38×10 −7 ) was observed. This suggests that the human classifier is partially pathogen specific since  E. coli  BSI could also be distinguished from healthy controls but not with the same degree of accuracy as  S. aureus  BSI. A heat map depicting these gene expression changes is presented in  FIG. 14 . 
     In the human  S. aureus  classifier described above, it is the inclusion of healthy controls that drives the discrimination from  S. aureus  BSI. Considering the clinical importance of differentiating Gram-positive from Gram-negative infections, rather than sick vs. healthy, a penalized binary regression model was created with the specific aim of differentiating human  S. aureus  (n=32) from  E. coli  (n=19) BSI. In this cohort, 52 factors were identified (different from the 79 factors identified when Healthy was included) of which only hFactor 40 remained in the top performing model after controlling for gender. Using leave-one-out cross-validation ( FIG. 4B ), this model had a sensitivity of 62.5% (20/32  S. aureus  BSIs correctly classified) but a specificity of 94.7% (18/19  E. coli  BSIs correctly classified). This corresponds to an AUC of 0.8503 (p=3.47×10 −5 ). 
     EXAMPLE 11 
     A Murine  S. aureus  Classifier Identifies  S. aureus  Infection in Humans 
     It was determined whether the murine  S. aureus  classifier could identify  S. aureus  BSI in humans. To accomplish this, the murine  S. aureus  classifier was projected onto human gene expression data. Specifically, Chip Comparer (available from URL:chipcomparer.genome.duke.edu/) provided a modified representation of the Affymetrix Mouse Genome 430 2.0 Array that only included orthologs of transcripts represented on the Affymetrix Human Genome U133A 2.0 Array. This resulted in a murine  S. aureus  classifier consisting only of genes with human orthologs (68.6% of the total array representation). This classifier was evaluated in the human cohort. To account for potential species specific variation in gene expression, predicted probabilities were plotted on a logit rather than a probabilistic scale. Using this murine  S. aureus  classifier, human patients with  S. aureus  BSI were distinguished from healthy controls (AUC=0.9484; p=4.00×10 −11 ) ( FIG. 5 ). Thus, the host response to  S. aureus  infection was sufficiently conserved that a predictive model generated in one species ( Mus musculus ) identified  S. aureus  BSI in another ( Homo sapiens ). However, the murine-derived  S. aureus  classifier did not differentiate between  S. aureus  and  E. coli  BSI in humans (AUC=0.5905; p=0.2883). 
     EXAMPLE 11 
     Validation of Murine and Human Classifiers in an Independent Pediatric Population 
     The murine and human  S. aureus  classifiers were externally validated in an independent human cohort. This validation cohort consisted of pediatric patients hospitalized due to invasive  S. aureus  infection (n=46) and healthy controls (n=10) who had gene expression data generated on a compatible platform (U133A array) with that used in this study. This cohort did not enroll children with  E. coli  infections. For this reason,  E. coli  infection was excluded from both classifiers. New murine and human  S. aureus  classifiers were developed in the same manner described above but without  E. coli -related expression data. This modified murine  S. aureus  classifier was comprised of mFactors 7, 15, and 26 but not mFactor23. The modified human  S. aureus  classifier only contained hFactor4. Both the murine and human  S. aureus  classifiers differentiated children with  S. aureus  infection from healthy controls in this validation cohort (murine classifier AUC=0.9522, p-value=9.03×10 −6  ( FIG. 6A ); human classifier AUC 0.9217, p-value 3.48×10 −5  ( FIG. 6B )). The converse was also true. A  S. aureus  classifier trained on this independent pediatric cohort accurately discriminated  S. aureus  infection from healthy controls in the CAPSOD human cohort (70/75 correctly classified; AUC=0.9775, p-value=2.03610212) and murine cohort (123/137 correctly classified; AUC=0.9255; p=4.56×10 −17 ). 
     EXAMPLE 11 
       S. aureus  Infection Induces Similar Host Gene-Expression Responses in Mouse and Human 
     Pairwise comparisons were performed to identify genes with significantly different levels of expression (after Bonferroni correction). Comparisons included  S. aureus  infection vs. Healthy,  E. coli  infection vs. Healthy, and  S. aureus  vs.  E. coli  infection in mice and humans. Genes from each pairing were entered into the GeneGo pathway map database. The 50 most significant biological pathways arising from the pairwise comparisons are presented in Tables 12-16, which show the pathway analysis for the genes from pairwise comparisons in the mouse and human study. The top 50 ranked pathways from GeneGo MetaCore pathway analysis based upon p-value are shown. Pathways that are present in both the mouse and human response to the specified pathogen are indicated with an asterisk (*). The genes represented within common pathways are presented in Table 17. Table 17 shows the genes in pathways common to murine and human responses to infection. Human genes and murine genes are separately indicated. 
     A similar number of pathways overlapped between the murine and human responses to  S. aureus  (12 of the top 50) and  E. coli  (14 of the top 50) infection. Most of the overlapping pathways in the murine and human responses to both  S. aureus  and  E. coli  belonged to the broad category of immune response including CD28, ICOS, and the MEF2 pathway. Cytoskeletal remodeling (TGF and WNT) and apoptosis were also common to both infection types in mice and humans. Some pathways were highly significant in the  S. aureus  vs. Healthy comparison but not manifest in  E. coli  vs. Healthy such as NF-kB-associated pathways; the CD40 immune response pathway; and clathrin-coated vesicle transport. As expected, these pathways were also differentially manifest in the direct comparison of murine  S. aureus  and  E. coli  infection. No statistically significant probes were identified that distinguished human  S. aureus  from  E. coli  BSI. One probe, corresponding to the F2RL3 gene, nearly met this statistical cutoff (p-value 5.94×10 −6  with a cutoff of 2.24×10 −6 ). F2RL3 encodes proteinase-activated receptor 4. This molecule is a G-protein coupled receptor activated by thrombin and trypsin but has not previously been implicated in the sepsis or immune response. It is expressed in multiple tissues with high levels in the lung, pancreas, thyroid, testis, and small intestine but not peripheral blood or lymphoid tissues. 
     EXAMPLE 12 
     Discussion of Examples 1-11 
     The current investigation contributes to this goal through three key findings. First,  S. aureus  infection induces conserved host gene expression responses in mice that can differentiate from  E. coli -infected or uninfected mice. This discovery was consistent and robust across multiple inbred mouse strains,  S. aureus  genetic backgrounds, time points, and was validated in outbred mice. The validation step strengthens generalizability and is an important improvement over previous murine gene-expression based classifiers that were developed and tested in only a single inbred mouse strain including the fields of infectious diseases; cancer progression; and aging. Furthermore, this murine predictor was specific for  S. aureus  infection and not simply a marker of illness based on the observation that mice with  E. coli  sepsis could not be distinguished from healthy, uninfected animals. The murine  S. aureus  classifier performed equally well at multiple time points despite progression of illness lending additional support to the specificity of this classifier. Second, human-derived host gene expression signatures differentiated  S. aureus  BSI from  E. coli  BSI or uninfected controls. In contrast to the murine-based classifier, the human-based model was less pathogen specific but still provided a significant degree of differentiation between  S. aureus  and  E. coli  BSI. Finally, the responses to  S. aureus  infection were highly conserved at the transcriptional and pathway level. This conserved response allowed the validation of the murine- and human-derived  S. aureus  classifiers in an independent cohort of  S. aureus -infected patients. 
     Previous efforts to identify a discriminatory host gene expression signature for Gram-positive versus Gram-negative infections have yielded inconsistent results. This is likely due to the observation that transcriptional data derived from complex phenotypes such as infection do not produce just one predictive gene set, but rather generate multiple gene sets associated with the phenotype in question. In the current investigation, well-established methodologies were utilized to derive predictors for  S. aureus  infection in both mice and humans from gene expression data. A key component of this methodology was a dimensional reduction step generating sets of co-expressed genes, termed “factors.” Multiple, individual factors differentiated between various infection states were observed although none performed universally well. For example, mFactor15 was associated with the lowest overall p-value during model generation. The AUC was 0.9587 for  S. aureus  vs. uninfected control mice but only 0.7942 for  S. aureus  vs.  E. coli . In contrast, mFactor23 had an AUC of 0.9800 for  S. aureus  vs.  E. coli  but an AUC of 0.5926 for  S. aureus  vs. uninfected control mice. In order to generate a more robust classifier, factors were used as independent variables to generate a binary regression model. Factor models are an excellent technique for estimating correlation structure in very high dimensional data sets. This comprised the second step in generating the  S. aureus  predictors. It was only by including all factors to build the classifier that the model could be validated in the broadest set of conditions including different bacterial pathogens. Although redundancy among the genes in a molecular classifier is expected and is a potential limitation, such redundancy can also improve robustness for a specific phenotype as is likely to be the case in discriminating  S. aureus  from  E. coli  infection in mice. Comparisons at the individual gene level, as with pairwise comparisons, are likely to reveal differences in relatively simple biological responses. In contrast, dimension reduction with factor modeling as utilized in this study incorporates differences across multiple pathways, allowing for the detection of changes in a more complex pathobiology. Additionally, the factor model construction does not incorporate known biological pathways. This leads to gene groupings that are sometimes difficult to interpret. The advantage of the approach is the extreme dimension reduction which allows for discovery and cross-validation on very small data sets. This is one possible explanation for why the human  S. aureus  classifier differentiated  S. aureus  from  E. coli  whereas no genes met the threshold for differential expression after Bonferroni correction in a pairwise comparison between these two patient populations. The strength of this approach is offset by the possibility that smaller or transient changes in gene expression might be missed. Furthermore, there are likely many combinations of genes and factors that would perform similarly to that described here. This study presents findings related to the best performing classifier using the described methodologies. 
     The murine model has been effectively used to gain insights into the pathophysiology of sepsis in general and  S. aureus  in particular. Murine-derived gene expression signatures have also been successfully translated to non-infectious human conditions such as radiation exposure and breast cancer. Here, the robust performance of a murine-derived  S. aureus  classifier in both mice and humans was described and also offer several lines of evidence supporting a partially conserved host response to  S. aureus  infection in both host species. First, the murine-based predictor could differentiate human  S. aureus  BSI from uninfected controls. Second, the genetic pathways were highly conserved. For example, most of the relevant murine pathways were also significantly associated with  S. aureus  BSI in humans. Finally, the murine-based predictor was highly accurate in classifying  S. aureus  infection in an independent human cohort. 
     The data presented here also indicates that the  S. aureus  classifiers are not being driven by lineage-specific transcript abundance. Specifically, the total leukocyte count and cell lineage distribution (based on routine automated differential measurements) were not different between patients with  S. aureus  infection and  E. coli  infection (15.7×10 9 /L with 86.2% neutrophils vs. 14.1×10 9 /L with 85.8% neutrophils, respectively). However, the human  S. aureus  classifier was still able to differentiate infection due to the two pathogens. The murine  S. aureus  classifier was highly successful in differentiating  S. aureus  infection from healthy and from  E. coli  infection yet was unable to differentiate  E. coli  from healthy. This result would not be expected if transcript abundance was driving the derivation of the classifier. 
     The overlap observed in the gene expression response to  S. aureus  infection in mouse and human was also consistent with published studies. NF-kB signaling pathways have been identified as a critical component of the murine response to infection, which was mirrored in the murine and human data presented here. Similar gene expression-based analyses of the human response to bacterial infection have also revealed the importance of other biological pathways including MHC class I and II antigen presentation, immunological synapse formation, TGF-b receptor signaling, TGF and WNT-dependent cytoskeleton remodeling, and T-cell receptor signaling, all of which were significantly associated with  S. aureus  infection in this study. Hence, mice and humans utilize many of the same or overlapping pathways in response to bacterial sepsis supporting the potential utility of murine-based diagnostics for human disease. 
     EXAMPLE 13 
     Gene Subsets for Diagnostic Assay 
     The mouse factors 7, 15, 23 and 26 together classify mice infected with  S. aureus  as distinct from healthy mice with an area-under-the-curve (AUC or classification accuracy) of 0.996 (where 1 is perfect). In another scenario, mouse factors 7, 15, and 26 translated to their human equivalent are sufficient to distinguish between humans infected with  S. aureus  and those who are healthy with an AUC of 0.9484. 
     In order to determine the subset of genes used in a diagnostic test, the relative contribution each gene makes to the factor&#39;s classification performance will be determined. Specifically, the number of genes required to achieve greater than 90%, 95%, 97%, and 99% of the factor&#39;s classification performance will be defined. Depending on the number of genes necessary to achieve these performance levels, a more limited gene set for diagnostic test development may be used. 
     An overview of the steps necessary for diagnostic test development is as follows: the optimal subset of genes will be identified from the presented factors that retains classification performance (as described above). As an example, the 200 top performing genes from each murine factor are presented. mRNA-specific probes will be generated for each. Patients with known diagnoses will be tested to verify the selected gene&#39;s mRNA can be detected by PCR or some other detection platform. Target gene expression will be measured relative to internal controls. Subsequently, an algorithm will produce a score or probability of  S. aureus  infection. Thresholds will be defined, above and below which a diagnosis will be made. This report would then be reported to the user. 
     It is understood that the foregoing detailed description and accompanying examples are merely illustrative and are not to be taken as limitations upon the scope of the invention, which is defined solely by the appended claims and their equivalents. 
     Various changes and modifications to the disclosed embodiments will be apparent to those skilled in the art. Such changes and modifications, including without limitation those relating to the chemical structures, substituents, derivatives, intermediates, syntheses, compositions, formulations, or methods of use of the invention, may be made without departing from the spirit and scope thereof 
     Any patents or publications mentioned in this specification are indicative of the levels of those skilled in the art to which the invention pertains. These patents and publications are herein incorporated by reference to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference. 
     One skilled in the art will readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The present examples along with the methods described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art which are encompassed within the spirit of the invention as defined by the scope of the claims. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Description of human subjects used to generate a  S. aureus  classifier. 
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                   
                 Subject 
                   
                   
                   
                 Source of 
                 Positive Culture 
                   
                   
               
               
                 Subject 
                 Category 
                 Race 
                 Age 
                 Gender 
                 Infection 
                 Sources 
                 WBC 
                 PMN % 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                 S1 
                 
                   S. aureus 
                 
                 White 
                 82 
                 Male 
                 Endocarditis 
                 Blood 
                 23.6 
                 96.4 
               
               
                 S2 
                 
                   S. aureus 
                 
                 White 
                 70 
                 Female 
                 Skin 
                 Blood, Wound, 
                 11.6 
                 N/A a   
               
               
                   
                   
                   
                   
                   
                   
                 Operative cultures 
               
               
                 S3 
                 
                   S. aureus 
                 
                 Black 
                 41 
                 Male 
                 Catheter b   
                 Blood 
                 14.8 
                 N/A 
               
               
                 S4 
                 
                   S. aureus 
                 
                 White 
                 81 
                 Male 
                 Skin 
                 Blood, Pleural fluid 
                 16.2 
                 N/A 
               
               
                 S5 
                 
                   S. aureus 
                 
                 White 
                 81 
                 Male 
                 Bone 
                 Blood 
                 17.3 
                 N/A 
               
               
                 S6 
                 
                   S. aureus 
                 
                 Black 
                 55 
                 Male 
                 Catheter 
                 Blood, Vascular 
                 14.3 
                 89.8 
               
               
                   
                   
                   
                   
                   
                   
                 catheter site 
               
               
                 S7 
                 
                   S. aureus 
                 
                 Black 
                 69 
                 Female 
                 Catheter 
                 Blood 
                 13 
                 N/A 
               
               
                 S8 
                 
                   S. aureus 
                 
                 Black 
                 44 
                 Female 
                 Catheter 
                 Blood 
                 13 
                 90 
               
               
                 S9 
                 
                   S. aureus 
                 
                 Black 
                 51 
                 Male 
                 Skin 
                 Blood 
                 6.9 
                 73 
               
               
                 S10 
                 
                   S. aureus 
                 
                 Black 
                 47 
                 Male 
                 Skin 
                 Blood 
                 12 
                 87 
               
               
                 S11 
                 
                   S. aureus 
                 
                 White 
                 36 
                 Female 
                 Endocarditis 
                 Blood 
                 22.7 
                 85 
               
               
                 S12 
                 
                   S. aureus 
                 
                 White 
                 54 
                 Male 
                 Bone 
                 Blood 
                 9.8 
                 88 
               
               
                 S13 
                 
                   S. aureus 
                 
                 Black 
                 55 
                 Male 
                 Bone 
                 Blood, Skin, 
                 18.3 
                 87 
               
               
                   
                   
                   
                   
                   
                   
                 Synovial fluid 
               
               
                 S14 
                 
                   S. aureus 
                 
                 Black 
                 42 
                 Male 
                 Unknown 
                 Blood, Urine, 
                 7.6 
                 82 
               
               
                   
                   
                   
                   
                   
                   
                 Sputum 
               
               
                 S15 
                 
                   S. aureus 
                 
                 Black 
                 52 
                 Male 
                 Bone 
                 Blood 
                 10.9 
                 79 
               
               
                 S16 
                 
                   S. aureus 
                 
                 Black 
                 55 
                 Male 
                 Bone 
                 Blood, Skin 
                 28.6 
                 95 
               
               
                 S17 
                 
                   S. aureus 
                 
                 White 
                 52 
                 Male 
                 Skin 
                 Blood, Skin 
                 17.9 
                 84 
               
               
                 S18 
                 
                   S. aureus 
                 
                 N/A 
                 51 
                 Female 
                 Lung 
                 Blood 
                 19.8 
                 78 
               
               
                 S19 c   
                 
                   S. aureus 
                 
                 Black 
                 40 
                 Male 
                 Skin 
                 Blood, Skin 
                 14.7 
                 93 
               
               
                 S20 
                 
                   S. aureus 
                 
                 White 
                 60 
                 Male 
                 Skin 
                 Blood 
                 N/A 
                 N/A 
               
               
                 S21 
                 
                   S. aureus 
                 
                 Black 
                 59 
                 Male 
                 Catheter 
                 Blood 
                 7.5 
                 75.5 
               
               
                 S22 
                 
                   S. aureus 
                 
                 Black 
                 58 
                 Male 
                 Bone 
                 Blood 
                 27.9 
                 N/A 
               
               
                 S23 
                 
                   S. aureus 
                 
                 Black 
                 77 
                 Male 
                 Urinary tract 
                 Blood, Urine, Skin 
                 9.8 
                 80.3 
               
               
                 S24 
                 
                   S. aureus 
                 
                 Black 
                 91 
                 Male 
                 Bone 
                 Blood 
                 15.1 
                 93 
               
               
                 S25 
                 
                   S. aureus 
                 
                 White 
                 75 
                 Female 
                 Catheter 
                 Blood 
                 6 
                 92 
               
               
                 S26 
                 
                   S. aureus 
                 
                 Black 
                 58 
                 Male 
                 Catheter 
                 Blood 
                 23.9 
                 87 
               
               
                 S27 
                 
                   S. aureus 
                 
                 Black 
                 24 
                 Male 
                 Urinary tract 
                 Blood, Urine, 
                 16 
                 76.4 
               
               
                   
                   
                   
                   
                   
                   
                 Sputum 
               
               
                 S28 
                 
                   S. aureus 
                 
                 White 
                 74 
                 Male 
                 Skin 
                 Blood, Abscess 
                 33.2 
                 89 
               
               
                 S29 c   
                 
                   S. aureus 
                 
                 Black 
                 70 
                 Male 
                 Skin 
                 Blood 
                 19.6 
                 82 
               
               
                 S30 
                 
                   S. aureus 
                 
                 White 
                 61 
                 Male 
                 Bone/CNS d   
                 Blood, Abscess 
                 10.4 
                 86 
               
               
                 S31 
                 
                   S. aureus 
                 
                 Black 
                 52 
                 Male 
                 Lung 
                 Blood ( S. aureus ); 
                 6.1 
                 93 
               
               
                   
                   
                   
                   
                   
                   
                 Antigen test ( S. pneumoniae ) 
               
               
                 S32 
                 
                   S. aureus 
                 
                 Black 
                 38 
                 Male 
                 Endocarditis 
                 Blood 
                 16.8 
                 94 
               
               
                 E1 
                 
                   E. coli 
                 
                 Black 
                 43 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 32.6 
                 87.3 
               
               
                 E2 
                 
                   E. coli 
                 
                 White 
                 49 
                 Female 
                 Urinary tract 
                 Blood 
                 14 
                 92.4 
               
               
                 E3 
                 
                   E. coli 
                 
                 Black 
                 44 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 15.7 
                 N/A 
               
               
                 E4 
                 
                   E. coli 
                 
                 White 
                 70 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 20.7 
                 88 
               
               
                 E5 
                 
                   E. coli 
                 
                 Black 
                 40 
                 Male 
                 Urinary tract 
                 Blood, Urine 
                 15 
                 83 
               
               
                 E6 
                 
                   E. coli 
                 
                 White 
                 91 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 5.6 
                 N/A 
               
               
                 E7 
                 
                   E. coli 
                 
                 Black 
                 25 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 11.1 
                 88 
               
               
                 E8 
                 
                   E. coli 
                 
                 White 
                 62 
                 Male 
                 Urinary tract 
                 Blood, Urine 
                 13.3 
                 N/A 
               
               
                 E9 
                 
                   E. coli 
                 
                 Black 
                 70 
                 Male 
                 Urinary tract 
                 Blood 
                 2.4 
                 94 
               
               
                 E10 
                 
                   E. coli 
                 
                 Black 
                 32 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 25.1 
                 N/A 
               
               
                 E11 
                 
                   E. coli 
                 
                 White 
                 54 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 10.8 
                 90 
               
               
                 E12 
                 
                   E. coli 
                 
                 White 
                 74 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 7.3 
                 97 
               
               
                 E13 
                 
                   E. coli 
                 
                 Black 
                 79 
                 Female 
                 Lung 
                 Blood 
                 16.9 
                 77 
               
               
                 E14 
                 
                   E. coli 
                 
                 Black 
                 41 
                 Male 
                 Urinary tract 
                 Blood, Urine 
                 14.3 
                 77.6 
               
               
                 E15 
                 
                   E. coli 
                 
                 White 
                 65 
                 Male 
                 Urinary tract 
                 Blood, Urine 
                 21.6 
                 85 
               
               
                 E16 
                 
                   E. coli 
                 
                 White 
                 63 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 8.5 
                 N/A 
               
               
                 E17 
                 
                   E. coli 
                 
                 White 
                 81 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 14.1 
                 86.5 
               
               
                 E18 
                 
                   E. coli 
                 
                 Black 
                 69 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 11.1 
                 67.6 
               
               
                 E19 
                 
                   E. coli 
                 
                 White 
                 55 
                 Female 
                 Urinary tract 
                 Blood, Urine 
                 7.2 
                 87.5 
               
               
                 H1 
                 Healthy 
                 Black 
                 27 
                 Male 
               
               
                 H2 
                 Healthy 
                 White 
                 24 
                 Female 
               
               
                 H3 
                 Healthy 
                 White 
                 29 
                 Female 
               
               
                 H4 
                 Healthy 
                 White 
                 26 
                 Male 
               
               
                 H5 
                 Healthy 
                 Asian 
                 30 
                 Male 
               
               
                 H6 
                 Healthy 
                 Black 
                 24 
                 Male 
               
               
                 H7 
                 Healthy 
                 White 
                 N/A 
                 Male 
               
               
                 H8 
                 Healthy 
                 Asian 
                 24 
                 Male 
               
               
                 H9 
                 Healthy 
                 Asian 
                 23 
                 Male 
               
               
                 H10 
                 Healthy 
                 White 
                 50 
                 Female 
               
               
                 H11 
                 Healthy 
                 White 
                 23 
                 Female 
               
               
                 H12 
                 Healthy 
                 White 
                 24 
                 Female 
               
               
                 H13 
                 Healthy 
                 White 
                 44 
                 Male 
               
               
                 H14 
                 Healthy 
                 White 
                 24 
                 Female 
               
               
                 H15 
                 Healthy 
                 White 
                 28 
                 Female 
               
               
                 H16 
                 Healthy 
                 White 
                 26 
                 Male 
               
               
                 H17 
                 Healthy 
                 Asian 
                 30 
                 Female 
               
               
                 H18 
                 Healthy 
                 Black 
                 26 
                 Male 
               
               
                 H19 
                 Healthy 
                 White 
                 25 
                 Male 
               
               
                 H20 
                 Healthy 
                 White 
                 24 
                 Male 
               
               
                 H21 
                 Healthy 
                 White 
                 24 
                 Male 
               
               
                 H22 
                 Healthy 
                 Asian 
                 25 
                 Female 
               
               
                 H23 
                 Healthy 
                 Black 
                 24 
                 Female 
               
               
                 H24 
                 Healthy 
                 White 
                 43 
                 Female 
               
               
                 H25 
                 Healthy 
                 White 
                 26 
                 Female 
               
               
                 H26 
                 Healthy 
                 Black 
                 59 
                 Male 
               
               
                 H27 
                 Healthy 
                 Black 
                 25 
                 Female 
               
               
                 H28 
                 Healthy 
                 White 
                 24 
                 Male 
               
               
                 H29 
                 Healthy 
                 White 
                 25 
                 Male 
               
               
                 H30 
                 Healthy 
                 White 
                 26 
                 Male 
               
               
                 H31 
                 Healthy 
                 White 
                 24 
                 Male 
               
               
                 H32 
                 Healthy 
                 White 
                 26 
                 Male 
               
               
                 H33 
                 Healthy 
                 N/A 
                 25 
                 Male 
               
               
                 H34 
                 Healthy 
                 White 
                 53 
                 Female 
               
               
                 H35 
                 Healthy 
                 Black 
                 45 
                 Female 
               
               
                 H36 
                 Healthy 
                 White 
                 23 
                 Male 
               
               
                 H37 
                 Healthy 
                 White 
                 26 
                 Female 
               
               
                 H38 
                 Healthy 
                 White 
                 27 
                 Male 
               
               
                 H39 
                 Healthy 
                 Asian 
                 43 
                 Female 
               
               
                 H40 
                 Healthy 
                 Black 
                 32 
                 Female 
               
               
                 H41 
                 Healthy 
                 N/A 
                 25 
                 Female 
               
               
                 H42 
                 Healthy 
                 Black 
                 43 
                 Female 
               
               
                 H43 
                 Healthy 
                 White 
                 N/A 
                 Female 
               
               
                   
               
               
                   a N/A—Not available. 
               
               
                   b Catheter refers to vascular catheters. 
               
               
                   c Gene expression data for S19 and S29 was generated from blood drawn on the second hospital day. Blood drawn on the day of admission was otherwise used for all other infected subjects. 
               
               
                   d This subject had vertebral osteomyelitis associated with an epidural abscess. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Characteristics of human subjects used for  S. aureus  classifier derivation. 
               
