# Patent

## Title
Methods and compositions for identifying minimal residual disease in acute lymphoblastic leukemia

## Abstract

This invention provides methods and kits for diagnosing, ascertaining the clinical course of minimal residual disease associated with acute lymphoblastic leukemia (ALL). Specifically the invention provides methods and kits useful in the diagnosis and determination of clinical parameters associated with diseases associated with ALL based on patterns of surface marker expression unique to ALL.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a 35 U.S.C. §273 U.S. National Stage of International Application PCT/US2012/028993 filed Mar. 14, 2012, which designates the U.S. and was published by the International Bureau in English on Oct. 4, 2012, and which claims the benefit of U.S. Provisional Application No. 61/470,056, filed Mar. 31, 2011, both of which are hereby incorporated by reference in their entirety.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with support under United States Government Grant CA60419 awarded by the National Institutes of Health. The United States Government has certain rights in this invention.


REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named 415313SEQLIST.txt, created on Mar. 6, 2012, and having a size of 225,858 bytes and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.
FIELD OF THE INVENTION
This invention relates generally to the detection of minimal residual disease in patients with acute lymphoblastic leukemia (ALL) and, more specifically, to a method to improve minimal residual disease monitoring for risk assignment and selection of therapeutic regimens.
BACKGROUND OF THE INVENTION
Leukemia relapse is the major cause of treatment failure for patients with acute lymphoblastic leukemia (ALL) (Pui et al. (2009) N Engl J Med. 360:2730-2741; Gokbuget and Hoelzer (2009) Semin. Hematol. 46:64-75; and Faderl et al. (2010) Cancer. 116:1165-1176). Relapse originates from leukemic cells that are resistant to chemotherapy but become undetectable after initial treatment in most cases. Nevertheless, methods more sensitive than microscopic examination can demonstrate leukemic cells in a proportion of samples with no morphologic evidence of leukemia, a finding termed “minimal residual disease (MRD)” (Campana (2009) Hematol. Oncol Clin North Am. 23:1083-98, vii).
MRD is currently the most powerful prognostic indicator in childhood ALL (Cave et al. (1998) N Engl J Med. 339:591-598; Coustan-Smith et al. (1998) Lancet. 351:550-554; van Dongen et al. (1998) Lancet. 352:1731-1738; Coustan-Smith et al. (2000) Blood. 96:2691-2696; Dworzak et al. (2002) Blood. 99:1952-1958; Nyvold et al. (2002) Blood. 99:1253-1258; Zhou et al. (2007) Blood. 110:1607-1611; Borowitz et al. (2008) Blood. 111:5477-5485. Basso et al. (2009) J Clin Oncol. 27:5168-5174; Canter et al. (2010) Blood. 115:3206-3214; Stow et al. (2010) Blood. 115:4657-4663). There is strong evidence supporting its prognostic significance in adult ALL (Krampera et al. (2003) Br J Haematol. 120:74-79; Vidriales, et al. (2003) Blood. 101:4695-4700; Raff et al. (2007) Blood. 109:910-915; Holowiecki et al. (2008) Br. J. Haematol. 142:227-237; Bassan et al. (2009) Blood. 113:4153-4162).
Thus, MRD monitoring has been introduced into many contemporary treatment protocols for risk assignment and selection of therapeutic regimens (Pui et al. (2009) N Engl J Med. 360:2730-2741; Gokbuget and Hoelzer. (2009) Semin. Hematol. 46:64-75; and Faderl et al. (2010) Cancer. 116:1165-1176). MRD measurements are also clinically useful in patients with relapsed ALL who achieve a second remission (Coustan-Smith et al. (2004) Leukemia 18:499-504; Paganin et al. (2008) Leukemia. 22:2193-2200; Raetz et al. (2008) J Clin. Oncol. 26:3971-3978), can help optimize the timing of hematopoietic stem cell transplantation (Bader et al. (2009) J Clin Oncol. 27:377-384), and guide decisions about donor lymphocyte infusion post-transplant (Lankester et al. (2010) Leukemia. 24:1462-1469).
Among methods for detecting MRD in ALL, PCR amplification of antigen-receptor genes has proven to be valuable and has been extensively standardized (Bruggemann, M., et al. (2010) Leukemia. 24:521-535) but the technical expertise and instrumentation required limit its application to specialized centers. PCR amplification of fusion transcripts may also provide useful clinical information but its applicability in ALL is restricted by the fact that molecular targets currently adaptable to routine MRD studies are present in only a minority of patients. Id. Flow cytometric detection of leukemia-specific markers has been shown to predict outcome in numerous clinical correlative studies (Coustan-Smith et al. (1998) Lancet. 351:550-554; Coustan-Smith et al. (2000) Blood. 96:2691-2696; Dworzak et al. (2002) Blood. 99:1952-1958; Borowitz, et al. (2008) Blood. 111:5477-5485; Basso et al. (2009) J Clin Oncol. 27:5168-5174; Krampera et al. (2003) Br J Haematol 120:74-79; Vidriales et al. (2003) Blood 101:4695-4700; Holowiecki et al. (2008) Br. J. Haematol. 142:227-237). The method holds potential for wider applicability than molecular techniques because flow cytometric methods for leukemia diagnosis are already established at most cancer centers worldwide (Campana (2009) Hematol. Oncol Clin North Am. 23:1083-98, vii).
MRD studies by flow cytometry rely on panels of antibodies to define unique immunophenotypic signatures of leukemic cells which must distinguish leukemic blasts from their normal counterparts, the CD19+ CD10+ lymphoid progenitors of the bone marrow (“hematogones”) (Campana (2009) Hematol. Oncol Clin North Am. 23:1083-98, vii; Bruggemann et al. (2010) Leukemia. 24:521-535; McKenna et al. (2001) Blood. 98:2498-2507; Lucio et al. (2001) Leukemia. 15:1185-1192).
Standard four-color flow cytometry can detect one leukemic cell in up to 10,000 normal bone marrow or peripheral blood cells but this task typically requires considerable interpretative expertise. Therefore, identification of new leukemia markers that are easily detectable and are stably expressed in a large proportion of ALL cases could simplify the application of MRD studies, and help extend their benefit to all patients and enhance the sensitivity of MRD detection.
BRIEF SUMMARY OF THE INVENTION
Methods and compositions are provided for identifying patients with minimal residual disease. The diagnostic methods generally comprise contacting a specimen from a patient with a plurality of probes, wherein each of said probes specifically binds to a distinct marker, wherein a first probe specifically binds to CD19, a second probe specifically binds to CD10, a third probe specifically binds to CD34, a fourth probe specifically binds to CD45, and at least two additional probes that specifically binds to any two of CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102, or CD300a. The complex formed between each of the probes and their marker is detected and a value is generated corresponding to an expression level of each of said marker. An expression profile is generated by combining the expression level values. In such methods, the expression of CD19, CD10, CD34 and CD45 and a modulated level of at least two of CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102, or CD300a relative to a normal control is indicative of minimal residual disease in acute lymphoblastic leukemia.
Additional methods for diagnosing minimal residual disease in a subject further include obtaining a specimen from a subject. The specimen is contacted with a plurality of probes, wherein each of the probes specifically binds to a distinct marker, wherein a first probe specifically binds to CD19 and a second probe specifically binds to CD10. A CD19+/CD10+ cell is isolated from the specimen. The expression level of at least two gene products expressed in said CD19+/CD10+ cell is determined, wherein the at least two gene products encode CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a. An expression profile is generated by combining the values generated of the expression levels of the indicated markers. The expression of CD19 and CD10 and a modulated level of at least two gene products encoding CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102, or CD300a relative to a normal control is indicative of minimal residual disease in acute lymphoblastic leukemia.
Kits for practicing the diagnostic methods of the invention are also provided, as well as, kits for evaluating the efficacy of a particular therapy for a subject with ALL.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a comparison of the relative mean fluorescence intensity of immunophenotypic markers expressed in ALL cells and in CD19+CD10+ B-cell progenitors as determined by flow cytometry.
FIG. 2 shows a comparison of the relative mean fluorescence intensity of immunophenotypic markers expressed in ALL cells and CD19+CD10+ B-cell progenitors as determined by flow cytometry.
FIG. 3 shows a comparison of new markers to standard markers using flow cytometry.
FIG. 4 graphically illustrates the expression of the new markers before, during, and at the end of remission induction therapy.
FIG. 5 is a heatmap showing the percentage of cases among the main genetic subtypes of childhood ALL in which the markers studied were differentially expressed by flow cytometry.
FIG. 6 is a graphic depiction of additional leukemia-associated markers that can improve resolution of MRD.