            
           
           
               
               
               
               
            
               
                   
                   S. aureus  (n = 32) 
                 Gram-negative (n = 19) 
                 Healthy (n = 43) 
               
               
                   
               
               
                 Age in years, mean (range) 
                 58 (24-91) 
                 58 (25-91) 
                 30 (23-59) 
               
               
                 Gender, n (%) 
                   
                   
                   
               
               
                 Female 
                  6 (19) 
                 14 (74) 
                 21 (49) 
               
               
                 Male 
                 26 (81) 
                  5 (26) 
                 22 (51) 
               
               
                 Race, n (%) 
                   
                   
                   
               
               
                 Black 
                 20 (63) 
                  9 (47) 
                  9 (21) 
               
               
                 White 
                 11 (34) 
                 10 (53) 
                 26 (60) 
               
               
                 Asian 
                  0 
                  0 
                  6 (14) 
               
               
                 Unknown 
                  1 (3) 
                  0 
                  2 (5) 
               
               
                 Dialysis, n (%) 
                 12 (38) 
                  0 
                  0 
               
               
                 Diabetes, n (%) 
                 13 (41) 
                  3 (16) 
                  0 
               
               
                 Immunosuppression, n (%) 
                  2 (6) 
                  2 (11) 
                  0 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Mouse Factor 7 
               
            
           
           
               
               
               
            
               
                 PROBE ID 
                 SYMBOL 
                 GENE NAME 
               
               
                   
               
               
                 1415741_at 
                 Tmem165 
                 transmembrane protein 165 
               
               
                 1415856_at 
                 Emb 
                 embigin 
               
               
                 1415899_at 
                 Junb 
                 Jun-B oncogene 
               
               
                 1416010_a_at 
                 Ehd1 
                 EH-domain containing 1 
               
               
                 1416035_at 
                 Hif1a 
                 hypoxia inducible factor 1 alpha subunit 
               
               
                 1416119_at 
                 Txn1 
                 thioredoxin 1 
               
               
                 1416249_at 
                 Nadk 
                 NAD kinase 
               
               
                 1416281_at 
                 Wdr45l 
                 Wdr45 like 
               
               
                 1416360_at 
                 Snx18 
                 sorting nexin 18 
               
               
                 1416378_at 
                 Pnkp 
                 polynucleotide kinase 3′-phosphatase 
               
               
                 1416381_a_at 
                 Prdx5 
                 peroxiredoxin 5 
               
               
                 1416440_at 
                 Cd164 
                 CD164 antigen 
               
               
                 1416442_at 
                 Ier2 
                 immediate early response 2 
               
               
                 1416522_a_at 
                 Grcc10 
                 gene rich cluster C10 gene 
               
               
                 1416527_at 
                 Rab32 
                 RAB32 member RAS oncogene family 
               
               
                 1416654_at 
                 Slc31a2 
                 solute carrier family 31 member 2 
               
               
                 1416983_s_at 
                 Foxo1 
                 forkhead box O1 
               
               
                 1417068_a_at 
                 Ptpn1 
                 protein tyrosine phosphatase non-receptor type 1 
               
               
                 1417190_at 
                 Nampt 
                 nicotinamide phosphoribosyltransferase 
               
               
                 1417230_at 
                 Ralgps2 
                 Ral GEF with PH domain and SH3 binding motif 2 
               
               
                 1417408_at 
                 F3 
                 coagulation factor III 
               
               
                 1417409_at 
                 Jun 
                 Jun oncogene 
               
               
                 1417478_a_at 
                 Ppp2r3c 
                 protein phosphatase 2 regulatory subunit B″ gamma 
               
               
                 1417564_at 
                 Med7 
                 mediator complex subunit 7 
               
               
                 1417730_at 
                 Ext1 
                 exostoses (multiple) 1 
               
               
                 1418154_at 
                 N4bp1 
                 NEDD4 binding protein 1 
               
               
                 1418300_a_at 
                 Mknk2 
                 MAP kinase-interacting serine/threonine kinase 2 
               
               
                 1418465_at 
                 Ncf4 
                 neutrophil cytosolic factor 4 
               
               
                 1418539_a_at 
                 Ptpre 
                 protein tyrosine phosphatase receptor type E 
               
               
                 1418797_at 
                 Ms4a8a 
                 membrane-spanning 4-domains subfamily A member 8A 
               
               
                 1418847_at 
                 Arg2 
                 arginase type II 
               
               
                 1418992_at 
                 F10 
                 coagulation factor X 
               
               
                 1418993_s_at 
                 F10 
                 coagulation factor X 
               
               
                 1419004_s_at 
                 NA 
                 NA 
               
               
                 1419006_s_at 
                 Peli2 
                 pellino 2 
               
               
                 1419178_at 
                 Cd3g 
                 CD3 antigen gamma polypeptide 
               
               
                 1419180_at 
                 Bcl9l 
                 B-cell CLL/lymphoma 9-like 
               
               
                 1419208_at 
                 Map3k8 
                 mitogen-activated protein kinase kinase kinase 8 
               
               
                 1419627_s_at 
                 Clec4n 
                 C-type lectin domain family 4 member n 
               
               
                 1419691_at 
                 Camp 
                 cathelicidin antimicrobial peptide 
               
               
                 1419766_at 
                 Sik1 
                 salt inducible kinase 1 
               
               
                 1420012_at 
                 Xbp1 
                 X-box binding protein 1 
               
               
                 1420197_at 
                 Gadd45b 
                 growth arrest and DNA-damage-inducible 45 beta 
               
               
                 1420631_a_at 
                 Blcap 
                 bladder cancer associated protein homolog (human) 
               
               
                 1420867_at 
                 Tmed2 
                 transmembrane emp24 domain trafficking protein 2 
               
               
                 1420868_s_at 
                 Tmed2 
                 transmembrane emp24 domain trafficking protein 2 
               
               
                 1421235_s_at 
                 Recql5 
                 RecQ protein-like 5 
               
               
                 1421326_at 
                 Csf2rb 
                 colony stimulating factor 2 receptor beta low-affinity 
               
               
                   
                   
                 (granulocyte-macrophage) 
               
               
                 1421411_at 
                 Pstpip2 
                 proline-serine-threonine phosphatase-interacting protein 2 
               
               
                 1421547_at 
                 Cd180 
                 CD180 antigen 
               
               
                 1422084_at 
                 Bmx 
                 BMX non-receptor tyrosine kinase 
               
               
                 1422506_a_at 
                 Cstb 
                 cystatin B 
               
               
                 1422508_at 
                 Atp6v1a 
                 ATPase H+ transporting lysosomal V1 subunit A 
               
               
                 1422791_at 
                 Pafah1b2 
                 platelet-activating factor acetylhydrolase isoform 1b subunit 
               
               
                   
                   
                 2 
               
               
                 1423100_at 
                 Fos 
                 FBJ osteosarcoma oncogene 
               
               
                 1423135_at 
                 Thy1 
                 thymus cell antigen 1 theta 
               
               
                 1423213_at 
                 Plxnc1 
                 plexin C1 
               
               
                 1423326_at 
                 Entpd1 
                 ectonucleoside triphosphate diphosphohydrolase 1 
               
               
                 1423346_at 
                 Degs1 
                 degenerative spermatocyte homolog 1 ( Drosophila ) 
               
               
                 1423411_at 
                 Rbm47 
                 RNA binding motif protein 47 
               
               
                 1423722_at 
                 Vmp1 
                 vacuole membrane protein 1 
               
               
                 1423904_a_at 
                 Pyr 
                 poliovirus receptor 
               
               
                 1423996_a_at 
                 Il4ra 
                 interleukin 4 receptor alpha 
               
               
                 1424256_at 
                 Rdh12 
                 retinol dehydrogenase 12 
               
               
                 1424302_at 
                 Lilrb3 
                 leukocyte immunoglobulin-like receptor subfamily B (with 
               
               
                   
                   
                 TM and ITIM domains) member 3 
               
               
                 1424424_at 
                 Slc39a1 
                 solute carrier family 39 (zinc transporter) member 1 
               
               
                 1424444_a_at 
                 1600014C10Rik 
                 RIKEN cDNA 1600014C10 gene 
               
               
                 1424509_at 
                 Cd177 
                 CD177 antigen 
               
               
                 1424996_at 
                 Cflar 
                 CASP8 and FADD-like apoptosis regulator 
               
               
                 1425406_at 
                 Clec4a2 
                 C-type lectin domain family 4 member a2 
               
               
                 1425587_a_at 
                 Ptprj 
                 protein tyrosine phosphatase receptor type J 
               
               
                 1425674_a_at 
                 Ssu72 
                 Ssu72 RNA polymerase II CTD phosphatase homolog 
               
               
                   
                   
                 (yeast) 
               
               
                 1425822_a_at 
                 Dtx1 
                 deltex 1 homolog ( Drosophila ) 
               
               
                 1426227_s_at 
                 Vps37c 
                 vacuolar protein sorting 37C (yeast) 
               
               
                 1426370_at 
                 Far1 
                 fatty acyl CoA reductase 1 
               
               
                 1426440_at 
                 Dhrs7 
                 dehydrogenase/reductase (SDR family) member 7 
               
               
                 1426575_at 
                 Sgms1 
                 sphingomyelin synthase 1 
               
               
                 1426600_at 
                 Slc2a1 
                 solute carrier family 2 (facilitated glucose transporter) 
               
               
                   
                   
                 member 1 
               
               
                 1426680_at 
                 Sepn1 
                 selenoprotein N1 
               
               
                 1426786_s_at 
                 Dhx38 
                 DEAH (Asp-Glu-Ala-His) box polypeptide 38 
               
               
                 1426808_at 
                 Lgals3 
                 lectin galactose binding soluble 3 
               
               
                 1427164_at 
                 Il13ra1 
                 interleukin 13 receptor alpha 1 
               
               
                 1427327_at 
                 Pilra 
                 paired immunoglobin-like type 2 receptor alpha 
               
               
                 1427683_at 
                 Egr2 
                 early growth response 2 
               
               
                 1428094_at 
                 Lamp2 
                 lysosomal-associated membrane protein 2 
               
               
                 1428191_s_at 
                 Mettl17 
                 methyltransferase like 17 
               
               
                 1428381_a_at 
                 Ppdpf 
                 pancreatic progenitor cell differentiation and proliferation 
               
               
                   
                   
                 factor homolog (zebrafish)RIKEN cDNA 2700038C09 gene 
               
               
                 1428466_at 
                 Chd3 
                 chromodomain helicase DNA binding protein 3 
               
               
                 1428579_at 
                 Fmnl2 
                 formin-like 2 
               
               
                 1428663_at 
                 Sgms2 
                 sphingomyelin synthase 2 
               
               
                 1428749_at 
                 Dmxl2 
                 Dmx-like 2 
               
               
                 1428750_at 
                 Cdc42ep2 
                 CDC42 effector protein (Rho GTPase binding) 2 
               
               
                 1428781_at 
                 Dmkn 
                 dermokine 
               
               
                 1428902_at 
                 Chst11 
                 carbohydrate sulfotransferase 11 
               
               
                 1428985_at 
                 Ints12 
                 integrator complex subunit 12 
               
               
                 1429352_at 
                 Mocos 
                 molybdenum cofactor sulfurase 
               
               
                 1429503_at 
                 Fam69a 
                 family with sequence similarity 69 member A 
               
               
                 1429527_a_at 
                 Plscr1 
                 phospholipid scramblase 1 
               
               
                 1429782_at 
                 Grcc10 
                 gene rich cluster C10 gene 
               
               
                 1429889_at 
                 Faim3 
                 Fas apoptotic inhibitory molecule 3 
               
               
                 1430289_a_at 
                 Wdr77 
                 WD repeat domain 77 
               
               
                 1431339_a_at 
                 Efhd2 
                 EF hand domain containing 2 
               
               
                 1433634_at 
                 Irf2bp2 
                 interferon regulatory factor 2 binding protein 2 
               
               
                 1433699_at 
                 Tnfaip3 
                 tumor necrosis factor alpha-induced protein 3 
               
               
                 1433968_a_at 
                 Megf9 
                 multiple EGF-like-domains 9 
               
               
                 1434015_at 
                 Slc2a6 
                 solute carrier family 2 (facilitated glucose transporter) 
               
               
                   
                   
                 member 6 
               
               
                 1434025_at 
                 NA 
                 NA 
               
               
                 1434310_at 
                 Bmpr2 
                 bone morphogenic protein receptor type II (serine/threonine 
               
               
                   
                   
                 kinase) 
               
               
                 1434334_at 
                 Prkd2 
                 protein kinase D2 
               
               
                 1434378_a_at 
                 Mxd4 
                 Max dimerization protein 4 
               
               
                 1434402_at 
                 Samd8 
                 sterile alpha motif domain containing 8 
               
               
                 1434418_at 
                 Lass6 
                 LAG1 homolog ceramide synthase 6 
               
               
                 1434758_at 
                 Crispld2 
                 cysteine-rich secretory protein LCCL domain containing 2 
               
               
                 1434774_at 
                 Rhbdf2 
                 rhomboid 5 homolog 2 ( Drosophila ) 
               
               
                 1434920_a_at 
                 Evl 
                 Ena-vasodilator stimulated phosphoprotein 
               
               
                 1435260_at 
                 Akt3 
                 thymoma viral proto-oncogene 3 
               
               
                 1435477_s_at 
                 Fcgr2b 
                 Fc receptor IgG low affinity IIb 
               
               
                 1435546_a_at 
                 1810013L24Rik 
                 RIKEN cDNA 1810013L24 gene 
               
               
                 1436499_at 
                 Sgms1 
                 sphingomyelin synthase 1 
               
               
                 1436590_at 
                 Ppp1r3b 
                 protein phosphatase 1 regulatory (inhibitor) subunit 3B 
               
               
                 1436819_at 
                 SEPT6 
                 septin 6 
               
               
                 1437152_at 
                 Mex3b 
                 mex3 homolog B ( C. elegans ) 
               
               
                 1437313_x_at 
                 Hmgb2 
                 high mobility group box 2 
               
               
                 1437421_at 
                 6330509M05Rik 
                 RIKEN cDNA 6330509M05 gene 
               
               
                 1438796_at 
                 Nr4a3 
                 nuclear receptor subfamily 4 group A member 3 
               
               
                 1438855_x_at 
                 Tnfaip2 
                 tumor necrosis factor alpha-induced protein 2 
               
               
                 1439814_at 
                 Atp8b4 
                 ATPase class I type 8B member 4 
               
               
                 1440458_at 
                 Cmah 
                 cytidine monophospho-N-acetylneuraminic acid 
               
               
                   
                   
                 hydroxylase 
               
               
                 1442122_at 
                 AI451458 
                 expressed sequence AI451458 
               
               
                 1444122_at 
                 Sycp2 
                 synaptonemal complex protein 2 
               
               
                 1445687_at 
                 Gm885 
                 predicted gene 885 
               
               
                 1447685_x_at 
                 Ets2 
                 E26 avian leukemia oncogene 2 3′ domain 
               
               
                 1448123_s_at 
                 Tgfbi 
                 transforming growth factor beta induced 
               
               
                 1448213_at 
                 Anxa1 
                 annexin A1 
               
               
                 1448231_at 
                 Fkbp5 
                 FK506 binding protein 5 
               
               
                 1448297_a_at 
                 Tnk2 
                 tyrosine kinase non-receptor2 
               
               
                 1448333_at 
                 Adprh 
                 ADP-ribosylarginine hydrolase 
               
               
                 1448443_at 
                 Serpini1 
                 serine (or cysteine) peptidase inhibitor Glade I member 1 
               
               
                 1448462_at 
                 Tdg 
                 thymine DNA glycosylase 
               
               
                 1448561_at 
                 Ncf2 
                 neutrophil cytosolic factor 2 
               
               
                 1448573_a_at 
                 Ceacam10 
                 carcinoembryonic antigen-related cell adhesion molecule 10 
               
               
                 1448618_at 
                 Mvp 
                 major vault protein 
               
               
                 1448700_at 
                 G0s2 
                 G0/G1 switch gene 2 
               
               
                 1448724_at 
                 Cish 
                 cytokine inducible SH2-containing protein 
               
               
                 1448993_at 
                 Atg3 
                 autophagy-related 3 (yeast) 
               
               
                 1449028_at 
                 Rhou 
                 ras homolog gene family member U 
               
               
                 1449037_at 
                 Crem 
                 cAMP responsive element modulator 
               
               
                 1449184_at 
                 Pglyrp1 
                 peptidoglycan recognition protein 1 
               
               
                 1449310_at 
                 Ptger2 
                 prostaglandin E receptor 2 (subtype EP2) 
               
               
                 1449317_at 
                 Cflar 
                 CASP8 and FADD-like apoptosis regulator 
               
               
                 1449336_a_at 
                 S1k 
                 STE20-like kinase (yeast) 
               
               
                 1449731_s_at 
                 Nfkbia 
                 nuclear factor of kappa light polypeptide gene enhancer in 
               
               
                   
                   
                 B-cells inhibitor alpha 
               
               
                 1450081_x_at 
                 Gpi1 
                 glucose phosphate isomerase 1 
               
               
                 1450214_at 
                 Adora2b 
                 adenosine A2b receptor 
               
               
                 1450829_at 
                 Tnfaip3 
                 tumor necrosis factor alpha-induced protein 3 
               
               
                 1451037_at 
                 Ptpn9 
                 protein tyrosine phosphatase non-receptor type 9 
               
               
                 1451201_s_at 
                 Rnh1 
                 ribonuclease/angiogenin inhibitor 1 
               
               
                 1451335_at 
                 Plac8 
                 placenta-specific 8 
               
               
                 1451340_at 
                 Arid5a 
                 AT rich interactive domain 5A (MRF1-like) 
               
               
                 1451507_at 
                 Mef2c 
                 myocyte enhancer factor 2C 
               
               
                 1451537_at 
                 Chi3l1 
                 chitinase 3-like 1 
               
               
                 1451775_s_at 
                 Il13ra1 
                 interleukin 13 receptor alpha 1 
               
               
                 1452197_at 
                 Smc4 
                 structural maintenance of chromosomes 4 
               
               
                 1452237_at 
                 Agfg1 
                 ArfGAP with FG repeats 1 
               
               
                 1452301_at 
                 Aldh3b1 
                 aldehyde dehydrogenase 3 family member B1 
               
               
                 1452732_at 
                 Asprv1 
                 aspartic peptidase retroviral-like 1 
               
               
                 1453009_at 
                 Cpm 
                 carboxypeptidase M 
               
               
                 1453851_a_at 
                 Gadd45g 
                 growth arrest and DNA-damage-inducible 45 gamma 
               
               
                 1454654_at 
                 Dirc2 
                 disrupted in renal carcinoma 2 (human) 
               
               
                 1454713_s_at 
                 Hdc 
                 histidine decarboxylase 
               
               
                 1454799_at 
                 Agpat9 
                 1-acylglycerol-3-phosphate O-acyltransferase 9 
               
               
                 1454897_at 
                 6330509M05Rik 
                 RIKEN cDNA 6330509M05 gene 
               
               
                 1455009_at 
                 Cpd 
                 carboxypeptidase D 
               
               
                 1455081_at 
                 Txnl4b 
                 thioredoxin-like 4B 
               
               
                 1455170_at 
                 2810001G20Rik 
                 RIKEN cDNA 2810001G20 gene 
               
               
                 1455197_at 
                 Rnd1 
                 Rho family GTPase 1 
               
               
                 1455229_x_at 
                 Pgs1 
                 phosphatidylglycerophosphate synthase 1 
               
               
                 1455332_x_at 
                 Fcgr2b 
                 Fc receptor IgG low affinity IIb 
               
               
                 1455353_at 
                 Tmcc1 
                 transmembrane and coiled coil domains 1 
               
               
                 1455405_at 
                 Pstpip2 
                 proline-serine-threonine phosphatase-interacting protein 2 
               
               
                 1455658_at 
                 Cggbp1 
                 CGG triplet repeat binding protein 1 
               
               
                 1455660_at 
                 Csf2rb 
                 colony stimulating factor 2 receptor beta low-affinity 
               
               
                   
                   
                 (granulocyte-macrophage) 
               
               
                 1455665_at 
                 Lonrf1 
                 LON peptidase N-terminal domain and ring finger 1 
               
               
                 1455860_at 
                 Pigh 
                 phosphatidylinositol glycan anchor biosynthesis class H 
               
               
                 1456028_x_at 
                 Marcks 
                 myristoylated alanine rich protein kinase C substrate 
               
               
                 1456055_x_at 
                 Pold1 
                 polymerase (DNA directed) delta 1 catalytic subunit 
               
               
                 1457035_at 
                 AI607873 
                 expressed sequence AI607873 
               
               
                 1457708_at 
                 Mbd4 
                 methyl-CpG binding domain protein 4 
               
               
                 1457728_at 
                 Fam129c 
                 family with sequence similarity 129 member C 
               
               
                 1458206_at 
                 NA 
                 NA 
               
               
                 1458351_s_at 
                 NA 
                 NA 
               
               
                 1459522_s_at 
                 Gyg 
                 glycogenin 
               
               
                 1459903_at 
                 Sema7a 
                 sema domain immunoglobulin domain (Ig) and GPI 
               
               
                   
                   
                 membrane anchor (semaphorin) 7A 
               
               
                 1460006_at 
                 Zfhx3 
                 zinc finger homeobox 3 
               
               
                 1460116_s_at 
                 Spred1 
                 sprouty protein with EVH-1 domain 1 related sequence 
               
               
                 1460227_at 
                 Timp1 
                 tissue inhibitor of metalloproteinase 1 
               
               
                 1460251_at 
                 Fas 
                 Fas (TNF receptor superfamily member 6) 
               
               
                 1460282_at 
                 Trem1 
                 triggering receptor expressed on myeloid cells 1 
               
               
                 1460329_at 
                 B4galt6 
                 UDP-Gal:betaGlcNAc beta 14-galactosyltransferase 
               
               
                   
                   
                 polypeptide 6 
               
               
                 1460335_at 
                 Lysmd3 
                 LysM putative peptidoglycan-binding domain containing 3 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Mouse Factor 15 
               
            
           
           
               
               
               
            
               
                 PROBE ID 
                 SYMBOL 
                 GENE NAME 
               
               
                   
               
               
                 1415741_at 
                 Tmem165 
                 transmembrane protein 165 
               
               
                 1415871_at 
                 Tgfbi 
                 transforming growth factor beta induced 
               
               
                 1415922_s_at 
                 Marcksl1 
                 MARCKS-like 1 
               
               
                 1416010_a_at 
                 Ehd1 
                 EH-domain containing 1 
               
               
                 1416298_at 
                 Mmp9 
                 matrix metallopeptidase 9 
               
               
                 1416359_at 
                 Snx18 
                 sorting nexin 18 
               
               
                 1416369_at 
                 Hiatl1 
                 hippocampus abundant transcript-like 1 
               
               
                 1416381_a_at 
                 Prdx5 
                 peroxiredoxin 5 
               
               
                 1416472_at 
                 Syap1 
                 synapse associated protein 1 
               
               
                 1416522_a_at  
                 Grcc10 
                 gene rich cluster C10 gene 
               
               
                 1416576_at 
                 Socs3 
                 suppressor of cytokine signaling 3 
               
               
                 1416908_s_at 
                 Tsn 
                 translin 
               
               
                 1417191_at 
                 Dnajb9 
                 DnaJ (Hsp40) homolog subfamily B 
               
               
                 1417250_at 
                 Rlim 
                 ring finger protein LIM domain interacting member 9 
               
               
                 1417266_at 
                 Cc16 
                 chemokine (C-C motif) ligand 6 
               
               
                 1417288_at 
                 Plekha2 
                 pleckstrin homology domain-containing family A 
               
               
                   
                   
                 (phosphoinositide binding specific) member 2 
               
               
                 1417291_at 
                 Tnfrsf1a 
                 tumor necrosis factor receptor superfamily member 1a 
               
               
                 1417297_at 
                 Itpr3 
                 inositol 14 
               
               
                 1417434_at 
                 Gpd2 
                 glycerol phosphate dehydrogenase 2 mitochondrial5- 
               
               
                   
                   
                 triphosphate receptor 3 
               
               
                 1417457_at 
                 Cks2 
                 CDC28 protein kinase regulatory subunit 2 
               
               
                 1417483_at 
                 Nfkbiz 
                 nuclear factor of kappa light polypeptide gene enhancer in 
               
               
                   
                   
                 B-cells inhibitor zeta 
               
               
                 1417508_at 
                 Rnf19a 
                 ring finger protein 19A 
               
               
                 1417542_at 
                 Rps6ka2 
                 ribosomal protein S6 kinase polypeptide 2 
               
               
                 1417544_a_at  
                 Flot2 
                 flotillin 2 
               
               
                 1417566_at 
                 Abhd5 
                 abhydrolase domain containing 5 
               
               
                 1417586_at 
                 Timeless 
                 timeless homolog ( Drosophila ) 
               
               
                 1417588_at 
                 Galnt3 
                 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- 
               
               
                   
                   
                 acetylgalactosaminyltransferase 3 
               
               
                 1417730_at 
                 Ext1 
                 exostoses (multiple) 1 
               
               
                 1418054_at 
                 Neurod4 
                 neurogenic differentiation 4 
               
               
                 1418133_at 
                 Bcl3 
                 B-cell leukemia/lymphoma 3 
               
               
                 1418154_at 
                 N4bp1 
                 NEDD4 binding protein 1 
               
               
                 1418300_a_at  
                 Mknk2 
                 MAP kinase-interacting serine/threonine kinase 2 
               
               
                 1418398_a_at 
                 Tspan32 
                 tetraspanin 32 
               
               
                 1418465_at 
                 Ncf4 
                 neutrophil cytosolic factor 4 
               
               
                 1418576_at 
                 Yipf5 
                 Yip1 domain family member 5 
               
               
                 1418578_at 
                 Dgka 
                 diacylglycerol kinase alpha 
               
               
                 1418992_at 
                 F10 
                 coagulation factor X 
               
               
                 1418993_s_at 
                 F10 
                 coagulation factor X 
               
               
                 1419208_at 
                 Map3k8 
                 mitogen-activated protein kinase kinase kinase 8 
               
               
                 1419406_a_at 
                 Bcl11a 
                 B-cell CLL/lymphoma 11A (zinc finger protein) 
               
               
                 1419432_at 
                 Spam1 
                 sperm adhesion molecule 1 
               
               
                 1419998_at 
                 NA 
                 NA 
               
               
                 1420197_at 
                 Gadd45b 
                 growth arrest and DNA-damage-inducible 45 beta 
               
               
                 1420394_s_at 
                 NA 
                 NA 
               
               
                 1420498_a_at 
                 Dab2 
                 disabled homolog 2 ( Drosophila ) 
               
               
                 1420631_a_at 
                 Blcap 
                 bladder cancer associated protein homolog (human) 
               
               
                 1421065_at 
                 Jak2 
                 Janus kinase 2 
               
               
                 1421326_at 
                 Csf2rb 
                 colony stimulating factor 2 receptor beta 
               
               
                 1421479_at 
                 Zfp318 
                 zinc finger protein 318 low-affinity (granulocyte- 
               
               
                   
                   
                 macrophage) 
               
               
                 1421895_at 
                 NA 
                 NA 
               
               
                 1422491_a_at 
                 Bnip2 
                 BCL2/adenovirus E1B interacting protein 2 
               
               
                 1422507_at 
                 Cstb 
                 cystatin B 
               
               
                 1422508_at 
                 Atp6v1a 
                 ATPase H+ transporting 
               
               
                 1422953_at 
                 Fpr2 
                 formyl peptide receptor 2 lysosomal V1 subunit A 
               
               
                 1423053_at 
                 Arf4 
                 ADP-ribosylation factor 4 
               
               
                 1423326_at 
                 Entpd1 
                 ectonucleoside triphosphate diphosphohydrolase 1 
               
               
                 1423345_at 
                 Degs1 
                 degenerative spermatocyte homolog 1 ( Drosophila ) 
               
               
                 1423558_at 
                 Ifngr2 
                 interferon gamma receptor 2 
               
               
                 1423588_at 
                 Arpc4 
                 actin related protein 2/3 complex subunit 4 
               
               
                 1423596_at 
                 Nek6 
                 NIMA (never in mitosis gene a)-related expressed kinase 6 
               
               
                 1423612_at 
                 Clp1 
                 CLP1 cleavage and polyadenylation factor I subunit 
               
               
                 1423989_at 
                 Tecpr1 
                 tectonin beta-propeller repeat containing 1 homolog ( S.   
               