DETAILED DESCRIPTION OF THE INVENTION
The present invention will now be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the inventions are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Like numbers refer to like elements throughout.
Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
Methods and compositions are provided for identifying patients with minimal residual disease in acute lymphoblastic leukemia (ALL). As discussed in further detail herein, genes expressed at different levels in ALL cells were compared to their normal counterparts. Using genome-wide gene analysis, expression profiles of 270 cases of newly diagnosed B-lineage ALL were compared to expression profiles of highly purified normal CD19+ CD10+ cells. Genes that had a substantially abnormal expression in leukemic cells were tested by flow cytometry to assess levels of protein expression. Promising molecules were examined in detail for optimization as MRD markers. Use of newly identified markers allows for the identification of unique leukemia profiles in ALL patients. Moreover, the compositions and methods disclosed herein allow for the detection of 1 leukemic cell in 100,000 normal bone marrow cells, thus significantly enhancing the power of flow cytometric monitoring of MRD in ALL.
Acute Lymphocytic Leukemia and Disease
Methods and compositions are provided herein directed to detection of minimal residual disease in acute B-lymphoblastic leukemia.
In specific methods, a specimen is taken from a subject with cancer, wherein the cancer is leukemia. Leukemia is a cancer of the bone marrow and blood. The four major types of leukemia are acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphoblastic leukemia (ALL) and chronic lymphocytic leukemia (CLL). Acute leukemia is a rapidly progressing cancer that produces blood cells that are not fully developed. Acute lymphocytic leukemia is often referred to as “acute lymphoblastic leukemia” because the leukemic cell that replaces the normal marrow cell is the (leukemic) lymphoblast. There are two principal ALL subtypes including a) the B-lymphocyte subtype—identified by finding cell surface markers on the leukemic blast cells common to normal B lymphocytes; and b) the T lymphocyte subtypes—identified by finding cell surface markers on the leukemic blast cells common to normal T lymphocytes. About 15% of cases are of the T-lymphocyte, and 85% of cases are of the precursor B-cell subtype.
The effects of ALL include uncontrolled and exaggerated growth and accumulation of lymphoblasts which fail to function as normal blood cells, and blockage of the production of normal marrow cells. The lack of production of normal marrow cells often leads to a deficiency of red cells (anemia), platelets (thrombocytopenia) and normal white cells, especially neutrophils (neutropenia), in the blood. ALL progresses rapidly without treatment, therefore the methods and compositions provided herein can be employed to allow for the early detection of acute lymphocytic leukemia.
“Diagnosing ALL” and/or “detecting minimal residual disease (MRD)” or “diagnosing minimal residual disease (MRD)” is intended to include, for example, diagnosing or detecting the presence of acute lymphoblastic leukemia (ALL) by identifying or detecting cells and/or cell products in specimens that are indicative of ALL, monitoring the progression of the disease, monitoring and/or detecting the recurrence of ALL disease in patients who had been previously treated for ALL, and monitoring and/or detecting minimal residual disease. The terms “diagnosing,” “detecting,” and “identifying” when used with acute lymphoblastic leukemia or minimal residual disease (MRD) are used interchangeably herein to refer to the identifying or detecting cells and/or cell products in specimens that are indicative of disease.
One method disclosed herein is directed to monitoring remission of leukemia. Remission is defined as the absence of outward signs of cancer, or in the case of ALL, the absence of detectable cancer cells in the body after a course of therapy. Remission in ALL can be characterized, for example, as a lack of detectable abnormal cells in the blood, bone marrow, and/or cerebrospinal fluid, and less than 5% blast cells in the bone marrow. Embodiments of the invention seek to detect cancer cells in instances where there is a relatively minimal amount of disease (minimal residual disease (MDR)) by phenotypic analysis. Standard detection methods define minimal residual disease as an incidence of less than one leukemic cell in 10,000 normal bone marrow/blood cells. The methods and compositions of the instant invention can detect minimal residual disease with an incidence of less than one in 100,000 cells.
Most ALL patients achieve at least an initial remission. However, some patients have residual leukemic cells in their marrow. Other patients achieve remission then “relapse” wherein they have a decrease in normal blood cells and a return of leukemia cells in the marrow. Embodiments of the invention detect leukemia and can help evaluate the risk for relapse after initial treatment. In addition to the detection of evidence of minimal residual disease, embodiments of the invention can further help to evaluate treatment regimens. For example, the detection and characterization of MRD can be indicative of the efficacy of certain treatment regimes, e.g., stem cell transplant.
In other embodiments of the invention, detection or diagnosing MRD can help determine whether additional treatment may be necessary. One of skill in the art will recognize that in these methods the term “therapy” can include any therapy for treating ALL, including but not limited to chemotherapy, radiation therapy, stem cell transplantation, and biological therapy (e.g., monoclonal antibody therapy). Depending on the subtype, specific drugs or drug combinations, drug dosages, duration of treatment, and other types of treatment, may be indicated to achieve optimal results.
In still other embodiments of the invention, methods for evaluating the efficacy of a therapy for treating ALL in a subject are provided. Embodiments of the invention can also be used to test specimens taken from a subject during the course of therapy to monitor the effects of treatment. Such methods typically comprise comparing the level of expression of a plurality of markers of the invention in a first specimen procured prior to the initiation of therapy with that from a second sample obtained following administration of at least a portion of the therapy. In some embodiments, a significantly lower and/or an undetectable level of expression of a marker in the second specimen relative to that of the first specimen obtained prior to the initiation of the therapy can be a positive indication of the efficacy of the therapy. In other embodiments, a significantly higher level of expression of a marker in the second sample can be a negative indication of the efficacy of the therapy. A positive indication of the efficacy of the therapy can mean that the therapy is producing beneficial results in the treatment of ALL and no minimal residual disease is detected. A negative indication of the efficacy of the therapy can mean that the therapy is not having beneficial effects with respect to treatment of ALL and minimal residual disease is detected.
Specimens from Subjects
In embodiments of the invention, the method comprises obtaining a “specimen” from a subject. The term “specimen” is intended to include blood cells, bone marrow cells, and cellular products that are derived from blood and bone marrow cells. Cellular products can include, but are not limited to, expressed proteins, expressed RNA, and DNA. In embodiments of the invention, a specimen can include cells derived from a variety of sources including, but not limited to, single cells, a collection of cells, tissue, cell culture, bone marrow, blood, or other bodily fluids. A tissue or cell source may include a tissue biopsy sample, a cell sorted population, cell culture, or a single cell. Sources for the specimen of the present invention include cells from peripheral blood or bone marrow, such as blast cells from peripheral blood or bone marrow. The term “specimen” can be used interchangeably with the term “sample” or “patient sample.”
A specimen may be processed in another embodiment to release or otherwise make available a nucleic acid or a protein for detection as described herein. Such processing may include, in one embodiment, steps of nucleic acid manipulation, e.g., preparing a cDNA by reverse transcription of RNA from the specimen. Thus, the nucleic acid to be amplified in one embodiment by the methods of the invention may be DNA or RNA. Isolation of protein, RNA, and DNA from the aforementioned sources is known to those of skill in the art, and is discussed herein.
In one embodiment, the method comprises obtaining a peripheral blood sample from a subject and analyzing the expression level of specific markers in leukocytes from the blood sample taken from the subject. To do blood tests, blood samples are generally taken from a vein in the subject's arm.
In another embodiment, the method comprises obtaining a bone marrow sample from a subject and analyzing the expression level of specific markers combinations in leukocytes from the blood sample taken from the subject. Specimens of marrow cells are obtained by bone marrow aspiration and biopsy.
The obtaining of a specimen uses methods well known in the art, as is the means to analyze leukocyte populations. For example, leukocyte populations can be prepared from whole blood by differential centrifugation, or for example, by density gradient centrifugation. The method can be conducted on leukocytes in blood samples which have not undergone any leukocyte enrichment, on whole blood samples, or where red blood cells have been lysed. In other embodiments the method can be conducted on enriched and purified subpopulations of cells, using methods well known in the art.
Analyzing Specimens
In embodiments of the invention, the method comprises “contacting” the specimen with a plurality of probes. In one embodiment, the term “contacting” is in reference to probes that are antibodies and generally referring to methods of “cell staining.” In a method of the invention, an antibody is added to a specimen and the antibody recognizes and binds to a specific protein for example, on the surface of cells in the specimen. A complex is thereby formed between the probe and the expressed protein. The complex can be detected and visualized by various techniques, as will be discussed herein. Combinations of antibody probes can be collectively added to a specimen and thereby “stain” the cell for later analysis by visualization with a flow cytometer or microscope, for example. One of skill in the art could determine whether a cell expressed a specific protein based on the level of antibody that bound to the cell using standard methods.
In embodiments of the invention the term “contacting” in reference to probes that are nucleic acids, refers to methods of detecting expression of an mRNA of interest in a specimen. A detectable complex can be formed when a nucleic acid probe specific to an expressed gene of interest hybridizes and binds an mRNA/cDNA expressed by cells in a specimen. One of skill in the art could determine whether a cell expressed a specific mRNA based on the level of detectable PCR product, for example, using standard methods.
Detecting Expression of Markers for Minimal Residual Disease
As used herein a “marker” can be any gene or protein whose level of expression in a tissue or cell is used comparatively to evaluate the level of expression to that of a normal or healthy cell or tissue. In particular embodiments of the invention, antibodies are used to detect marker expression at the protein level. In other aspects of the invention, marker expression is detected at the nucleic acid level.
Markers of the invention may be referred to herein interchangeably as “markers,” “immunophenotypic markers,” “leukemia-associated phenotypic markers,” “phenotypic markers,” or “cell markers.” “Leukemia-associated markers” can refer to particular combinations of markers used to diagnosis a particular leukemia, for example, an expression profile of different combinations of markers may be particular to a patient with ALL. In particular embodiments of the invention, markers can refer to “antigenic markers,” “antigens,” or “cell surface antigens,” referring to proteins that are expressed on the cell surface. Combinations of markers of the invention are selective for ALL, and specifically minimal residual disease.
The various markers employed in the methods and compositions disclosed herein, can have a modulated level of expression when compared to an appropriate control. Alternatively, a given marker need not show a modulated level of expression, but rather must only be expressed in the given sample. Specific expression profiles of the given marker combinations that are predictive of the various states disclosed herein are discussed in further detail elsewhere herein.
As used herein, a “modulated level” of a marker can comprise any statistically significant increase (overexpression) or decrease (underexpression) of the given marker when compared to an appropriate control. The modulated level can be assayed by monitoring either the concentration of and/or activity of the marker polypeptide and/or the level of the mRNA encoding the marker polypeptide. In general, a modulate level of marker can include either an increase or a decrease of at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or higher relative to an appropriate control.
By “overexpressed” it is intended that the marker of interest is overexpressed in ALL cells but is not overexpressed in conditions classified as nonmalignant, benign, and/or any conditions that are not considered to be indicative of clinical disease. In general, an overexpressed marker can include any statistically significant increase in expression when compared to an appropriate control, including for example, an increase of at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or higher relative to an appropriate control.
By “underexpressed” it is intended that the marker of interest is underexpressed in ALL cells but is not underexpressed in conditions classified as nonmalignant, benign, and/or any conditions that are not considered to be indicative of clinical disease. Thus, detection of various combinations of markers of the invention permit the differentiation of specimens indicative of an increased likelihood of minimal residual disease associated with ALL as compared to those of normal control specimens that are indicative of nonmalignant and benign proliferation.
The level of expression of a particular marker that is sufficient to constitute “overexpression” will vary depending on the specific marker used. In particular embodiments of the invention, a “threshold level” of expression over a normal control is established for a particular marker, wherein expression levels above this value are deemed overexpression. Overexpression of a particular marker can refer to an increase in the percentage of a population detected as expressing a particular marker or marker combination. Overexpression can also refer to the level of expression on a population of cells as detected by an increase in the mean fluorescence intensity (MFI). For example, in one embodiment of the invention, “overexpression” may be determined if the marker MFI for the specimen is at least three-fold above the normal control, wherein a three-fold increase in MFI is the “threshold level.” In other embodiments, an overexpressed marker can include any statistically significant decrease in expression when compared to an appropriate control, including for example, an increase of at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or higher relative to an appropriate control or at least at least a 1 fold, 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 10 fold or higher expression level relative to an appropriate control.
The level of expression of a particular marker that is sufficient to constitute “underexpression” will vary depending on the specific marker used. In particular embodiments of the invention, a “threshold level” of expression is established for a particular marker, wherein expression levels below this value are deemed underexpression. Underexpression of a particular marker can refer to a decrease in the percentage of a population detected as expressing a particular marker or marker combination. Underexpression can also refer to the level of expression on a population of cells as detected by a decrease in the mean fluorescence intensity (MFI). For example, in one embodiment of the invention, “underexpression” may be determined for that particular marker if the marker MFI for the specimen is less than the normal control by at least half, wherein a 50% reduction MFI is the “threshold level”. In other embodiments, an underexpressed marker can include any statistically significant decrease in expression when compared to an appropriate control, including for example, a decrease of at least at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or lower relative to an appropriate control or at least at least a 1 fold, 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 10 fold or lower expression level relative to an appropriate control.
The methods of the invention comprise diagnosing minimal residual disease in a sample taken from a subject by detecting the expression of a plurality of markers that are modulated in ALL. Markers CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, and CD49f were analyzed and found differentially expressed in up to 81.4% of ALL cases. Embodiments of the invention can include, but are not limited to, compositions and methods related to new markers for the detection of minimal residual disease (MRD) comprising: CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, and CD49f.
In yet other embodiments, diagnosing minimal residual disease in a sample taken from a subject can comprise the detection of combinations of markers including, but not limited to markers CD19, CD10, CD34, and CD45, in combination with markers comprising: CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
In yet other embodiments, diagnosing minimal residual disease in a sample taken from a subject can comprise the detection of combinations of markers including, but not limited to: CD19, CD10, CD34, and CD45, in combination with marker comprising: CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a.
The methods of the invention can comprise MRD detection by flow cytometry with preferred combinations of probes to specific markers. MRD detection can be combined with at least 4 different probes, and can include in some embodiments at least 5, 6, 7, 8, 9, 10, 11, and 12 different probes. When incorporated with at least 6-probes, the new marker combinations afford the detection of one leukemic cell amongst 105 bone marrow cells. These new markers allow MRD studies in all B-lineage ALL patients, and increase the sensitivity of detecting minimal residual disease.
Probes to Detect Markers of Minimal Residual Disease
The term “probe” refers to any molecule that is capable of specifically binding to an intended target molecule, for example, a nucleotide transcript or a protein encoded by a marker gene. RNA/DNA probes can be synthesized by one of skill in the art, or derived from appropriate biological preparations. Likewise, antibody probes to specific targets can be generated by one of skill in the art, or derived from appropriate sources. Probes may be specifically designed to be labeled. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molecules.
By “specifically binds,” it is generally meant that an antibody binds to an epitope via its antigen binding domain, and that the binding entails some complementarity between the antigen binding domain and the epitope. An epitope is a site on an antigen or marker where the antibody binds via its variable region. The epitope is therefore a part of the antigen or marker, but the epitope is only a portion of the marker recognized by the antibody. According to this definition, an antibody is said to “specifically bind” to an epitope or have “antigen specificity” when it binds to that epitope, via its antigen binding domain more readily than it would bind to a random, unrelated epitope. As used herein, therefore, “specifically binds” is used interchangeably with recognition of a defined epitope on an antigen or marker, or any epitope contained in the antigen or marker. For example the term “specifically binds” when used in conjunction with a particular antibody is used to indicate that there is recognition of a certain epitope of the antigen and the interaction between the antibody and epitope is a non-random interaction indicative of the presence or “expression” of the certain epitope. The term “specifically binds” when used in conjunction with a particular marker is used to indicate that there is recognition of a certain antigen or marker and the interaction between the antibody and antigen or marker is a non-random interaction indicative of the presence or “expression” of the certain antigen or marker.
Embodiments of the invention, include methods and kits comprising probes to detect markers and combinations of markers in TABLE 1 comprising genes overexpressed in B-lineage ALL.
Embodiments of the invention, include methods and kits comprising probes to detect markers and combinations of markers in TABLE 2 comprising genes underexpressed in B-lineage ALL.
Embodiments of the invention include methods and kits comprising probes to detect markers and combinations of markers comprising CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
Embodiments of the invention, include methods and kits comprising a plurality of probes to detect markers and combinations of markers comprising CD19, CD10, CD34, and CD45, and any two of CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a (See TABLE 3).
Embodiments of the invention include methods and kits comprising contacting a specimen with a plurality of probes to detect expression levels of markers comprising CD19, CD10, CD34, and CD45, and any two of CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
In one embodiment of the invention, a method comprises obtaining a specimen from a subject and contacting the specimen with plurality of probes to detect expression levels of markers. As a first step, the specimen is contacted by a plurality of probes to CD19, CD10, CD34 and CD45 wherein a first probe specifically binds to CD19, a second probe specifically binds to CD10, a third probe specifically binds to CD34, and a fourth probe specifically binds to CD45, and at least two additional probes specifically bind to any two of CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a. As a third step, at least one complex formed between each of said probes and said markers is detected and a value generated, wherein the value corresponds to an expression level of each of said marker. As a fourth step, an expression profile is generated by combining said values generated. The expression profile displaying each of the markers from step one and those selected in step two is compared to a normal control expression profile. The expression of CD19 and CD10, a modulated level of CD34, and CD45, and a modulated level of at least one of CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a is indicative of minimal residual disease in acute lymphoblastic leukemia.
In yet another embodiment of the invention, the method further comprises contacting the specimen with at least three, four, five, six, seven, or eight additional probes to detect expression levels of markers comprising CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a.
In another embodiment of the invention, the method further comprises permeabilization of cells in the specimen prior to the contacting the specimen with a probe to detect expression levels of markers comprising CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a.
In yet another embodiment of the invention, said plurality of probes specifically bind distinct markers comprising: (a) CD10, CD19, CD34, CD45, CD38, CD24, and CD44; (b) CD10, CD19, CD34, CD45, CD38, CD58, and CD44; (c) CD10, CD19, CD34, CD45, CD38, CD73, and CD15; (d) CD10, CD19, CD34, CD45, CD38, CD200, and CD44; (e) CD10, CD19, CD34, CD45, CD66c, CD123, and CD86; (f) CD10, CD19, CD34, CD45, CD72, CD13, and CD33; or (g) CD10, CD19, CD34, CD45, CD79b, HSPB1, and Bcl-2.
In another embodiment of the invention said modulated level comprises the expression of CD34 of CD45.
In yet another embodiment of the invention said modulated level comprises the overexpression of CD44, CD58, CD73, CD200, CD86, HSPB1, BCL2, CD164, CD97, CD99, or CD300a and/or the underexpression of CD38, CD72, or CD79b, relative to a normal control.
Generating Expression Profiles
As used herein, an “expression profile” comprises one or more values corresponding to a measurement of the relative abundance of a gene expression product (i.e., a marker). Such values may include measurements of RNA levels or protein abundance. Thus, an expression profile can comprise values representing the measurement of the transcriptional state or the translational state of the gene. As is known to those of skill in the art, the transcriptional state and translational state are related.
In embodiments of the invention, an “expression profile” of a specimen can include the identities and relative abundance, or “expression level,” of the RNA species, especially mRNAs present in populations of cells in the specimen. Preferably, a sufficient fraction or mRNA is used generate an expression profile using combinations of markers predictive of minimal residual disease. An expression profile can be conveniently determined by measuring transcript abundance by any of several existing gene expression technologies.
In embodiments, an “expression profile” of a specimen can include the identities and relative abundance, or “expression level”, of the constituent protein species expressed in populations of cells in the specimen. Expression profiles according to the invention comprise one or more values representing the expression level of a gene having differential expression in minimal residual disease as compared to a normal control specimen. Each expression profile can contain a sufficient number of values such that the profile can be used to distinguish samples containing a minimal number of leukemic cells or minimal residual disease as compared to specimens taken from normal controls. In some embodiments, an expression profile can comprise four values. In other embodiments, an expression profile can comprise more than four values corresponding to differentially expressed genes, for example at least 5, 6, 7, 8, 9, 10, 11, or 12 values.
In other embodiments of the invention, an expression profile can comprise values corresponding to mRNA expression levels as detected by nucleic acid probes. In exemplary embodiments, it may be advantageous to use a greater number of probes and therefore analyze the expression of a greater number of genes simultaneously. Therefore, in other embodiments of the invention 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 130, 140, 150, 160, 170. 180, 190, 200, or >200 probes are reasonable. Embodiments of the invention, can include, but are not limited to, the detection of mRNA expression with probe sets shown in TABLE 1 comprising genes overexpressed in B-lineage ALL. Other embodiments of the invention, can include, but are not limited to, the detection of mRNA expression with probe sets shown in TABLE 2 comprising genes underexpressed in B-lineage ALL.