               
                   
                   
                   cerevisiae ) 
               
               
                 1424141_at 
                 Hectd1 
                 HECT domain containing 1 
               
               
                 1424444_a_at 
                 1600014C10Rik 
                 RIKEN cDNA 1600014C10 gene 
               
               
                 1424724_a_at 
                 D16Ertd472e 
                 DNA segment Chr 16 
               
               
                 1424727_at 
                 CcrS 
                 chemokine (C-C motif) receptor 5 ERATO Doi 472 
               
               
                   
                   
                 expressed 
               
               
                 1424779_at 
                 Reep3 
                 receptor accessory protein 3 
               
               
                 1424852_at 
                 Mef2c 
                 myocyte enhancer factor 2C 
               
               
                 1424990_at 
                 Orai1 
                 ORAI calcium release-activated calcium modulator 1 
               
               
                 1425289_a_at 
                 Cr2 
                 complement receptor 2 
               
               
                 1425485_at 
                 Mtmr6 
                 myotubularin related protein 6 
               
               
                 1425486_s_at 
                 Mtmr6 
                 myotubularin related protein 6 
               
               
                 1425493_at 
                 Bmpr1a 
                 bone morphogenetic protein receptor type 1A 
               
               
                 1425611_a_at 
                 Cux1 
                 cut-like homeobox 1 
               
               
                 1425706_a_at 
                 Ddb2 
                 damage specific DNA binding protein 2 
               
               
                 1426369_at 
                 Far1 
                 fatty acyl CoA reductase 1 
               
               
                 1426373_at 
                 Ski 
                 ski sarcoma viral oncogene homolog (avian) 
               
               
                 1426377_at 
                 Zfp281 
                 zinc finger protein 281 
               
               
                 1426390_a_at 
                 Arf1 
                 ADP-ribosylation factor 1 
               
               
                 1426473_at 
                 Dnajc9 
                 DnaJ (Hsp40) homolog subfamily C 
               
               
                 1426550_at 
                 Sidt1 
                 SID1 transmembrane family member 1 member 9 
               
               
                 1426565_at 
                 Igf1r 
                 insulin-like growth factor I receptor 
               
               
                 1426818_at 
                 Arrdc4 
                 arrestin domain containing 4 
               
               
                 1426977_at 
                 Usp47 
                 ubiquitin specific peptidase 47 
               
               
                 1427164_at 
                 Il13ra1 
                 interleukin 13 receptor alpha 1 
               
               
                 1427532_at 
                 Trat1 
                 T cell receptor associated transmembrane adaptor 1 
               
               
                 1427689_a_at 
                 Tnip1 
                 TNFAIP3 interacting protein 1 
               
               
                 1428141_at 
                 Gga2 
                 golgi associated gamma adaptin ear containing 
               
               
                 1428191_s_at 
                 Mettl17 
                 methyltransferase like 17 ARF binding protein 2 
               
               
                 1428207_at 
                 Bcl7a 
                 B-cell CLL/lymphoma 7A 
               
               
                 1428214_at 
                 Tomm7 
                 translocase of outer mitochondrial membrane 7 homolog 
               
               
                   
                   
                 (yeast) 
               
               
                 1428381_a_at 
                 Ppdpf 
                 pancreatic progenitor cell differentiation and proliferation 
               
               
                   
                   
                 factor homolog (zebrafish)RIKEN cDNA 2700038C09 
               
               
                   
                   
                 gene 
               
               
                 1428545_at 
                 0610007L01Rik 
                 RIKEN cDNA 0610007L01 gene 
               
               
                 1428579_at 
                 Fmnl2 
                 formin-like 2 
               
               
                 1428669_at 
                 Bmyc 
                 brain expressed myelocytomatosis oncogene 
               
               
                 1429321_at 
                 Rnf149 
                 ring finger protein 149 
               
               
                 1429400_at 
                 ClcnS 
                 chloride channel 5 
               
               
                 1433864_at 
                 Lrp12 
                 low density lipoprotein-related protein 12 
               
               
                 1433939_at 
                 Aff3 
                 AF4/FMR2 family member 3 
               
               
                 1433943_at 
                 NA 
                 NA 
               
               
                 1434054_at 
                 NA 
                 NA 
               
               
                 1434123_at 
                 Fut11 
                 fucosyltransferase 11 
               
               
                 1434175_s_at 
                 Tecpr1 
                 tectonin beta-propeller repeat containing 1 
               
               
                 1434402_at 
                 Samd8 
                 sterile alpha motif domain containing 8 
               
               
                 1434521_at 
                 Rfx7 
                 regulatory factor X7 
               
               
                 1434547_at 
                 Cpd 
                 carboxypeptidase D 
               
               
                 1434573_at 
                 Traf3ip3 
                 TRAF3 interacting protein 3 
               
               
                 1434705_at 
                 Ctbp2 
                 C-terminal binding protein 2 
               
               
                 1435260_at 
                 Akt3 
                 thymoma viral proto-oncogene 3 
               
               
                 1435517_x_at 
                 Ralb 
                 v-ral simian leukemia viral oncogene homolog B (ras 
               
               
                   
                   
                 related) 
               
               
                 1435793_at 
                 Aph1b 
                 anterior pharynx defective 1b homolog ( C. elegans ) 
               
               
                 1436511_at 
                 BC031781 
                 cDNA sequence BC031781 
               
               
                 1436921_at 
                 Atp7a 
                 ATPase Cu++ transporting 
               
               
                 1436999_at 
                 Pid1 
                 phosphotyrosine interaction domain containing 1 alpha 
               
               
                   
                   
                 polypeptide 
               
               
                 1437152_at 
                 Mex3b 
                 mex3 homolog B ( C. elegans ) 
               
               
                 1437270_a_at 
                 Clcf1 
                 cardiotrophin-like cytokine factor 1 
               
               
                 1437421_at 
                 6330509M05Rik  
                 RIKEN cDNA 6330509M05 gene 
               
               
                 1437591_a_at 
                 Wdr1 
                 WD repeat domain 1 
               
               
                 1437870_at 
                 Slco4c1 
                 solute carrier organic anion transporter family member 4C1 
               
               
                 1437992_x_at 
                 Gja1 
                 gap junction protein alpha 1 
               
               
                 1438044_at 
                 1700047M11Rik  
                 RIKEN cDNA 1700047M11 gene 
               
               
                 1438670_at 
                 Ptpn1 
                 protein tyrosine phosphatase non-receptor type 1 
               
               
                 1439160_at 
                 Pramef8 
                 PRAME family member 8 
               
               
                 1439443_x_at 
                 Tkt 
                 transketolase 
               
               
                 1439457_x_at 
                 Atg12 
                 autophagy-related 12 (yeast) 
               
               
                 1439814_at 
                 Atp8b4 
                 ATPase class I 
               
               
                 1440458_at 
                 Cmah 
                 cytidine monophospho-N-acetylneuraminic acid 
               
               
                   
                   
                 hydroxylase type 8B member 4 
               
               
                 1443021_at 
                 Mthfs 
                 5 10-methenyltetrahydrofolate synthetase 
               
               
                 1444459_at 
                 NA 
                 NA 
               
               
                 1448204_at 
                 Sav1 
                 salvador homolog 1 ( Drosophila ) 
               
               
                 1448443_at 
                 Serpini1 
                 serine (or cysteine) peptidase inhibitor Glade I 
               
               
                 1448561_at 
                 Ncf2 
                 neutrophil cytosolic factor 2 member 1 
               
               
                 1448573_a_at 
                 Ceacam10 
                 carcinoembryonic antigen-related cell adhesion molecule 10 
               
               
                 1448617_at 
                 Cd53 
                 CD53 antigen 
               
               
                 1448700_at 
                 G0s2 
                 G0/G1 switch gene 2 
               
               
                 1448742_at 
                 Snai1 
                 snail homolog 1 ( Drosophila ) 
               
               
                 1448758_at 
                 Nrbf2 
                 nuclear receptor binding factor 2 
               
               
                 1448786_at 
                 Plbd1 
                 phospholipase B domain containing 1 
               
               
                 1449037_at 
                 Crem 
                 cAMP responsive element modulator 
               
               
                 1449324_at 
                 Ero1l 
                 ERO1-like ( S. cerevisiae ) 
               
               
                 1449336_a_at 
                 Slk 
                 STE20-like kinase (yeast) 
               
               
                 1449677_s_at 
                 Tmem38b 
                 transmembrane protein 38B 
               
               
                 1449947_s_at 
                 Zfhx3 
                 zinc finger homeobox 3 
               
               
                 1450116_at 
                 Fam48a 
                 family with sequence similarity 48 member A 
               
               
                 1450214_at 
                 Adora2b 
                 adenosine A2b receptor 
               
               
                 1450377_at 
                 Thbs1 
                 thrombospondin 1 
               
               
                 1450424_a_at 
                 Il18bp 
                 interleukin 18 binding protein 
               
               
                 1450459_at 
                 2010106G01Rik  
                 RIKEN cDNA 2010106G01 gene 
               
               
                 1451079_at 
                 Adpgk 
                 ADP-dependent glucokinase 
               
               
                 1451486_at 
                 Slc46a3 
                 solute carrier family 46 member 3 
               
               
                 1451507_at 
                 Mef2c 
                 myocyte enhancer factor 2C 
               
               
                 1451767_at 
                 Ncf1 
                 neutrophil cytosolic factor 1 
               
               
                 1452093_at 
                 Tmem185b 
                 transmembrane protein 185B 
               
               
                 1452197_at 
                 Smc4 
                 structural maintenance of chromosomes 4 
               
               
                 1452205_x_at 
                 NA 
                 NA 
               
               
                 1452301_at 
                 Aldh3b1 
                 aldehyde dehydrogenase 3 family member B1 
               
               
                 1452316_at 
                 Ints12 
                 integrator complex subunit 12 
               
               
                 1452414_s_at 
                 Ccdc86 
                 coiled-coil domain containing 86 
               
               
                 1452922_at 
                 Ppp1r3d 
                 protein phosphatase 1 regulatory subunit 3D 
               
               
                 1453283_at 
                 Pgm1 
                 phosphoglucomutase 1 
               
               
                 1454976_at 
                 Sod2 
                 superoxide dismutase 2 mitochondrial 
               
               
                 1454984_at 
                 Lifr 
                 leukemia inhibitory factor receptor 
               
               
                 1455019_x_at 
                 Ckap4 
                 cytoskeleton-associated protein 4 
               
               
                 1455089_at 
                 Gng12 
                 guanine nucleotide binding protein (G protein) gamma 12 
               
               
                 1455104_at 
                 Mxd1 
                 MAX dimerization protein 1 
               
               
                 1455133_s_at 
                 AI848100 
                 expressed sequence AI848100 
               
               
                 1455197_at 
                 Rnd1 
                 Rho family GTPase 1 
               
               
                 1455660_at 
                 Csf2rb 
                 colony stimulating factor 2 receptor beta 
               
               
                 1455729_at 
                 Gnaq 
                 guanine nucleotide binding protein alpha q polypeptide 
               
               
                   
                   
                 low-affinity (granulocyte-macrophage) 
               
               
                 1455899_x_at 
                 Socs3 
                 suppressor of cytokine signaling 3 
               
               
                 1456135_s_at 
                 Pxn 
                 paxillin 
               
               
                 1456545_at 
                 Il18rap 
                 interleukin 18 receptor accessory protein 
               
               
                 1456700_x_at 
                 Marcks 
                 myristoylated alanine rich protein kinase C substrate 
               
               
                 1457404_at 
                 Nfkbiz 
                 nuclear factor of kappa light polypeptide gene enhancer in 
               
               
                   
                   
                 B-cells inhibitor zeta 
               
               
                 1457579_at 
                 D11Ertd717e 
                 DNA segment Chr 11 
               
               
                 1457644_s_at  
                 Cxcl1 
                 chemokine (C-X-C motif) ligand 1 ERATO Doi 717 
               
               
                   
                   
                 expressed 
               
               
                 1457753_at 
                 Tlr13 
                 toll-like receptor 13 
               
               
                 1457793_a_at  
                 Whsc1l1 
                 Wolf-Hirschhorn syndrome candidate 1-like 1 (human) 
               
               
                 1457825_x_at  
                 Tcn2 
                 transcobalamin 2 
               
               
                 1457976_at 
                 2010002M12Rik 
                 RIKEN cDNA 2010002M12 gene 
               
               
                 1458308_at 
                 Sbno2 
                 strawberry notch homolog 2 ( Drosophila ) 
               
               
                 1458351_s_at  
                 NA 
                 NA 
               
               
                 1458518_at 
                 Cpeb2 
                 cytoplasmic polyadenylation element binding protein 2 
               
               
                 1458525_at 
                 NA 
                 NA 
               
               
                 1458668_at 
                 Tpd52 
                 tumor protein D52 
               
               
                 1458933_at 
                 Slc22a15 
                 solute carrier family 22 (organic anion/cation transporter) 
               
               
                   
                   
                 member 15 
               
               
                 1459522_s_at 
                 Gyg 
                 glycogenin 
               
               
                 1459718_x_at 
                 Klf6 
                 Kruppel-like factor 6 
               
               
                 1459961_a_at 
                 Stat3 
                 signal transducer and activator of transcription 3 
               
               
                 1460006_at 
                 Zfhx3 
                 zinc finger homeobox 3 
               
               
                 1460033_at 
                 A330023F24Rik 
                 RIKEN cDNA A330023F24 gene 
               
               
                 1460197_a_at 
                 Steap4 
                 STEAP family member 4 
               
               
                 1460227_at 
                 Timp1 
                 tissue inhibitor of metalloproteinase 1 
               
               
                 1460251_at 
                 Fas 
                 Fas (TNF receptor superfamily member 6) 
               
               
                 1460282_at 
                 Trem1 
                 triggering receptor expressed on myeloid cells 1 
               
               
                 1460338_a_at 
                 Crlf3 
                 cytokine receptor-like factor 3 
               
               
                 1460458_at 
                 Crispld2 
                 cysteine-rich secretory protein LCCL domain containing 2 
               
               
                 1460510_a_at 
                 Coq10b 
                 coenzyme Q10 homolog B ( S. cerevisiae ) 
               
               
                 1460573_at 
                 AI848100 
                 expressed sequence AI848100 
               
               
                 1460598_at 
                 Il28ra 
                 interleukin 28 receptor alpha 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Mouse Factor 23 
               
            
           
           
               
               
               
            
               
                 PROBE ID 
                 SYMBOL 
                 GENE NAME 
               
               
                   
               
               
                 1415734_at 
                 Rab7 
                 RAB7 member RAS oncogene family 
               
               
                 1415778_at 
                 Morf412 
                 mortality factor 4 like 2 
               
               
                 1415826_at 
                 Atp6v1h 
                 ATPase H+ transporting lysosomal V1 subunit H 
               
               
                 1415856_at 
                 Emb 
                 embigin 
               
               
                 1415871_at 
                 Tgfbi 
                 transforming growth factor beta induced 
               
               
                 1416011_x_at 
                 Ehd1 
                 EH-domain containing 1 
               
               
                 1416012_at 
                 Ehd1 
                 EH-domain containing 1 
               
               
                 1416067_at 
                 Ifrd1 
                 interferon-related developmental regulator 1 
               
               
                 1416082_at 
                 Rab1 
                 RAB1 member RAS oncogene family 
               
               
                 1416459_at 
                 Arf2 
                 ADP-ribosylation factor 2 
               
               
                 1416466_at 
                 Vapa 
                 vesicle-associated membrane protein associated protein A 
               
               
                 1416467_at 
                 Ddx3x 
                 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3 X- 
               
               
                   
                   
                 linked 
               
               
                 1416496_at 
                 Mrfap1 
                 Morf4 family associated protein 1 
               
               
                 1417218_at 
                 Calhm2 
                 calcium homeostasis modulator 2 
               
               
                 1417268_at 
                 Cd14 
                 CD14 antigen 
               
               
                 1417291_at 
                 Tnfrsf1a 
                 tumor necrosis factor receptor superfamily member 1a 
               
               
                 1417392_a_at  
                 Slc7a7 
                 solute carrier family 7 (cationic amino acid transporter y+ 
               
               
                   
                   
                 system) member 7 
               
               
                 1417478_a_at 
                 Ppp2r3c 
                 protein phosphatase 2 regulatory subunit B″ gamma 
               
               
                 1417564_at 
                 Med7 
                 mediator complex subunit 7 
               
               
                 1417591_at 
                 Ptges2 
                 prostaglandin E synthase 2 
               
               
                 1417597_at 
                 Cd28 
                 CD28 antigen 
               
               
                 1417730_at 
                 Ext1 
                 exostoses (multiple) 1 
               
               
                 1417741_at 
                 Pygl 
                 liver glycogen phosphorylase 
               
               
                 1418300_a_at 
                 Mknk2 
                 MAP kinase-interacting serine/threonine kinase 2 
               
               
                 1418465_at 
                 Ncf4 
                 neutrophil cytosolic factor 4 
               
               
                 1418468_at 
                 Anxa11 
                 annexin All 
               
               
                 1418841_s_at  
                 Cdk11b 
                 cyclin-dependent kinase 11B 
               
               
                 1418992_at 
                 F10 
                 coagulation factor X 
               
               
                 1418993_s_at  
                 F10 
                 coagulation factor X 
               
               
                 1419091_a_at 
                 Anxa2 
                 annexin A2 
               
               
                 1419180_at 
                 Bcl91 
                 B-cell CLL/lymphoma 9-like 
               
               
                 1419607_at 
                 Tnf 
                 tumor necrosis factor 
               
               
                 1419609_at 
                 Ccr1 
                 chemokine (C-C motif) receptor 1 
               
               
                 1419722_at 
                 K1k8 
                 kallikrein related-peptidase 8 
               
               
                 1420012_at 
                 Xbp1 
                 X-box binding protein 1 
               
               
                 1420361_at 
                 Slc11a1 
                 solute carrier family 11 (proton-coupled divalent metal ion 
               
               
                   
                   
                 transporters) member 1 
               
               
                 1420886_a_at  
                 Xbp1 
                 X-box binding protein 1 
               
               
                 1420997_a_at  
                 Gpi1 
                 glucose phosphate isomerase 1 
               
               
                 1421291_at 
                 Il18rap 
                 interleukin 18 receptor accessory protein 
               
               
                 1421463_at 
                 Siglece 
                 sialic acid binding Ig-like lectin E 
               
               
                 1421478_a_at  
                 Zfp318 
                 zinc finger protein 318 
               
               
                 1421855_at 
                 Fgl2 
                 fibrinogen-like protein 2 
               
               
                 1422002_at 
                 Mxd1 
                 MAX dimerization protein 1 
               
               
                 1422013_at 
                 Clec4a2 
                 C-type lectin domain family 4 member a2 
               
               
                 1422046_at 
                 Itgam 
                 integrin alpha M 
               
               
                 1422573_at 
                 Ampd3 
                 adenosine monophosphate deaminase 3 
               
               
                 1422631_at 
                 Ahr 
                 aryl-hydrocarbon receptor 
               
               
                 1422791_at 
                 Pafah1b2 
                 platelet-activating factor acetylhydrolase isoform 1b subunit 
               
               
                   
                   
                 2 
               
               
                 1422879_at 
                 Sypl 
                 synaptophysin-like protein 
               
               
                 1422880_at 
                 Sypl 
                 synaptophysin-like protein 
               
               
                 1422887_a_at 
                 Ctbp2 
                 C-terminal binding protein 2 
               
               
                 1422931_at 
                 Fosl2 
                 fos-like antigen 2 
               
               
                 1423053_at 
                 Arf4 
                 ADP-ribosylation factor 4 
               
               
                 1423100_at 
                 Fos 
                 FBJ osteosarcoma oncogene 
               
               
                 1423112_at 
                 Ube2d3 
                 ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog 
               
               
                   
                   
                 yeast) 
               
               
                 1423135_at 
                 Thy1 
                 thymus cell antigen 1 theta 
               
               
                 1423170_at 
                 Taf7 
                 TAF7 RNA polymerase II TATA box binding protein 
               
               
                   
                   
                 (TBP)-associated factor 
               
               
                 1423326_at 
                 Entpd1 
                 ectonucleoside triphosphate diphosphohydrolase 1 
               
               
                 1423361_at 
                 Yme1l1 
                 YME1-like 1 ( S. cerevisiae ) 
               
               
                 1423383_a_at 
                 Osbpl9 
                 oxysterol binding protein-like 9 
               
               
                 1423466_at 
                 Ccr7 
                 chemokine (C-C motif) receptor 7 
               
               
                 1423558_at 
                 Ifngr2 
                 interferon gamma receptor 2 
               
               
                 1423596_at 
                 Nek6 
                 NIMA (never in mitosis gene a)-related expressed kinase 6 
               
               
                 1423706_a_at 
                 Pgd 
                 phosphogluconate dehydrogenase 
               
               
                 1423854_a_at 
                 Rasl11b 
                 RAS-like family 11 member B 
               
               
                 1423903_at 
                 Pvr 
                 poliovirus receptor 
               
               
                 1424027_at 
                 Pxn 
                 paxillin 
               
               
                 1424441_at 
                 Slc27a4 
                 solute carrier family 27 (fatty acid transporter) member 4 
               
               
                 1424942_a_at 
                 Myc 
                 myelocytomatosis oncogene 
               
               
                 1425128_at 
                 B3gnt8 
                 UDP-GlcNAc:betaGal beta-13-N- 
               
               
                   
                   
                 acetylglucosaminyltransferase 8 
               
               
                 1425346_at 
                 Zfp318 
                 zinc finger protein 318 
               
               
                 1425347_a_at 
                 Zfp318 
                 zinc finger protein 318 
               
               
                 1425485_at 
                 Mtmr6 
                 myotubularin related protein 6 
               
               
                 1425486_s_at 
                 Mtmr6 
                 myotubularin related protein 6 
               
               
                 1425663_at 
                 Il1rn 
                 interleukin 1 receptor antagonist 
               
               
                 1425674_a_at 
                 Ssu72 
                 Ssu72 RNA polymerase II CTD phosphatase homolog 
               
               
                   
                   
                 (yeast) 
               
               
                 1426112_a_at 
                 Cd72 
                 CD72 antigen 
               
               
                 1426227_s_at 
                 Vps37c 
                 vacuolar protein sorting 37C (yeast) 
               
               
                 1426299_at 
                 Snx20 
                 sorting nexin 20 
               
               
                 1426312_at 
                 Bre 
                 brain and reproductive organ-expressed protein 
               
               
                 1426377_at 
                 Zfp281 
                 zinc finger protein 281 
               
               
                 1426396_at 
                 Cd247 
                 CD247 antigen 
               
               
                 1426473_at 
                 Dnajc9 
                 DnaJ (Hsp40) homolog subfamily C member 9 
               
               
                 1426501_a_at 
                 Tifa 
                 TRAF-interacting protein with forkhead-associated domain 
               
               
                 1426554_a_at 
                 Pgam1 
                 phosphoglycerate mutase 1 
               
               
                 1426565_at 
                 Igf1r 
                 insulin-like growth factor I receptor 
               
               
                 1426648_at 
                 Mapkapk2 
                 MAP kinase-activated protein kinase 2 
               
               
                 1426722_at 
                 Slc38a2 
                 solute carrier family 38 member 2 
               
               
                 1426755_at 
                 Ckap4 
                 cytoskeleton-associated protein 4 
               
               
                 1426798_a_at 
                 Ppp1r15b 
                 protein phosphatase 1 regulatory (inhibitor) subunit 15b 
               
               
                 1426808_at 
                 Lgals3 
                 lectin galactose binding soluble 3 
               
               
                 1426988_at 
                 KlhdcS 
                 kelch domain containing 5 
               
               
                 1427102_at 
                 Slfn4 
                 schlafen 4 
               
               
                 1427227_at 
                 Gabrg1 
                 gamma-aminobutyric acid (GABA) A receptor subunit 
               
               
                   
                   
                 gamma 1 
               
               
                 1427314_at 
                 Tmed7 
                 transmembrane emp24 protein transport domain containing 
               
               
                   
                   
                 7 
               
               
                 1427747_a_at 
                 Lcn2 
                 lipocalin 2 
               
               
                 1427899_at 
                 Rnf6 
                 ring finger protein (C3H2C3 type) 6 
               
               
                 1428141_at 
                 Gga2 
                 golgi associated gamma adaptin ear containing ARF 
               
               
                   
                   
                 binding protein 2 
               
               
                 1428192_at 
                 Kbtbd7 
                 kelch repeat and BTB (POZ) domain containing 7 
               
               
                 1428243_at 
                 1700021K19Rik 
                 RIKEN cDNA 1700021K19 gene 
               
               
                 1428720_s_at 
                 NA 
                 NA 
               
               
                 1428875_at 
                 Golim4 
                 golgi integral membrane protein 4 
               
               
                 1428942_at 
                 Mt2 
                 metallothionein 2 
               
               
                 1429413_at 
                 Cpm 
                 carboxypeptidase M 
               
               
                 1429527_a_at 
                 Plscr1 
                 phospholipid scramblase 1 
               
               
                 1429693_at 
                 Dab2 
                 disabled homolog 2 ( Drosophila ) 
               
               
                 1430443_at 
                 Anxa10 
                 annexin A10 
               
               
                 1431339_a_at 
                 Efhd2 
                 EF hand domain containing 2 
               
               
                 1431774_a_at 
                 Lyrm1 
                 LYR motif containing 1 
               
               
                 1433508_at 
                 Klf6 
                 Kruppel-like factor 6 
               
               
                 1433939_at 
                 Aff3 
                 AF4/FMR2 family member 3 
               
               
                 1433943_at 
                 NA 
                 NA 
               
               
                 1434402_at 
                 Samd8 
                 sterile alpha motif domain containing 8 
               
               
                 1434418_at 
                 Lass6 
                 LAG1 homolog ceramide synthase 6 
               
               
                 1434432_at 
                 Rffl 
                 ring finger and FYVE like domain containing protein 
               
               
                 1434502_x_at 
                 Slc4a1 
                 solute carrier family 4 (anion exchanger) member 1 
               
               
                 1434556_at 
                 Tmem170b 
                 transmembrane protein 170B 
               
               
                 1435176_a_at 
                 Id2 
                 inhibitor of DNA binding 2 
               
               
                 1435260_at 
                 Akt3 
                 thymoma viral proto-oncogene 3 
               
               
                 1435449_at 
                 Bc12l11 
                 BCL2-like 11 (apoptosis facilitator) 
               
               
                 1435517_x_at 
                 Ralb 
                 v-ral simian leukemia viral oncogene homolog B (ras 
               
               
                   
                   
                 related) 
               
               
                 1435644_at 
                 Sh3pxd2b 
                 SH3 and PX domains 2B 
               
               
                 1436333_a_at 
                 Synj1 
                 synaptojanin 1 
               
               
                 1436590_at 
                 Ppp1r3b 
                 protein phosphatase 1 regulatory (inhibitor) subunit 3B 
               
               
                 1436763_a_at 
                 Klf9 
                 Kruppel-like factor 9 
               
               
                 1436921_at 
                 Atp7a 
                 ATPase Cu++ transporting alpha polypeptide 
               
               
                 1436986_at 
                 Sntb2 
                 syntrophin basic 2 
               
               
                 1436999_at 
                 Pid1 
                 phosphotyrosine interaction domain containing 1 
               
               
                 1437152_at 
                 Mex3b 
                 mex3 homolog B ( C. elegans ) 
               
               
                 1437270_a_at 
                 Clcf1 
                 cardiotrophin-like cytokine factor 1 
               
               
                 1437271_at 
                 Clcf1 
                 cardiotrophin-like cytokine factor 1 
               
               
                 1437313_x_at 
                 Hmgb2 
                 high mobility group box 2 
               
               
                 1437363_at 
                 Homer1 
                 homer homolog 1 ( Drosophila ) 
               
               
                 1437870_at 
                 Slco4c1 
                 solute carrier organic anion transporter family member 4C1 
               
               
                 1438021_at 
                 Rbm47 
                 RNA binding motif protein 47 
               
               
                 1438044_at 
                 1700047M11Rik 
                 RIKEN cDNA 1700047M11 gene 
               
               
                 1438627_x_at 
                 Pgd 
                 phosphogluconate dehydrogenase 
               
               
                 1438650_x_at 
                 Gja1 
                 gap junction protein alpha 1 
               
               
                 1438657_x_at 
                 NA 
                 NA 
               
               
                 1440458_at 
                 Cmah 
                 cytidine monophospho-N-acetylneuraminic acid 
               
               
                   
                   
                 hydroxylase 
               
               
                 1441843_s_at 
                 NA 
                 NA 
               
               
                 1444402_at 
                 Zc3h12c 
                 zinc finger CCCH type containing 12C 
               
               
                 1445687_at 
                 Gm885 
                 predicted gene 885 
               
               
                 1448165_at 
                 Casp2 
                 caspase 2 
               
               
                 1448190_at 
                 Mrpl33 
                 mitochondrial ribosomal protein L33 
               
               
                 1448199_at 
                 Ankrd10 
                 ankyrin repeat domain 10 
               
               
                 1448210_at 
                 Rab1 
                 RAB1 member RAS oncogene family 
               
               
                 1448231_at 
                 Fkbp5 
                 FK506 binding protein 5 
               
               
                 1448291_at 
                 Mmp9 
                 matrix metallopeptidase 9 
               
               
                 1448318_at 
                 Plin2 
                 perilipin 2 
               
               
                 1448377_at 
                 Slpi 
                 secretory leukocyte peptidase inhibitor 
               
               
                 1448511_at 
                 Ptprcap 
                 protein tyrosine phosphatase receptor type C polypeptide- 
               
               
                   
                   
                 associated protein 
               
               
                 1448617_at 
                 Cd53 
                 CD53 antigen 
               
               
                 1448648_at 
                 Fam114a1 
                 family with sequence similarity 114 member A1 
               
               
                 1448728_a_at 
                 Nfkbiz 
                 nuclear factor of kappa light polypeptide gene enhancer in 
               
               
                   
                   
                 B-cells inhibitor zeta 
               
               
                 1448795_a_at 
                 NA 
                 NA 
               
               
                 1448861_at 
                 Traf5 
                 TNF receptor-associated factor 5 
               
               
                 1448898_at 
                 Ccl9 
                 chemokine (C-C motif) ligand 9 
               
               
                 1449303_at 
                 Sesn3 
                 sestrin 3 
               
               
                 1449310_at 
                 Ptger2 
                 prostaglandin E receptor 2 (subtype EP2) 
               
               
                 1449336_a_at 
                 Slk 
                 STE20-like kinase (yeast) 
               
               
                 1449342_at 
                 Ptplb 
                 protein tyrosine phosphatase-like (proline instead of 
               
               
                   
                   
                 catalytic arginine) member b 
               
               
                 1450513_at 
                 Cd33 
                 CD33 antigen 
               
               
                 1450654_a_at 
                 Dhdds 
                 dehydrodolichyl diphosphate synthase 
               
               
                 1450858_a_at 
                 Ube2d3 
                 ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog 
               
               
                   
                   
                 yeast) 
               
               
                 1451097_at 
                 Vasp 
                 vasodilator-stimulated phosphoprotein 
               
               
                 1452045_at 
                 Zfp281 
                 zinc finger protein 281 
               
               
                 1452163_at 
                 Ets1 
                 E26 avian leukemia oncogene 1 5′ domain 
               
               
                 1452181_at 
                 Ckap4 
                 cytoskeleton-associated protein 4 
               
               
                 1452443_s_at 
                 Helz 
                 helicase with zinc finger domain 
               
               
                 1452922_at 
                 Ppp1r3d 
                 protein phosphatase 1 regulatory subunit 3D 
               
               
                 1453985_at 
                 0610007P08Rik 
                 RIKEN cDNA 0610007P08 gene 
               
               
                 1454064_a_at 
                 Rnf138 
                 ring finger protein 138 
               
               
                 1454699_at 
                 Sesn1 
                 sestrin 1 
               
               
                 1454762_at 
                 Xkrx 
                 X Kell blood group precursor related X linked 
               
               
                 1454896_at 
                 Rbpj 
                 recombination signal binding protein for immunoglobulin 
               
               
                   
                   
                 kappa J region 
               
               
                 1454976_at 
                 Sod2 
                 superoxide dismutase 2 mitochondrial 
               
               
                 1454984_at 
                 Lifr 
                 leukemia inhibitory factor receptor 
               
               
                 1455229_x_at 
                 Pgs1 
                 phosphatidylglycerophosphate synthase 1 
               
               
                 1455353_at 
                 Tmcc1 
                 transmembrane and coiled coil domains 1 
               
               
                 1455729_at 
                 Gnaq 
                 guanine nucleotide binding protein alpha q polypeptide 
               
               
                 1456037_x_at 
                 Preb 
                 prolactin regulatory element binding 
               
               
                 1456307_s_at 
                 Adcy7 
                 adenylate cyclase 7 
               
               
                 1456388_at 
                 Atp11a 
                 ATPase class VI type 11A 
               
               
                 1456545_at 
                 Il18rap 
                 interleukin 18 receptor accessory protein 
               
               
                 1457035_at 
                 AI607873 
                 expressed sequence AI607873 
               
               
                 1457645_at 
                 C130079G13Rik 
                 RIKEN cDNA C130079G13 gene 
               
               
                 1457917_at 
                 Lck 
                 lymphocyte protein tyrosine kinase 
               
               
                 1458067_at 
                 Fam179b 
                 family with sequence similarity 179 member B 
               
               
                 1458518_at 
                 Cpeb2 
                 cytoplasmic polyadenylation element binding protein 2 
               
               
                 1458668_at 
                 Tpd52 
                 tumor protein D52 
               
               
                 1460197_a_at 
                 Steap4 
                 STEAP family member 4 
               
               
                 1460227_at 
                 Timp1 
                 tissue inhibitor of metalloproteinase 1 
               
               
                 1460271_at 
                 Trem3 
                 triggering receptor expressed on myeloid cells 3 
               
               
                 1460329_at 
                 B4galt6 
                 UDP-Gal:betaGlcNAc beta 14-galactosyltransferase 
               
               
                   
                   
                 polypeptide 6 
               
               
                 1460335_at 
                 Lysmd3 
                 LysM putative peptidoglycan-binding domain containing 3 
               
               
                 1460408_at 
                 Gabrg1 
                 gamma-aminobutyric acid (GABA) A receptor subunit 
               
               
                   
                   
                 gamma 1 
               
               
                 1460510_a_at 
                 Coq10b 
                 coenzyme Q10 homolog B ( S. cerevisiae ) 
               
               
                 1460573_at 
                 AI848100 
                 expressed sequence AI848100 
               
               
                 1460735_at 
                 Svil 
                 supervillin 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Mouse Factor 26 
               
            
           
           
               
               
               
            
               
                 PROBE ID 
                 SYMBOL 
                 GENE NAME 
               
               
                   
               
               
                 1415686_at 
                 Rab14 
                 RAB14 member RAS oncogene family 
               
               
                 1415800_at 
                 Gja1 
                 gap junction proteinalpha 1 
               
               
                 1415830_at 
                 OrcS 
                 origin recognition complex subunit 5 
               
               
                 1415871_at 
                 Tgfbi 
                 transforming growth factor beta induced 
               
               
                 1416019_at 
                 Dr1 
                 down-regulator of transcription 1 
               
               
                 1416234_at 
                 Lrrc59 
                 leucine rich repeat containing 59 
               
               
                 1416360_at 
                 Snx18 
                 sorting nexin 18 
               
               
                 1416369_at 
                 Hiatl1 
                 hippocampus abundant transcript-like 1 
               
               
                 1416435_at 
                 Ltbr 
                 lymphotoxin B receptor 
               
               
                 1416502_a_at 
                 Preb 
                 prolactin regulatory element binding 
               
               
                 1416522_a_at 
                 Grcc10 
                 gene rich cluster C10 gene 
               
               
                 1416527_at 
                 Rab32 
                 RAB32 member RAS oncogene family 
               
               
                 1416543_at 
                 Nfe2l2 
                 nuclear factor erythroid derived 2 like 2 
               
               
                 1416573_at 
                 Pofut2 
                 protein O-fucosyltransferase 2 
               
               
                 1416576_at 
                 Socs3 
                 suppressor of cytokine signaling 3 
               
               
                 1416700_at 
                 Rnd3 
                 Rho family GTPase 3 
               
               
                 1416881_at 
                 Mcl1 
                 myeloid cell leukemia sequence 1 
               
               
                 1416981_at 
                 Foxo1 
                 forkhead box O1 
               
               
                 1416983_s_at  
                 Foxo1 
                 forkhead box O1 
               
               
                 1417297_at 
                 Itpr3 
                 inositol 145-triphosphate receptor 3 
               
               
                 1417392_a_at  
                 Slc7a7 
                 solute carrier family 7 (cationic amino acid transporter y+ 
               
               
                   
                   
                 system) member 7 
               
               
                 1417446_at 
                 Slc12a4 
                 solute carrier family 12 member 4 
               
               
                 1417460_at 
                 Ifitm2 
                 interferon induced transmembrane protein 2 
               
               
                 1417509_at 
                 Rnf19a 
                 ring finger protein 19A 
               
               
                 1417566_at 
                 Abhd5 
                 abhydrolase domain containing 5 
               
               
                 1417661_at 
                 Rdm1 
                 RAD52 motif 1 
               
               
                 1417696_at 
                 Soat1 
                 sterol O-acyltransferase 1 
               
               
                 1417744_a_at  
                 Ralb 
                 v-ral simian leukemia viral oncogene homolog B (ras 
               
               
                   
                   
                 related) 
               
               
                 1417859_at 
                 Gas7 
                 growth arrest specific 7 
               
               
                 1417890_at 
                 Pdxp 
                 pyridoxal (pyridoxine vitamin B6) phosphatase 
               
               
                 1417985_at 
                 Nrarp 
                 Notch-regulated ankyrin repeat protein 
               
               
                 1418133_at 
                 Bcl3 
                 B-cell leukemia/lymphoma 3 
               
               
                 1418468_at 
                 Anxa11 
                 annexin A11 
               
               
                 1418574_a_at  
                 Shfm1 
                 split hand/foot malformation (ectrodactyly) type 1 
               
               
                 1418612_at 
                 Slfn1 
                 schlafen 1 
               
               
                 1418798_s_at  
                 Srpk3 
                 serine/arginine-rich protein specific kinase 3 
               
               
                 1418901_at 
                 Cebpb 
                 CCAAT/enhancer binding protein (C/EBP) beta 
               
               
                 1418930_at 
                 Cxcl10 
                 chemokine (C-X-C motif) ligand 10 
               
               
                 1419006_s_at  
                 Peli2 
                 pellino 2 
               
               
                 1419178_at 
                 Cd3g 
                 CD3 antigen gamma polypeptide 
               
               
                 1419508_at 
                 Ripk1 
                 receptor (TNFRSF)-interacting serine-threonine kinase 1 
               
               
                 1419641_at 
                 Purb 
                 purine rich element binding protein B 
               
               
                 1419709_at 
                 Stfa3 
                 stefin A3 
               
               
                 1419721_at 
                 Niacr1 
                 niacin receptor 1 
               
               
                 1419722_at 
                 Klk8 
                 kallikrein related-peptidase 8 
               
               
                 1420369_a_at  
                 Csn2 
                 casein beta 
               
               
                 1420394_s_at  
                 NA 
                 NA 
               
               
                 1420591_at 
                 Gpr84 
                 G protein-coupled receptor 84 
               
               
                 1420873_at 
                 Twf1 
                 twinfilin actin-binding protein homolog 1 ( Drosophila ) 
               
               
                 1421366_at 
                 Clec5a 
                 C-type lectin domain family 5 member a 
               
               
                 1421547_at 
                 Cd180 
                 CD180 antigen 
               
               
                 1421863_at 
                 Vampl1 
                 vesicle-associated membrane protein 1 
               
               
                 1422013_at 
                 Clec4a2 
                 C-type lectin domain family 4 member a2 
               
               
                 1422506_a_at 
                 Cstb 
                 cystatin B 
               
               
                 1422519_at 
                 Cask 
                 calcium/calmodulin-dependent serine protein kinase 
               
               
                   
                   
                 (MAGUK family) 
               
               
                 1422557_s_at 
                 Mt1 
                 metallothionein 1 
               
               
                 1423167_at 
                 Mobkl3 
                 MOB1 Mps One Binder kinase activator-like 3 (yeast) 
               
               
                 1423313_at 
                 Pde7a 
                 phosphodiesterase 7A 
               
               
                 1423383_a_at 
                 Osbpl9 
                 oxysterol binding protein-like 9 
               
               
                 1423632_at 
                 Gpr146 
                 G protein-coupled receptor 146 
               
               
                 1423670_a_at 
                 Srpr 
                 signal recognition particle receptor (‘docking protein’) 
               
               
                 1423743_at 
                 Arcn1 
                 archain 1 
               
               
                 1423754_at 
                 Ifitm3 
                 interferon induced transmembrane protein 3 
               
               
                 1423838_s_at 
                 2400003C14Rik 
                 RIKEN cDNA 2400003C14 gene 
               
               
                 1423989_at 
                 Tecpr1 
                 tectonin beta-propeller repeat containing 1 
               
               
                 1424032_at 
                 Hven1 
                 hydrogen voltage-gated channel 1 
               
               
                 1424254_at 
                 Ifitm1 
                 interferon induced transmembrane protein 1 
               
               
                 1424256_at 
                 Rdh12 
                 retinol dehydrogenase 12 
               
               
                 1424564_at 
                 2410001C21Rik 
                 RIKEN cDNA 2410001C21 gene 
               
               
                 1424573_at 
                 Tmed5 
                 transmembrane emp24 protein transport domain containing 
               
               
                   
                   
                 5 
               
               
                 1424906_at 
                 Pqlc3 
                 PQ loop repeat containing 
               
               
                 1425128_at 
                 B3gnt8 
                 UDP-GlcNAc:betaGal beta-13-N- 
               
               
                   
                   
                 acetylglucosaminyltransferase 8 
               
               
                 1425407_s_at 
                 NA 
                 NA 
               
               
                 1425492_at 
                 Bmpr1a 
                 bone morphogenetic protein receptor type 1A 
               
               
                 1425587_a_at 
                 Ptprj 
                 protein tyrosine phosphatase receptor type J 
               
               
                 1425933_a_at 
                 Nt5c2 
                 5′-nucleotidase cytosolic II 
               
               
                 1425977_a_at 
                 Slk 
                 STE20-like kinase (yeast) 
               
               
                 1426063_a_at 
                 Gem 
                 GTP binding protein (gene overexpressed in skeletal muscle) 
               
               
                 1426368_at 
                 Rin2 
                 Ras and Rab interactor 2 
               
               
                 1426369_at 
                 Far1 
                 fatty acyl CoA reductase 1 
               
               
                 1426708_at 
                 Antxr2 
                 anthrax toxin receptor 2 
               
               
                 1426865_a_at 
                 Ncam1 
                 neural cell adhesion molecule 1 
               
               
                 1426899_at 
                 Tbc1d23 
                 TBC1 domain family member 23 
               
               
                 1426978_at 
                 NA 
                 NA 
               
               
                 1427243_at 
                 Rell1 
                 RELT-like 1 
               
               
                 1428141_at 
                 Gga2 
                 golgi associated gamma adaptin ear containing ARF binding 
               
               
                   
                   
                 protein 2 
               
               
                 1428214_at 
                 Tomm7 
                 translocase of outer mitochondrial membrane 7 homolog 
               
               
                   
                   
                 (yeast) 
               
               
                 1428231_at 
                 Cpsf6 
                 cleavage and polyadenylation specific factor 6 
               
               
                 1428357_at 
                 2610019F03Rik  
                 RIKEN cDNA 2610019F03 gene 
               
               
                 1428702_at 
                 Ddx28 
                 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 
               
               
                 1428719_at 
                 NA 
                 NA 
               
               
                 1428985_at 
                 Ints12 
                 integrator complex subunit 12 
               
               
                 1429115_at 
                 NA 
                 NA 
               
               
                 1429321_at 
                 Rnf149 
                 ring finger protein 149 
               
               
                 1429466_s_at  
                 NA 
                 NA 
               
               
                 1429527_a_at  
                 Plscr1 
                 phospholipid scramblase 1 
               
               
                 1429775_a_at  
                 NA 
                 NA 
               
               
                 1433454_at 
                 Abtb2 
                 ankyrin repeat and BTB (POZ) domain containing 2 
               
               
                 1433815_at 
                 Jakmip1 
                 janus kinase and microtubule interacting protein 1 
               
               
                 1434025_at 
                 NA 
                 NA 
               
               
                 1434054_at 
                 NA 
                 NA 
               
               
                 1434070_at 
                 Jag1 
                 jagged 1 
               
               
                 1434126_at 
                 4930402H24Rik 
                 RIKEN cDNA 4930402H24 gene 
               
               
                 1434310_at 
                 Bmpr2 
                 bone morphogenic protein receptor type II (serine/threonine 
               
               
                   
                   
                 kinase) 
               
               
                 1434311_at 
                 Cnot6l 
                 CCR4-NOT transcription complex subunit 6-like 
               
               
                 1434431_x_at  
                 Adora2b 
                 adenosine A2b receptor 
               
               
                 1434484_at 
                 1100001G20Rik 
                 RIKEN cDNA 1100001G20 gene 
               
               
                 1434487_at 
                 Mef2d 
                 myocyte enhancer factor 2D 
               
               
                 1434773_a_at  
                 Slc2a1 
                 solute carrier family 2 (facilitated glucose transporter) 
               
               
                   
                   
                 member 1 
               
               
                 1434814_x_at 
                 Gpi1 
                 glucose phosphate isomerase 1 
               
               
                 1435077_at 
                 Asxl1 
                 additional sex combs like 1 ( Drosophila ) 
               
               
                 1435176_a_at 
                 Id2 
                 inhibitor of DNA binding 2 
               
               
                 1435231_at 
                 Coq4 
                 coenzyme Q4 homolog (yeast) 
               
               
                 1435458_at 
                 Pim1 
                 proviral integration site 1 
               
               
                 1435996_at 
                 Card11 
                 caspase recruitment domain family member 11 
               
               
                 1436077_a_at  
                 Fcho1 
                 FCH domain only 1 
               
               
                 1436103_at 
                 Rab3ip 
                 RAB3A interacting protein 
               
               
                 1436666_at 
                 NA 
                 NA 
               
               
                 1437111_at 
                 Zc3h12c 
                 zinc finger CCCH type containing 12C 
               
               
                 1437225_x_at  
                 Gnai3 
                 guanine nucleotide binding protein (G protein) alpha 
               
               
                   
                   
                 inhibiting 3 
               
               
                 1437270_a_at 
                 Clcf1 
                 cardiotrophin-like cytokine factor 1 
               
               
                 1437313_x_at 
                 Hmgb2 
                 high mobility group box 2 
               
               
                 1438031_at 
                 Rasgrp3 
                 RAS guanyl releasing protein 3 
               
               
                 1438627_x_at 
                 Pgd 
                 phosphogluconate dehydrogenase 
               
               
                 1439443_x_at 
                 Tkt 
                 transketolase 
               
               
                 1439662_at 
                 Homer1 
                 homer homolog 1 ( Drosophila ) 
               
               
                 1439799_at 
                 NA 
                 NA 
               
               
                 1441079_at 
                 Mbd4 
                 methyl-CpG binding domain protein 4 
               
               
                 1441962_at 
                 Alox5 
                 arachidonate 5-lipoxygenase 
               
               
                 1442122_at 
                 AI451458 
                 expressed sequence AI451458 
               
               
                 1444090_at 
                 Pram1 
                 PML-RAR alpha-regulated adaptor molecule 1 
               
               
                 1444985_at 
                 NA 
                 NA 
               
               
                 1447918_x_at 
                 Iglv1 
                 immunoglobulin lambda variable 1 
               
               
                 1448159_at 
                 Rab7 
                 RAB7 member RAS oncogene family 
               
               
                 1448306_at 
                 Nfkbia 
                 nuclear factor of kappa light polypeptide gene enhancer in 
               
               
                   
                   
                 B-cells inhibitor alpha 
               
               
                 1448333_at 
                 Adprh 
                 ADP-ribosylarginine hydrolase 
               
               
                 1448377_at 
                 Slpi 
                 secretory leukocyte peptidase inhibitor 
               
               
                 1448543_at 
                 Slmo2 
                 slowmo homolog 2 ( Drosophila ) 
               
               
                 1448559_at 
                 Flot1 
                 flotillin 1 
               
               
                 1448604_at 
                 Uck2 
                 uridine-cytidine kinase 2 
               
               
                 1448856_a_at 
                 Msra 
                 methionine sulfoxide reductase A 
               
               
                 1448948_at 
                 Slc50a1 
                 solute carrier family 50 (sugar transporter) member 1 
               
               
                 1448957_at 
                 Rbpj 
                 recombination signal binding protein for immunoglobulin 
               
               
                   
                   
                 kappa J region 
               
               
                 1449028_at 
                 Rhou 
                 ras homolog gene family member U 
               
               
                 1449455_at 
                 Hck 
                 hemopoietic cell kinase 
               
               
                 1449591_at 
                 Casp4 
                 caspase 4 apoptosis-related cysteine peptidase 
               
               
                 1449712_s_at 
                 Atp6v1e1 
                 ATPase H+ transporting lysosomal V1 subunit El 
               
               
                 1449829_at 
                 Itgb2l 
                 integrin beta 2-like 
               
               
                 1449858_at 
                 Cd86 
                 CD86 antigen 
               
               
                 1450295_s_at 
                 Pvr 
                 poliovirus receptor 
               
               
                 1450459_at 
                 2010106G01Rik 
                 RIKEN cDNA 2010106G01 gene 
               
               
                 1450742_at 
                 Bysl 
                 bystin-like 
               
               
                 1450786_x_at 
                 Pdlim5 
                 PDZ and LIM domain 5 
               
               
                 1450882_s_at 
                 NA 
                 NA 
               
               
                 1450913_at 
                 B4galt6 
                 UDP-Gal:betaGlcNAc beta 14-galactosyltransferase 
               
               
                   
                   
                 polypeptide 6 
               
               
                 1450937_at 
                 Lin7c 
                 lin-7 homolog C ( C. elegans ) 
               
               
                 1450971_at 
                 Gadd45b 
                 growth arrest and DNA-damage-inducible 45 beta 
               
               
                 1451015_at 
                 Tkt 
                 transketolase 
               
               
                 1451037_at 
                 Ptpn9 
                 protein tyrosine phosphatase non-receptor type 9 
               
               
                 1451079_at 
                 Adpgk 
                 ADP-dependent glucokinase 
               
               
                 1451171_at 
                 2310008H04Rik 
                 RIKEN cDNA 2310008H04 gene 
               
               
                 1451275_at 
                 Uhrf1bp1l 
                 UHRF1 (ICBP90) binding protein 1-like 
               
               
                 1451317_at 
                 Ythdf2 
                 YTH domain family 2 
               
               
                 1451387_s_at  
                 Cuta 
                 cutA divalent cation tolerance homolog ( E. coli ) 
               
               
                 1451436_at 
                 Sbno1 
                 sno strawberry notch homolog 1 ( Drosophila ) 
               
               
                 1451458_at 
                 Tmem2 
                 transmembrane protein 2 
               
               
                 1451537_at 
                 Chi3l1 
                 chitinase 3-like 1 
               
               
                 1451713_a_at  
                 Fcer2a 
                 Fc receptor IgE low affinity II alpha polypeptide 
               
               
                 1451767_at 
                 Ncf1 
                 neutrophil cytosolic factor 1 
               
               
                 1452024_a_at  
                 Ldb1 
                 LIM domain binding 1 
               
               
                 1452118_at 
                 Rrp1b 
                 ribosomal RNA processing 1 homolog B ( S. cerevisiae ) 
               
               
                 1452162_at 
                 Wdr48 
                 WD repeat domain 48 
               
               
                 1452163_at 
                 Ets1 
                 E26 avian leukemia oncogene 1 5′ domain 
               
               
                 1452306_at 
                 Zfyve26 
                 zinc finger FYVE domain containing 26 
               
               
                 1452408_at 
                 NA 
                 NA 
               
               
                 1452483_a_at 
                 Cd44 
                 CD44 antigen 
               
               
                 1452732_at 
                 Asprv1 
                 aspartic peptidase retroviral-like 1 
               
               
                 1453009_at 
                 Cpm 
                 carboxypeptidase M 
               
               
                 1454197_a_at  
                 Ccdc86 
                 coiled-coil domain containing 86 
               
               
                 1454654_at 
                 Dirc2 
                 disrupted in renal carcinoma 2 (human) 
               
               
                 1454711_at 
                 Trio 
                 triple functional domain (PTPRF interacting) 
               
               
                 1454880_s_at  
                 Bmf 
                 BCL2 modifying factor 
               
               
                 1454979_at 
                 Diap1 
                 diaphanous homolog 1 ( Drosophila ) 
               
               
                 1455000_at 
                 Gpr68 
                 G protein-coupled receptor 68 
               
               
                 1455002_at 
                 Ptp4a1 
                 protein tyrosine phosphatase 4a1 
               
               
                 1455032_at 
                 Ccnyl1 
                 cyclin Y-like 1 
               
               
                 1455300_at 
                 Tet2 
                 tet oncogene family member 2 
               
               
                 1455332_x_at  
                 Fcgr2b 
                 Fc receptor IgG low affinity IIb 
               
               
                 1456037_x_at 
                 Preb 
                 prolactin regulatory element binding 
               
               
                 1456341_a_at 
                 Klf9 
                 Kruppel-like factor 9 
               
               
                 1456875_at 
                 Gm19906 
                 predicted gene19906 
               
               
                 1457376_at 
                 NA 
                 NA 
               
               
                 1457753_at 
                 Tlr13 
                 toll-like receptor 13 
               
               
                 1457825_x_at 
                 Tcn2 
                 transcobalamin 2 
               
               
                 1459903_at 
                 Sema7a 
                 sema domain immunoglobulin domain (Ig) and GPI 
               
               
                   
                   
                 membrane anchor (semaphorin) 7A 
               
               
                 1459916_at 
                 Gm19980 
                 predicted gene19980 
               
               
                 1460257_a_at 
                 NA 
                 NA 
               
               
                 1460282_at 
                 Trem1 
                 triggering receptor expressed on myeloid cells 1 
               
               
                 1460287_at 
                 Timp2 
                 tissue inhibitor of metalloproteinase 2 
               
               
                 1460351_at 
                 S100a11 
                 5100 calcium binding protein A11 (calgizzarin) 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Human Factor 4 
               
            
           
           
               
               
               
            
               
                 PROBE ID 
                 SYMBOL 
                 GENE NAME 
               
               
                   
               
               
                 200060_s_at 
                 RNPS1 
                 RNA binding protein S1 serine-rich domain 
               
               
                 200633_at 
                 UBB 
                 ubiquitin B 
               
               
                 200675_at 
                 CD81 
                 CD81 molecule 
               
               
                 200693_at 
                 YWHAQ 
                 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase 
               
               
                   
                   
                 activation protein theta polypeptide 
               
               
                 200702_s_at 
                 DDX24 
                 DEAD (Asp-Glu-Ala-Asp) box polypeptide 24 
               
               
                 200717_x_at 
                 RPL7 
                 ribosomal protein L7 
               
               
                 200739_s_at 
                 SUMO3 
                 SMT3 suppressor of mif two 3 homolog 3 ( S .  cerevisiae ) 
               
               
                 200741_s_at 
                 RPS27 
                 ribosomal protein S27 
               
               
                 200743_s_at 
                 TPP1 
                 tripeptidyl peptidase I 
               
               
                 200764_s_at 
                 CTNNA1 
                 catenin (cadherin-associated protein) alpha 1 102 kDa 
               
               
                 200766_at 
                 CTSD 
                 cathepsin D 
               
               
                 200767_s_at 
                 FAM120A 
                 family with sequence similarity 120A 
               
               
                 200874_s_at 
                 NOP56 
                 NOP56 ribonucleoprotein homolog (yeast) 
               
               
                 200875_s_at 
                 NOP56 
                 NOP56 ribonucleoprotein homolog (yeast) 
               
               
                 200881_s_at 
                 DNAJA1 
                 DnaJ (Hsp40) homolog subfamily A member 1 
               
               
                 200886_s_at 
                 PGAM1 
                 phosphoglycerate mutase 1 (brain) 
               
               
                 200947_s_at 
                 GLUD1 
                 glutamate dehydrogenase 1 
               
               
                 200951_s_at 
                 CCND2 
                 cyclin D2 
               
               
                 200954_at 
                 ATP6V0C 
                 ATPase H+ transporting lysosomal 16 kDa V0 subunit c 
               
               
                 200955_at 
                 IMMT 
                 inner membrane protein mitochondrial 
               
               
                 200968_s_at 
                 PPIB 
                 peptidylprolyl isomerase B (cyclophilin B) 
               
               
                 200969_at 
                 SERP1 
                 stress-associated endoplasmic reticulum protein 1 
               
               
                 200984_s_at 
                 CD59 
                 CD59 molecule complement regulatory protein 
               
               
                 200985_s_at 
                 CD59 
                 CD59 molecule complement regulatory protein 
               
               
                 200998_s_at 
                 CKAP4 
                 cytoskeleton-associated protein 4 
               
               
                 201015_s_at 
                 JUP 
                 junction plakoglobin 
               
               
                 201055_s_at 
                 HNRNPA0 
                 heterogeneous nuclear ribonucleoprotein A0 
               
               
                 201087_at 
                 PXN 
                 paxillin 
               
               
                 201243_s_at 
                 ATP1B1 
                 ATPase Na+/K+ transporting beta 1 polypeptide 
               
               
                 201260_s_at 
                 SYPL1 
                 synaptophysin-like 1 
               
               
                 201332_s_at 
                 STAT6 
                 signal transducer and activator of transcription 6 
               
               
                 201353_s_at 
                 BAZ2A 
                 bromodomain adjacent to zinc finger domain 2A 
               
               
                 201369_s_at 
                 ZFP36L2 
                 zinc finger protein 36 C3H type-like 2 
               
               
                 201395_at 
                 RBMS 
                 RNA binding motif protein 5 
               
               
                 201396_s_at 
                 SGTA 
                 small glutamine-rich tetratricopeptide repeat (TPR)-containing 
               
               
                   
                   
                 alpha 
               
               
                 201449_at 
                 TIA1 
                 TIA1 cytotoxic granule-associated RNA binding protein 
               
               
                 201525_at 
                 APOD 
                 apolipoprotein D 
               
               
                 201530_x_at 
                 EIF4A1 
                 eukaryotic translation initiation factor 4A1 
               
               
                 201532_at 
                 PSMA3 
                 proteasome (prosome macropain) subunit alpha type 3 
               
               
                 201556_s_at 
                 VAMP2 
                 vesicle-associated membrane protein 2 (synaptobrevin 2) 
               
               
                 201601_x_at 
                 IFITM1 
                 interferon induced transmembrane protein 1 (9-27) 
               
               
                 201602_s_at 
                 PPP1R12A 
                 protein phosphatase 1 regulatory (inhibitor) subunit 12A 
               
               
                 201614_s_at 
                 RUVBL1 
                 RuvB-like 1 ( E .  coli ) 
               
               
                 201650_at 
                 KRT19 
                 keratin 19 
               
               
                 201699_at 
                 PSMC6 
                 proteasome (prosome macropain) 26S subunit ATPase 6 
               
               
                 201700_at 
                 CCND3 
                 cyclin D3 
               
               
                 201701_s_at 
                 PGRMC2 
                 progesterone receptor membrane component 2 
               
               
                 201737_s_at 
                 6-Mar 
                 membrane-associated ring finger (C3HC4) 6 
               
               
                 201751_at 
                 JOSD1 
                 Josephin domain containing 1 
               
               
                 201840_at 
                 NEDD8 
                 neural precursor cell expressed developmentally down-regulated 8 
               
               
                 201881_s_at 
                 ARIH1 
                 ariadne homolog ubiquitin-conjugating enzyme E2 binding 
               
               
                   
                   
                 protein 1 ( Drosophila ) 
               
               
                 201903_at 
                 UQCRC1 
                 ubiquinol-cytochrome c reductase core protein I 
               
               
                 201960_s_at 
                 MYCBP2 
                 MYC binding protein 2 
               
               
                 201984_s_at 
                 EGFR 
                 epidermal growth factor receptor 
               
               
                 202007_at 
                 NID1 
                 nidogen 1 
               
               
                 202008_s_at 
                 NID1 
                 nidogen 1 
               
               
                 202054_s_at 
                 ALDH3A2 
                 aldehyde dehydrogenase 3 family member A2 
               
               
                 202056_at 
                 KPNA1 
                 karyopherin alpha 1 (importin alpha 5) 
               
               
                 202057_at 
                 KPNA1 
                 karyopherin alpha 1 (importin alpha 5) 
               
               
                 202162_s_at 
                 CNOT8 
                 CCR4-NOT transcription complex subunit 8 
               
               
                 202234_s_at 
                 SLC16A1 
                 solute carrier family 16 member 1 (monocarboxylic acid 
               
               
                   
                   
                 transporter 1) 
               
               
                 202240_at 
                 PLK1 
                 polo-like kinase 1 
               
               
                 202273_at 
                 PDGFRB 
                 platelet-derived growth factor receptor beta polypeptide 
               
               
                 202329_at 
                 CSK 
                 c-src tyrosine kinase 
               
               
                 202360_at 
                 MAML1 
                 mastermind-like 1 ( Drosophila ) 
               
               
                 202368_s_at 
                 TRAM2 
                 translocation associated membrane protein 2 
               
               
                 202382_s_at 
                 GNPDA1 
                 glucosamine-6-phosphate deaminase 1 
               
               
                 202426_s_at 
                 RXRA 
                 retinoid X receptor alpha 
               
               
                 202508_s_at 
                 SNAP25 
                 synaptosomal-associated protein 25 kDa 
               
               
                 202548_s_at 
                 ARHGEF7 
                 Rho guanine nucleotide exchange factor (GEF) 7 
               
               
                 202566_s_at 
                 SVIL 
                 supervillin 
               
               
                 202623_at 
                 EAPP 
                 E2F-associated phosphoprotein 
               
               
                 202624_s_at 
                 CABIN1 
                 calcineurin binding protein 1 
               
               
                 202636_at 
                 RNF103 
                 ring finger protein 103 
               
               
                 202693_s_at 
                 STK17A 
                 serine/threonine kinase 17a 
               
               
                 202694_at 
                 STK17A 
                 serine/threonine kinase 17a 
               
               
                 202709_at 
                 FMOD 
                 fibromodulin 
               
               
                 202750_s_at 
                 TFIP11 
                 tuftelin interacting protein 11 
               
               
                 202756_s_at 
                 GPC1 
                 glypican 1 
               
               
                 202787_s_at 
                 MAPKAPK3 
                 mitogen-activated protein kinase-activated protein kinase 3 
               
               
                 202795_x_at 
                 TRIOBP 
                 TRIO and F-actin binding protein 
               
               
                 202796_at 
                 SYNPO 
                 synaptopodin 
               
               
                 202830_s_at 
                 SLC37A4 
                 solute carrier family 37 (glucose-6-phosphate transporter) 
               
               
                   
                   
                 member 4 
               
               
                 202859_x_at 
                 IL8 
                 interleukin 8 
               
               
                 202972_s_at 
                 FAM13A 
                 family with sequence similarity 13 member A 
               
               
                 202973_x_at 
                 FAM13A 
                 family with sequence similarity 13 member A 
               
               
                 202985_s_at 
                 BAGS 
                 BCL2-associated athanogene 5 
               
               
                 203023_at 
                 NOP16 
                 NOP16 nucleolar protein homolog (yeast) 
               
               
                 203199_s_at 
                 MTRR 
                 5-methyltetrahydrofolate-homocysteine methyltransferase 
               