TABLE 1







Probe sets overexpressed in 25% of more of B-lineage ALL cases (n = 270) as compared to normal bone marrow CD19+CD10+ cells from 4


healthy donors















CD10+
CD10+


% ALL





CD19+
CD19+

ALL
over ex-




probe set ID
max
min
ALL max
min
pressed
Title
Symbol

















205270_s_at
63.1
12.7
2315.9
175.2
100.0
lymphocyte cytosolic protein 2 (SH2 domain containing
LCP2








leukocyte protein of 76 kDa)



213915_at
23.3
7.7
3934.2
11.6
98.1
natural killer cell group 7 sequence
NKG7


211745_x_at
907.2
271.5
267381.8
226.1
97.4
hemoglobin, alpha 1 /// hemoglobin, alpha 1
HBA1


214414_x_at
615.5
165.5
196027.6
18.1
97.4
hemoglobin, alpha 2 /// hemoglobin, alpha 2
HBA2


209458_x_at
1028.1
164.7
274466.9
252.3
97.0
hemoglobin, alpha 1 ///hemoglobin, alpha 2
HBA1 /// HBA2


211699_x_at
795.5
176
224904.8
286.1
97.0
hemoglobin, alpha 1 ///hemoglobin, alpha 2
HBA1 /// HBA2


215411_s_at
280
87.6
7183.4
88.9
97.0
TRAF3 interacting protein 2
TRAF3IP2


217414_x_at
445.7
33.4
158800.9
23.6
97.0
hemoglobin, alpha 2
HBA2


209116_x_at
941.1
229.3
313970.9
235.5
96.7
hemoglobin, beta
HBB


211696_x_at
1594.2
428.4
334867.9
455.7
96.7
hemoglobin, beta
HBB


204018_x_at
1005.5
299.1
283177.3
26.8
96.7
hemoglobin, alpha 1 /// hemoglobin, alpha 2
HBA1 /// HBA2


212901_s_at
47.5
36.6
930.7
44.5
96.3
cleavage stimulation factor, 3′ pre-RNA, subunit 2,
CSTF2T








64 kDa, tau variant



217232_x_at
1632.4
439.5
318351.3
441.5
96.3
hemoglobin, beta
HBB


212195_at
166
116.4
4130.3
211.7
95.9
MRNA; cDNA DKFZp564F053 (from clone
—








DKFZp564F053)



208469_s_at
33.4
25.9
517.3
14.1
94.8
palmitoyl-protein thioesterase 2 /// EGF-like-domain,
PPT2 /// EGFL8








multiple 8



208820_at
18.3
5.4
1678
6.5
94.8
PTK2 protein tyrosine kinase 2
PTK2


212812_at
247.8
122.3
13345.6
70.7
94.8
CDNA: FLJ22642 fis, clone HSI06970
—


214617_at
130.8
94.1
6399.6
159.5
94.4
perforin 1 (pore forming protein) /// perforin 1 (pore
PRF1








forming protein)



204848_x_at
50.9
16.5
120790.8
19.7
94.1
hemoglobin, gamma A /// hemoglobin, gamma G
HBG1 /// HBG2


213515_x_at
356.4
139.2
88491.2
58.9
94.1
hemoglobin, gamma A /// hemoglobin, gamma G
HBG1 /// HBG2


219243_at
37.3
8.5
3807.4
14.9
93.0
GTPase, IMAP family member 4
GIMAP4


206834_at
252.4
49.8
105121.3
49.3
92.2
hemoglobin, delta /// hemoglobin, delta
HBD


218805_at
108.4
57.2
4940.9
80.9
92.2
GTPase, IMAP family member 5 /// GTPase, IMAP family
GIMAP5








member 5



215806_x_at
114.2
99.1
8980
33.2
92.2
T cell receptor gamma constant 2 /// T cell receptor
TRGC2 ///








gamma variable 9 ///
TRGV9 ///


204419_x_at
277.7
152.9
124214.1
48.5
92.2
hemoglobin, gamma A /// hemoglobin, gamma G
HBG1 /// HBG2


209200_at
605.5
306.8
8617.6
49.7
92.2
MADS box transcription enhancer factor 2, polypeptide C
MEF2C








(myocyte enhancer factor 2C)



200770_s_at
62.9
33.2
793
25.7
91.5
laminin, gamma 1 (formerly LAMB2)
LAMC1


204497_at
12.9
7.2
3587.5
8.1
91.5
adenylate cyclase 9
ADCY9


213095_x_at
40.2
29
3845.6
28
91.5
allograft inflammatory factor 1
AIF1


203745_at
132.4
83.6
1181.3
77.4
90.7
holocytochrome c synthase (cytochrome c heme-lyase)
HCCS


205950_s_at
223.3
39.9
70148.2
131
90.7
carbonic anhydrase I
CA1


210031_at
60.9
26.7
4613.9
22.6
90.7
CD3Z antigen, zeta polypeptide (TiT3 complex)
CD3Z


208923_at
349.8
238
7825.2
220.5
90.4
cytoplasmic FMR1 interacting protein 1
CYFIP1


212136_at
369.4
317.4
3062.7
228.2
90.4
ATPase, Ca++ transporting, plasma membrane 4
ATP2B4


218589_at
179.1
114.7
11915.5
71.2
90.4
purinergic receptor P2Y, G-protein coupled, 5
P2RY5


220992_s_at
63.6
42.9
664.5
16.6
90.4
chromosome 1 open reading frame 25 /// chromosome 1
C1orf25








open reading frame 25



205898_at
69.3
11.1
4165.5
6.9
90.0
chemokine (C—X3—C motif) receptor 1
CX3CR1


213539_at
160.4
53
7872.8
89.4
90.0
CD3D antigen, delta polypeptide (TiT3 complex)
CD3D


203685_at
229
149.1
5203.8
150.1
89.6
B-cell CLL/lymphoma 2
BCL2


209813_x_at
19.8
9.6
8796.6
11.2
88.9
T cell receptor gamma constant 2 /// T cell receptor
TRGC2 ///








gamma variable 9 ///
TRGV9 ///


205269_at
99.5
58.2
1135.6
60.5
88.5
lymphocyte cytosolic protein 2 (SH2 domain containing
LCP2








leukocyte protein of 76 kDa)



212560_at
629
507.9
13410.1
337.8
88.1
chromosome 11 open reading frame 32
C11orf32


215051_x_at
110.9
60.4
8954.9
40.8
88.1
allograft inflammatory factor 1
AIF1


218244_at
284.7
193.9
2035.2
146.7
88.1
nucleolar protein 8
NOL8


65585_at
62.8
19.8
610.3
26.2
87.8
family with sequence similarity 86, member B1
FAM86B1


205592_at
70.1
24.9
36020.7
26.5
87.4
Solute carrier family 4, anion exchanger, member 1
SLC4A1








(erythrocyte membrane protein band 3, Diego blood









group)



215920_s_at
46.3
21.2
631
9.7
87.4
hypothetical protein LOC283970 /// similar to nuclear pore
LOC283970 ///








complex interacting protein
LOC440350


213500_at
47.6
12.2
836.8
15.8
87.0
Mitochondrial ribosomal protein S22
MRPS22


201841_s_at
302
15.6
8938.9
36.4
86.7
heat shock 27 kDa protein 1
HSPB1


215967_s_at
46.2
15.6
1629.1
15.5
86.7
lymphocyte antigen 9
LY9


204774_at
305.5
167.7
6766.7
297.7
86.3
ecotropic viral integration site 2A
EVI2A


202771_at
211.8
40.7
4946.6
19.9
86.3
family with sequence similarity 38, member A
FAM38A


217865_at
188.7
14.9
3581.1
11.3
85.9
ring finger protein 130
RNF130


202615_at
551.3
390.3
4195
16.1
85.9
Guanine nucleotide binding protein (G protein), q
GNAQ








polypeptide



219654_at
160.3
106.9
4702.9
17.2
85.9
protein tyrosine phosphatase-like (proline instead of
PTPLA








catalytic arginine), member a



1405j_at
22
5.7
2700.9
7.6
85.6
chemokine (C-C motif) ligand 5
CCL5


200696_s_at
510.4
417
11239.7
359.9
84.8
gelsolin (amyloidosis, Finnish type)
GSN


204547_at
19.3
5.2
885.8
4.4
84.8
RAB40B, member RAS oncogene family
RAB40B


209901_x_at
47.7
36.8
4211
22.6
84.8
allograft inflammatory factor 1
AIF1


207643_s_at
234.7
94.4
3029.5
28
84.1
tumor necrosis factor receptor superfamily, member 1A
TNFRSF1A


210933_s_at
7.4
2.6
785.5
3.3
83.7
fascin homolog 1, actin-bundling protein
FSCN1








(Strongylocentrotus purpuratus)



211821_x_at
26.2
13.7
32574.5
6.5
83.7
glycophorin A (includes MN blood group)
GYPA


32625_at
50.2
34.8
1977.7
13.2
83.7
natriuretic peptide receptor A/guanylate cyclase A
NPR1








(atrionatriuretic peptide receptor A)



203388_at
365.8
102.9
3514.3
116.5
83.3
arrestin, beta 2
ARRB2


203372_s_at
1002.4
316.3
13986.4
31.5
83.3
suppressor of cytokine signaling 2
SOCS2


213541_s_at
631
253.7
9628.5
89.7
82.6
v-ets erythroblastosis virus E26 oncogene like (avian)
ERG


214181_x_at
171.8
56.6
11593.5
15.6
82.2
leukocyte specific transcript 1
LST1


215633_x_at
233.3
128.3
11473.5
22.7
82.2
leukocyte specific transcript 1
LST1


203373_at
1943.6
895.5
26597.2
73.1
82.2
suppressor of cytokine signaling 2
SOCS2


202594_at
453.3
354.8
2346.8
399.3
81.9
leptin receptor overlapping transcript-like 1
LEPROTL1


205173_x_at
604
304.7
7457.7
227.5
81.9
CD58 antigen, (lymphocyte function-associated antigen
CD58








3)



214761_at
244.1
157.3
3051.9
6.8
81.9
zinc finger protein 423
ZNF423


201280_s_at
16.7
7.8
647.9
7.8
81.5
disabled homolog 2, mitogen-responsive phosphoprotein
DAB2








(Drosophila)



201906_s_at
37.3
16
2193.9
12.8
81.1
CTD (carboxy-terminal domain, RNA polymerase II,
CTDSPL








polypeptide A) small phosphatase-like



213123_at
165.8
55.4
1188.1
20.9
81.1
Microfibrillar-associated protein 3
MFAP3


201681_s_at
25.7
7.4
685.1
3.8
80.7
discs, large homolog 5 (Drosophila)
DLG5


203596_s_at
97.2
22.5
2083.3
34.8
80.7
interferon-induced protein with tetratricopeptide repeats 5
IFIT5


209409_at
203.3
102.3
2142.6
97
80.7
growth factor receptor-bound protein 10
GRB10


209933_s_at
126.1
59.1
1481.7
29.3
80.7
CD300A antigen
CD300A


218831_s_at
55.9
42.5
4423.1
18.8
80.7
Fc fragment of IgG, receptor, transporter, alpha
FCGRT


218689_at
42.1
20
997.9
13.5
80.4
Fanconi anemia, complementation group F
FANCF


202910_s_at
303.4
149.2
6537
31.5
80.4
CD97 antigen
CD97


216942_s_at
275.1
129.2
4763
48.2
80.4
CD58 antigen, (lymphocyte function-associated antigen
CD58








3)



210202_s_at
141.1
45.9
2799.5
18.1
80.4
bridging integrator 1
BIN1


202426_s_at
12.4
10.1
1492.4
6.3
80.0
retinoid X receptor, alpha
RXRA


209568_s_at
371.5
262.5
4854.8
163.5
80.0
ral guanine nucleotide dissociation stimulator-like 1
RGL1


212298_at
10.6
5.6
2155.1
3.3
80.0
neuropilin 1
NRP1


216050_at
9.3
4.5
2263.8
0.9
80.0
CDNA: FLJ20931 fis, clone ADSE01282
—


208010_s_at
15.4
6.4
550.2
2.9
80.0
protein tyrosine phosphatase, non-receptor type 22
PTPN22








(lymphoid)



215836_s_at
220.6
114.5
4999.1
75.2
79.6
protocadherin gamma subfamily A1
PCDHGA1


219777_at
45
2.4
3845.4
1.2
79.6
GTPase, IMAP family member 6
GIMAP6


221879_at
67.6
32.7
1584.5
13.1
79.6
calmodulin-like 4
CALML4


219349_s_at
123
63.1
709.7
12.8
79.6
SECS-like 1 (S. cerevisiae)
SEC5L1


219938_s_at
67.1
43.3
1226.2
10.9
79.6
proline-serine-threonine phosphatase interacting protein 2
PSTPIP2


211582_x_at
295.3
27.2
9348.4
23.1
79.3
leukocyte specific transcript 1
LST1


212070_at
179.3
13.7
7815.2
33.7
79.3
G protein-coupled receptor 56
GPR56


203427_at
262.2
115.7
1968.9
47
79.3
ASF1 anti-silencing function 1 homolog A (S. cerevisiae)
ASF1A


201105_at
33.8
10.7
24467.4
7.8
78.9
lectin, galactoside-binding, soluble, 1 (galectin 1)
LGALS1


205099_s_at
17.7
8.1
958.1
7.1
78.9
chemokine (C-C motif) receptor 1
CCR1


202917_s_at
379.2
230.5
76685.5
107.5
78.9
S100 calcium binding protein A8 (calgranulin A)
S100A8


200953_s_at
556.9
302.6
15144.4
183.6
78.5
cyclin D2
CCND2


204563_at
415.7
288.1
16680.8
205
78.5
selectin L (lymphocyte adhesion molecule 1)
SELL


211560_s_at
32.4
17.8
59803.8
11.7
78.1
aminolevulinate, delta-, synthase 2
ALAS2








(sideroblastic/hypochromic anemia)



212267_at
177.1
117.9
2050.8
127.1
78.1
KIAA0261
KIAA0261


222116_s_at
65.2
11.5
991.4
9.7
78.1
TBC1 domain family, member 16
TBC1D16


57715_at
138.8
41.2
1448.5
48.3
78.1
family with sequence similarity 26, member B
FAM26B


210916_s_at
109.2
40.8
4864.2
18.8
78.1
CD44 antigen (homing function and Indian blood group
CD44








system)



209199_s_at
1762.1
1338.9
12199.4
66.6
78.1
MADS box transcription enhancer factor 2, polypeptide C
MEF2C








(myocyte enhancer factor 2C)



203232_s_at
7.8
4.1
916.3
4
77.8
ataxin 1
ATXN1


222061_at
60.7
6.9
864.5
13.9
77.8
CD58 antigen, (lymphocyte function-associated antigen
CD58








3)



209129_at
186.6
102.1
1556.4
77.3
77.4
thyroid hormone receptor interactor 6
TRIP6


211986_at
187.8
24.6
7591.2
30.9
77.4
AHNAK nucleoprotein (desmoyokin)
AHNAK


212135_s_at
881.2
583.9
6848.7
471.1
77.4
ATPase, Ca++ transporting, plasma membrane 4
ATP2B4


212349_at
32.2
14.1
413.8
11.1
77.4
protein O-fucosyltransferase 1
POFUT1


209163_at
64.7
37.7
1725.6
9.9
77.4
cytochrome b-561
CYB561


210164_at
56.7
5.5
1828.8
6.5
77.0
granzyme B (granzyme 2, cytotoxic T-lymphocyte-
GZMB








associated serine esterase 1) ///



212602_at
79.7
18.9
1360.4
9.6
76.7
WD repeat and FYVE domain containing 3
WDFY3


200878_at
23.4
9.6
1992
6.1
76.3
endothelial PAS domain protein 1
EPAS1


209195_s_at
228.5
65.3
2349.2
62.6
76.3
adenylate cyclase 6
ADCY6


210629_x_at
374.2
216.5
6073.9
65.3
76.3
leukocyte specific transcript 1
LST1


222101_s_at
98.5
31.8
1276
15.3
76.3
dachsous 1 (Drosophila)
DCHS1


218199_s_at
72
66.6
632.1
28.1
76.3
nucleolar protein family 6 (RNA-associated)
NOL6


215543_s_at
281.3
56
1778.6
25.9
75.9
like-glycosyltransferase
LARGE


217730_at
151.8
114.9
1923.4
34.6
75.9
transmembrane BAX inhibitor motif containing 1
TMBIM1


219161_s_at
370.4
214.7
4079.9
48.4
75.9
chemokine-like factor
CKLF


201666_at
287.5
234.5
6650.2
156.8
75.6
TIMP metallopeptidase inhibitor 1
TIMP1


203186_s_at
545.5
147.1
14516.7
171.2
75.6
calvasculin, metastasin, murine placental homolog)
S100A4


203508_at
145.6
13.6
2176.2
28.1
75.6
tumor necrosis factor receptor superfamily, member 1B
TNFRSF1B


205354_at
49.1
25
799.3
13.2
75.6
guanidinoacetate N-methyltransferase
GAMT


210784_x_at
64.6
35.1
1105.8
21.4
75.6
leukocyte immunoglobulin-like receptor, subfamily B (with
LILRB2 ///








TM and ITIM domains), member 2 /// leukocyte
LILRB3








immunoglobulin-like receptor, subfamily B (with TM and









ITIM domains), member 3



211744_s_at
428.3
296.5
5561.2
148.4
75.6
CD58 antigen, (lymphocyte function-associated antigen
CD58








3) /// CD58 antigen, (lymphocyte function-associated









antigen 3)



219672_at
212.5
68.3
31465.9
32.8
75.6
erythroid associated factor
ERAF


202535_at
134.1
94.1
756.6
21.9
75.2
Fas (TNFRSF6)-associated via death domain
FADD


205488_at
133.2
17.6
8624.2
18.7
74.8
granzyme A (granzyme 1, cytotoxic T-lymphocyte-
GZMA








associated serine esterase 3)



205708_s_at
237.2
32
2798.1
131.5
74.8
transient receptor potential cation channel, subfamily M,
TRPM2








member 2



214574_x_at
530.6
84
10726.8
34.4
74.8
leukocyte specific transcript 1
LST1


215177_s_at
145.9
31.5
12400.9
14.6
74.8
integrin, alpha 6
ITGA6


211101_x_at
604.8
512.8
5777.6
123.3
74.8
leukocyte immunoglobulin-like receptor, subfamily A (with
LILRA2








TM domain), member 2



208634_s_at
1744.4
1323.4
8823.5
766
74.4
microtubule-actin crosslinking factor 1
MACF1


209949_at
177.6
37
3712.2
28.7
74.4
neutrophil cytosolic factor 2 (65 kDa, chronic
NCF2








granulomatous disease, autosomal 2)



212678_at
181.2
55.4
902.4
70
74.4
Neurofibromin 1 (neurofibromatosis, von Recklinghausen
NF1








disease, Watson disease)



219837_s_at
43.5
15.8
8209.4
9.7
74.4
cytokine-like 1
CYTL1


202269_x_at
70.2
15
4634.3
4.2
74.4
guanylate binding protein 1, interferon-inducible, 67 kDa ///
GBP1








guanylate binding protein 1, interferon-inducible, 67 kDa



202481_at
170.6
37.7
3015.7
23.6
74.1
dehydrogenase/reductase (SDR family) member 3
DHRS3


220206_at
62.6
20.4
507.2
7.4
74.1
zinc finger, MYM-type 1
ZMYM1


219753_at
462.7
331.5
29780.3
31
74.1
stromal antigen 3
STAG3


217728_at
358.4
166.7
11349.1
220.3
73.7
S100 calcium binding protein A6 (calcyclin)
S100A6


222217_s_at
459.8
324.6
4162.3
181.3
73.7
solute carrier family 27 (fatty acid transporter), member 3
SLC27A3


210146_x_at
144.2
20.9
2389.3
12.7
73.3
leukocyte immunoglobulin-like receptor, subfamily B (with
LILRB2








TM and ITIM domains), member 2



210225_x_at
74.9
39
1132.5
21.1
73.3
leukocyte immunoglobulin-like receptor, subfamily B (with
LILRB2 ///








TM and ITIM domains), member 2 /// leukocyte
LILRB3








immunoglobulin-like receptor, subfamily B (with TM and









ITIM domains), member 3



217188_s_at
44.3
31.3
866.3
21.9
73.3
chromosome 14 open reading frame 1
C14orf1


207338_s_at
158.2
115.3
967.9
20.4
73.3
zinc finger protein 200
ZNF200


201301_s_at
149.8
88.7
3595.6
11.2
73.3
annexin A4
ANXA4


203591_s_at
55.4
21.3
2647.9
6.6
73.0
colony stimulating factor 3 receptor (granulocyte) ///
CSF3R








colony stimulating factor 3 receptor (granulocyte)



204344_s_at
60.7
28.2
753.9
24
72.6
Sec23 homolog A (S. cerevisiae)
SEC23A


212501_at
158.1
115.9
7067.4
15.6
72.6
CCAAT/enhancer binding protein (C/EBP), beta
CEBPB


204249_s_at
863.3
418.4
19159.9
415.6
71.9
LIM domain only 2 (rhombotin-like 1)
LMO2


219326_s_at
671.4
509.7
4219.2
395.1
71.9
UDP-GlcNAc:betaGal beta-1,3-N-
B3GNT1








acetylglucosaminyltransferase 1



202894_at
182
58.6
1507.8
27.6
71.9
EPH receptor B4
EPHB4


218988_at
352.1
173.3
12424.3
59.3
71.9
solute carrier family 35, member E3
SLC35E3


209583_s_at
423.9
313.2
3955.4
42.3
71.9
CD200 antigen
CD200


213817_at
111.9
9.6
1451.4
2
71.9
MRNA; cDNA DKFZp586B0220 (from clone
—








DKFZp586B0220)



208047_s_at
40.8
4
714.4
4.9
71.5
NGFI-A binding protein 1 (EGR1 binding protein 1)
NAB1


216920_s_at
169
132.3
9679.7
22.7
71.5
T cell receptor gamma constant 2 /// T cell receptor
TRGC2 ///








gamma variable 9
TRGV9


204959_at
26.5
7.5
8089.4
3.1
71.5
myeloid cell nuclear differentiation antigen /// myeloid cell
MNDA








nuclear differentiation antigen



204438_at
114.4
83.8
12305
5.7
71.5
mannose receptor, C type 1 /// mannose receptor, C type
MRC1 ///








1-like 1
MRC1L1


203948_s_at
66.5
15.8
53188
9.1
71.1
myeloperoxidase
MPO


209365_s_at
416.3
51.2
10277.5
46.2
70.7
extracellular matrix protein 1
ECM1


214407_x_at
207
13.6
29217.6
7.7
70.7
alycophorin B (includes Ss blood group)
GYPB


221756_at
235.7
94.4
3467.9
56.7
70.7
HGFL gene /// HGFL gene
MGC17330


216511_s_at
239.9
89
2129.1
12.7
70.7
transcription factor 7-like 2 (T-cell specific, HMG-box)
TCF7L2


206207_at
51.8
26.6
10212
7.2
70.7
Charcot-Leyden crystal protein /// Charcot-Leyden crystal
CLC








protein



210547_x_at
39.2
12.8
665.6
13.8
70.4
islet cell autoantigen 1, 69 kDa
ICA1


213056_at
257.6
173.8
3516
11.2
70.4
FERM domain containing 4B
FRMD4B


219530_at
137.7
45.3
759
31.1
70.0
hypothetical protein FLJ21816
FLJ21816


222079_at
159.9
99.5
1043.2
38.1
70.0
—
—


207788_s_at
93.1
58.2
2250.2
12.5
70.0
sorbin and SH3 domain containing 3
SORBS3


212196_at
258.2
132.8
3733.9
106
69.6
MRNA; cDNA DKFZp564F053 (from clone
—








DKFZp564F053)



215844_at
21.6
10.7
305.1
7
69.6
transportin 2 (importin 3, karyopherin beta 2b)
TNPO2


215706_x_at
363.3
176.5
3611.6
78.6
69.6
zyxin
ZYX


201564_s_at
24.6
9.8
895.5
8.1
69.3
fascin homolog 1, actin-bundling protein
FSCN1








(Strongylocentrotus purpuratus)



208683_at
362.3
288.9
5110.1
178
69.3
calpain 2, (m/II) large subunit
CAPN2


221861_at
202.8
34.1
1381.3
46
69.3
MRNA; cDNA DKFZp762M127 (from clone
—








DKFZp762M127)



200951_s_at
27.7
15.2
2127.3
6
69.3
cyclin D2
CCND2


201328_at
751.6
331.4
7886.4
286.8
68.9
v-ets erythroblastosis virus E26 oncogene homolog 2
ETS2








(avian)



209344_at
630.8
208.5
7920.4
383.3
68.9
tropomyosin 4
TPM4


222303_at
604.5
422
8580.9
42
68.9
—
—


211160_x_at
41.3
19.1
1744.4
10.3
68.5
actinin, alpha 1
ACTN1


204083_s_at
84.2
9.9
1854.6
7.3
68.1
tropomyosin 2 (beta)
TPM2


211100_x_at
604.9
372.9
6014.8
326.2
68.1
leukocyte immunoglobulin-like receptor, subfamily A (with
LILRA2








TM domain), member 2



221679_s_at
24.6
5.4
479
2.9
68.1
abhydrolase domain containing 6
ABHD6


218729_at
227
131.9
5414.4
61.7
68.1
latexin
LXN


221773_at
864.6
342.2
11369.1
83.4
68.1
ELK3, ETS-domain protein (SRF accessory protein 2)
ELK3


200808_s_at
336.8
99.6
3372.4
243
67.8
zyxin
ZYX


205837_s_at
18.2
1.6
5044
1.6
67.8
glycophorin A (includes MN blood group)
GYPA


222062_at
16.1
8.9
674.4
6.8
67.8
interleukin 27 receptor, alpha
IL27RA


218820_at
151
83.1
2129.3
27.9
67.8
chromosome 14 open reading frame 132
C14orf132


204648_at
71.3
15.4
1100
10
67.4
natriuretic peptide receptor A/guanylate cyclase A
NPR1








(atrionatriuretic peptide receptor A)



205289_at
81.6
5.2
3030
5.3
67.4
bone morphogenetic protein 2
BMP2


211066_x_at
362.3
258.9
7663.5
115.2
67.4
protocadherin gamma subfamily A1
PCDHGA1


205067_at
698.3
430.6
6951.6
85.9
67.4
interleukin 1, beta
IL1B


202878_s_at
348.1
242.3
3646.4
147.1
67.0
complement component 1, q subcomponent, receptor 1
C1QR1


211581_x_at
485.2
62.8
6222.2
32.4
67.0
leukocyte specific transcript 1
LST1


212772_s_at
208.1
171.5
1656.3
86.3
67.0
ATP-binding cassette, sub-family A (ABC1), member 2
ABCA2


218522_s_at
241.8
148.4
1323.8
151.3
67.0
BPY2 interacting protein 1
BPY2IP1


221188_s_at
257.9
146.8
1620.6
76
67.0
cell death-inducing DFFA-like effector b
CIDEB


216850_at
23.1
14.9
437.5
4.5
67.0
small nuclear ribonucleoprotein polypeptide N
SNRPN


218532_s_at
220
175.4
3786.7
11.2
67.0
hypothetical protein FLJ20152
FLJ20152


203370_s_at
118.2
45.6
1223
24.7
66.7
PDZ and LIM domain 7 (enigma)
PDLIM7


206337_at
256
77.9
7065.2
126.8
66.7
chemokine (C-C motif) receptor 7 /// chemokine (C-C
CCR7








motif) receptor 7



219411_at
35.5
17.4
554.2
11.3
66.7
engulfment and cell motility 3 (ced-12 homolog, C. elegans)
ELMO3


203939_at
121.1
54.3
5133.9
5
66.7
5′-nucleotidase, ecto (CD73)
NT5E


206769_at
43.1
15.2
740.5
10.2
66.3
thymosin, beta 4, Y-linked
TMSB4Y


215076_s_at
18.8
10.3
618.7
7.8
66.3
collagen, type III, alpha 1 (Ehlers-Danlos syndrome type
COL3A1








IV, autosomal dominant)



202711_at
77.2
35.2
769.5
10.5
66.3
ephrin-B1
EFNB1


201976_s_at
76.5
12
3468
10
65.9
myosin X
MYO10


209468_at
35.5
9
518.6
9.5
65.9
low density lipoprotein receptor-related protein 5
LRP5