               
                   
                   
                 reductase 
               
               
                 203236_s_at 
                 LGALS9 
                 lectin galactoside-binding soluble 9 
               
               
                 203376_at 
                 CDC40 
                 cell division cycle 40 homolog ( S .  cerevisiae ) 
               
               
                 203460_s_at 
                 PSEN1 
                 presenilin 1 
               
               
                 203610_s_at 
                 TRIM38 
                 tripartite motif containing 38 
               
               
                 203693_s_at 
                 E2F3 
                 E2F transcription factor 3 
               
               
                 203718_at 
                 PNPLA6 
                 patatin-like phospholipase domain containing 6 
               
               
                 203764_at 
                 DLGAP5 
                 discs large ( Drosophila ) homolog-associated protein 5 
               
               
                 203794_at 
                 CDC42BPA 
                 CDC42 binding protein kinase alpha (DMPK-like) 
               
               
                 203863_at 
                 ACTN2 
                 actinin alpha 2 
               
               
                 203864_s_at 
                 ACTN2 
                 actinin alpha 2 
               
               
                 204217_s_at 
                 RTN2 
                 reticulon 2 
               
               
                 204218_at 
                 C11orf51 
                 chromosome 11 open reading frame 51 
               
               
                 204237_at 
                 GULP1 
                 GULP engulfment adaptor PTB domain containing 1 
               
               
                 204238_s_at 
                 C6orf108 
                 chromosome 6 open reading frame 108 
               
               
                 204242_s_at 
                 ACOX3 
                 acyl-CoA oxidase 3 pristanoyl 
               
               
                 204249_s_at 
                 LMO2 
                 LIM domain only 2 (rhombotin-like 1) 
               
               
                 204250_s_at 
                 CEP164 
                 centrosomal protein 164 kDa 
               
               
                 204287_at 
                 SYNGR1 
                 synaptogyrin 1 
               
               
                 204447_at 
                 ProSAPiP1 
                 ProSAPiP1 protein 
               
               
                 204464_s_at 
                 EDNRA 
                 endothelin receptor type A 
               
               
                 204491_at 
                 PDE4D 
                 phosphodiesterase 4D cAMP-specific 
               
               
                 204496_at 
                 STRN3 
                 striatin calmodulin binding protein 3 
               
               
                 204497_at 
                 ADCY9 
                 adenylate cyclase 9 
               
               
                 204597_x_at 
                 STC1 
                 stanniocalcin 1 
               
               
                 204697_s_at 
                 CHGA 
                 chromogranin A (parathyroid secretory protein 1) 
               
               
                 205053_at 
                 PRIM1 
                 primase DNA polypeptide 1 (49 kDa) 
               
               
                 205064_at 
                 SPRR1B 
                 small proline-rich protein 1B 
               
               
                 205067_at 
                 IL1B 
                 interleukin 1 beta 
               
               
                 205144_at 
                 NA 
                 NA 
               
               
                 205151_s_at 
                 TRIL 
                 TLR4 interactor with leucine-rich repeats 
               
               
                 205182_s_at 
                 ZNF324 
                 zinc finger protein 324 
               
               
                 205225_at 
                 ESR1 
                 estrogen receptor 1 
               
               
                 205243_at 
                 SLC13A3 
                 solute carrier family 13 (sodium-dependent dicarboxylate 
               
               
                   
                   
                 transporter) member 3 
               
               
                 205296_at 
                 RBL1 
                 retinoblastoma-like 1 (p107) 
               
               
                 205340_at 
                 ZBTB24 
                 zinc finger and BTB domain containing 24 
               
               
                 205364_at 
                 ACOX2 
                 acyl-CoA oxidase 2 branched chain 
               
               
                 205396_at 
                 SMAD3 
                 SMAD family member 3 
               
               
                 205483_s_at 
                 ISG15 
                 ISG15 ubiquitin-like modifier 
               
               
                 205590_at 
                 RASGRP1 
                 RAS guanyl releasing protein 1 (calcium and DAG-regulated) 
               
               
                 205680_at 
                 MMP10 
                 matrix metallopeptidase 10 (stromelysin 2) 
               
               
                 205734_s_at 
                 AFF3 
                 AF4/FMR2 family member 3 
               
               
                 205887_x_at 
                 MSH3 
                 mutS homolog 3 ( E .  coli ) 
               
               
                 206099_at 
                 PRKCH 
                 protein kinase C eta 
               
               
                 206147_x_at 
                 SCML2 
                 sex comb on midleg-like 2 ( Drosophila ) 
               
               
                 206266_at 
                 GPLD1 
                 glycosylphosphatidylinositol specific phospholipase D1 
               
               
                 206421_s_at 
                 SERPINB7 
                 serpin peptidase inhibitor Glade B (ovalbumin) member 7 
               
               
                 206614_at 
                 GDF5 
                 growth differentiation factor 5 
               
               
                 206653_at 
                 POLR3G 
                 polymerase (RNA) III (DNA directed) polypeptide G (32 kD) 
               
               
                 206931_at 
                 ZNF141 
                 zinc finger protein 141 
               
               
                 206932_at 
                 CH25H 
                 cholesterol 25-hydroxylase 
               
               
                 207022_s_at 
                 LDHC 
                 lactate dehydrogenase C 
               
               
                 207076_s_at 
                 ASS1 
                 argininosuccinate synthase 1 
               
               
                 207086_x_at 
                 NA 
                 NA 
               
               
                 207160_at 
                 IL12A 
                 interleukin 12A (natural killer cell stimulatory factor 1 cytotoxic 
               
               
                   
                   
                 lymphocyte maturation factor 1 p35) 
               
               
                 207174_at 
                 GPC5 
                 glypican 5 
               
               
                 207385_at 
                 TFDP3 
                 transcription factor Dp family member 3 
               
               
                 207588_at 
                 NA 
                 NA 
               
               
                 207759_s_at 
                 NA 
                 NA 
               
               
                 207908_at 
                 KRT2 
                 keratin 2 
               
               
                 208043_at 
                 NA 
                 NA 
               
               
                 208113_x_at 
                 PABPC3 
                 poly(A) binding protein cytoplasmic 3 
               
               
                 208114_s_at 
                 ISG20L2 
                 interferon stimulated exonuclease gene 20 kDa-like 2 
               
               
                 208334_at 
                 NDST4 
                 N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4 
               
               
                 208340_at 
                 NA 
                 NA 
               
               
                 208381_s_at 
                 SGPL1 
                 sphingosine-1-phosphate lyase 1 
               
               
                 208556_at 
                 GPR31 
                 G protein-coupled receptor 31 
               
               
                 208683_at 
                 CAPN2 
                 calpain 2 (m/II) large subunit 
               
               
                 208709_s_at 
                 NRD1 
                 nardilysin (N-arginine dibasic convertase) 
               
               
                 208710_s_at 
                 AP3D1 
                 adaptor-related protein complex 3 delta 1 subunit 
               
               
                 208729_x_at 
                 HLA-B 
                 major histocompatibility complex class I B 
               
               
                 208738_x_at 
                 SUMO2 
                 SMT3 suppressor of mif two 3 homolog 2 ( S .  cerevisiae ) 
               
               
                 208748_s_at 
                 FLOT1 
                 flotillin 1 
               
               
                 208750_s_at 
                 ARF1 
                 ADP-ribosylation factor 1 
               
               
                 208765_s_at 
                 HNRNPR 
                 heterogeneous nuclear ribonucleoprotein R 
               
               
                 208786_s_at 
                 MAP1LC3B 
                 microtubule-associated protein 1 light chain 3 beta 
               
               
                 208800_at 
                 SRP72 
                 signal recognition particle 72 kDa 
               
               
                 208817_at 
                 COMT 
                 catechol-O-methyltransferase 
               
               
                 208820_at 
                 PTK2 
                 PTK2 protein tyrosine kinase 2 
               
               
                 208852_s_at 
                 CANX 
                 calnexin 
               
               
                 208853_s_at 
                 CANX 
                 calnexin 
               
               
                 208856_x_at 
                 RPLP0 
                 ribosomal protein large P0 
               
               
                 208857_s_at 
                 PCMT1 
                 protein-L-isoaspartate (D-aspartate) O-methyltransferase 
               
               
                 208875_s_at 
                 PAK2 
                 p21 protein (Cdc42/Rac)-activated kinase 2 
               
               
                 209021_x_at 
                 ATG13 
                 ATG13 autophagy related 13 homolog ( S .  cerevisiae ) 
               
               
                 209047_at 
                 AQP1 
                 aquaporin 1 (Colton blood group) 
               
               
                 209055_s_at 
                 CDCSL 
                 CDCS cell division cycle 5-like ( S .  pombe ) 
               
               
                 209087_x_at 
                 MCAM 
                 melanoma cell adhesion molecule 
               
               
                 209088_s_at 
                 UBN1 
                 ubinuclein 1 
               
               
                 209169_at 
                 GPM6B 
                 glycoprotein M6B 
               
               
                 209170_s_at 
                 GPM6B 
                 glycoprotein M6B 
               
               
                 209197_at 
                 SYT11 
                 synaptotagmin XI 
               
               
                 209225_x_at 
                 TNPO1 
                 transportin 1 
               
               
                 209253_at 
                 SORBS3 
                 sorbin and SH3 domain containing 3 
               
               
                 209352_s_at 
                 SIN3B 
                 SIN3 homolog B transcription regulator (yeast) 
               
               
                 209393_s_at 
                 EIF4E2 
                 eukaryotic translation initiation factor 4E family member 2 
               
               
                 209479_at 
                 CCDC28A 
                 coiled-coil domain containing 28A 
               
               
                 209556_at 
                 NCDN 
                 neurochondrin 
               
               
                 209623_at 
                 MCCC2 
                 methylcrotonoyl-CoA carboxylase 2 (beta) 
               
               
                 209666_s_at 
                 CHUK 
                 conserved helix-loop-helix ubiquitous kinase 
               
               
                 209689_at 
                 CCDC93 
                 coiled-coil domain containing 93 
               
               
                 209726_at 
                 CA11 
                 carbonic anhydrase XI 
               
               
                 209822_s_at 
                 VLDLR 
                 very low density lipoprotein receptor 
               
               
                 209865_at 
                 SLC35A3 
                 solute carrier family 35 (UDP-N-acetylglucosamine (UDP- 
               
               
                   
                   
                 GlcNAc) transporter) member A3 
               
               
                 209866_s_at 
                 LPHN3 
                 latrophilin 3 
               
               
                 209972_s_at 
                 AIMP2 
                 aminoacyl tRNA synthetase complex-interacting multifunctional 
               
               
                   
                   
                 protein 2 
               
               
                 209973_at 
                 NFKBIL1 
                 nuclear factor of kappa light polypeptide gene enhancer in B-cells 
               
               
                   
                   
                 inhibitor-like 1 
               
               
                 210158_at 
                 ERCC4 
                 excision repair cross-complementing rodent repair deficiency 
               
               
                   
                   
                 complementation group 4 
               
               
                 210163_at 
                 CXCL11 
                 chemokine (C-X-C motif) ligand 11 
               
               
                 210251_s_at 
                 RUFY3 
                 RUN and FYVE domain containing 3 
               
               
                 210344_at 
                 OSBPL7 
                 oxysterol binding protein-like 7 
               
               
                 210346_s_at 
                 CLK4 
                 CDC-like kinase 4 
               
               
                 210377_at 
                 ACSM3 
                 acyl-CoA synthetase medium-chain family member 3 
               
               
                 210470_x_at 
                 NONO 
                 non-POU domain containing octamer-binding 
               
               
                 210613_s_at 
                 SYNGR1 
                 synaptogyrin 1 
               
               
                 210627_s_at 
                 MOGS 
                 mannosyl-oligosaccharide glucosidase 
               
               
                 210677_at 
                 SOAT2 
                 sterol O-acyltransferase 2 
               
               
                 210731_s_at 
                 LGALS8 
                 lectin galactoside-binding soluble 8 
               
               
                 210732_s_at 
                 LGALS8 
                 lectin galactoside-binding soluble 8 
               
               
                 210823_s_at 
                 PTPRS 
                 protein tyrosine phosphatase receptor type S 
               
               
                 210919_at 
                 PHLPP1 
                 PH domain and leucine rich repeat protein phosphatase 1 
               
               
                 211054_at 
                 INVS 
                 inversin 
               
               
                 211055_s_at 
                 INVS 
                 inversin 
               
               
                 211070_x_at 
                 DBI 
                 diazepam binding inhibitor (GABA receptor modulator acyl-CoA 
               
               
                   
                   
                 binding protein) 
               
               
                 211165_x_at 
                 EPHB2 
                 EPH receptor B2 
               
               
                 211190_x_at 
                 CD84 
                 CD84 molecule 
               
               
                 211224_s_at 
                 ABCB11 
                 ATP-binding cassette sub-family B (MDR/TAP) member 11 
               
               
                 211334_at 
                 MRE11A 
                 MRE11 meiotic recombination 11 homolog A ( S .  cerevisiae ) 
               
               
                 211375_s_at 
                 ILF3 
                 interleukin enhancer binding factor 3 90 kDa 
               
               
                 211380_s_at 
                 PRKG1 
                 protein kinase cGMP-dependent type I 
               
               
                 211413_s_at 
                 PADI4 
                 peptidyl arginine deiminase type IV 
               
               
                 211555_s_at 
                 GUCY1B3 
                 guanylate cyclase 1 soluble beta 3 
               
               
                 211775_x_at 
                 MGC13053 
                 hypothetical MGC13053 
               
               
                 211794_at 
                 FYB 
                 FYN binding protein 
               
               
                 211833_s_at 
                 BAX 
                 BCL2-associated X protein 
               
               
                 211954_s_at 
                 IPO5 
                 importin 5 
               
               
                 211964_at 
                 COL4A2 
                 collagen type IV alpha 2 
               
               
                 211995_x_at 
                 ACTG1 
                 actin gamma 1 
               
               
                 211996_s_at 
                 NA 
                 NA 
               
               
                 212037_at 
                 PNN 
                 pinin desmosome associated protein 
               
               
                 212075_s_at 
                 CSNK2A1 
                 casein kinase 2 alpha 1 polypeptide 
               
               
                 212152_x_at 
                 ARID1A 
                 AT rich interactive domain 1A (SWI-like) 
               
               
                 212154_at 
                 SDC2 
                 syndecan 2 
               
               
                 212274_at 
                 LPIN1 
                 lipin 1 
               
               
                 212282_at 
                 TMEM97 
                 transmembrane protein 97 
               
               
                 212307_s_at 
                 OGT 
                 O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N- 
               
               
                   
                   
                 acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) 
               
               
                 212328_at 
                 LIMCH1 
                 LIM and calponin homology domains 1 
               
               
                 212387_at 
                 TCF4 
                 transcription factor 4 
               
               
                 212439_at 
                 IP6K1 
                 inositol hexakisphosphate kinase 1 
               
               
                 212440_at 
                 SNRNP27 
                 small nuclear ribonucleoprotein 27 kDa (U4/U6.U5) 
               
               
                 212738_at 
                 ARHGAP19 
                 Rho GTPase activating protein 19 
               
               
                 212854_x_at 
                 NA 
                 NA 
               
               
                 212938_at 
                 COL6A1 
                 collagen type VI alpha 1 
               
               
                 212951_at 
                 GPR116 
                 G protein-coupled receptor 116 
               
               
                 212966_at 
                 HIC2 
                 hypermethylated in cancer 2 
               
               
                 213022_s_at  
                 UTRN 
                 utrophin 
               
               
                 213039_at 
                 ARHGEF18 
                 Rho/Rac guanine nucleotide exchange factor (GEF) 18 
               
               
                 213067_at 
                 MYH10 
                 myosin heavy chain 10 non-muscle 
               
               
                 213073_at 
                 ZFYVE26 
                 zinc finger FYVE domain containing 26 
               
               
                 213135_at 
                 TIAM1 
                 T-cell lymphoma invasion and metastasis 1 
               
               
                 213168_at 
                 SP3 
                 Sp3 transcription factor 
               
               
                 213185_at 
                 KIAA0556 
                 KIAA0556 
               
               
                 213188_s_at  
                 MINA 
                 MYC induced nuclear antigen 
               
               
                 213334_x_at  
                 HAUS7 
                 HAUS augmin-like complex subunit 7 
               
               
                 213351_s_at  
                 TMCC1 
                 transmembrane and coiled-coil domain family 1 
               
               
                 213395_at 
                 MLC1 
                 megalencephalic leukoencephalopathy with subcortical cysts 1 
               
               
                 213397_x_at  
                 NA 
                 NA 
               
               
                 213436_at 
                 CNR1 
                 cannabinoid receptor 1 (brain) 
               
               
                 213439_x_at  
                 RUNDC3A 
                 RUN domain containing 3A 
               
               
                 213659_at 
                 ZNF75D 
                 zinc finger protein 75D 
               
               
                 213687_s_at  
                 RPL35A 
                 ribosomal protein L35a 
               
               
                 213816_s_at  
                 MET 
                 met proto-oncogene (hepatocyte growth factor receptor) 
               
               
                 213874_at 
                 SERPINA4 
                 serpin peptidase inhibitor clade A (alpha-1 antiproteinase 
               
               
                   
                   
                 antitrypsin) member 4 
               
               
                 214319_at 
                 FRY 
                 furry homolog ( Drosophila ) 
               
               
                 214349_at 
                 NA 
                 NA 
               
               
                 214380_at 
                 PRPF31 
                 PRP31 pre-mRNA processing factor 31 homolog ( S .  cerevisiae ) 
               
               
                 214387_x_at 
                 SFTPC 
                 surfactant protein C 
               
               
                 214565_s_at  
                 NA 
                 NA 
               
               
                 214727_at 
                 BRCA2 
                 breast cancer 2 early onset 
               
               
                 214915_at 
                 ZNF362 
                 zinc finger protein 362 
               
               
                 214952_at 
                 NCAM1 
                 neural cell adhesion molecule 1 
               
               
                 215067_x_at 
                 PRDX2 
                 peroxiredoxin 2 
               
               
                 215240_at 
                 ITGB3 
                 integrin beta 3 (platelet glycoprotein IIIa antigen CD61) 
               
               
                 215254_at 
                 RCAN1 
                 regulator of calcineurin 1 
               
               
                 215510_at 
                 ETV2 
                 ets variant 2 
               
               
                 215727_x_at  
                 NA 
                 NA 
               
               
                 215974_at 
                 HCG4B 
                 HLA complex group 4B (non-protein coding) 
               
               
                 216048_s_at 
                 RHOBTB3 
                 Rho-related BTB domain containing 3 
               
               
                 216752_at 
                 PIK3R4 
                 phosphoinositide-3-kinase regulatory subunit 4 
               
               
                 216971_s_at 
                 PLEC 
                 plectin 
               
               
                 217455_s_at 
                 SSTR2 
                 somatostatin receptor 2 
               
               
                 217544_at 
                 NA 
                 NA 
               
               
                 217640_x_at 
                 SKA1 
                 spindle and kinetochore associated complex subunit 1 
               
               
                 217641_at 
                 GPR135 
                 G protein-coupled receptor 135 
               
               
                 217740_x_at 
                 RPL7A 
                 ribosomal protein L7a 
               
               
                 217799_x_at 
                 UBE2H 
                 ubiquitin-conjugating enzyme E2H 
               
               
                 217889_s_at 
                 CYBRD1 
                 cytochrome b reductase 1 
               
               
                 217903_at 
                 STRN4 
                 striatin calmodulin binding protein 4 
               
               
                 217924_at 
                 C6orf106 
                 chromosome 6 open reading frame 106 
               
               
                 217928_s_at 
                 PPP6R3 
                 protein phosphatase 6 regulatory subunit 3 
               
               
                 217941_s_at 
                 ERBB2IP 
                 erbb2 interacting protein 
               
               
                 217992_s_at 
                 EFHD2 
                 EF-hand domain family member D2 
               
               
                 217996_at 
                 PHLDA1 
                 pleckstrin homology-like domain family A member 1 
               
               
                 218006_s_at 
                 ZNF22 
                 zinc finger protein 22 (KOX 15) 
               
               
                 218028_at 
                 ELOVL1 
                 ELOVL fatty acid elongase 1 
               
               
                 218048_at 
                 COMMD3 
                 COMM domain containing 3 
               
               
                 218049_s_at 
                 MRPL13 
                 mitochondrial ribosomal protein L13 
               
               
                 218358_at 
                 CRELD2 
                 cysteine-rich with EGF-like domains 2 
               
               
                 218380_at 
                 NA 
                 NA 
               
               
                 218390_s_at 
                 FAM204A 
                 family with sequence similarity 204 member A 
               
               
                 218541_s_at 
                 C8orf4 
                 chromosome 8 open reading frame 4 
               
               
                 218580_x_at 
                 AURKAIP1 
                 aurora kinase A interacting protein 1 
               
               
                 218625_at 
                 NRN1 
                 neuritin 1 
               
               
                 218694_at 
                 ARMCX1 
                 armadillo repeat containing X-linked 1 
               
               
                 218710_at 
                 TTC27 
                 tetratricopeptide repeat domain 27 
               
               
                 218771_at 
                 PANK4 
                 pantothenate kinase 4 
               
               
                 218920_at 
                 FAM193B 
                 family with sequence similarity 193 member B 
               
               
                 219051_x_at 
                 METRN 
                 meteorin glial cell differentiation regulator 
               
               
                 219058_x_at 
                 TINAGL1 
                 tubulointerstitial nephritis antigen-like 1 
               
               
                 219388_at 
                 GRHL2 
                 grainyhead-like 2 ( Drosophila ) 
               
               
                 219485_s_at 
                 PSMD10 
                 proteasome (prosome macropain) 26S subunit non-ATPase 10 
               
               
                 219495_s_at 
                 ZNF180 
                 zinc finger protein 180 
               
               
                 219528_s_at 
                 BCL11B 
                 B-cell CLL/lymphoma 11B (zinc finger protein) 
               
               
                 219829_at 
                 ITGB1BP2 
                 integrin beta 1 binding protein (melusin) 2 
               
               
                 219975_x_at 
                 OLAH 
                 oleoyl-ACP hydrolase 
               
               
                 219988_s_at 
                 RNF220 
                 ring finger protein 220 
               
               
                 220156_at 
                 EFCAB1 
                 EF-hand calcium binding domain 1 
               
               
                 220243_at 
                 ZBTB44 
                 zinc finger and BTB domain containing 44 
               
               
                 220357_s_at 
                 SGK2 
                 serum/glucocorticoid regulated kinase 2 
               
               
                 220403_s_at 
                 TP53AIP1 
                 tumor protein p53 regulated apoptosis inducing protein 1 
               
               
                 220650_s_at 
                 SLC9A5 
                 solute carrier family 9 (sodium/hydrogen exchanger) member 5 
               
               
                 220663_at 
                 IL1RAPL1 
                 interleukin 1 receptor accessory protein-like 1 
               
               
                 220750_s_at 
                 LEPRE1 
                 leucine proline-enriched proteoglycan (leprecan) 1 
               
               
                 220769_s_at 
                 WDR78 
                 WD repeat domain 78 
               
               
                 220991_s_at 
                 RNF32 
                 ring finger protein 32 
               
               
                 221036_s_at 
                 APH1B 
                 anterior pharynx defective 1 homolog B ( C .  elegans ) 
               
               
                 221066_at 
                 RXFP3 
                 relaxin/insulin-like family peptide receptor 3 
               
               
                 221080_s_at 
                 DENND1C 
                 DENN/MADD domain containing 1C 
               
               
                 221102_s_at 
                 TRPM6 
                 transient receptor potential cation channel subfamily M member 6 
               
               
                 221280_s_at 
                 PARD3 
                 par-3 partitioning defective 3 homolog ( C .  elegans ) 
               
               
                 221296_at 
                 TECTA 
                 tectorin alpha 
               
               
                 221510_s_at 
                 GLS 
                 glutaminase 
               
               
                 221625_at 
                 ZNF506 
                 zinc finger protein 506 
               
               
                 221888_at 
                 CC2D1A 
                 coiled-coil and C2 domain containing 1A 
               
               
                 221896_s_at 
                 HIGD1A 
                 HIG1 hypoxia inducible domain family member 1A 
               
               
                 222014_x_at 
                 MTO1 
                 mitochondrial translation optimization 1 homolog ( S .  cerevisiae ) 
               
               
                 222015_at 
                 CSNK1E 
                 casein kinase 1 epsilon 
               
               
                 222062_at 
                 IL27RA 
                 interleukin 27 receptor alpha 
               
               
                 222144_at 
                 KIF17 
                 kinesin family member 17 
               
               
                 222158_s_at 
                 PPPDE1 
                 PPPDE peptidase domain containing 1 
               
               
                 222165_x_at 
                 C9orf16 
                 chromosome 9 open reading frame 16 
               
               
                 222226_at 
                 SAA3P 
                 serum amyloid A3 pseudogene 
               
               
                 31845_at 
                 ELF4 
                 E74-like factor 4 (ets domain transcription factor) 
               
               
                 34063_at 
                 RECQL5 
                 RecQ protein-like 5 
               
               
                 35160_at 
                 LDB1 
                 LIM domain binding 1 
               
               
                 37943_at 
                 ZFYVE26 
                 zinc finger FYVE domain containing 26 
               
               
                 38398_at 
                 MADD 
                 MAP-kinase activating death domain 
               
               
                 40359_at 
                 RASSF7 
                 Ras association (RalGDS/AF-6) domain family (N-terminal) 
               
               
                   
                   
                 member 7 
               
               
                 41512_at 
                 BRAP 
                 BRCA1 associated protein 
               
               
                 54632_at 
                 THADA 
                 thyroid adenoma associated 
               
               
                 65635_at 
                 ENGASE 
                 endo-beta-N-acetylglucosaminidase 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Human Factor 20 
               
            
           
           
               
               
               
            
               
                 PROBE ID 
                 SYMBOL 
                 GENE NAME 
               
               
                   
               
               
                 200992_at 
                 IPO7 
                 importin 7 
               
               
                 201034_at 
                 ADD3 
                 adducin 3 (gamma) 
               
               
                 201149_s_at 
                 TIMP3 
                 TIMP metallopeptidase inhibitor 3 
               
               
                 201412_at 
                 LRP10 
                 low density lipoprotein receptor-related protein 10 
               
               
                 201565_s_at 
                 ID2 
                 inhibitor of DNA binding 2 dominant negative helix-loop-helix 
               
               
                   
                   
                 protein 
               
               
                 201651_s_at 
                 PACSIN2 
                 protein kinase C and casein kinase substrate in neurons 2 
               
               
                 201662_s_at 
                 ACSL3 
                 acyl-CoA synthetase long-chain family member 3 
               
               
                 201721_s_at 
                 LAPTM5 
                 lysosomal protein transmembrane 5 
               
               
                 201761_at 
                 MTHFD2 
                 methylenetetrahydrofolate dehydrogenase (NADP+ dependent)  
               
               
                   
                   
                 2 methenyltetrahydrofolate cyclohydrolase 
               
               
                 202350_s_at 
                 MATN2 
                 matrilin 2 
               
               
                 202628_s_at 
                 SERPINE1 
                 serpin peptidase inhibitor Glade E (nexin plasminogen activator 
               
               
                   
                   
                 inhibitor type 1) member 1 
               
               
                 203191_at 
                 ABCB6 
                 ATP-binding cassette sub-family B (MDR/TAP) member 6 
               
               
                 203216_s_at 
                 MYO6 
                 myosin VI 
               
               
                 203229_s_at 
                 CLK2 
                 CDC-like kinase 2 
               
               
                 203879_at 
                 PIK3CD 
                 phosphoinositide-3-kinase catalytic delta polypeptide 
               
               
                 203884_s_at 
                 RAB11FIP2 
                 RAB11 family interacting protein 2 (class I) 
               
               
                 203950_s_at 
                 CLCN6 
                 chloride channel 6 
               
               
                 204025_s_at 
                 PDCD2 
                 programmed cell death 2 
               
               
                 204060_s_at 
                 NA 
                 NA 
               
               
                 204215_at 
                 C7orf23 
                 chromosome 7 open reading frame 23 
               
               
                 204316_at 
                 RGS10 
                 regulator of G-protein signaling 10 
               
               
                 204387_x_at 
                 MRP63 
                 mitochondrial ribosomal protein 63 
               
               
                 206541_at 
                 KLKB1 
                 kallikrein B plasma (Fletcher factor) 1 
               
               
                 208461_at 
                 HIC1 
                 hypermethylated in cancer 1 
               
               
                 208742_s_at 
                 SAP18 
                 Sin3A-associated protein 18 kDa 
               
               
                 209043_at 
                 PAPSS1 
                 3′-phosphoadenosine 5′-phosphosulfate synthase 1 
               
               
                 209115_at 
                 UBA3 
                 ubiquitin-like modifier activating enzyme 3 
               
               
                 209146_at 
                 MSMO1 
                 methylsterol monooxygenase 1 
               
               
                 209227_at 
                 TUSC3 
                 tumor suppressor candidate 3 
               
               
                 209743_s_at 
                 ITCH 
                 itchy E3 ubiquitin protein ligase homolog (mouse) 
               
               
                 210545_at 
                 ITSN2 
                 intersectin 2 
               
               
                 212027_at 
                 RBM25 
                 RNA binding motif protein 25 
               
               
                 212668_at 
                 SMURF1 
                 SMAD specific E3 ubiquitin protein ligase 1 
               
               
                 212871_at 
                 MAPKAPK5 
                 mitogen-activated protein kinase-activated protein kinase 5 
               
               
                 212969_x_at 
                 EML3 
                 echinoderm microtubule associated protein like 3 
               
               
                 212983_at 
                 HRAS 
                 v-Ha-ras Harvey rat sarcoma viral oncogene homolog 
               