213589_s_at
13.2
8.1
555.7
8.5
65.9
hypothetical protein LOC146712 /// UDP-GlcNAc:betaGal
LOC146712 ///








beta-1,3-N-acetylglucosaminyltransferase-like 1
B3GNTL1


216352_x_at
21.4
12.4
635.4
7
65.9
protocadherin gamma subfamily A, 3
PCDHGA3


212364_at
56.6
15.9
1780.2
6.8
65.9
myosin IB
MYO1B


209101_at
428
135.6
25930.7
14.5
65.9
connective tissue growth factor
CTGF


201295_s_at
97.5
48.6
1881.2
32.4
65.6
WD repeat and SOCS box-containing 1
WSB1


203470_s_at
138.4
59.7
2050.7
27.3
65.6
pleckstrin
PLEK


209079_x_at
370.2
206.7
7185.2
78.4
65.6
protocadherin gamma subfamily A1
PCDHGA1


219539_at
116.7
24.4
771.3
10.8
65.6
gem (nuclear organelle) associated protein 6
GEMIN6


210299_s_at
280.5
132.8
4488.4
28
65.6
four and a half LIM domains 1
FHL1


210298_x_at
363.7
190.1
7144.3
24.8
65.6
four and a half LIM domains 1
FHL1


207857_at
394.5
181.8
4403.8
146.9
65.2
leukocyte immunoglobulin-like receptor, subfamily A (with
LILRA2








TM domain), member 2



209930_s_at
133.8
7.8
10314
6
65.2
nuclear factor (erythroid-derived 2), 45 kDa
NFE2


213694_at
301.2
211.7
3478.4
133.6
65.2
round spermatid basic protein 1
RSBN1


214880_x_at
22.8
6.3
610
3.6
65.2
caldesmon 1
CALD1


211126_s_at
411.4
157.2
4771.5
35.4
65.2
cysteine and glycine-rich protein 2
CSRP2


208146_s_at
25.5
18.8
1653.4
7.6
65.2
carboxypeptidase, vitellogenic-like /// carboxypeptidase,
CPVL








vitellogenic-like



213620_s_at
983
871.1
7321.1
233.8
65.2
intercellular adhesion molecule 2
ICAM2


219667_s_at
709.4
360.7
6837.7
12.4
65.2
B-cell scaffold protein with ankyrin repeats 1
BANK1


203957_at
45.1
21.8
893.1
14.2
64.8
E2F transcription factor 6
E2F6


216035_x_at
254.4
26.8
1646.6
26.1
64.8
transcription factor 7-like 2 (T-cell specific, HMG-box)
TCF7L2


207827_x_at
199.3
183
30767.9
21.7
64.8
synuclein, alpha (non A4 component of amyloid
SNCA








precursor)



212158_at
35.5
9.5
3320.4
4
64.8
syndecan 2 (heparan sulfate proteoglycan 1, cell surface-
SDC2








associated, fibroglycan)



204422_s_at
9.3
6.5
388.3
2.3
64.8
fibroblast growth factor 2 (basic)
FGF2


211031_s_at
554.3
418.8
4347.1
103.8
64.8
cytoplasmic linker 2 /// cytoplasmic linker 2
CYLN2


214022_s_at
886.2
395.4
26636.7
334.7
64.4
interferon induced transmembrane protein 1 (9-27)
IFITM1


204466_s_at
374.1
223
72280.7
90.1
64.4
synuclein, alpha (non A4 component of amyloid
SNCA








precursor)



204683_at
740.3
498.1
4022.8
292.4
64.1
intercellular adhesion molecule 2
ICAM2


210116_at
14.8
3.6
1595.3
4.4
64.1
SH2 domain protein 1A, Duncan's disease
SH2D1A








(lymphoproliferative syndrome)



202023_at
54.6
31.9
1763.8
9.4
64.1
ephrin-A1
EFNA1


204845_s_at
23.5
5.7
406.1
1.2
64.1
glutamyl aminopeptidase (aminopeptidase A)
ENPEP


207979_s_at
120.4
38.6
2307.3
20.4
63.7
CD8 antigen, beta polypeptide 1 (p37)
CD8B1


210140_at
178.3
40.7
5369.7
30.9
63.7
cystatin F (leukocystatin)
CST7


211135_x_at
81.3
25.3
984.1
27.2
63.7
leukocyte immunoglobulin-like receptor, subfamily B (with
LILRB2 ///








TM and ITIM domains), member 2 /// leukocyte
LILRB3








immunoglobulin-like receptor, subfamily B (with TM and









ITIM domains), member 3



208871_at
55.3
20.9
836.6
9.7
63.7
atrophin 1
ATN1


209683_at
217.1
49.1
2479.7
14
63.7
Family with sequence similarity 49, member A
FAM49A


201944_at
759.8
517
3132.4
663.7
63.3
hexosaminidase B (beta polypeptide)
HEXB


213103_at
56.2
12.6
763.7
10.9
63.3
START domain containing 13
STARD13


202893_at
134.7
39.5
1480.8
15.9
63.3
unc-13 homolog B (C. elegans)
UNC13B


207651_at
42.2
20.3
8734.2
8
63.3
G protein-coupled receptor 171
GPR171


207075_at
23.2
10.2
638.2
8.8
63.0
cold autoinflammatory syndrome 1
CIAS1


212728_at
85.7
26.5
958
27
63.0
discs, large homolog 3 (neuroendocrine-dig, Drosophila)
DLG3


212063_at
733.2
361.3
15874.7
140.4
63.0
CD44 antigen (homing function and Indian blood group
CD44








system)



201508_at
139.5
45.9
2084.8
20.8
63.0
insulin-like growth factor binding protein 4
IGFBP4


218025_s_at
296.9
257.9
1696.4
72.7
63.0
peroxisomal D3,D2-enoyl-CoA isomerase
PECI


202270_at
62.8
14.1
1821.4
4.4
63.0
guanylate binding protein 1, interferon-inducible, 67 kDa ///
GBP1








guanylate binding protein 1, interferon-inducible, 67 kDa



214551_s_at
14.1
5.8
1524.8
3.8
62.6
CD7 antigen (p41)
CD7


220146_at
26.7
3.5
1010.1
2.1
62.6
toll-like receptor 7
TLR7


221786_at
214.2
173.5
1433.7
16.9
62.6
chromosome 6 open reading frame 120
C6orf120


206584_at
99.8
78.1
1102.1
13
62.6
lymphocyte antigen 96
LY96


201601_x_at
604.7
162.7
22080.6
147
62.2
interferon induced transmembrane protein 1 (9-27)
IFITM1


208130_s_at
30.5
11.4
714.8
7.5
62.2
thromboxane A synthase 1 (platelet, cytochrome P450,
TBXAS1








family 5, subfamily A)



210370_s_at
193.2
9
1151.2
11.5
62.2
lymphocyte antigen 9
LY9


218607_s_at
446.2
365
1711.3
254.7
62.2
SDA1 domain containing 1
SDAD1


218613_at
251.9
109.2
2485
44.6
62.2
pleckstrin and Sec7 domain containing 3
PSD3


212975_at
687.4
618.3
10417.7
23
62.2
DENN/MADD domain containing 3
DENND3


207697_x_at
402.5
221.4
4154.4
31.9
62.2
leukocyte immunoglobulin-like receptor, subfamily B (with
LILRB2








TM and ITIM domains), member 2



203192_at
85.8
61
1923.4
18
61.9
ATP-binding cassette, sub-family B (MDR/TAP), member 6
ABCB6


200660_at
38.2
13.9
2700.3
7.8
61.5
S100 calcium binding protein A11 (calgizzarin)
S100A11


202747_s_at
82.5
46.5
7009.4
39.7
61.5
integral membrane protein 2A
ITM2A


203061_s_at
59.9
34
667.2
17.6
61.5
mediator of DNA damage checkpoint 1
MDC1


214450_at
30.1
16.7
2250.8
16.9
61.5
cathepsin W (lymphopain) /// cathepsin W (Iymphopain)
CTSW


204304_s_at
115.5
22
13206.2
6.9
61.5
prominin 1
PROM1


218999_at
116.1
33.7
811.4
10.4
61.5
hypothetical protein FLJ11000
FLJ11000


220230_s_at
162.6
11.7
7143.3
4.2
61.5
cytochrome b5 reductase 2
CYB5R2


202242_at
318.5
109
4053.5
17.3
61.5
tetraspanin 7
TSPAN7


214505_s_at
632
262.1
9639.8
188.3
61.1
four and a half LIM domains 1
FHL1


200771_at
309.6
153.2
1480.6
18.1
61.1
laminin, gamma 1 (formerly LAMB2)
LAMC1


220640_at
29.3
13.3
665.2
5.6
61.1
casein kinase 1, gamma 1
CSNK1G1


201809_s_at
398.3
237.2
7012.1
84.2
61.1
endoglin (Osler-Rendu-Weber syndrome 1)
ENG


206718_at
54.8
32.7
691
9.3
61.1
LIM domain only 1 (rhombotin 1)
LMO1


39402_at
495.8
318.6
4822.3
44.9
61.1
interleukin 1, beta
IL1B


201858_s_at
619.5
277.2
69794.9
28.2
61.1
proteoglycan 1, secretory granule
PRG1


202371_at
217.8
113.5
2896.9
9.1
61.1
transcription elongation factor A (SII)-like 4
TCEAL4


218569_s_at
54.1
43.4
610.7
21.8
60.7
ketch repeat and BTB (POZ) domain containing 4
KBTBD4


32502_at
128.3
52.3
758.7
38.5
60.7
glycerophosphodiester phosphodiesterase domain
GDPD5








containing 5



218764_at
696.6
275.3
8459
79
60.7
protein kinase C, eta
PRKCH


219686_at
796.9
90
8383
15.6
60.7
serine/threonine kinase 32B
STK32B


220770_s_at
52.6
12.1
360.7
2.5
60.4
transposon-derived Buster3 transposase-like
LOC63920


202664_at
976.9
593.1
6117.3
314.8
60.0
Wiskott-Aldrich syndrome protein interacting protein
WASPIP


219865_at
142.4
71.9
1295.9
40.9
60.0
HSPC157 protein
HSPC157


202430_s_at
120.4
26.3
3812.6
8.4
60.0
phospholipid scramblase 1
PLSCR1


209234_at
97.8
28.5
926.3
9.7
60.0
kinesin family member 1B
KIF1B


222201_s_at
245.9
136.7
1241.3
48.4
60.0
CASP8 associated protein 2
CASP8AP2


209360_s_at
704.4
281
4550
124.2
60.0
runt-related transcription factor 1 (acute myeloid leukemia
RUNX1








1; aml1 oncogene)



210895_s_at
106.9
31.9
1392.7
13.6
60.0
CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)
CD86


209035_at
195.8
41.2
4059.5
10.9
60.0
midkine (neurite growth-promoting factor 2)
MDK


208370_s_at
726.8
529.7
10489.7
85.9
60.0
Down syndrome critical region gene 1
DSCR1


203535_at
311.5
255.2
52168.5
24.2
60.0
S100 calcium binding protein A9 (calgranulin B)
S100A9


201656_at
136.6
3.2
6443.6
1.7
59.6
integrin, alpha 6
ITGA6


221523_s_at
177.2
83.5
1807.4
64.7
59.6
Ras-related GTP binding D
RRAGD


221565_s_at
167.9
33.8
1912.9
20.9
59.6
family with sequence similarity 26, member B
FAM26B


206434_at
12.7
2.4
810.5
0.7
59.6
sparc/osteonectin, cwcv and kazal-like domains
SPOCK3








proteoglycan (testican) 3



206506_s_at
190.3
45.2
2364.9
19
59.6
suppressor of Ty 3 homolog (S. cerevisiae)
SUPT3H


208891_at
997
526.4
13003.4
128.7
59.6
dual specificity phosphatase 6
DUSP6


207785_s_at
445.7
232.5
5173.6
231
59.3
recombining binding protein suppressor of hairless
RBPSUH








(Drosophila)



212154_at
129.4
6.7
4850.1
6.7
59.3
syndecan 2 (heparan sulfate proteoglycan 1, cell surface-
SDC2








associated, fibroglycan)



221797_at
76.7
17.6
562.9
9.9
59.3
hypothetical protein LOC339229
LOC339229


202663_at
272.6
108.1
1844.3
50.5
59.3
Wiskott-Aldrich syndrome protein interacting protein
WASPIP


206991_s_at
87.3
60.1
1388.1
29
59.3
chemokine (C-C motif) receptor 5
CCR5


207735_at
228.9
162.1
2162.1
21.7
59.3
ring finger protein 125
RNF125


211144_x_at
179.3
73.4
7308.1
11.8
59.3
T cell receptor gamma constant 2
TRGC2


201315_x_at
2600.3
1198.3
27908.8
1041.3
58.9
interferon induced transmembrane protein 2 (1-8D)
IFITM2


202524_s_at
393.7
350.1
4971.7
235
58.9
sparc/osteonectin, cwcv and kazal-like domains
SPOCK2








proteoglycan (testican) 2



209728_at
22
16.3
20171.1
9.5
58.9
major histocompatibility complex, class II, DR beta 4
HLA-DRB4


209892_at
228.2
110.3
3825.8
173.9
58.9
fucosyltransferase 4 (alpha (1,3) fucosyltransferase,
FUT4








myeloid-specific)



212768_s_at
8.8
2.4
6175.5
1.6
58.9
olfactomedin 4
OLFM4


214966_at
42.2
11.3
563.1
5.9
58.9
glutamate receptor, ionotropic, kainate 5
GRIK5


217078_s_at
16
4.5
519.5
2.4
58.9
CD300A antigen
CD300A


206582_s_at
54.3
43.6
2710.8
14.3
58.9
G protein-coupled receptor 56
GPR56


214467_at
154.9
77.3
1080.3
55.8
58.5
G protein-coupled receptor 65
GPR65


205571_at
237.2
172.1
1201.6
71.9
58.5
lipoyltransferase 1
LIPT1


220134_x_at
84.4
22.9
803.2
9
58.5
chromosome 1 open reading frame 78
C1orf78


203680_at
168.3
39.3
2787.8
6.3
58.5
protein kinase, cAMP-dependent, regulatory, type II, beta
PRKAR2B


217800_s_at
168.2
122.5
2297.2
7.4
58.5
Nedd4 family interacting protein 1
NDFIP1


203828_s_at
18.5
8.1
3620.8
8.2
58.1
interleukin 32 /// interleukin 32
IL32


217321_x_at
11.7
3.3
310.1
2.2
58.1
Ataxin 3
ATXN3


219423_x_at
103.9
11.1
1087.9
14.1
58.1
tumor necrosis factor receptor superfamily, member 25
TNFRSF25


220187_at
6.4
3
200.6
1.7
58.1
STEAP family member 4
STEAP4


204944_at
6.1
5.3
368.8
2.2
58.1
protein tyrosine phosphatase, receptor type, G
PTPRG


204277_s_at
19.9
11.2
342.4
11.4
57.8
thymidine kinase 2, mitochondrial
TK2


205685_at
76.9
7.2
1077.2
5
57.8
CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)
CD86


215933_s_at
1121.5
787.7
11058
214.8
57.8
hematopoietically expressed homeobox
HHEX


218751_s_at
339.1
208
8267.8
45
57.8
F-box and WD-40 domain protein 7 (archipelago
FBXW7








homolog, Drosophila)



211796_s_at
382.6
210.2
13295.6
10.4
57.8
T cell receptor beta variable 21-1 /// T cell receptor beta
TRBV21-1 ///








variable 19 /// T cell receptor beta variable 5-4 /// T cell
TRBV19 ///








receptor beta variable 3-1 /// T cell receptor beta constant 1
TRBV5-4 ///









TRBV3-1 ///









TRBC1


206666_at
123.4
33.3
5218.3
20.4
57.4
granzyme K (granzyme 3; tryptase II) /// granzyme K
GZMK








(granzyme 3; tryptase II)



212671_s_at
1304.7
118.8
18591.5
149
57.4
major histocompatibility complex, class II, DQ alpha 1 ///
HLA-DQA1 ///








DQ alpha 2
HLA-DQA2


213262_at
154.3
93.2
1110
21.5
57.4
spastic ataxia of Charlevoix-Saguenay (sacsin)
SACS


218627_at
347.9
213.1
4194.7
69.3
57.4
hypothetical protein FLJ11259
FLJ11259


203354_s_at
37.7
20.5
814.1
8.2
57.4
pleckstrin and Sec7 domain containing 3
PSD3


217572_at
24.3
12.9
2948
4.9
57.4
Transcribed locus, strongly similar to NP_032244.1
—








hemoglobin alpha 1 chain [Mus musculus]



213993_at
15.3
8.7
815
2.8
57.4
spondin 1, extracellular matrix protein
SPON1


212170_at
164.8
106.1
770.6
12.4
57.4
RNA binding motif protein 12
RBM12


205786_s_at
168.7
50.4
5191.4
29.6
57.0
integrin, alpha M
ITGAM


221748_s_at
281.6
132.5
11141.1
85.8
57.0
tensin 1 /// tensin 1
TNS1


222155_s_at
158.3
39.8
1291.3
23.6
57.0
G protein-coupled receptor 172A
GPR172A


200665_s_at
101.3
17.2
3081.6
6.6
57.0
secreted protein, acidic, cysteine-rich (osteonectin) ///
SPARC








secreted protein, acidic, cysteine-rich (osteonectin)



211795_s_at
118.4
40.8
2108
20.1
57.0
FYN binding protein (FYB-120/130)
FYB


201212_at
34.6
14.8
1137
4.4
57.0
legumain
LGMN


218695_at
49.5
32.4
816.6
13
57.0
exosome component 4
EXOSC4


208886_at
582.5
77.7
15547
11.8
57.0
H1 histone family, member 0
H1F0


218136_s_at
409
344.1
18019.6
205.2
56.7
solute carrier family 25, member 37
SLC25A37


206734_at
113.3
42.2
701.8
13.9
56.7
jerky homolog-like (mouse)
JRKL


209651_at
114.5
58
865.7
6.7
56.7
transforming growth factor beta 1 induced transcript 1
TGFB1I1


214690_at
13.1
8.5
360.6
2.8
56.7
TATA box binding protein (TBP)-associated factor, RNA
TAF1B








polymerase I, B, 63 kDa



201279_s_at
106.6
14.2
1243.9
7.6
56.3
disabled homolog 2, mitogen-responsive phosphoprotein
DAB2








(Drosophila)



210999_s_at
224.7
70.5
3092.9
70.1
56.3
growth factor receptor-bound protein 10
GRB10


212498_at
912.7
724.8
4480.2
570.3
56.3
CDNA FLJ31636 fis, clone NT2RI2003481
—


206229_x_at
46.9
20.7
548.4
8.7
56.3
paired box gene 2
PAX2


219945_at
21.8
13.4
261.9
5.4
56.3
DEAD (Asp-Glu-Ala-Asp) box polypeptide 25
DDX25


206852_at
57.4
10
1522.9
1.8
56.3
EPH receptor A7
EPHA7


209485_s_at
28.9
12.4
1427.2
3.8
56.3
oxysterol binding protein-like 1A
OSBPL1A


204457_s_at
19
7.9
3486.7
4.9
55.9
growth arrest-specific 1
GAS1


206498_at
62.6
26.2
1115.7
18.8
55.9
oculocutaneous albinism II (pink-eye dilution homolog,
OCA2








mouse)



209691_s_at
42.9
11
706.7
8
55.9
docking protein 4
DOK4


202446_s_at
557.8
361
16437.5
52.3
55.9
phospholipid scramblase 1
PLSCR1


206674_at
496.6
291.7
11241.8
143.6
55.9
fms-related tyrosine kinase 3
FLT3


217983_s_at
2911.2
1695.5
23933.1
798.4
55.9
ribonuclease T2
RNASET2


219812_at
398.9
90.5
5223.7
44.7
55.9
hypothetical protein MGC2463
MGC2463


205285_s_at
92.8
32.2
933.9
8.6
55.9
FYN binding protein (FYB-120/130)
FYB


202688_at
217.4
76.5
3385.9
50.9
55.6
tumor necrosis factor (ligand) superfamily, member 10
TNFSF10


202710_at
258.9
138.5
1342.8
82.5
55.6
BET1 homolog (S. cerevisiae)
BET1


204116_at
1213.2
604
8123.4
574.9
55.6
interleukin 2 receptor, gamma (severe combined
IL2RG








immunodeficiency)



206332_s_at
2150.8
1433.4
10919.1
739.6
55.6
interferon, gamma-inducible protein 16
IFI16


206752_s_at
83.6
13.6
681.7
10.6
55.6
DNA fragmentation factor, 40 kDa, beta polypeptide
DFFB








(caspase-activated DNase)



208657_s_at
138.4
25.5
3249.4
25.4
55.6
septin 9
SEPT9


219487_at
59.7
1.6
551.4
3.1
55.6
hypothetical protein FLJ23560
FLJ23560


203386_at
193.2
109
1626.1
18.5
55.6
TBC1 domain family, member 4
TBC1D4


205640_at
56.9
35.6
1153
15.1
55.6
aldehyde dehydrogenase 3 family, member B1
ALDH3B1


203069_at
66.8
19
844.4
13
55.2
synaptic vesicle glycoprotein 2A
SV2A


204302_s_at
68.2
26.7
944.7
21.1
55.2
KIAA0427
KIAA0427


205290_s_at
176.5
13.9
9212
8.5
55.2
bone morphogenetic protein 2
BMP2


205881_at
117.4
11.6
790.2
25.2
55.2
zinc finger protein 74 (Cos52)
ZNF74


215574_at
78.3
19.4
2858
12.2
55.2
CDNA FLJ11454 fis, clone HEMBA1001463
—


215471_s_at
45.3
17
1245.8
15.9
54.8
microtubule-associated protein 7
MAP7


217936_at
251.3
158.7
1327.8
122.5
54.8
Rho GTPase activating protein 5
ARHGAP5


203264_s_at
75.9
25.6
513.6
9.9
54.8
Cdc42 guanine nucleotide exchange factor (GEF) 9
ARHGEF9


221058_s_at
279.4
210.1
2060.4
24.2
54.8
chemokine-like factor
CKLF


202845_s_at
663.8
459.5
2955
268.7
54.4
ralA binding protein 1
RALBP1


202931_x_at
553.1
343.6
3782.7
233.6
54.4
bridging integrator 1
BIN1


209555_s_at
81.9
8.9
8745.9
6.3
54.4
CD36 antigen (collagen type I receptor, thrombospondin
CD36








receptor)



210201_x_at
795.6
608.4
5732.9
359.2
54.4
bridging integrator 1
BIN1


211627_x_at
10.8
4.1
257
2.9
54.4
estrogen receptor 1 /// estrogen receptor 1
ESR1


213193_x_at
720.7
601.7
16080.3
353.1
54.4
T cell receptor beta variable 19 /// T cell receptor beta
TRBV19 ///








variable 19 /// T cell receptor beta constant 1 /// T cell
TRBC1








receptor beta constant 1



218510_x_at
249.7
41.2
4634.1
20.6
54.4
hypothetical protein FLJ20152
FLJ20152


218706_s_at
22.8
5.6
759.6
4
54.4
HCV NS3-transactivated protein 2
NS3TP2


212905_at
250.8
141.5
1185.6
50.5
54.4
cleavage stimulation factor, 3′ pre-RNA, subunit 2,
CSTF2T








64 kDa, tau variant



206234_s_at
105.2
27.5
839
12.8
54.4
matrix metallopeptidase 17 (membrane-inserted)
MMP17


203678_at
352.4
188.6
1567.1
175.4
54.1
KIAA1018 protein
KIAA1018


204720_s_at
31.5
7.3
1142.5
4.4
54.1
DnaJ (Hsp40) homolog, subfamily C, member 6
DNAJC6


210061_at
74.6
27.7
511.4
14.1
54.1
zinc finger protein 589
ZNF589


220974_x_at
30.1
15.8
1382.3
10.7
54.1
sideroflexin 3 /// sideroflexin 3
SFXN3


204067_at
191.3
43.9
958.5
21.1
54.1
sulfite oxidase
SUOX


200670_at
2422.4
1523
17638.7
508.3
54.1
X-box binding protein 1
XBP1


212731_at
220.1
158.7
830.8
14.9
54.1
ankyrin repeat domain 46
ANKRD46


221527_s_at
136.3
40.6
694.5
10.4
54.1
par-3 partitioning defective 3 homolog (C. elegans)
PARD3


211339_s_at
193
76.6
4748.8
110.2
53.7
IL2-inducible T-cell kinase
ITK


220969_s_at
122.5
79.9
614.7
58.2
53.7
—
—


219130_at
264.9
180.4
1083.9
47.7
53.7
hypothetical protein FLJ10287
FLJ10287


219335_at
165.2
77.7
1285
34.2
53.7
armadillo repeat containing, X-linked 5
ARMCX5


206275_s_at
35.9
9.6
506.5
3.2
53.7
microtubule associated monoxygenase, calponin and LIM
MICAL2








domain containing 2



219871_at
36.5
11.9
819.2
4.3
53.7
hypothetical protein FLJ13197
FLJ13197


209213_at
80
41.3
944.1
8.2
53.7
carbonyl reductase 1
CBR1


210746_s_at
51.5
22.9
22040.8
16.6
53.3
erythrocyte membrane protein band 4.2 /// erythrocyte
EPB42








membrane protein band 4.2



219528_s_at
139.2
37.1
1828.2
42.7
53.3
B-cell CLL/lymphoma 11B (zinc finger protein)
BCL11B


202336_s_at
22.2
10.3
4372.9
4.8
53.3
peptidylglycine alpha-amidating monooxygenase
PAM


210215_at
54.2
13.4
2653.7
5.7
53.3
transferrin receptor 2
TFR2


216321_s_at
756.7
523.2
10606.3
260.3
53.3
nuclear receptor subfamily 3, group C, member 1
NR3C1








(glucocorticoid receptor)



202932_at
96.3
14
1478.6
3.4
53.3
v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1
YES1


221920_s_at
275.2
71.1
16582.5
15.1
53.3
solute carrier family 25, member 37
SLC25A37


208071_s_at
465.6
298.2
3598.8
36.7
53.3
leukocyte-associated Ig-like receptor 1
LAIR1


201061_s_at
426
245.6
17977.3
186.3
53.0
stomatin
STOM


212408_at
828.7
649.6
4117
668.9
53.0
torsin A interacting protein 1
TOR1AIP1


221005_s_at
38.9
14.8
491.4
11.5
53.0
phosphatidylserine synthase 2 /// phosphatidylserine
PTDSS2








synthase 2



212956_at
276.4
23.5
5870
4.7
53.0
KIAA0882 protein
KIAA0882


217948_at
27.1
19.1
371.1
5.9
53.0
DKFZP564B147 protein
DKFZP564B147


216011_at
47.5
26.8
508
7.3
53.0
Solute carrier family 39 (zinc transporter), member 9
SLC39A9


202949_s_at
33.3
13.6
1345.9
7.5
52.6
four and a half LIM domains 2
FHL2


203387_s_at
266.9
209.8
1701.4
132.2
52.6
TBC1 domain family, member 4
TBC1D4


201540_at
1847.7
885.4
22279.2
224
52.6
four and a half LIM domains 1
FHL1


219315_s_at
171.4
63.4
2139.8
19.8
52.6
chromosome 16 open reading frame 30
C16orf30


205739_x_at
409.9
270.6
4446.8
95.8
52.6
zinc finger protein 588
ZNF588


211909_x_at
7.6
3.7
231
1
52.6
prostaglandin E receptor 3 (subtype EP3) ///
PTGER3








prostaglandin E receptor 3 (subtype EP3)



212488_at
794.1
481.3
6100.5
39.7
52.6
collagen, type V, alpha 1
COL5A1


211368_s_at
187.8
104.4
1699.1
4.5
52.6
caspase 1, apoptosis-related cysteine peptidase
CASP1








(interleukin 1, beta, convertase)



203349_s_at
218.6
56.9
3919.9
36.4
52.2
ets variant gene 5 (ets-related molecule)
ETV5


206099_at
521.1
140.5
6649.5
98
52.2
protein kinase C, eta
PRKCH


209176_at
78.5
12.3
645.9
10.5
52.2
—
—


215111_s_at
486.3
376.5
8516
194.7
52.2
TSC22 domain family, member 1
TSC22D1


218086_at
26
10.9
3310.3
8.8
52.2
neural proliferation, differentiation and control, 1
NPDC1


217977_at
88.7
35.5
4936.5
15.4
52.2
selenoprotein X, 1
SEPX1


212473_s_at
118.4
85.5
10655.4
6.7
52.2
microtubule associated monoxygenase, calponin and LIM
MICAL2








domain containing 2



205717_x_at
452.2
265.9
4246.6
159.1
51.9
protocadherin gamma subfamily A, 1
PCDHGA1


212343_at
43.5
20.4
580.2
13.2
51.9
Yip1 domain family, member 6
YIPF6


202342_s_at
66.7
9.5
492.8
3.4
51.9
tripartite motif-containing 2
TRIM2


216913_s_at
24.9
19.3
1027.2
9.6
51.9
KIAA0690
KIAA0690


211546_x_at
238.6
220.9
24574.6
38.4
51.9
synuclein, alpha (non A4 component of amyloid
SNCA








precursor)