               
                 213336_at 
                 BAZ1B 
                 bromodomain adjacent to zinc finger domain 1B 
               
               
                 214140_at 
                 SLC25A16 
                 solute carrier family 25 (mitochondrial carrier; Graves disease 
               
               
                   
                   
                 autoantigen) member 16 
               
               
                 214355_x_at 
                 NA 
                 NA 
               
               
                 215169_at 
                 NA 
                 NA 
               
               
                 215420_at 
                 IHH 
                 Indian hedgehog 
               
               
                 216975_x_at 
                 NPAS1 
                 neuronal PAS domain protein 1 
               
               
                 217837_s_at 
                 VPS24 
                 vacuolar protein sorting 24 homolog ( S .  cerevisiae ) 
               
               
                 217891_at 
                 C16orf58 
                 chromosome 16 open reading frame 58 
               
               
                 217994_x_at 
                 CPSF3L 
                 cleavage and polyadenylation specific factor 3-like 
               
               
                 218136_s_at 
                 SLC25A37 
                 solute carrier family 25 member 37 
               
               
                 218478_s_at 
                 ZCCHC8 
                 zinc finger CCHC domain containing 8 
               
               
                 218675_at 
                 SLC22A17 
                 solute carrier family 22 member 17 
               
               
                 218756_s_at 
                 DHRS11 
                 dehydrogenase/reductase (SDR family) member 11 
               
               
                 218882_s_at 
                 WDR3 
                 WD repeat domain 3 
               
               
                 221087_s_at 
                 APOL3 
                 apolipoprotein L3 
               
               
                 221778_at 
                 JHDM1D 
                 jumonji C domain containing histone demethylase 1 homolog D 
               
               
                   
                   
                 ( S .  cerevisiae ) 
               
               
                 221823_at 
                 C5orf30 
                 chromosome 5 open reading frame 30 
               
               
                 222255_at 
                 PRX 
                 periaxin 
               
               
                 40472_at 
                 LPCAT4 
                 lysophosphatidylcholine acyltransferase 4 
               
               
                 44617_at 
                 OGFOD2 
                 2-oxoglutarate and iron-dependent oxygenase domain  
               
               
                   
                   
                 containing 2 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 9 
               
             
            
               
                   
               
               
                 Human Factor 40 
               
            
           
           
               
               
               
            
               
                 PROBE ID 
                 SYMBOL 
                 GENE NAME 
               
               
                   
               
               
                 200989_at 
                 HIF1A 
                 hypoxia inducible factor 1 alpha subunit (basic helix-loop-helix 
               
               
                   
                   
                 transcription factor) 
               
               
                 201772_at 
                 AZIN1 
                 antizyme inhibitor 1 
               
               
                 202116_at 
                 DPF2 
                 D4 zinc and double PHD fingers family 2 
               
               
                 202552_s_at 
                 CRIM1 
                 cysteine rich transmembrane BMP regulator 1 (chordin-like) 
               
               
                 203607_at 
                 INPP5F 
                 inositol polyphosphate-5-phosphatase F 
               
               
                 203643_at 
                 ERF 
                 Ets2 repressor factor 
               
               
                 204161_s_at 
                 ENPP4 
                 ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative) 
               
               
                 204284_at 
                 PPP1R3C 
                 protein phosphatase 1 regulatory (inhibitor) subunit 3C 
               
               
                 204452_s_at 
                 FZD1 
                 frizzled family receptor 1 
               
               
                 207583_at 
                 ABCD2 
                 ATP-binding cassette sub-family D (ALD) member 2 
               
               
                 208701_at 
                 APLP2 
                 amyloid beta (A4) precursor-like protein 2 
               
               
                 209054_s_at 
                 WHSC1 
                 Wolf-Hirschhorn syndrome candidate 1 
               
               
                 209593_s_at 
                 TOR1B 
                 torsin family 1 member B (torsin B) 
               
               
                 209840_s_at 
                 LRRN3 
                 leucine rich repeat neuronal 3 
               
               
                 210736_x_at 
                 DTNA 
                 dystrobrevin alpha 
               
               
                 213611_at 
                 AQP5 
                 aquaporin 5 
               
               
                 214062_x_at 
                 NFKBIB 
                 nuclear factor of kappa light polypeptide gene enhancer in B-cells 
               
               
                   
                   
                 inhibitor beta 
               
               
                 214952_at 
                 NCAM1 
                 neural cell adhesion molecule 1 
               
               
                 216222_s_at 
                 MYO10 
                 myosin X 
               
               
                 216869_at 
                 PDE1C 
                 phosphodiesterase 1C calmodulin-dependent 70 kDa 
               
               
                 220585_at 
                 HKDC1 
                 hexokinase domain containing 1 
               
               
                 221402_at 
                 OR1F1 
                 olfactory receptor family 1 subfamily F member 1 
               
               
                 221651_x_at 
                 NA 
                 NA 
               
               
                 221708_s_at 
                 UNC45A 
                 unc-45 homolog A ( C .  elegans ) 
               
               
                 222296_at 
                 NA 
                 NA 
               
               
                 222316_at 
                 NA 
                 NA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 10 
               
             
            
               
                   
               
               
                 Human Factor 74 
               
            
           
           
               
               
               
            
               
                 PROBE ID 
                 SYMBOL 
                 GENE NAME 
               
               
                   
               
               
                 1487_at 
                 ESRRA 
                 estrogen-related receptor alpha 
               
               
                 201045_s_at 
                 RAB6A 
                 RAB6A member RAS oncogene family 
               
               
                 201046_s_at 
                 RAD23A 
                 RAD23 homolog A ( S .  cerevisiae ) 
               
               
                 201751_at 
                 JOSD1 
                 Josephin domain containing 1 
               
               
                 201752_s_at 
                 ADD3 
                 adducin 3 (gamma) 
               
               
                 201753_s_at 
                 ADD3 
                 adducin 3 (gamma) 
               
               
                 201951_at 
                 ALCAM 
                 activated leukocyte cell adhesion molecule 
               
               
                 202058_s_at 
                 KPNA1 
                 karyopherin alpha 1 (importin alpha 5) 
               
               
                 202579_x_at 
                 HMGN4 
                 high mobility group nucleosomal binding domain 4 
               
               
                 202786_at 
                 STK39 
                 serine threonine kinase 39 
               
               
                 202813_at 
                 TARBP1 
                 TAR (HIV-1) RNA binding protein 1 
               
               
                 202814_s_at 
                 HEXIM1 
                 hexamethylene bis-acetamide inducible 1 
               
               
                 202954_at 
                 UBE2C 
                 ubiquitin-conjugating enzyme E2C 
               
               
                 203092_at 
                 TIMM44 
                 translocase of inner mitochondrial membrane 44 homolog (yeast) 
               
               
                 203100_s_at 
                 CDYL 
                 chromodomain protein Y-like 
               
               
                 203276_at 
                 LMNB1 
                 lamin B1 
               
               
                 203694_s_at 
                 DHX16 
                 DEAH (Asp-Glu-Ala-His) box polypeptide 16 
               
               
                 203763_at 
                 DYNC2LI1 
                 dynein cytoplasmic 2 light intermediate chain 1 
               
               
                 203806_s_at 
                 FANCA 
                 Fanconi anemia complementation group A 
               
               
                 203848_at 
                 AKAP8 
                 A kinase (PRKA) anchor protein 8 
               
               
                 203984_s_at 
                 CASP9 
                 caspase 9 apoptosis-related cysteine peptidase 
               
               
                 203991_s_at 
                 KDM6A 
                 lysine (K)-specific demethylase 6A 
               
               
                 204056_s_at 
                 MVK 
                 mevalonate kinase 
               
               
                 204109_s_at 
                 NFYA 
                 nuclear transcription factor Y alpha 
               
               
                 204244_s_at 
                 DBF4 
                 DBF4 homolog ( S .  cerevisiae ) 
               
               
                 204403_x_at 
                 FAM115A 
                 family with sequence similarity 115 member A 
               
               
                 204535_s_at 
                 REST 
                 RE1-silencing transcription factor 
               
               
                 204632_at 
                 RPS6KA4 
                 ribosomal protein S6 kinase 90 kDa polypeptide 4 
               
               
                 205000_at 
                 DDX3Y 
                 DEAD (Asp-Glu-Ala-Asp) box polypeptide 3 Y-linked 
               
               
                 205098_at 
                 CCR1 
                 chemokine (C-C motif) receptor 1 
               
               
                 205150_s_at 
                 TRIL 
                 TLR4 interactor with leucine-rich repeats 
               
               
                 205315_s_at 
                 SNTB2 
                 syntrophin beta 2 (dystrophin-associated protein A1 59 kDa basic 
               
               
                   
                   
                 component 2) 
               
               
                 205345_at 
                 BARD1 
                 BRCA1 associated RING domain 1 
               
               
                 205513_at 
                 TCN1 
                 transcobalamin I (vitamin B12 binding protein R binder family) 
               
               
                 205591_at 
                 OLFM1 
                 olfactomedin 1 
               
               
                 205718_at 
                 ITGB7 
                 integrin beta 7 
               
               
                 205848_at 
                 GAS2 
                 growth arrest-specific 2 
               
               
                 205908_s_at 
                 OMD 
                 osteomodulin 
               
               
                 205948_at 
                 PTPRT 
                 protein tyrosine phosphatase receptor type T 
               
               
                 205980_s_at 
                 NA 
                 NA 
               
               
                 206045_s_at 
                 NOL4 
                 nucleolar protein 4 
               
               
                 206173_x_at 
                 GABPB1 
                 GA binding protein transcription factor beta subunit 1 
               
               
                 206253_at 
                 DLG2 
                 discs large homolog 2 ( Drosophila ) 
               
               
                 206302_s_at 
                 NA 
                 NA 
               
               
                 206445_s_at 
                 PRMT1 
                 protein arginine methyltransferase 1 
               
               
                 206525_at 
                 GABRR1 
                 gamma-aminobutyric acid (GABA) receptor rho 1 
               
               
                 206805_at 
                 SEMA3A 
                 sema domain immunoglobulin domain (Ig) short basic domain 
               
               
                   
                   
                 secreted (semaphorin) 3A 
               
               
                 206806_at 
                 DGKI 
                 diacylglycerol kinase iota 
               
               
                 207029_at 
                 KITLG 
                 KIT ligand 
               
               
                 207700_s_at 
                 NCOA3 
                 nuclear receptor coactivator 3 
               
               
                 207864_at 
                 SCN7A 
                 sodium channel voltage-gated type VII alpha 
               
               
                 207871_s_at 
                 ST7 
                 suppression of tumorigenicity 7 
               
               
                 208017_s_at 
                 MCF2 
                 MCF.2 cell line derived transforming sequence 
               
               
                 208311_at 
                 GPR50 
                 G protein-coupled receptor 50 
               
               
                 208955_at 
                 DUT 
                 deoxyuridine triphosphatase 
               
               
                 209192_x_at 
                 KAT5 
                 K(lysine) acetyltransferase 5 
               
               
                 209346_s_at 
                 PI4K2A 
                 phosphatidylinositol 4-kinase type 2 alpha 
               
               
                 209412_at 
                 TRAPPC10 
                 trafficking protein particle complex 10 
               
               
                 209598_at 
                 PNMA2 
                 paraneoplastic antigen MA2 
               
               
                 209620_s_at 
                 ABCB7 
                 ATP-binding cassette sub-family B (MDR/TAP) member 7 
               
               
                 209621_s_at 
                 PDLIM3 
                 PDZ and LIM domain 3 
               
               
                 209658_at 
                 CDC16 
                 cell division cycle 16 homolog ( S .  cerevisiae ) 
               
               
                 209829_at 
                 FAM65B 
                 family with sequence similarity 65 member B 
               
               
                 210033_s_at 
                 SPAG6 
                 sperm associated antigen 6 
               
               
                 210034_s_at 
                 RPLS 
                 ribosomal protein L5 
               
               
                 210078_s_at 
                 KCNAB1 
                 potassium voltage-gated channel shaker-related subfamily beta 
               
               
                   
                   
                 member 1 
               
               
                 210386_s_at 
                 MTX1 
                 metaxin 1 
               
               
                 210394_x_at 
                 NA 
                 NA 
               
               
                 210470_x_at 
                 NONO 
                 non-POU domain containing octamer-binding 
               
               
                 210491_at 
                 NA 
                 NA 
               
               
                 210493_s_at 
                 MFAP3L 
                 microfibrillar-associated protein 3-like 
               
               
                 210697_at 
                 ZNF257 
                 zinc finger protein 257 
               
               
                 211238_at 
                 ADAM7 
                 ADAM metallopeptidase domain 7 
               
               
                 211691_x_at 
                 NA 
                 NA 
               
               
                 212125_at 
                 RANGAP1 
                 Ran GTPase activating protein 1 
               
               
                 212338_at 
                 MYO1D 
                 myosin ID 
               
               
                 212340_at 
                 YIPF6 
                 Yip1 domain family member 6 
               
               
                 212408_at 
                 TOR1AIP1 
                 torsin A interacting protein 1 
               
               
                 212412_at 
                 PDLIMS 
                 PDZ and LIM domain 5 
               
               
                 212413_at 
                 6-Sep 
                 septin 6 
               
               
                 212614_at 
                 ARID5B 
                 AT rich interactive domain 5B (MRF1-like) 
               
               
                 212615_at 
                 CHD9 
                 chromodomain helicase DNA binding protein 9 
               
               
                 212696_s_at 
                 RNF4 
                 ring finger protein 4 
               
               
                 212739_s_at 
                 NME4 
                 non-metastatic cells 4 protein expressed in 
               
               
                 212774_at 
                 ZNF238 
                 zinc finger protein 238 
               
               
                 212849_at 
                 AXIN1 
                 axin 1 
               
               
                 213370_s_at 
                 SFMBT1 
                 Scm-like with four mbt domains 1 
               
               
                 213621_s_at 
                 GUK1 
                 guanylate kinase 1 
               
               
                 213793_s_at 
                 HOMER1 
                 homer homolog 1 ( Drosophila ) 
               
               
                 213912_at 
                 TBC1D30 
                 TBC1 domain family member 30 
               
               
                 214937_x_at 
                 PCM1 
                 pericentriolar material 1 
               
               
                 215367_at 
                 KIAA1614 
                 KIAA1614 
               
               
                 215927_at 
                 ARFGEF2 
                 ADP-ribosylation factor guanine nucleotide-exchange factor 2 
               
               
                   
                   
                 (brefeldin A-inhibited) 
               
               
                 215945_s_at 
                 TRIM2 
                 tripartite motif containing 2 
               
               
                 216064_s_at 
                 AGA 
                 aspartylglucosaminidase 
               
               
                 216718_at 
                 LINC00302 
                 long intergenic non-protein coding RNA 302 
               
               
                 216753_at 
                 NA 
                 NA 
               
               
                 217436_x_at 
                 NA 
                 NA 
               
               
                 217440_at 
                 NA 
                 NA 
               
               
                 217496_s_at 
                 IDE 
                 insulin-degrading enzyme 
               
               
                 217892_s_at 
                 LIMA1 
                 LIM domain and actin binding 1 
               
               
                 217996_at 
                 PHLDA1 
                 pleckstrin homology-like domain family A member 1 
               
               
                 218111_s_at 
                 CMAS 
                 cytidine monophosphate N-acetylneuraminic acid synthetase 
               
               
                 218962_s_at 
                 TMEM168 
                 transmembrane protein 168 
               
               
                 218987_at 
                 ATF7IP 
                 activating transcription factor 7 interacting protein 
               
               
                 219045_at 
                 RHOF 
                 ras homolog gene family member F (in filopodia) 
               
               
                 219086_at 
                 ZNF839 
                 zinc finger protein 839 
               
               
                 219136_s_at 
                 LMF1 
                 lipase maturation factor 1 
               
               
                 219507_at 
                 RSRC1 
                 arginine/serine-rich coiled-coil 1 
               
               
                 219508_at 
                 GCNT3 
                 glucosaminyl (N-acetyl) transferase 3 mucin type 
               
               
                 219569_s_at 
                 TMEM22 
                 transmembrane protein 22 
               
               
                 219677_at 
                 SPSB1 
                 splA/ryanodine receptor domain and SOCS box containing 1 
               
               
                 219680_at 
                 NLRX1 
                 NLR family member X1 
               
               
                 219744_at 
                 FN3K 
                 fructosamine 3 kinase 
               
               
                 219747_at 
                 NDNF 
                 neuron-derived neurotrophic factor 
               
               
                 220068_at 
                 VPREB3 
                 pre-B lymphocyte 3 
               
               
                 220077_at 
                 CCDC134 
                 coiled-coil domain containing 134 
               
               
                 220385_at 
                 JPH2 
                 junctophilin 2 
               
               
                 221240_s_at 
                 B3GNT4 
                 UDP-GlcNAc:betaGal beta-13-N-acetylglucosaminyltransferase 4 
               
               
                 221245_s_at 
                 FZD5 
                 frizzled family receptor 5 
               
               
                 221428_s_at 
                 TBL1XR1 
                 transducin (beta)-like 1 X-linked receptor 1 
               
               
                 221592_at 
                 NA 
                 NA 
               
               
                 221607_x_at 
                 ACTG1 
                 actin gamma 1 
               
               
                 221608_at 
                 WNT6 
                 wingless-type MMTV integration site family member 6 
               
               
                 221630_s_at 
                 DDX4 
                 DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 
               
               
                 222150_s_at 
                 PION 
                 pigeon homolog ( Drosophila ) 
               
               
                 222285_at 
                 NA 
                 NA 
               
               
                 222288_at 
                 NA 
                 NA 
               
               
                 222289_at 
                 KCNC2 
                 potassium voltage-gated channel Shaw-related subfamily  
               
               
                   
                   
                 member 2 
               
               
                 35201_at 
                 HNRNPL 
                 heterogeneous nuclear ribonucleoprotein L 
               
               
                 38487_at 
                 STAB1 
                 stabilin 1 
               
               
                 38703_at 
                 DNPEP 
                 aspartyl aminopeptidase 
               
               
                 39549_at 
                 NPAS2 
                 neuronal PAS domain protein 2 
               
               
                 41657_at 
                 STK11 
                 serine/threonine kinase 11 
               
               
                 41858_at 
                 PGAP2 
                 post-GPI attachment to proteins 2 
               
               
                 52255_s_at  
                 COL5A3 
                 collagen type V alpha 3 
               
               
                 74694_s_at  
                 RABEP2 
                 rabaptin RAB GTPase binding effector protein 2 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 11 
               
             
            
               
                   
               
               
                 MRSA v. MSSA 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Gene 
                   
                 Entrez 
                   
               
               
                 Probe Set ID 
                 Symbol 
                 Gene Title 
                 Gene ID 
                 p-value 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 1420021_s_at 
                 Suz12 
                 suppressor of zeste 12 homolog ( Drosophila ) 
                 52615 
                 5.54E−07 
               
               
                 1422842_at 
                 Xrn2 
                 5′-3′ exoribonuclease 2 
                 24128 
                 9.49E−07 
               
               
                 1429432_at 
                 Bat212 
                 HLA-B associated transcript 2-like 2 
                 226562 
                 7.86E−07 
               
               
                 1434391_at 
                 AI503316 
                 expressed sequence AI503316 
                 105860 
                 1.02E−06 
               
               
                 1439247_at 
                 Dock10 
                 dedicator of cytokinesis 10 
                 210293 
                 1.02E−06 
               
               
                 1444279_at 
                 Huwe1 
                 HECT, UBA and WWE domain containing 1 
                 59026 
                 3.22E−07 
               
               
                 1446384_at 
                 — 
                 (Unannotated) 
                 — 
                 1.33E−07 
               
               
                 1446512_at 
                 Zc3h15 
                 zinc finger CCCH-type containing 15 
                 69082 
                 2.34E−07 
               
               
                 1449578_at 
                 Supt16h 
                 suppressor of Ty 16 homolog ( S .  cerevisiae ) 
                 114741 
                 2.91E−07 
               
               
                 1450051_at 
                 Atrx 
                 alpha thalassemia/mental retardation syndrome 
                 22589 
                 6.07E−07 
               
               
                   
                   
                 X-linked homolog (human) 
                   
                   
               
               
                 1451685_at 
                 Mllt6 
                 myeloid/lymphoid or mixed-lineage leukemia 
                 246198 
                 8.09E−07 
               
               
                   
                   
                 (trithorax homolog,  Drosophila ); translocated to, 6 
                   
                   
               
               
                 1452470_at 
                 Cep350 
                 centrosomal protein 350 
                 74081 
                 1.03E−06 
               
               
                 1456112_at 
                 Tpr 
                 translocated promoter region 
                 108989 
                 8.10E−07 
               
               
                 1457731_at 
                 Snapc3 
                 small nuclear RNA activating complex, 
                 77634 
                 3.80E−07 
               
               
                   
                   
                 polypeptide 3 
                   
                   
               
               
                 1459398_at 
                 Peli1 
                 Pellino 1 
                 67245 
                 7.47E−07 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 12 
               
             
            
               
                   
               
               
                 Pathway analysis for the genes from pairwise comparisons in the 
               
               
                 mouse and human study. Asterisk (*) indicates pathways that  
               
               
                 are present in both the mouse and human response to 
               
               
                 the specified pathogen. 
               
            
           
           
               
               
               
            
               
                   
                 MOUSE  S.   aureus  VS HEALTHY CONTROLS 
                   
               
               
                 # 
                 Pathway 
                 p-value 
               
               
                   
               
            
           
           
               
               
               
            
               
                 1 
                 Immune response_HMGB1/RAGE signaling pathway 
                 1.58E−14 
               
               
                 2 
                 * Immune response_T cell receptor signaling pathway 
                 7.40E−14 
               
               
                 3 
                 * Immune response_CD28 signaling 
                 2.75E−13 
               
               
                 4 
                 * Transcription_NF-kB signaling pathway 
                 5.45E−13 
               
               
                 5 
                 Immune response_Oncostatin M signaling via MAPK in 
                 1.24E−12 
               
               
                   
                 human cells 
                   
               
               
                 6 
                 * Transport_Clathrin-coated vesicle cycle 
                 1.29E−12 
               
               
                 7 
                 Signal transduction_JNK pathway 
                 5.29E−12 
               
               
                 8 
                 Apoptosis and survival_APRIL and BAFF signaling 
                 5.95E−12 
               
               
                 9 
                 Immune response_Regulation of T cell function by 
                 6.32E−12 
               
               
                   
                 CTLA-4 
                   
               
               
                 10 
                 * Immune response_ICOS pathway in T-helper cell 
                 8.69E−12 
               
               
                 11 
                 * Immune response_TCR and CD28 co-stimulation in 
                 1.24E−11 
               
               
                   
                 activation of NF-kB 
                   
               
               
                 12 
                 Immune response_IL-3 activation and signaling pathway 
                 1.38E−11 
               
               
                 13 
                 Development_Flt3 signaling 
                 2.06E−11 
               
               
                 14 
                 Immune response_IL-1 signaling pathway 
                 2.06E−11 
               
               
                 15 
                 Immune response_CD137 signaling in immune cell 
                 3.03E−11 
               
               
                 16 
                 Immune response_Oncostatin M signaling via MAPK in 
                 3.18E−11 
               
               
                   
                 mouse cells 
                   
               
               
                 17 
                 G-protein signaling_Regulation of p38 and JNK signaling 
                 5.86E−11 
               
               
                   
                 mediated by G-proteins 
                   
               
               
                 18 
                 Immune response_IL-17 signaling pathways 
                 5.88E−11 
               
               
                 19 
                 Reproduction_GnRH signaling 
                 7.27E−11 
               
               
                 20 
                 * Immune response_CD40 signaling 
                 1.05E−10 
               
               
                 21 
                 Development_TGF-beta-dependent induction of EMT 
                 1.30E−10 
               
               
                   
                 via MAPK 
                   
               
               
                 22 
                 Development_Prolactin receptor signaling 
                 1.39E−10 
               
               
                 23 
                 Apoptosis and survival_Lymphotoxin-beta receptor 
                 4.08E−10 
               
               
                   
                 signaling 
                   
               
               
                 24 
                 Immune response_Gastrin in inflammatory response 
                 6.02E−10 
               
               
                 25 
                 * Development_GM-CSF signaling 
                 6.76E−10 
               
               
                 26 
                 * Immune response_Function of MEF2 in T lymphocytes 
                 6.76E−10 
               
               
                 27 
                 Immune response_IL-22 signaling pathway 
                 7.58E−10 
               
               
                 28 
                 Immune response_CCR5 signaling in macrophages and 
                 8.59E−10 
               
               
                   
                 T lymphocytes 
                   
               
               
                 29 
                 Immune response_MIF in innate immunity response 
                 9.71E−10 
               
               
                 30 
                 Immune response_Fc epsilon RI pathway 
                 1.27E−09 
               
               
                 31 
                 * Immune response_Immunological synapse formation 
                 1.36E−09 
               
               
                 32 
                 * Immune response_CXCR4 signaling via second 
                 1.52E−09 
               
               
                   
                 messenger 
                   
               
               
                 33 
                 Chemotaxis_CXCR4 signaling pathway 
                 1.52E−09 
               
               
                 34 
                 Immune response_MIF-mediated glucocorticoid regulation 
                 1.68E−09 
               
               
                 35 
                 * Cytoskeleton remodeling_TGF, WNT and cytoskeletal 
                 1.68E−09 
               
               
                   
                 remodeling 
                   
               
               
                 36 
                 Apoptosis and survival_Anti-apoptotic TNFs/NF-kB/ 
                 1.76E−09 
               
               
                   
                 Bcl-2 pathway 
                   
               
               
                 37 
                 Immune response_IL-15 signaling 
                 2.14E−09 
               
               
                 38 
                 Immune response_CD16 signaling in NK cells 
                 3.12E−09 
               
               
                 39 
                 Cell adhesion_Chemokines and adhesion 
                 3.81E−09 
               
               
                 40 
                 Cytokine production by Th17 cells in CF 
                 4.20E−09 
               
               
                 41 
                 Mucin expression in CF via TLRs, EGFR signaling 
                 4.38E−09 
               
               
                   
                 pathways 
                   
               
               
                 42 
                 G-protein signaling_Ras family GTPases in kinase 
                 4.44E−09 
               
               
                   
                 cascades (scheme) 
                   
               
               
                 43 
                 Immune response_HMGB1/TLR signaling pathway 
                 5.51E−09 
               
               
                 44 
                 Chemotaxis_Leukocyte chemotaxis 
                 6.15E−09 
               
               
                 45 
                 Apoptosis and survival_Regulation of Apoptosis by 
                 6.98E−09 
               
               
                   
                 Mitochondrial Proteins 
                   
               
               
                 46 
                 G-protein signaling_N-RAS regulation pathway 
                 6.98E−09 
               
               
                 47 
                 * Immune response_NFAT in immune response 
                 7.06E−09 
               
               
                 48 
                 Immune response_TREM1 signaling pathway 
                 7.58E−09 
               
               
                 49 
                 * Immune response_IL-27 signaling pathway 
                 1.01E−08 
               
               
                 50 
                 * Development_NOTCH1-mediated pathway for NF-KB 
                 1.31E−08 
               
               
                   
                 activity modulation 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 13 
               
             
            
               
                   
               
               
                 Pathway analysis for the genes from pairwise comparisons in the 
               
               
                 mouse and human study. Asterisk (*) indicates pathways that are 
               
               
                 present in both the mouse and human response to the specified pathogen. 
               