220330_s_at
76.6
55.8
1219.5
1.9
51.9
SAM domain, SH3 domain and nuclear localisation
SAMSN1








signals, 1



201313_at
59.3
11.7
806.8
8.4
51.5
enolase 2 (gamma, neuronal)
ENO2


209677_at
59.3
10
494.2
6.6
51.5
protein kinase C, iota
PRKCI


208534_s_at
60.8
12.2
1464.6
6
51.5
RAS p21 protein activator 4 /// hypothetical protein
RASA4 ///








FLJ21767
FLJ21767


212504_at
241.7
71.4
2483.2
32
51.5
KIAA0934
KIAA0934


201329_s_at
863.4
379.9
7961
122.2
51.5
v-ets erythroblastosis virus E26 oncogene homolog 2
ETS2








(avian)



209146_at
118.9
64.6
825.4
6.9
51.5
sterol-C4-methyl oxidase-like
SC4MOL


221526_x_at
245.3
109.5
1393
29.7
51.5
par-3 partitioning defective 3 homolog (C. elegans)
PARD3


214156_at
42.4
17.2
1686.2
3.8
51.5
myosin VIIA and Rab interacting protein
MYRIP


219014_at
1928.5
1774.4
18056.6
300
51.5
placenta-specific 8
PLAC8


200050_at
747.8
270.7
2799
232.9
51.1
zinc finger protein 146 /// zinc finger protein 146
ZNF146


201790_s_at
103.8
21.9
1309.1
15.1
51.1
7-dehydrocholesterol reductase
DHCR7


203611_at
1976.8
1120.4
37006.1
737.2
51.1
telomeric repeat binding factor 2
TERF2


209835_x_at
477.3
245.5
9995.9
168.9
51.1
CD44 antigen (homing function and Indian blood group
CD44








system)



212183_at
100.8
17
1555.8
18.8
51.1
nudix (nucleoside diphosphate linked moiety X)-type motif 4
NUDT4


212598_at
41.3
12
536.8
6.1
51.1
WD repeat and FYVE domain containing 3
WDFY3


218113_at
229
70
1840
54.7
51.1
transmembrane protein 2
TMEM2


218486_at
132.3
10.8
3794.5
4.8
51.1
Kruppel-like factor 11
KLF11


54037_at
362.4
285.4
2749.7
98.4
51.1
Hermansky-Pudlak syndrome 4
HPS4


207813_s_at
34.9
27
288.2
8
51.1
ferredoxin reductase
FDXR


207120_at
22.2
11
322.9
2.7
51.1
zinc finger protein 667
ZNF667


214321_at
35.5
22.5
3390.7
3.4
51.1
nephroblastoma overexpressed gene
NOV


204546_at
60.8
16
772.7
8
50.7
KIAA0513
KIAA0513


205467_at
194.7
41.4
1696.3
27.4
50.7
caspase 10, apoptosis-related cysteine peptidase
CASP10


210176_at
198.1
109.2
1127.4
115.6
50.7
toll-like receptor 1
TLR1


211828_s_at
25
7.9
521.9
7.4
50.7
TRAF2 and NCK interacting kinase
TNIK


200999_s_at
220.7
113.6
3758.8
26.4
50.7
cytoskeleton-associated protein 4
CKAP4


206011_at
183.1
75.1
1908.8
12.4
50.7
caspase 1, apoptosis-related cysteine peptidase
CASP1








(interleukin 1, beta, convertase)



202517_at
273.9
170.4
6850.3
28.3
50.7
collapsin response mediator protein 1
CRMP1


204747_at
282.2
196.5
5497.8
129.3
50.4
interferon-induced protein with tetratricopeptide repeats 3
IFIT3


205838_at
28.5
9.3
8663.8
6.7
50.4
glycophorin A (includes MN blood group)
GYPA


206098_at
35.9
3.4
206
2.4
50.4
zinc finger protein 482
ZNF482


218825_at
270.2
16.8
3402.2
15.1
50.4
EGF-like-domain, multiple 7
EGFL7


209215_at
294
224.3
2545
82
50.4
tetracycline transporter-like protein
TETRAN


212077_at
70.8
60.4
5341.6
3.6
50.4
caldesmon 1
CALD1


207723_s_at
14
6.5
1469.8
3.3
50.0
killer cell lectin-like receptor subfamily C, member 3
KLRC3


219743_at
71.1
15.2
2565.5
7.9
50.0
hairy/enhancer-of-split related with YRPW motif 2
HEY2


201422_at
434.5
286.1
6636.6
46.9
50.0
interferon, gamma-inducible protein 30
IFI30


201859_at
820.4
406.8
24186.7
181.1
50.0
proteoglycan 1, secretory granule
PRG1


206232_s_at
140.2
32
1423.6
8.3
50.0
UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase,
B4GALT6








polypeptide 6



200762_at
1427.6
1083.2
10880.8
344.9
50.0
dihydropyrimidinase-like 2
DPYSL2


209679_s_at
361
105.6
2891.8
34.3
50.0
small trans-membrane and glycosylated protein
LOC57228


203153_at
46
5.9
4357.9
7
49.6
interferon-induced protein with tetratricopeptide repeats 1
IFIT1


204310_s_at
24.1
10.3
346.6
5.8
49.6
natriuretic peptide receptor B/guanylate cyclase B
NPR2








(atrionatriuretic peptide receptor B)



206866_at
38.8
11.3
1138.2
6
49.6
cadherin 4, type 1, R-cadherin (retinal)
CDH4


211133_x_at
167.6
48.7
831.3
33.3
49.6
leukocyte immunoglobulin-like receptor, subfamily B (with
LILRB2 ///








TM and ITIM domains), member 2 /// leukocyte
LILRB3








immunoglobulin-like receptor, subfamily B (with TM and









ITIM domains), member 3



212605_s_at
456.6
387.3
2803.4
247.1
49.6
Nudix (nucleoside diphosphate linked moiety X)-type
NUDT3








motif 3



213273_at
114.6
12.6
2460
10.9
49.6
odz, odd Oz/ten-m homolog 4 (Drosophila)
ODZ4


218983_at
90.8
24.9
833.9
10.5
49.6
complement component 1, r subcomponent-like
C1RL


201028_s_at
2047.8
1148.8
19384.2
325.4
49.6
CD99 antigen
CD99


211429_s_at
128.8
61.2
4692.5
21.8
49.6
serpin peptidase inhibitor, clade A (alpha-1
SERPINA1








antiproteinase, antitrypsin), member 1



205041_s_at
8.5
3.2
1537.4
2.6
49.3
orosomucoid 1 /// orosomucoid 2
ORM1 /// ORM2


205418_at
133.4
15.3
890.2
11.3
49.3
feline sarcoma oncogene
FES


205495_s_at
165.1
14.8
3464.4
14.4
49.3
granulysin /// granulysin
GNLY


210314_x_at
176.8
16.3
1177.3
20.7
49.3
tumor necrosis factor (ligand) superfamily, member 13 ///
TNFSF13 ///








tumor necrosis factor (ligand) superfamily, member 12-
TNFSF12-








member 13
TNFSF13


209241_x_at
205.9
152.8
1195.2
26.5
49.3
misshapen-like kinase 1 (zebrafish)
MINK1


202145_at
160.4
71.4
2972.7
28.1
49.3
lymphocyte antigen 6 complex, locus E
LY6E


204352_at
516.8
346.2
3368.9
89.5
49.3
TNF receptor-associated factor 5
TRAF5


213233_s_at
508.3
399.2
2437.2
33.5
49.3
kelch-like 9 (Drosophila)
KLHL9


211367_s_at
177.9
76.1
1385.3
6.2
49.3
caspase 1, apoptosis-related cysteine peptidase
CASP1








(interleukin 1, beta, convertase)



218690_at
84
56.9
637.1
17.8
49.3
PDZ and LIM domain 4
PDLIM4


220448_at
169.6
93.8
5928.5
4.3
49.3
potassium channel, subfamily K, member 12
KCNK12


201012_at
202.4
40.4
15217.5
79.3
48.9
annexin A1
ANXA1


201325_s_at
41.6
9.2
2026.9
7.8
48.9
epithelial membrane protein 1
EMP1


206871_at
33.4
11.3
43391
8.5
48.9
elastase 2, neutrophil
ELA2


204489_s_at
491.6
46.5
6193.8
22.5
48.9
CD44 antigen (homing function and Indian blood group
CD44








system)



212675_s_at
649.7
387.7
3942.6
127.4
48.9
—
—


207733_x_at
133.5
44.8
804.2
11.6
48.9
pregnancy specific beta-1-glycoprotein 9
PSG9


215469_at
9.1
6
491
2.4
48.9
CDNA FLJ11627 fis, clone HEMBA1004225
—


202052_s_at
113.2
17
783.9
9
48.5
retinoic acid induced 14
RAI14


211571_s_at
20.8
5.6
6316.7
4.8
48.5
chondroitin sulfate proteoglycan 2 (versican)
CSPG2


221942_s_at
495.9
272.4
6805.3
76.1
48.5
guanylate cyclase 1, soluble, alpha 3
GUCY1A3


208636_at
475.1
235
5700.3
22
48.5
Actinin, alpha 1
ACTN1


212503_s_at
243.6
152.1
2682.6
52.9
48.5
KIAA0934
KIAA0934


213746_s_at
181.5
133.1
2479.4
15.3
48.5
filamin A, alpha (actin binding protein 280)
FLNA


210262_at
18.9
11.2
1040.7
3.6
48.5
cysteine-rich secretory protein 2
CRISP2


206082_at
517.7
281.3
3082.3
26.6
48.5
—
—


203814_s_at
45.7
11.7
1307.6
6.4
48.1
NAD(P)H dehydrogenase, quinone 2
NQO2


207426_s_at
405.2
164.3
4003.1
88.9
48.1
tumor necrosis factor (ligand) superfamily, member 4 (tax-
TNFSF4








transcriptionally activated glycoprotein 1, 34 kDa)



217382_at
27.6
2.8
671.1
1.5
48.1
similar to Chloride intracellular channel protein 1 (Nuclear
LOC390363








chloride ion channel 27) (NCC27) (p64 CLCP) (Chloride









channel ABP)



218152_at
397.3
264.4
2145.1
196.1
48.1
high-mobility group 20A
HMG20A


219570_at
98.5
13.1
722.8
12.4
48.1
chromosome 20 open reading frame 23
C20orf23


214439_x_at
738.3
423.3
5005.2
34.9
48.1
bridging integrator 1
BIN1


219956_at
150.6
83.3
1080.7
16.4
48.1
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-
GALNT6








acetylgalactosaminyltransferase 6 (GalNAc-T6)



212820_at
167.8
54.4
2069.3
11.1
48.1
Dmx-like 2
DMXL2


218694_at
175.4
122.2
1524.5
24.4
48.1
armadillo repeat containing, X-linked 1
ARMCX1


205653_at
99.7
74.7
24713.5
17
48.1
cathepsin G
CTSG


205804_s_at
239.2
196.7
1677.1
25.1
48.1
TRAF3 interacting protein 3
TRAF3IP3


203167_at
27.5
21.2
755.1
11.8
47.8
TIMP metallopeptidase inhibitor 2
TIMP2


209286_at
109.6
17.3
3085.9
13.9
47.8
CDC42 effector protein (Rho GTPase binding) 3
CDC42EP3


218758_s_at
122.6
44
901.4
17.9
47.8
DNA segment on chromosome 21 (unique) 2056
D21S2056E








expressed sequence



220618_s_at
78.8
35.1
864.5
14
47.8
zinc finger, CW type with PWWP domain 1
ZCWPW1


216056_at
37.5
20.4
1647.5
6.6
47.8
CD44 antigen (Indian blood group)
CD44


204122_at
194.7
37.7
4519.8
38.5
47.4
TYRO protein tyrosine kinase binding protein
TYROBP


211820_x_at
154
9.9
16977.4
10.9
47.4
glycophorin A (includes MN blood group)
GYPA


213975_s_at
385.3
20.4
11329.4
7.7
47.4
lysozyme (renal amyloidosis) /// leukocyte
LYZ /// LILRB1








immunoglobulin-like receptor, subfamily B (with TM and









ITIM domains), member 1



203305_at
477
331.4
17615.2
50.6
47.4
coagulation factor XIII, A1 polypeptide
F13A1


203923_s_at
307.5
200.6
2691.8
94.1
47.4
cytochrome b-245, beta polypeptide (chronic
CYBB








granulomatous disease)



207705_s_at
244.4
101.3
1962.5
21
47.4
KIAA0980 protein
KIAA0980


218935_at
225.6
98.8
1666.1
18.2
47.4
EH-domain containing 3
EHD3


214433_s_at
176.1
92.2
37065.6
8.9
47.4
selenium binding protein 1 /// selenium binding protein 1
SELENBP1


202382_s_at
27.2
13.3
709.5
6.9
47.0
glucosamine-6-phosphate deaminase 1
GNPDA1


210589_s_at
50.6
33.4
1138.1
22.4
47.0
glucosidase, beta; acid (includes glucosylceramidase) ///
GBA /// GBAP








glucosidase, beta; acid, pseudogene



221709_s_at
59.4
16.6
632
15.8
47.0
chromosome 14 open reading frame 131 /// chromosome
C14orf131








14 open reading frame 131



218276_s_at
222.1
153.4
1251.9
51.4
47.0
salvador homolog 1 (Drosophila)
SAV1


216155_at
107.9
19
814.4
5
47.0
Neuron navigator 1
NAV1


219691_at
139
37.5
921.3
10
47.0
sterile alpha motif domain containing 9
SAMD9


215449_at
65.7
45.5
6842.1
16
47.0
benzodiazapine receptor (peripheral)-like 1
BZRPL1


201372_s_at
37.6
12.1
384.9
4.6
47.0
cullin 3
CUL3


207104_x_at
116.2
21.1
980.6
14.4
46.7
leukocyte immunoglobulin-like receptor, subfamily B (with
LILRB1








TM and ITIM domains), member 1



209370_s_at
401.4
81.6
4041.7
110.9
46.7
SH3-domain binding protein 2
SH3BP2


219359_at
272.8
98
4034.5
56.4
46.7
hypothetical protein FLJ22635
FLJ22635


37145_at
188.7
20.9
2719.8
16.5
46.7
granulysin
GNLY


213117_at
176.9
40.6
1268
13.6
46.7
kelch-like 9 (Drosophila)
KLHL9


210321_at
33.3
16.6
1557.9
6.2
46.7
granzyme H (cathepsin G-like 2, protein h-CCPX) ///
GZMH








granzyme H (cathepsin G-like 2, protein h-CCPX)