            
           
           
               
               
               
            
               
                   
                 HUMAN  S.   aureus  VS. HEALTHY CONTROLS 
                   
               
               
                 # 
                 Pathway 
                 p-value 
               
               
                   
               
            
           
           
               
               
               
            
               
                 1 
                 * Cytoskeleton remodeling_TGF, WNT and cytoskeletal 
                 5.45E−11 
               
               
                   
                 remodeling 
                   
               
               
                 2 
                 * Immune response_NFAT in immune response 
                 1.13E−10 
               
               
                 3 
                 Cytoskeleton remodeling_Cytoskeleton remodeling 
                 1.45E−09 
               
               
                 4 
                 Protein folding and maturation_POMC processing 
                 1.79E−09 
               
               
                 5 
                 Immune response_IL-4 signaling pathway 
                 1.43E−08 
               
               
                 6 
                 Oxidative phosphorylation 
                 1.47E−08 
               
               
                 7 
                 * Immune response_CD28 signaling 
                 2.13E−08 
               
               
                 8 
                 * Immune response_T cell receptor signaling pathway 
                 3.90E−08 
               
               
                 9 
                 * Immune response_ICOS pathway in T-helper cell 
                 4.51E−08 
               
               
                 10 
                 * Immune response_TCR and CD28 co-stimulation in 
                 4.70E−08 
               
               
                   
                 activation of NF-kB 
                   
               
               
                 11 
                 * Immune response_Function of MEF2 in T lymphocytes 
                 7.12E−08 
               
               
                 12 
                 Transcription_Role of heterochromatin protein 1 (HP1) 
                 1.31E−07 
               
               
                   
                 family in transcriptional silencing 
                   
               
               
                 13 
                 Signal transduction_Activation of PKC via G-Protein 
                 1.90E−07 
               
               
                   
                 coupled receptor 
                   
               
               
                 14 
                 Signal transduction_AKT signaling 
                 2.59E−07 
               
               
                 15 
                 Development_TGF-beta receptor signaling 
                 3.47E−07 
               
               
                 16 
                 Development_Role of HDAC and calcium/calmodulin- 
                 4.73E−07 
               
               
                   
                 dependent kinase (CaMK) in control of skeletal  
                   
               
               
                   
                 myogenesis 
                   
               
               
                 17 
                 Immune response_BCR pathway 
                 4.73E−07 
               
               
                 18 
                 Some pathways of EMT in cancer cells 
                 5.51E−07 
               
               
                 19 
                 Regulation of degradation of deltaF508 CFTR in CF 
                 8.47E−07 
               
               
                 20 
                 Apoptosis and survival_Granzyme A signaling 
                 9.21E−07 
               
               
                 21 
                 Immune response_NF-AT signaling and leukocyte 
                 1.16E−06 
               
               
                   
                 interactions 
                   
               
               
                 22 
                 Apoptosis and survival_Endoplasmic reticulum stress 
                 1.32E−06 
               
               
                   
                 response pathway 
                   
               
               
                 23 
                 Development_WNT signaling pathway. Part 2 
                 1.32E−06 
               
               
                 24 
                 Immune response_Antigen presentation by MHC class I 
                 1.67E−06 
               
               
                 25 
                 Development_PIP3 signaling in cardiac myocytes 
                 1.83E−06 
               
               
                 26 
                 * Immune response_CD40 signaling 
                 2.34E−06 
               
               
                 27 
                 Cytoskeleton remodeling_Regulation of actin 
                 2.68E−06 
               
               
                   
                 cytoskeleton by Rho GTPases 
                   
               
               
                 28 
                 Immune response_IL-10 signaling pathway 
                 3.01E−06 
               
               
                 29 
                 Development_PDGF signaling via STATs and NF-kB 
                 3.09E−06 
               
               
                 30 
                 * Immune response_Immunological synapse formation 
                 3.58E−06 
               
               
                 31 
                 Immune response_IL-2 activation and signaling pathway 
                 4.34E−06 
               
               
                 32 
                 Translation_Regulation of EIF4F activity 
                 5.37E−06 
               
               
                 33 
                 * Immune response_IL-27 signaling pathway 
                 5.44E−06 
               
               
                 34 
                 Immune response_Bacterial infections in normal airways 
                 6.52E−06 
               
               
                 35 
                 Immune response_Th1 and Th2 cell differentiation 
                 7.07E−06 
               
               
                 36 
                 Development_Leptin signaling via PI3K-dependent 
                 7.86E−06 
               
               
                   
                 pathway 
                   
               
               
                 38 
                 * Development_NOTCH1-mediated pathway for NF-KB 
                 9.05E−06 
               
               
                   
                 activity modulation 
                   
               
               
                 37 
                 * Immune response_CXCR4 signaling via second 
                 9.05E−06 
               
               
                   
                 messenger 
                   
               
               
                 39 
                 CFTR folding and maturation (norm and CF) 
                 9.76E−06 
               
               
                 40 
                 Immune response_CCR3 signaling in eosinophils 
                 1.02E−05 
               
               
                 41 
                 PGE2 pathways in cancer 
                 1.14E−05 
               
               
                 42 
                 Develosment_IGF-1 receptor signaling 
                 1.41E−05 
               
               
                 43 
                 Immune response_Antigen presentation by MHC class II 
                 1.51E−05 
               
               
                 44 
                 * Transport_Clathrin-coated vesicle cycle 
                 1.67E−05 
               
               
                 45 
                 Translation_Insulin regulation of translation 
                 1.71E−05 
               
               
                 46 
                 Signal transduction_IP3 signaling 
                 1.73E−05 
               
               
                 47 
                 Apoptosis and survival_nAChR in apoptosis inhibition 
                 1.82E−05 
               
               
                   
                 and cell cycle progression 
                   
               
               
                 48 
                 * Transcription_NF-kB signaling pathway 
                 2.03E−05 
               
               
                 49 
                 G-protein signaling_Regulation of RAC1 activity 
                 2.37E−05 
               
               
                 50 
                 * Development_GM-CSF signaling 
                 2.52E−05 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 14 
               
             
            
               
                   
               
               
                 Pathway analysis for the genes from pairwise comparisons in the 
               
               
                 mouse and human study. Asterisk (*) indicates pathways that are 
               
               
                 present in both the mouse and human response to the specified pathogen. 
               
            
           
           
               
               
            
               
                   
                 MOUSE  E.   coli  VS. HEALTHY CONTROLS 
               
            
           
           
               
               
               
            
               
                 # 
                 Pathway 
                 p-value 
               
               
                   
               
            
           
           
               
               
               
            
               
                 1 
                 * Development VEGF signaling via VEGFR2 - generic 
                 5.51E−14 
               
               
                   
                 cascades 
                   
               
               
                 2 
                 Immune response_CCR5 signaling in macrophages and 
                 4.40E−13 
               
               
                   
                 T lymphocytes 
                   
               
               
                 3 
                 * Immune response_CD28 signaling 
                 6.16E−12 
               
               
                 4 
                 Development_A2A receptor signaling 
                 3.10E−11 
               
               
                 5 
                 Cytoskeleton remodeling_Role of PKA in cytoskeleton 
                 7.11E−11 
               
               
                   
                 reorganisation 
                   
               
               
                 6 
                 Apoptosis and survival_Granzyme B signaling 
                 1.13E−10 
               
               
                 7 
                 * Immune response_Gastrin in inflammatory response 
                 2.52E−10 
               
               
                 8 
                 * Development_Prolactin receptor signaling 
                 2.63E−10 
               
               
                 9 
                 * Immune response_HMGB1/RAGE signaling pathway 
                 2.97E−10 
               
               
                 10 
                 Apoptosis and survival_BAD phosphorylation 
                 1.82E−09 
               
               
                 11 
                 Immune response_TREM1 signaling pathway 
                 2.69E−09 
               
               
                 12 
                 Apoptosis and survival_Anti-apoptotic action of Gastrin 
                 2.81E−09 
               
               
                 13 
                 * Cytoskeleton remodeling_TGF, WNT and cytoskeletal 
                 3.96E−09 
               
               
                   
                 remodeling 
                   
               
               
                 14 
                 Immune response_IL-1 signaling pathway 
                 4.27E−09 
               
               
                 15 
                 Development_GM-CSF signaling 
                 5.64E−09 
               
               
                 16 
                 * Immune response_Function of MEF2 in T lymphocytes 
                 5.64E−09 
               
               
                 17 
                 Development_Growth hormone signaling via STATs and 
                 6.47E−09 
               
               
                   
                 PLC/IP3 
                   
               
               
                 18 
                 Cytoskeleton remodeling_Reverse signaling by ephrin B 
                 9.11E−09 
               
               
                 19 
                 Immune response_HMGB1 release from the cell 
                 1.04E−08 
               
               
                 20 
                 Immune response_HMGB1/TLR signaling pathway 
                 1.04E−08 
               
               
                 21 
                 Immune response_Inhibitory action of Lipoxins on pro- 
                 1.38E−08 
               
               
                   
                 inflammatory TNF-alpha signaling 
                   
               
               
                 22 
                 Blood coagulation_GPCRs in platelet aggregation 
                 1.73E−08 
               
               
                 23 
                 * Immune response_Histamine H1 receptor signaling in 
                 2.00E−08 
               
               
                   
                 immune response 
                   
               
               
                 24 
                 * Immune response_IFN gamma signaling pathway 
                 2.29E−08 
               
               
                 25 
                 * Immune response_IL-22 signaling pathway 
                 2.45E−08 
               
               
                 26 
                 Signal transduction_cAMP signaling 
                 2.51E−08 
               
               
                 27 
                 * Cell adhesion_Chemokines and adhesion 
                 3.31E−08 
               
               
                 28 
                 Development_Flt3 signaling 
                 3.40E−08 
               
               
                 29 
                 Signal transduction_Erk Interactions: Inhibition of Erk 
                 3.89E−08 
               
               
                 30 
                 G-protein signaling G-Protein alpha-q signaling cascades 
                 3.89E−08 
               
               
                 31 
                 Development_Gastrin in cell growth and proliferation 
                 4.41E−08 
               
               
                 32 
                 Chemotaxis_Leukocyte chemotaxis 
                 5.03E−08 
               
               
                 33 
                 Development_EGFR signaling pathway 
                 5.89E−08 
               
               
                 34 
                 Chemotaxis_Lipoxin inhibitory action on fMLP-induced 
                 7.04E−08 
               
               
                   
                 neutrophil chemotaxis 
                   
               
               
                 35 
                 * Immune response_ICOS pathway in T-helper cell 
                 7.04E−08 
               
               
                 36 
                 * Immune response_IL-15 signaling 
                 7.81E−08 
               
               
                 37 
                 Signal transduction_Activation of PKC via G-Protein 
                 7.83E−08 
               
               
                   
                 coupled receptor 
                   
               
               
                 38 
                 Regulation of CFTR activity (norm and CF) 
                 8.05E−08 
               
               
                 39 
                 Immune response_Fc gamma R-mediated phagocytosis in 
                 9.96E−08 
               
               
                   
                 macrophages 
                   
               
               
                 40 
                 G-protein signaling_G-Protein alpha-12 signaling pathway 
                 1.39E−07 
               
               
                 41 
                 Cell adhesion_Role of tetraspanins in the integrin- 
                 1.39E−07 
               
               
                   
                 mediated cell adhesion 
                   
               
               
                 42 
                 Apoptosis and survival_HTR1A signaling 
                 2.65E−07 
               
               
                 43 
                 Immune response_Bacterial infections in normal airways 
                 2.65E−07 
               
               
                 44 
                 HIV-1 signaling via CCR5 in macrophages and T 
                 2.99E−07 
               
               
                   
                 lymphocytes 
                   
               
               
                 45 
                 Transcription_NF-kB signaling pathway 
                 2.99E−07 
               
               
                 46 
                 Immune response_CXCR4 signaling via second 
                 3.39E−07 
               
               
                   
                 messenger 
                   
               
               
                 47 
                 Cell adhesion_Ephrin signaling 
                 3.44E−07 
               
               
                 48 
                 Cell adhesion_Histamine H1 receptor signaling in the 
                 3.44E−07 
               
               
                   
                 interruption of cell barrier integrity 
                   
               
               
                 49 
                 * Immune response_NFAT in immune response 
                 3.60E−07 
               
               
                 50 
                 Some pathways of EMT in cancer cells 
                 3.60E−07 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 15 
               
             
            
               
                   
               
               
                 Pathway analysis for the genes from pairwise comparisons in the 
               
               
                 mouse and human study. Asterisk (*) indicates pathways that are 
               
               
                 present in both the mouse and human response to the specified 
               
               
                 pathogen. 
               
            
           
           
               
               
               
            
               
                   
                 HUMAN  E.   coli  VS. HEALTHY CONTROLS 
                   
               
               
                 # 
                 Pathway 
                 p-value 
               
               
                   
               
            
           
           
               
               
               
            
               
                 1 
                 * Cytoskeleton remodeling_TGF, WNT and cytoskeletal 
                 2.76E−10 
               
               
                   
                 remodeling 
                   
               
               
                 2 
                 * Immune response_HMGB1/RAGE signaling pathway 
                 1.15E−09 
               
               
                 3 
                 Development_EPO-induced Jak-STAT pathway 
                 6.64E−09 
               
               
                 4 
                 Immune response_Oncostatin M signaling via MAPK in 
                 6.64E−09 
               
               
                   
                 mouse cells 
                   
               
               
                 5 
                 Cytoskeleton remodeling_Cytoskeleton remodeling 
                 7.59E−09 
               
               
                 6 
                 Protein folding and maturation_POMC processing 
                 9.88E−09 
               
               
                 7 
                 * Development_Prolactin receptor signaling 
                 1.59E−08 
               
               
                 8 
                 Immune response_IL-2 activation and signaling pathway 
                 2.29E−08 
               
               
                 9 
                 * Immune response_ICOS pathway in T-helper cell 
                 2.48E−08 
               
               
                 10 
                 Immune response_Immunological synapse formation 
                 2.56E−08 
               
               
                 11 
                 Immune response_Oncostatin M signaling via MAPK in 
                 2.64E−08 
               
               
                   
                 human cells 
                   
               
               
                 12 
                 * Immune response_NFAT in immune response 
                 6.40E−08 
               
               
                 13 
                 Transcription_Role of heterochromatin protein 1 (HP1) 
                 8.70E−08 
               
               
                   
                 family in transcriptional silencing 
                   
               
               
                 14 
                 Immune response_T cell receptor signaling pathway 
                 1.04E−07 
               
               
                 15 
                 * Immune response_Function of MEF2 in T lymphocytes 
                 1.95E−07 
               
               
                 16 
                 Immune response_IL-4 signaling pathway 
                 2.55E−07 
               
               
                 18 
                 * Immune response__IFN gamma signaling pathway 
                 2.63E−07 
               
               
                 19 
                 Immune response_BCR pathway 
                 2.63E−07 
               
               
                 17 
                 * Immune response_CD28 signaling 
                 2.63E−07 
               
               
                 20 
                 * Immune response_Histamine H1 receptor signaling in 
                 3.65E−07 
               
               
                   
                 immune response 
                   
               
               
                 21 
                 Immune response_CD16 signaling in NK cells 
                 3.87E−07 
               
               
                 22 
                 PGE2 pathways in cancer 
                 4.07E−07 
               
               
                 23 
                 * Development_VEGF signaling via VEGFR2 - generic 
                 4.14E−07 
               
               
                   
                 cascades 
                   
               
               
                 24 
                 Development_Thrombopoietin-regulated cell processes 
                 4.21E−07 
               
               
                 25 
                 Immune response_IL-4 - antiapoptotic action 
                 5.94E−07 
               
               
                 26 
                 Normal and pathological TGF-beta-mediated regulation 
                 5.96E−07 
               
               
                   
                 of cell proliferation 
                   
               
               
                 27 
                 Immune response_Th1 and Th2 cell differentiation 
                 8.97E−07 
               
               
                 28 
                 Development_TGF-beta receptor signaling 
                 9.11E−07 
               
               
                 29 
                 Chemotaxis_CXCR4 signaling pathway 
                 1.07E−06 
               
               
                 30 
                 Development_PIP3 signaling in cardiac myocytes 
                 1.09E−06 
               
               
                 31 
                 Development_Role of HDAC and calcium/calmodulin- 
                 1.15E−06 
               
               
                   
                 dependent kinase (CaMK) in control of skeletal 
                   
               
               
                   
                 myogenesis 
                   
               
               
                 32 
                 * Immune response_Gastrin in inflammatory response 
                 1.44E−06 
               
               
                 33 
                 * Cell adhesion_Chemokines and adhesion 
                 1.52E−06 
               
               
                 34 
                 Transcription_Role of AP-1 in regulation of cellular 
                 1.69E−06 
               
               
                   
                 metabolism 
                   
               
               
                 35 
                 Transcription_Sin3 and NuRD in transcription regulation 
                 1.69E−06 
               
               
                 37 
                 Development_Growth hormone signaling via PI3K/AKT  
                 2.40E−06 
               
               
                   
                 and MAPK cascades 
                   
               
               
                 36 
                 Translation_Insulin regulation of translation 
                 2.40E−06 
               
               
                 38 
                 Signal transduction_IP3 signaling 
                 2.61E−06 
               
               
                 39 
                 Translation_Regulation of EIF2 activity 
                 2.78E−06 
               
               
                 40 
                 Immune response_NF-AT signaling and leukocyte 
                 3.16E−06 
               
               
                   
                 interactions 
                   
               
               
                 43 
                 Immune response_IL-12-induced IFN-gamma production 
                 3.17E−06 
               
               
                 42 
                 Immune response_IL-9 signaling pathway 
                 3.17E−06 
               
               
                 41 
                 Immune response_Regulation of T cell function by 
                 3.17E−06 
               
               
                   
                 CTLA-4 
                   
               
               
                 44 
                 Translation_Regulation of EIF4F activity 
                 3.18E−06 
               
               
                 45 
                 * Immune response_IL-15 signaling 
                 3.32E−06 
               
               
                 47 
                 G-protein signaling_N-RAS regulation pathway 
                 3.52E−06 
               
               
                 46 
                 * Immune response_IL-22 signaling pathway 
                 3.52E−06 
               
               
                 48 
                 Immune response_IL-27 signaling pathway 
                 3.77E−06 
               
               
                 49 
                 Apoptosis and survival_Granzyme A signaling 
                 3.78E−06 
               
               
                 50 
                 Immune response_Signaling pathway mediated by IL-6 
                 3.78E−06 
               
               
                   
                 and IL-1 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 16 
               
             
            
               
                   
               
               
                 Pathway analysis for the genes from pairwise comparisons in the mouse and human study. 
               
               
                 MOUSE  S .  aureus  VS.  E .  coli   
               
            
           
           
               
               
               
            
               
                 # 
                 Pathway 
                 p-value 
               
               
                   
               
               
                  1 
                 Cytoskeleton remodeling_TGF, WNT and cytoskeletal remodeling 
                 4.98E−13 
               
               
                  2 
                 Development_IGF-1 receptor signaling 
                 1.17E−12 
               
               
                  3 
                 Transport_Clathrin-coated vesicle cycle 
                 1.27E−12 
               
               
                  4 
                 Development_PIP3 signaling in cardiac myocytes 
                 2.24E−12 
               
               
                  5 
                 Immune response_HMGB1/RAGE signaling pathway 
                 2.32E−12 
               
               
                  6 
                 Immune response_IL-15 signaling 
                 6.07E−12 
               
               
                  7 
                 Immune response_IL-2 activation and signaling pathway 
                 9.24E−12 
               
               
                  8 
                 Development_GM-CSF signaling 
                 1.80E−11 
               
               
                  9 
                 Immune response_HMGB1/TLR signaling pathway 
                 2.74E−11 
               
               
                 10 
                 Apoptosis and survival_APRIL and BAFF signaling 
                 3.22E−11 
               
               
                 11 
                 Immune response_IL-3 activation and signaling pathway 
                 3.84E−11 
               
               
                 12 
                 Cell adhesion_Chemokines and adhesion 
                 4.55E−11 
               
               
                 13 
                 Immune response_CD40 signaling 
                 6.24E−11 
               
               
                 14 
                 Signal transduction_AKT signaling 
                 7.25E−11 
               
               
                 15 
                 Immune response_Gastrin in inflammatory response 
                 8.44E−11 
               
               
                 16 
                 Cytoskeleton remodeling_Cytoskeleton remodeling 
                 3.97E−10 
               
               
                 17 
                 Development_NOTCH1-mediated pathway for NF-KB activity modulation 
                 5.11E−10 
               
               
                 18 
                 Cell cycle_Influence of Ras and Rho proteins on G1/S Transition 
                 7.37E−10 
               
               
                 19 
                 Apoptosis and survival_HTR1A signaling 
                 8.53E−10 
               
               
                 20 
                 Immune response_IL-1 signaling pathway 
                 1.06E−09 
               
               
                 21 
                 Transcription_NF-kB signaling pathway 
                 2.25E−09 
               
               
                 22 
                 Immune response_Regulation of T cell function by CTLA-4 
                 2.27E−09 
               
               
                 23 
                 Immune response_IL-17 signaling pathways 
                 4.61E−09 
               
               
                 24 
                 Immune response_Bacterial infections in normal airways 
                 5.21E−09 
               
               
                 25 
                 Mucin expression in CF via TLRs, EGFR signaling pathways 
                 5.21E−09 
               
               
                 26 
                 Development_TGF-beta-dependent induction of EMT via MAPK 
                 6.16E−09 
               
               
                 27 
                 Apoptosis and survival_Anti-apoptotic TNFs/NF-kB/Bcl-2 pathway 
                 7.98E−09 
               
               
                 28 
                 Development_EPO-induced Jak-STAT pathway 
                 9.02E−09 
               
               
                 29 
                 Development_VEGF signaling via VEGFR2-generic cascades 
                 1.01E−08 
               
               
                 30 
                 Immune response_Histamine H1 receptor signaling in immune response 
                 1.06E−08 
               
               
                 31 
                 Apoptosis and survival_Regulation of Apoptosis by Mitochondrial Proteins 
                 1.80E−08 
               
               
                 32 
                 Apoptosis and survival_Endoplasmic reticulum stress response pathway 
                 2.37E−08 
               
               
                 33  
                 Immune response_Oncostatin M signaling via MAPK in human cells 
                 3.27E−08 
               
               
                 34  
                 Development_Role of HDAC and calcium/calmodulin-dependent kinase 
                 3.79E−08 
               
               
                   
                 (CaMK) in control of skeletal myogenesis 
                   
               
               
                 35 
                 Development_FGFR signaling pathway 
                 3.79E−08 
               
               
                 36 
                 Immune response_BCR pathway 
                 3.79E−08 
               
               
                 37 
                 Development_Flt3 signaling 
                 4.37E−08 
               
               
                 38  
                 Immune response_CCR5 signaling in macrophages and T lymphocytes 
                 4.62E−08 
               
               
                 39  
                 Apoptosis and survival_Granzyme B signaling 
                 7.07E−08 
               
               
                 40  
                 NGF activation of NF-kB 
                 7.15E−08 
               
               
                 41  
                 Development_Thrombopoietin-regulated cell processes 
                 7.35E−08 
               
               
                 42  
                 Apoptosis and survival_Lymphotoxin-beta receptor signaling 
                 8.88E−08 
               
               
                 43  
                 Development_Growth hormone signaling via PI3K/AKT and MAPK cascades 
                 8.88E−08 
               
               
                 44  
                 Development_PEDF signaling 
                 9.68E−08 
               
               
                 45 
                 Development_A3 receptor signaling 
                 9.68E−08 
               
               
                 46  
                 Transcription_Receptor-mediated HIF regulation 
                 1.05E−07 
               
               
                 47  
                 IL-1 beta-dependent CFTR expression 
                 1.19E−07 
               
               
                 48  
                 Translation_Regulation of EIF4F activity 
                 1.20E−07 
               
               
                 49  
                 Immune response_ICOS pathway in T-helper cell 
                 1.21E−07 
               
               
                 50  
                 Proteolysis_Role of Parkin in the Ubiquitin-Proteasomal Pathway 
                 1.31E−07 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17 
               
             
            
               
                   
               
               
                 Genes in pathways common to murine and human responses to infection. 
               
            
           
           
               
               
               
            
               
                 Pairwise 
                   
                   
               
               
                 comparison 
                 Pathway 
                 Genes 
               
               
                   
               
               
                 
                   S. 
                   aureus 
                 
                 Cytoskeleton 
                 Human genes: 
               
               
                 vs. Healthy 
                 remodeling_TGF, WNT 
                 AKT1 AKT3 ACTG1 ACTR3 ACTR3B ARPC1A ARPC2 
               
               
                   
                 and cytoskeletal 
                 AXIN1 CRK CSNK2A1 CSNK2B COL4A2 COL4A3 
               
               
                   
                 remodeling 
                 DSTN DVL1 DVL2 DVL3 PTK2 FZD3 FZD5 FZD7 
               
               
                   
                   
                 GSK3B CHUK LIMK2 LAMA1 LAMC1 MYL6 MYL6B 
               
               
                   
                   
                 PPP1CB PPP1R12A MMP13 MKNK1 MYL12A MYL12B 
               
               
                   
                   
                 RPS6KA5 NCL PIK3CB PIK3R1 PIK3R3 PLAUR PPARD 
               
               
                   
                   
                 RHEB ROCK2 SMAD3 SOS2 TAB1 TCF7L2 TGFB1 
               
               
                   
                   
                 TGFBR1 TLN2 LEF1 TCF7 TSC2 VAV1 VEGFA VCL 
               
               
                   
                   
                 MYC SRC MTOR CDKN2B MAPK13 MAPK14 TP53 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Acta2 Actb Actg1 Actn4 Actr2 Actr3 Arpc1b 
               
               
                   
                   
                 Arpc4 Arpc5 Axin2 Ctnnb1 Cdc42 Crk Col4a2 Dstn Dvl2 
               
               
                   
                   
                 Mapk1 Fzd1 Fzd7 Grb2 Mdm2 Ppp1r12a Map3k11 Rps6ka5 
               
               
                   
                   
                 Nlk Serpine1 Pak1 Plaur Ppard Pxn Rheb Rhoa Sos1 Sos2 
               
               
                   
                   
                 Map3k7 Tgfbr2 Lef1 Tcf7 Vav1 Jun Myc Raf1 Eif4e 
               
               
                   
                   
                 Cdkn1a Mapk11 Mapk13 
               
               
                   
                 Immune response_NFAT 
                 Human genes: 
               
               
                   
                 in immune response 
                 AKT1 AKT3 BLNK CD28 CD247 CD3D CD3E CD3G 
               
               
                   
                   
                 CD79A CD79B PPP3CC CALM1 CALM3 FCER1A 
               
               
                   
                   
                 FCER1G GSK3B NFKBIA CHUK IKBKB ITPR1 ITPR3 
               
               
                   
                   
                 ITK IGHV3-23 IGKC IGK@ IGL@ IGHM LAT LCK LYN 
               
               
                   
                   
                 HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 
               
               
                   
                   
                 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA- 
               
               
                   
                   
                 DRA HLA-DRB1 HLA-DRB3 HLA-DRB4 HLA-DRB5 
               
               
                   
                   
                 NFAT5 NFATC1 NFATC3 REL RELA PIK3CB PIK3R1 
               
               
                   
                   
                 PIK3R3 PRKCQ PLCG1 TRAC TRA@ TRAT1 VAV1 
               
               
                   
                   
                 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Blnk Cd28 Cd247 Cd3d Cd3e Cd3g Cd79a 
               
               
                   
                   
                 Cd79b Cd80 Cd86 Fcer1g Ms4a2 Nfkbia Nfkbib Nfkbie 
               
               
                   
                   
                 Ikbkb Itpr2 Itpr3 Itk Igk Lat Lck H2-Eb2 Nfatc2 Nfatc3 Relb 
               
               
                   
                   
                 Nfkb2 Rel Rela Prkcq Plcg1 Lcp2 Tcrb-J Trat1 Vav1 Zap70 
               
               
                   
                 Immune response_CD28 
                 Human genes: 
               
               
                   
                 signaling 
                 AKT1 AKT3 BAD BCL2L1 CD28 CD247 CD3D CD3E 
               
               
                   
                   
                 CD3G PPP3CC CALM1 CALM3 FYN GRAP2 GSK3B 
               
               
                   
                   
                 NFKBIA CHUK IKBKB ITPR1 ITPR3 ITK LAT LCK 
               
               
                   
                   
                 NFAT5 NFATC1 NFATC3 REL RELA PIK3CB PIK3R1 
               
               
                   
                   
                 PIK3R3 PRKCQ PLCG1 TRAC TRA@ VAV1 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Bad Bcl2l1 Cd28 Cd247 Cd3d Cd3e Cd3g Cd80 
               
               
                   
                   
                 Cd86 Fyn Grap2 Grb2 Nfkbia Nfkbib Nfkbie Ikbkb Itpr2 
               
               
                   
                   
                 Itpr3 Itk Mapk8 Lat Lck Map2k4 Map2k7 Nfatc2 Nfatc3 
               
               
                   
                   
                 Relb Nfkb2 Rel Rela Pak1 Prkcq Plcg1 Lcp2 Tcrb-J Vav1 
               
               
                   
                   
                 Zap70 Jun 
               
               
                   
                 Immune response_T cell 
                 Human genes: 
               
               
                   
                 receptor signaling 
                 CD247 CD3D CD3E CD3G CD4 RASGRP1 PPP3CC 
               
               
                   
                 pathway 
                 CALM1 CALM3 ELK1 FYN NFKBIA CHUK IKBKB 
               
               
                   
                   
                 ITPR1 ITPR3 ITK LAT LCK MALT1 HLA-DMA HLA- 
               
               
                   
                   
                 DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 
               
               
                   
                   
                 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA HLA- 
               
               
                   
                   
                 DRB1 HLA-DRB3 HLA-DRB4 HLA-DRB5 NFATC1 
               
               
                   
                   
                 NFATC3 REL RELA PRKCQ PLCG1 SOS2 TRAC TRA@ 
               
               
                   
                   
                 TRAT1 VAV1 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Bcl10 Card11 Cd247 Cd3d Cd3e Cd3g Cd4 Rasgrp1 Mapk1 
               
               
                   
                   
                 Elk1 Fyn Grb2 Nfkbia Nfkbib Nfkbie Ikbkb Itpr2 Itpr3 Itk 
               
               
                   
                   
                 Lat Lck H2-Eb2 Ube2v2 Nfatc2 Nfatc3 Relb Nfkb2 Rel 
               
               
                   
                   
                 Rela Prkcq Plcg1 Sos1 Sos2 Lcp2 Tcrb-J Trat1 Vav1 Zap70 
               
               
                   
                   
                 Fos Raf1 
               
               
                   
                 Immune response_ICOS 
                 Human genes: 
               
               
                   
                 pathway in T-helper cell 
                 AKT1 AKT3 BAD CD28 CD247 CD3D CD3E CD3G 
               
               
                   
                   
                 PPP3CC CALM1 CALM3 GNA15 GNB5 GNB1 GNG10 
               
               
                   
                   
                 GNG3 GNG5 NFKBIA ICOS IKBKB ITPR1 ITPR3 ITK 
               
               
                   
                   
                 LAT LCK HLA-DMA HLA-DMB HLA-DOA HLA-DOB 
               
               
                   
                   
                 HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA- 
               
               
                   
                   
                 DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB4 
               
               
                   
                   
                 HLA-DRB5 REL RELA PIK3CB PIK3R1 PIK3R3 PRKCQ 
               
               
                   
                   
                 PLCG1 TRAC TRA@ TRAT1 VAV1 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Bad Cd28 Cd247 Cd3d Cd3e Cd3g Cd80 Cd86 
               
               
                   
                   
                 Cdc42 Gnb1 Gnb2 Gng12 Gng2 Gab2 Grb2 Nfkbia Nfkbib 
               
               
                   
                   
                 Nfkbie Ikbkb Itpr2 Itpr3 Itk Lat Lck H2-Eb2 Nfatc2 Relb 
               
               
                   
                   
                 Nfkb2 Rel Rela Pik3r5 Prkcq Plcg1 Lcp2 Tcrb-J Trat1 Vav1 
               
               
                   
                   
                 Zap70 
               
               
                   
                 Immune response_TCR 
                 Human genes: 
               
               
                   
                 and CD28 co-stimulation 
                 AKT1 AKT3 CD28 CD247 CD3D CD3E CD3G CD4 
               
               
                   
                 in activation of NF-kB 
                 GRAP2 NFKBIA CHUK IKBKB ITK LAT LCK MALT1 
               
               
                   
                   
                 HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 
               
               
                   
                   
                 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA- 
               
               
                   
                   
                 DRA HLA-DRB1 HLA-DRB3 HLA-DRB4 HLA-DRB5 
               
               
                   
                   
                 REL RELA PIK3CB PIK3R1 PIK3R3 PRKCQ PLCG1 
               
               
                   
                   
                 TRAC TRA@ VAV1 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Bcl10 Card11 Cd28 Cd247 Cd3d Cd3e Cd3g Cd4 
               
               
                   
                   
                 Cd80 Cd86 Grap2 Grb2 Nfkbia Nfkbib Nfkbie Ikbkb Itk Lat 
               
               
                   
                   
                 Lck H2-Eb2 Ube2v2 Relb Nfkb2 Rel Rela Prkcq Plcg1 Lcp2 
               
               
                   
                   
                 Tcrb-J Vav1 Zap70 
               
               
                   
                 Immune 
                 Human genes: 
               
               
                   
                 response_Function of 
                 CABIN1 CALM1 CALM3 CAMK4 CAMKK2 CARM1 
               
               
                   
                 MEF2 in T lymphocytes 
                 CD247 CD3D CD3E CD3G HDAC1 HDAC4 HDAC5 
               
               
                   
                   
                 HDAC9 ITPR1 ITPR3 LAT LCK MAP2K5 MAP2K6 
               
               
                   
                   
                 MAPK14 MEF2A MEF2B MEF2C NCOA2 PLCG1 
               
               
                   
                   
                 PPP3CC PRKCA PRKCG PRKCH PRKCQ PRKCZ 
               
               
                   
                   
                 PRKD3 TRA@ TRAC YWHAQ ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Cabin1 Camk4 Camkk1 Cd247 Cd3d Cd3e Cd3g Hdac4 
               
               
                   
                   
                 Hdac7 Il2 Itpr2 Itpr3 Jun Lat Lck Map2k6 Map3k3 Mapk11 
               
               
                   
                   
                 Mef2c Mef2d Ncoa2 Nfatc2 Nr4a1 Plcg1 Prkcd Prkce Prkcq 
               
               
                   
                   
                 Prkd2 Prkd3 Tcrb-J Ywhab Ywhae Ywhag Zap70 
               
               
                   
                 Immune response_CD40 
                 Human genes: 
               
               
                   
                 signaling 
                 AKT1 AKT3 BCL2L1 CCND2 CD40LG CFLAR CHUK 
               
               
                   
                   
                 FAS FASLG FCER2 ICAM1 IKBKB JAK2 JAK3 LTA 
               
               
                   
                   
                 LYN MAP3K14 MAPK13 MAPK14 NFKBIA PIK3CB 
               
               
                   
                   
                 PIK3R1 REL RELA TNFAIP3 TP53 TRAF1 TRAF3IP2 
               
               
                   
                   
                 TRAF5 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Bcl2l1 Cbl Ccl12 Cd80 Cd86 Cflar Fas Fcer2a 
               
               
                   
                   
                 Icam1 Ikbkb Il6 Irf1 Jak2 Jun Map2k4 Map3k14 Map3k7 
               
               
                   
                   
                 Mapk11 Mapk13 Mapk8 Nfkb2 Nfkbia Nfkbib Nfkbie Ptgs2 
               
               
                   
                   
                 Rel Rela Relb Smpd1 Stat3 Tnfaip3 Traf1 Traf5 Traf6 
               
               
                   
                 Immune 
                 Human genes: 
               
               
                   
                 response_Immunological 
                 ACTG1 ACTR3 ACTR3B ARF6 ARPC1A ARPC2 CD2 
               
               
                   
                 synapse formation 
                 CD247 CD28 CD3D CD3E CD3G CD4 CD58 CRKL 
               
               
                   
                   
                 CXCR4 CYTH1 DOCK2 FYN GNB1 GNB5 GNG10 
               
               
                   
                   
                 GNG3 GNG5 HLA-DMA HLA-DMB HLA-DOA HLA- 
               
               
                   
                   
                 DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 
               
               
                   
                   
                 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA- 
               
               
                   
                   
                 DRB4 HLA-DRB5 ICAM1 ICAM2 ITPR1 ITPR3 PIK3CB 
               
               
                   
                   
                 PIK3R1 PIK3R3 PLCG1 RASGRP2 SKAP1 TLN2 TRA@ 
               
               
                   
                   
                 TRAC VAV1 VCL 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Actb Actg1 Actn4 Actr2 Actr3 Arf6 Arpc1b Arpc4 Arpc5 
               
               
                   
                   
                 Cbl Cd2 Cd247 Cd28 Cd3d Cd3e Cd3g Cd4 Cd80 Cd86 
               
               
                   
                   
                 Cdc42 Cxcr4 Fyn Gnb1 Gnb2 Gng12 Gng2 Grb2 H2-Eb2 
               
               
                   
                   
                 Icam1 Icam2 Itgb2 Itpr2 Itpr3 Lcp2 Pik3r5 Plcg1 Rac2 
               
               
                   
                   
                 Rasgrp2 Skap1 Tcrb-J Vav1 
               
               
                   
                 Immune response_IL-27 
                 Human genes: 
               
               
                   
                 signaling pathway 
                 CD28 ICAM1 IFNGR1 IL10 IL12RB2 EBI3 IL27RA IL6ST 
               
               
                   
                   
                 JAK1 JAK2 REL RELA SOCS3 STAT1 TBX21 MYC 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Cd28 Icam1 Ifng Ifngr2 Il10 Il2 Ebi3 Il27ra Il6st Jak2 Relb 
               
               
                   
                   
                 Nfkb2 Rel Rela Pim1 Socs3 Stat1 Stat3 Itgb2 Myc 
               
               
                   
                 Development_NOTCH1- 
                 Human genes: 
               
               
                   
                 mediated pathway for 
                 ADAM17 HDAC1 RBBP4 RBBP7 H3F3A H3F3B 
               
               
                   
                 NF-KB activity 
                 HIST1H4B HIST1H4D HIST1H4E HIST1H4F HIST1H4H 
               
               
                   
                 modulation 
                 HIST1H4J HIST1H4K HIST2H4A HIST2H4B NFKBIA 
               
               
                   
                   
                 CHUK IKBKB IL1A IL1R1 JAG1 NCOR1 REL RELA 
               
               
                   
                   
                 MAP3K14 RBPJ SAP30 NCOR2 APH1B PSEN1 PSENEN 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Adam17 Rbbp4 H3f3b Hist1h4j Nfkbia Nfkbib Nfkbie 
               
               
                   
                   
                 Ikbkb Il1a Irak2 Jag1 Ncor1 Relb Nfkb2 Rel Rela Map3k14 
               
               
                   
                   
                 Notch1 Rbpj Sap30 Traf6 Aph1a Aph1b Aph1c Ncstn Psen1 
               
               
                   
                 Immune 
                 Human genes: 
               
               
                   
                 response_CXCR4 
                 AKT1 AKT3 CXCR4 FYN GNAI3 GNAZ GNB5 GNB1 
               
               
                   
                 signaling via second 
                 GNG10 GNG3 GNG5 NFKBIA CHUK IKBKB ITPR1 
               
               
                   
                 messenger 
                 ITPR3 ITK LAT LCK REL RELA PRKCQ PLCG1 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Cxcr4 Fyn Gnai1 Gnai2 Gnai3 Gnb1 Gnb2 
               
               
                   
                   
                 Gng12 Gng2 Nfkbia Nfkbib Nfkbie Ikbkb Itpr2 Itpr3 Itk Lat 
               
               
                   
                   
                 Lck Relb Nfkb2 Rel Rela Pik3r5 Prkcq Plcb3 Plcg1 Ptk2b 
               
               
                   
                   
                 Lcp2 Zap70 
               
               
                   
                 Transport_Clathrin- 
                 Human genes: 
               
               
                   
                 coated vesicle cycle 
                 AP1G1 AP1S1 AP2M1 ACTG1 BIN1 SAR1A SAR1B 
               
               
                   
                   
                 SEC24A SEC24C SEC24D SEC31A SEC31B CLTC COPA 
               
               
                   
                   
                 COPB1 COPZ1 SH3GLB1 EPN1 HIP1R MYO1E NSF 
               
               
                   
                   
                 PIK3C3 PIK3R4 RABGEF1 RAB11A RAB4A RAB7A 
               
               
                   
                   
                 RAB11FIP1 STX12 STX16 STX7 STX8 PLIN3 VAMP2 
               
               
                   
                   
                 VAMP4 VAMP7 YKT 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Ap1b1 Ap1g1 Ap1g2 Ap2a2 Ap2b1 Arf1 Acta2 Actb Actg1 
               
               
                   
                   
                 Bin1 Sar1a Sec23b Sec24b Sec24d Cltc Cltb Arcn1 Copb1 
               
               
                   
                   
                 Dab2 Eea1 Gosr1 Hip1 Hip1r Nsf Picalm Pikfyve Preb 
               
               
                   
                   
                 Rabgef1 Rab4b Rab5a Rab7 Rab8a Rab11fip1 Stx12 Stx16 
               
               
                   
                   
                 Stx6 Stx7 Vamp2 Vamp4 Vamp8 Vti1a Vti1b Ykt6 
               
               
                   
                 Transcription_NF-kB  
                 Human genes: 
               
               
                   
                 signaling pathway 
                 AKT1 AKT3 CD28 NFKBIA IKBKAP CHUK IKBKB 
               
               
                   
                   
                 IL1A IL1R1 IRAK3 LY96 MYD88 REL RELA MAP3K14 
               
               
                   
                   
                 PRKCQ TRAC TRA@ TNFRSF1B LTA TRADD 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Cd14 Cd28 Nfkbia Nfkbib Nfkbie Ikbkb Il1a 
               
               
                   
                   
                 Il1rap Irak2 Irak3 Lbp Ltbr Ly96 Myd88 Relb Nfkb2 Rel 
               
               
                   
                   
                 Rela Map3k14 Prkcq Ripk2 Tcrb-J Tlr4 Tnfrsf1a Tnfrsf1b 
               
               
                   
                   
                 Tnf Traf6 
               
               
                   
                 Development_GM-CSF 
                 Human genes: 
               
               
                   
                 signaling 
                 AKT1 AKT3 BAD BCL2 BCL2L1 CSF2RA CASP3 ELK1 
               
               
                   
                   
                 HCK NFKBIA CHUK IKBKB JAK2 LYN REL RELA 
               
               
                   
                   
                 PIK3CB PIK3R1 GNB2L1 SOS2 STAT5B MYC 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt3 Bad Bcl2 Bcl2l1 Ccl12 Cish Csf2ra Csf2rb Egr1 
               
               
                   
                   
                 Mapk1 Elk1 Grb2 Hck Nfkbia Nfkbib Nfkbie Ikbkb Jak2 
               
               
                   
                   
                 Mcl1 Relb Nflcb2 Rel Rela Pim1 Sos1 Sos2 Stat3 Fos Myc 
               
               
                   E.   coli  vs. 
                 Cytoskeleton 
                 Human genes: 
               
               
                 Healthy 
                 remodeling_TGF, WNT 
                 AKT1 AKT3 ACTG1 ARPC1A ARPC2 SERPING1 CRK 
               
               
                   
                 and cytoskeletal 
                 CSNK2A1 CCND1 DVL2 DVL3 MAPK1 PTK2 FZD5 
               
               
                   
                 remodeling 
                 GRB2 GSK3B LIMK2 LAMA1 MYL6 MYL6B PPP1R12A 
               
               
                   
                   
                 MMP13 MKNK1 MYL12A MYL12B RPS6KA5 NCL 
               
               
                   
                   
                 PIK3CB PIK3R1 PIK3R3 PLAUR PPARD SMAD2 
               
               
                   
                   
                 SMAD3 SOS2 SHC1 TCF7L2 TGFB1 TGFBR1 LEF1 
               
               
                   
                   
                 TCF7 TSC2 VAV1 VCL WNT11 WNT8B XIAP JUN MYC 
               
               
                   
                   
                 SRC MTOR CDKN2B MAPK13 MAPK14 TP53 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt2 Akt3 Acta2 Actb Actg1 Actr2 Arpc4 Ctnnb1 
               
               
                   
                   
                 Cdc42 Crk Csnk2a1 Csnk2a2 Cfl2 Col4a2 Dock1 Dstn Dvl3 
               
               
                   
                   
                 Ptk2 Foxo3 Fn1 Fzd1 Fzd3 Grb2 Chuk Limk2 Lamc1 Mdm2 
               
               
                   
                   
                 Ppp1cb Ppp1r12a Map3k11 Mknk1 My12 Rps6ka5 Ncl 
               
               
                   
                   
                 Serpine1 Pik3r3 Plaur Pxn Rheb Rock1 Rock2 Smad2 Sos1 
               
               
                   
                   
                 Sos2 Shc1 Map3k7 Tgfbr1 Vcl Wnt8b Wnt16 Wnt5a Jun 
               
               
                   
                   
                 Myc Raf1 Eif4e Mtor Cdkn1a Mapk13 Mapk14 
               
               
                   
                 Immune 
                 Human genes: 
               
               
                   
                 response_HMGB1/RAGE 
                 AKT1 AKT3 DIAPH1 MAPK1 PTK2 HMGB1 NFKBIA 
               
               
                   
                 signaling pathway 
                 NFKBIB ICAM1 IL1A IL1B IL1RN MAPK9 KRAS 
               
               
                   
                   
                 MEF2A MEF2C MAP2K6 MYOG RELB PIK3CB PIK3R1 
               
               
                   
                   
                 AGER TLR2 TNF JUN SRC NOS2 MAPK13 MAPK14 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt2 Akt3 Cdc42 Diap1 Ptk2 Nflcbia Nfkbib Icam1 
               
               
                   
                   
                 Il1a Il1b Il6 Il1rn Kras Mef2a Mef2c Map2k6 Ccl4 Relb 
               
               
                   
                   
                 Nfkb2 Rel Rela Serpine1 Pxn Scg2 Tlr2 Tlr4 Tnf F3 Vcam1 
               
               
                   
                   
                 Jun Raf1 Mapk13 Mapk14 Rps6ka3 
               
               
                   
                 Development_Prolactin 
                 Human genes: 
               
               
                   
                 receptor signaling 
                 AKT1 AKT3 BCL2 CEBPB CREBBP CCND1 MAPK1 
               
               
                   
                   
                 FYN GRB2 IRS1 JAK2 NEK3 NMI PIK3CB PIK3R1 
               
               
                   
                   
                 PLCG1 PRL PTPN11 SOCS1 SOCS3 SOS2 STAT1 
               
               
                   
                   
                 STAT5B SHC1 VAV1 CBL JUN MYC SRC 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt2 Akt3 Bcl2 Bcl2l1 Csn2 Cebpb Nr3c1 Grb2 Jak2 
               
               
                   
                   
                 Rela Socs1 Socs3 Sos1 Sos2 Stat3 Stat5a Shc1 Vav2 Cbl 
               
               
                   
                   
                 Jun Myc Raf1 
               
               
                   
                 Immune response_ICOS 
                 Human genes: 
               
               
                   
                 pathway in T-helper cell 
                 AKT1 AKT3 BAD CD28 CD247 CD3D CD3E CD3G 
               
               
                   
                   
                 PPP3CC CALM1 GNA15 GNB5 GNB1 GNG10 GNG5 
               
               
                   
                   
                 GRB2 NFKBIA NFKBIB ICOS IKBKB ITPR1 ITPR2 
               
               
                   
                   
                 ITPR3 ITK LAT LCK HLA-DMA HLA-DMB HLA-DOB 
               
               
                   
                   
                 HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA- 
               
               
                   
                   
                 DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB4 
               
               
                   
                   
                 HLA-DRB5 RELB PIK3CB PIK3CG PIK3R1 PIK3R3 
               
               
                   
                   
                 PRKCQ PLCG1 TRAC TRA@ VAV1 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt2 Akt3 Cd247 Cd3g Cd80 Cd86 Cdc42 Ppp3ca 
               
               
                   
                   
                 Ppp3cb Gnb1 Gnb5 Gng10 Gng12 Gng13 Gngt1 Gngt2 
               
               
                   
                   
                 Gab2 Grb2 Nfkbia Nfkbib Icos1 Ikbkb Itpr3 Lat Lck H2-Eb2 
               
               
                   
                   
                 Nfatc2 Relb Nfkb2 Rel Rela Pdpk1 Pik3r3 Pik3r5 Lcp2 
               
               
                   
                   
                 Tcrb-J Trat1 Zap70 
               
               
                   
                 Immune response_NFAT 
                 Human genes: 
               
               
                   
                 in immune response 
                 AKT1 AKT3 BLNK CD28 CD247 CD3D CD3E CD3G 
               
               
                   
                   
                 CD79A CD79B PPP3CC CALM1 FCER1A FCER1G 
               
               
                   
                   
                 GSK3B NFKBIA NFKBIB IKBKB ITPR1 ITPR2 ITPR3 
               
               
                   
                   
                 ITK IGHV3-23 IGKC IGK@ IGL@ IGHM LAT LCK LYN 
               
               
                   
                   
                 HLA-DMA HLA-DMB HLA-DOB HLA-DPA1 HLA- 
               
               
                   
                   
                 DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA 
               
               
                   
                   
                 HLA-DRB1 HLA-DRB3 HLA-DRB4 HLA-DRB5 NFAT5 
               
               
                   
                   
                 NFATC1 NFATC3 RELB PIK3CB PIK3R1 PIK3R3 
               
               
                   
                   
                 PRKCQ PLCG1 TRAC TRA@ VAV1 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt2 Akt3 Cd247 Cd3g Cd79a Cd79b Cd80 Cd86 
               
               
                   
                   
                 Ppp3ca Ppp3cb Ms4a2 Nfkbia Nfkbib Chuk Ikbkb Itpr3 Igk 
               
               
                   
                   
                 Lat Lck Lyn H2-Eb2 Nfat5 Nfatc2 Relb Nfkb2 Rel Rela 
               
               
                   
                   
                 Pik3r3 Lcp2 Syk Tcrb-J Trat1 Zap70 
               
               
                   
                 Immune 
                 Human genes: 
               
               
                   
                 response_Function of 
                 CABIN1 CALM1 CAMK4 CAMKK2 CD247 CD3D CD3E 
               
               
                   
                 MEF2 in T lymphocytes 
                 CD3G HDAC1 HDAC4 HDAC9 ITPR1 ITPR2 ITPR3 JUN 
               
               
                   
                   
                 LAT LCK MAP2K5 MAP2K6 MAPK14 MEF2A MEF2B 
               
               
                   
                   
                 MEF2C NCOA2 PLCG1 PPP3CC PRKCA PRKCH 
               
               
                   
                   
                 PRKCQ PRKD3 TRA@ TRAC YWHAQ ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Cd247 Cd3g Hdac2 Hdac7 Itpr3 Jun Kat2b Lat Lck Map2k5 
               
               
                   
                   
                 Map2k6 Mapk14 Mapk7 Mef2a Mef2c Mef2d Ncoa2 Nfatc2 
               
               
                   
                   
                 Ppp3ca Ppp3cb Prkci Prkd2 Tcrb-J Ywhab Ywhae Ywhag 
               
               
                   
                   
                 Ywhaq Ywhaz Zap70 
               
               
                   
                 Immune response__IFN 
                 Human genes: 
               
               
                   
                 gamma signaling pathway 
                 AKT1 AKT3 CALM1 CAMK2G CBL CEBPB CREBBP 
               
               
                   
                   
                 CRKL ICAM1 IFNGR1 IFNGR2 ITPR1 ITPR2 ITPR3 
               
               
                   
                   
                 JAK1 JAK2 MAP2K6 MAP3K4 MAPK1 MAPK13 
               
               
                   
                   
                 MAPK14 MCM5 MYC PIK3CB PIK3R1 PIK3R3 PRKCA 
               
               
                   
                   
                 PTPN11 SMAD7 SOCS1 SRC STAT1 STAT2 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Afap1 Akt1 Akt2 Akt3 Cebpb Crk1 Icam1 Itpr3 Stat2 Jak2 
               
               
                   
                   
                 Mcm5 Map2k6 Map3k4 Pdpk1 Pik3r3 Ptk2b Smad7 Socs1 
               
               
                   
                   
                 Cbl Myc Cdkn1a Mapk13 Mapk14 
               
               
                   
                 Immune response_CD28 
                 Human genes: 
               
               
                   
                 signaling 
                 AKT1 AKT3 BAD CALM1 CD247 CD28 CD3D CD3E 
               
               
                   
                   
                 CD3G FYN GRB2 GSK3B IKBKB ITK ITPR1 ITPR2 
               
               
                   
                   
                 ITPR3 JUN LAT LCK MAPK9 NFAT5 NFATC1 NFATC3 
               
               
                   
                   
                 NFKBIA NFKBIB PIK3CB PIK3R1 PIK3R3 PLCG1 
               
               
                   
                   
                 PPP3CC PRKCQ RELB TRA@ TRAC VAV1 ZAP70 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt2 Akt3 Bcl2l1 Cd247 Cd3g Cd80 Cd86 Chuk 
               
               
                   
                   
                 Grap2 Grb2 Ikbkb Itpr3 Jun Lat Lck Lcp2 Map2k4 Nfat5 
               
               
                   
                   
                 Nfatc2 Nfkb2 Nfkbia Nfkbib Pik3r3 Pip5k1a Ppp3ca Ppp3cb 
               
               
                   
                   
                 Rel Rela Relb Tcrb-J Zap70 
               
               
                   
                 Immune 
                 Human genes: 
               
               
                   
                 response_Histamine H1 
                 CALM1 GNA11 GNB1 GNB5 GNG10 GNG5 ICAM1 
               
               
                   
                 receptor signaling in 
                 IKBKB ITPR1 ITPR2 ITPR3 JUN MAPK1 MAPK13 
               
               
                   
                 immune response 
                 MAPK14 MAPK9 MMP1 MMP13 MMP3 MMP9 NFATC1 
               
               
                   
                   
                 NFKBIA NFKBIB NOS2 PLA2G4A PLCB2 PPP3CC 
               
               
                   
                   
                 PRKCA TNF 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Chuk F3 Fos Gnaq Gnb1 Gnb5 Gng10 Gng12 Gng13 Gngt1 
               
               
                   
                   
                 Gngt2 Icam1 Ikbkb Il6 Itpr3 Jun Mapk13 Mapk14 Mmp1a 
               
               
                   
                   
                 Nfkbia Nfkbib Nos3 Pla2g4a Pla2g4c Plcb1 Plcb4 Ppp3ca 
               
               
                   
                   
                 Ppp3cb Ppp3r1 Raf1 Rela Tnf Vcam1 
               
               
                   
                 Development_VEGF 
                 Human genes: 
               
               
                   
                 signaling via VEGFR2 - 
                 ACTG1 AKT1 AKT3 FYN GRB2 GSK3B HSP90AA1 
               
               
                   
                 generic cascades 
                 HSPB1 IKBKB ITPR1 ITPR2 ITPR3 JUN MAPK1 
               
               
                   
                   
                 MAPK13 MAPK14 MAPKAPK2 NF1 NFATC1 NFKBIA 
               
               
                   
                   
                 NFKBIB NOS2 PIK3CB PIK3R1 PIK3R3 PLAUR PLCG1 
               
               
                   
                   
                 PPP3CC PRKCA PRKCH PRKCQ PRKD3 PTGS1 PTK2  
               
               
                   
                   
                 SH2D2A SHC1 SOS2 SRC TCF7L2 TRAP1 VCL 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Actb Actg1 Akt1 Akt2 Akt3 Cdc42 Chuk Ctnnb1 Fos Grb2 
               
               
                   
                   
                 Hsp90aa1 Hsp90b1 Hspb1 Ikbkb Itpr3 Jun Mapk13 Mapk14 
               
               
                   
                   
                 Mapkapk2 Nck1 Nf1 Nfkbia Nfkbib Nos3 Pak2 Pdpk1 
               
               
                   
                   
                 Pik3r3 Plaur Ppp3ca Ppp3cb Prkci Prkd2 Ptgs2 Ptk2 Pxn 
               
               
                   
                   
                 Raf1 Rela Rock1 Shc1 Sos1 Sos2 Sphk1 Vcl 
               
               
                   
                 Immune 
                 Human genes: 
               
               
                   
                 response_Gastrin in 
                 AKT1 AKT3 ELAVL1 GNA11 GRB2 IKBKB IRS1 ITPR1 
               
               
                   
                 inflammatory response 
                 ITPR2 ITPR3 JUN MAP2K5 MAP2K6 MAP3K14 MAPK1 
               
               
                   
                   
                 MAPK14 MAPK9 MEF2A MEF2B MEF2C MMP3 
               
               
                   
                   
                 NFKBIA NFKBIB PIK3CB PIK3R1 PLCG1 PRKCA PTK2 
               
               
                   
                   
                 SERPINB2 SHC1 SOS2 SRC 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Akt1 Akt2 Akt3 Chuk Cxcl1 Elavl1 Elk1 Fos Gnaq Grb2 
               
               
                   
                   
                 Hbegf Ikbkb Itpr3 Jun Map2k4 Map2k5 Map2k6 Map3k14 
               
               
                   
                   
                 Map3k7 Mapk14 Mapk7 Mef2a Mef2c Mef2d Nfkbia 
               
               
                   
                   
                 Nfkbib Pdpk1 Ptgs2 Ptk2 Raf1 Rela Serpinb2 Shc1 Sos1 
               
               
                   
                   
                 Sos2 Traf6 
               
               
                   
                 Cell 
                 Human genes: 
               
               
                   
                 adhesion_Chemokines 
                 ACTG1 AKT1 AKT3 ARPC1A ARPC2 CAV2 CCR1 CD44 
               
               
                   
                 and adhesion 
                 CD47 CRK FLNA FLOT2 GNAI3 GNB1 GNB5 GNG10 
               
               
                   
                   
                 GNG5 GRB2 GSK3B ITGA6 ITGB1 JUN LAMA1 LEF1 
               
               
                   
                   
                 LIMK2 MAPK1 MMP1 MMP13 MSN MYC PIK3CB 
               
               
                   
                   
                 PIK3CG PIK3R1 PIK3R3 PLAUR PTEN PTK2 RAP1GAP 
               
               
                   
                   
                 RELB SDC2 SHC1 SOS2 SRC TCF7 TCF7L2 TRIO VAV1 
               
               
                   
                   
                 VCL 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Acta2 Actb Actg1 Actr2 Akt1 Akt2 Akt3 Arpc4 Braf Cav2 
               
               
                   
                   
                 Ccr1 Cd44 Cd47 Cdc42 Cfl2 Col1a2 Col4a2 Crk Ctnnb1 
               
               
                   
                   
                 Cxcl3 Cxcl5 Dock1 Flot2 Fn1 Gnai1 Gnai2 Gnai3 Gnb1 
               
               
                   
                   
                 Gnb5 Gng10 Gng12 Gng13 Gngt1 Gngt2 Grb2 Itgb1 Jun 
               
               
                   
                   
                 Lamc1 Limk2 Mmpla Msn Myc Nfkb2 Pik3r3 Pik3r5 Plaur 
               
               
                   
                   
                 Pten Ptk2 Pxn Raf1 Rap1gap Rel Rela Relb Rock1 Rock2 
               
               
                   
                   
                 Serpine1 Shc1 Sos1 Sos2 Thbs1 Trio Vcl 
               
               
                   
                 Immune response_IL-15 
                 Human genes: 
               
               
                   
                 signaling 
                 ADAM17 AKT1 AKT3 BCL2 FKBP1A GRB2 IKBKB 
               
               
                   
                   
                 IL15RA IL2RB LCK MAP2K6 MAP3K14 MAPK1 
               
               
                   
                   
                 MAPK13 MAPK14 MKNK1 MTOR MYB MYC NFKBIA 
               
               
                   
                   
                 NFKBIB PIK3CB PIK3R1 PLCG1 PTK2 SHC1 SOS2 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Adam17 Akt1 Akt2 Akt3 Bcl2 Bcl2l1 Chuk Eif4e Ets1 
               
               
                   
                   
                 Fkbp1a Fos Gab2 Grb2 Ikbkb Il15ra Il6 Lck Map2k4 
               
               
                   
                   
                 Map2k6 Map3k14 Mapk13 Mapk14 Mcl1 Mknk1 Mtor Myc 
               
               
                   
                   
                 Nfkbia Nfkbib Pdpk1 Plcb1 Ptk2 Raf1 Rela Rps6kb1 Shc1 
               
               
                   
                   
                 Sos1 Sos2 Syk 
               
               
                   
                 Immune response_IL-22 
                 Human genes: 
               
               
                   
                 signaling pathway 
                 BCL2 CD28 CD4 HLA-DMA HLA-DMB HLA-DOB HLA- 
               
               
                   
                   
                 DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 
               
               
                   
                   
                 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB4 HLA- 
               
               
                   
                   
                 DRB5 IL10RB IL12RB2 IL2RA IL2RB JAK1 JAK2 JAK3 
               
               
                   
                   
                 JUN MAPK1 MAPK13 MAPK14 MAPK9 MYC SOCS3 
               
               
                   
                   
                 STAT1 STAT4 STAT5B TRA@ TRAC 
               
               
                   
                   
                 Murine genes: 
               
               
                   
                   
                 Bcl2 Bcl2l1 Cd86 Fos H2-Eb2 Il10rb Il2ra Jak2 Jak3 Jun 
               
               
                   
                   
                 Mapk13 Mapk14 Mcl1 Myc Socs3 Stat3 Stat5a Tcrb-J