212509_s_at
874.8
669.9
16097.8
208.4
46.7
matrix-remodelling associated 7
MXRA7


206518_s_at
35.2
14.3
1009.6
2.9
46.7
regulator of G-protein signalling 9
RGS9


205899_at
81.3
41.1
5746.4
6.7
46.7
cyclin A1
CCNA1


219952_s_at
44.5
10.4
1155.8
14.4
46.3
mucolipin 1
MCOLN1


220734_s_at
86.1
20.6
492.2
15.8
46.3
hypothetical protein MGC10334
MGC10334


221014_s_at
150.6
5.4
789.2
61.9
46.3
RAB33B, member RAS oncogene family /// RAB33B,
RAB33B








member RAS oncogene family



220615_s_at
206.2
22.1
2746.1
9.3
46.3
male sterility domain containing 1
MLSTD1


200615_s_at
283.8
215.7
2222.3
31.7
46.3
adaptor-related protein complex 2, beta 1 subunit
AP2B1


218954_s_at
51.1
31.2
548.7
8
46.3
BRF2, subunit of RNA polymerase III transcription
BRF2








initiation factor, BRF1-like



221724_s_at
32.3
26.6
1445.2
9.7
46.3
C-type lectin domain family 4, member A
CLEC4A


212013_at
1198.6
779.9
6768.7
10.4
46.3
peroxidasin homolog (Drosophila)
PXDN


201060_x_at
351.6
243.5
9900.6
143.4
45.9
stomatin
STOM


204928_s_at
26.6
16.4
605.2
12.6
45.9
solute carrier family 10 (sodium/bile acid cotransporter
SLC10A3








family), member 3



205758_at
251.6
28.5
2296.3
26.2
45.9
CD8 antigen, alpha polypeptide (p32) /// D8 antigen,
CD8A








alpha polypeptide (p32)



214692_s_at
36.8
18.8
697.7
12.1
45.9
jerky homolog (mouse)
JRK


217904_s_at
54.5
20
988.3
7.2
45.9
beta-site APP-cleaving enzyme 1
BACE1


205391_x_at
97.2
24.1
5144.8
10.1
45.9
ankyrin 1, erythrocytic /// ankyrin 1, erythrocytic
ANK1


215666_at
10.4
4
4868.5
1.7
45.9
major histocompatibility complex, class II, DR beta 4
HLA-DRB4


32042_at
93.3
75.7
657
18.1
45.9
cytosolic ovarian carcinoma antigen 1
COVA1


221485_at
159.7
88.1
2565.1
13.4
45.9
UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase,
B4GALT5








polypeptide 5



219504_s_at
74.9
32.1
647.3
5.1
45.9
chromosome 1 open reading frame 82
C1orf82


219154_at
139.2
34.7
1223.9
32.3
45.6
ras homolog gene family, member F (in filopodia)
RHOF


201964_at
592.6
317.4
2559.5
146.2
45.6
amyotrophic lateral sclerosis 4
ALS4


206414_s_at
172.8
30.4
1356.5
12.5
45.6
development and differentiation enhancing factor 2
DDEF2


209297_at
64.6
28.3
2212.4
12.9
45.6
intersectin 1 (SH3 domain protein)
ITSN1


221040_at
31.9
7.5
818.7
3.6
45.6
calpain 10
CAPN10


211474_s_at
583.1
390.7
2625.8
126.3
45.6
serpin peptidase inhibitor, clade B (ovalbumin), member 6
SERPINB6


204924_at
164.9
53.5
1519.3
16.7
45.6
toll-like receptor 2
TLR2


218625_at
309.9
197.7
7686.5
59.9
45.6
neuritin 1
NRN1


64408_s_at
69.9
34.2
431.4
7.2
45.6
calmodulin-like 4
CALML4


204030_s_at
777.4
335.9
5350.9
17.8
45.6
schwannomin interacting protein 1
SCHIP1


206048_at
26.8
6
296.3
6
45.2
ovo-like 2 (Drosophila)
OVOL2


207417_s_at
179.2
129.8
960.4
71.8
45.2
zinc finger protein 177
ZNF177


221682_s_at
55.4
3.5
615.7
2.5
45.2
protocadherin gamma subfamily B, 6
PCDHGB6


217143_s_at
148.2
47
2102.9
22.5
45.2
T cell receptor alpha locus /// T cell receptor delta locus
TRA@ /// TRD@


219200_at
193.1
136.2
791
40.9
45.2
hypothetical protein MGC5297
MGC5297


203952_at
98
67.6
671.4
26.8
45.2
activating transcription factor 6
ATF6


205878_at
39.3
19.3
420.9
6.1
45.2
POU domain, class 6, transcription factor 1
POU6F1


212062_at
18.9
10.9
2294.2
4.1
45.2
ATPase, Class II, type 9A
ATP9A


221788_at
76.1
20.4
718.2
4.8
45.2
Phosphoglucomutase 3
PGM3


207821_s_at
245.4
65
1131.2
54.3
44.8
PTK2 protein tyrosine kinase 2
PTK2


222312_s_at
50.8
9
422.6
8.3
44.8
CDNA clone IMAGE: 6186815
—


207459_x_at
272.7
55.5
20138.4
19.3
44.8
glycophorin B (includes Ss blood group)
GYPB


218298_s_at
440.3
284.8
2624.6
118.3
44.8
chromosome 14 open reading frame 159
C14orf159


202202_s_at
47.6
9.8
586.4
2.7
44.8
laminin, alpha 4
LAMA4


215354_s_at
147.9
86.6
605
23.4
44.8
proline-, glutamic acid-, leucine-rich protein 1
PELP1


203355_s_at
319.3
149.7
2993.9
23.7
44.8
pleckstrin and Sec7 domain containing 3
PSD3


207030_s_at
394.1
147.2
4873.1
24.3
44.8
cysteine and glycine-rich protein 2
CSRP2


215807_s_at
69
40.2
1184.6
13.1
44.8
plexin B1
PLXNB1


212235_at
152.9
16.9
1270
13.7
44.4
plexin D1
PLXND1


218608_at
170.7
14.9
1358.1
12.8
44.4
ATPase type 13A2
ATP13A2


34726_at
210.8
91.9
901.7
87
44.4
calcium channel, voltage-dependent, beta 3 subunit
CACNB3


202201_at
261.3
56.9
23262.7
27.3
44.4
biliverdin reductase B (flavin reductase (NADPH))
BLVRB


203148_s_at
276.3
157.7
1480.8
42.5
44.4
tripartite motif-containing 14
TRIM14


215719_x_at
61.1
13.9
1175.1
5.9
44.4
Fas (TNF receptor superfamily, member 6)
FAS


222126_at
161
95
1827.7
26
44.4
Insulin receptor substrate 3-like
HRBL


212372_at
618.7
397.6
4614.1
115.8
44.4
myosin, heavy polypeptide 10, non-muscle
MYH10


221994_at
36.1
13.4
347.7
3.8
44.4
PDZ and LIM domain 5
PDLIM5


215028_at
97.8
15.6
1792.1
2.9
44.4
sema domain, transmembrane domain (TM), and
SEMA6A








cytoplasmic domain, (semaphorin) 6A



212192_at
127.9
35.5
3244.7
2.6
44.4
potassium channel tetramerisation domain containing 12
KCTD12


203325_s_at
265.4
137.3
2845.4
11.5
44.4
collagen, type V, alpha 1
COL5A1


200699_at
294.6
228
1197.6
124.3
44.1
KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein
KDELR2








retention receptor 2



218899_s_at
164.5
10.8
3140.6
10.1
44.1
brain and acute leukemia, cytoplasmic
BAALC


217519_at
30.4
4.6
285
2.2
44.1
Microtubule-actin crosslinking factor 1
MACF1


218807_at
562.5
419.2
4141.9
204.2
44.1
vav 3 oncogene
VAV3


210151_s_at
365.9
274.5
1788.9
42.5
44.1
dual-specificity tyrosine-(Y)-phosphorylation regulated
DYRK3








kinase 3



215894_at
82.6
6.9
1987
2.1
44.1
prostaglandin D2 receptor (DP)
PTGDR


210783_x_at
163
40.1
1631.4
13
44.1
C-type lectin domain family 11, member A
CLEC11A


205154_at
38
17.4
1093.7
11.5
43.7
leucine rich repeat neuronal 5
LRRN5


210430_x_at
45.3
24.4
5655.9
16.2
43.7
Rhesus blood group, D antigen
RHD


211148_s_at
10.3
4.4
593
4.2
43.7
angiopoietin 2
ANGPT2


222144_at
28.4
13
709.7
10.4
43.7
kinesin family member 17
KIF17


210613_s_at
450.3
135.3
2720.5
25.2
43.7
synaptogyrin 1
SYNGR1


204929_s_at
343.3
181
2094.2
33.4
43.7
vesicle-associated membrane protein 5 (myobrevin)
VAMP5


201807_at
874.5
680.8
4594.7
473.5
43.3
vacuolar protein sorting 26 homolog A (yeast)
VPS26A


207846_at
9.9
1.7
407.8
0.9
43.3
POU domain, class 1, transcription factor 1 (Pit1, growth
POU1F1








hormone factor 1)



200923_at
674.8
262.5
6976.3
63.3
43.3
lectin, galactoside-binding, soluble, 3 binding protein
LGALS3BP


211419_s_at
38.7
9.4
731
4
43.3
chimerin (chimaerin) 2
CHN2


209582_s_at
413.4
242.1
2897.2
106.3
43.3
CD200 antigen
CD200


205131_x_at
255
36.1
2512.6
11.9
43.3
C-type lectin domain family 11, member A
CLEC11A


208322_s_at
188
60.7
2898.8
15.2
43.3
ST3 beta-galactoside alpha-2,3-sialyltransferase 1
ST3GAL1


208198_x_at
73.6
66.4
647.4
21.5
43.3
killer cell immunoglobulin-like receptor, two domains,
KIR2DS1








short cytoplasmic tail, 1



217584_at
61.9
28.2
750.6
4.8
43.3
Niemann-Pick disease, type C1
NPC1


205330_at
200.9
114.6
3525.1
24.7
43.3
meningioma (disrupted in balanced translocation) 1
MN1


214475_x_at
190.4
85.4
4205.9
10.1
43.3
calpain 3, (p94)
CAPN3


211709_s_at
559.3
441.1
5273.2
17.1
43.3
C-type lectin domain family 11, member A /// C-type lectin
CLEC11A








domain family 11, member A



204032_at
75.1
13.4
409.7
7.3
43.0
breast cancer anti-estrogen resistance 3
BCAR3


205109_s_at
96.9
8.6
2788.5
5.2
43.0
Rho guanine nucleotide exchange factor (GEF) 4
ARHGEF4


218525_s_at
191.5
59.4
973.3
40.3
43.0
hypoxia-inducible factor 1, alpha subunit inhibitor
HIF1AN


221771_s_at
414.5
191.6
1621.4
150.2
43.0
M-phase phosphoprotein, mpp8
HSMPP8


221933_at
30.4
5.8
1889.4
3.6
43.0
neuroligin 4, X-linked
NLGN4X


202826_at
43.2
36.7
620.2
12.9
43.0
serine peptidase inhibitor, Kunitz type 1
SPINT1


213618_at
578.7
308
2951.3
141.6
43.0
centaurin, delta 1
CENTD1


219376_at
112.3
45.6
439
22.2
43.0
zinc finger protein 322B
ZNF322B


220986_s_at
22.1
2.9
250.7
0.9
43.0
tigger transposable element derived 6 /// tigger
TIGD6








transposable element derived 6



205349_at
542.8
279.4
9728.6
79.3
43.0
guanine nucleotide binding protein (G protein), alpha 15
GNA15








(Gq class)



206001_at
1156.7
435.3
13016
73.3
43.0
neuropeptide Y
NPY


201617_x_at
30.9
6.3
1133.6
1.6
43.0
caldesmon 1
CALD1


205407_at
153.9
62.7
1103.5
6.8
43.0
reversion-inducing-cysteine-rich protein with kazal motifs
RECK


214920_at
71.5
13.9
7696.6
1
43.0
hypothetical protein LOC221981
LOC221981


203509_at
1408.7
987.3
19247.5
644.6
42.6
sortilin-related receptor, L(DLR class) A repeats-
SORL1








containing



203756_at
63.4
33.9
985.4
17.2
42.6
Rho guanine nucleotide exchange factor (GEF) 17
ARHGEF17


215247_at
37
14.1
505.1
8.8
42.6
hypothetical protein LOC339692
LOC339692


204490_s_at
358.2
177
6178.3
80.2
42.6
CD44 antigen (homing function and Indian blood group
CD44








system)



202990_at
129.3
80.2
2758.5
19.8
42.6
phosphorylase, glycogen; liver (Hers disease, glycogen
PYGL








storage disease type VI)



209617_s_at
68.7
23.3
424.5
6
42.6
catenin (cadherin-associated protein), delta 2 (neural
CTNND2








plakophilin-related arm-repeat protein)



210432_s_at
126
7
8051.5
3
42.6
sodium channel, voltage-gated, type III, alpha
SCN3A


202786_at
516.7
381.8
3315.8
115.1
42.6
serine threonine kinase 39 (STE20/SPS1 homolog, yeast)
STK39


203595_s_at
211.8
106.6
2067.3
39.1
42.6
interferon-induced protein with tetratricopeptide repeats 5
IFIT5


201375_s_at
570.8
376.1
3830.3
343.5
42.2
protein phosphatase 2 (formerly 2A), catalytic subunit,
PPP2CB








beta isoform



201640_x_at
90.8
14.3
542.2
14.8
42.2
cleft lip and palate associated transmembrane protein 1
CLPTM1


201894_s_at
782.9
494.9
3984.2
463.8
42.2
signal sequence receptor, alpha (translocon-associated
SSR1








protein alpha)



210854_x_at
157.5
33
5300.7
25.1
42.2
solute carrier family 6 (neurotransmitter transporter,
SLC6A8








creatine), member 8



212014_x_at
406.8
193.4
8862.5
103.3
42.2
CD44 antigen (homing function and Indian blood group
CD44








system)



212366_at
238.2
143.6
1029.8
72.6
42.2
zinc finger protein 292
ZNF292


212606_at
216.6
9.2
1437.3
6.1
42.2
WD repeat and FYVE domain containing 3
WDFY3


218676_s_at
240.6
17.7
3374.1
9.2
42.2
phosphatidylcholine transfer protein
PCTP


219485_s_at
568.5
437.9
3387.7
256.5
42.2
proteasome (prosome, macropain) 26S subunit, non-
PSMD10








ATPase, 10



219491_at
33.9
14
393.9
10.4
42.2
leucine rich repeat and fibronectin type III domain
LRFN4








containing 4



219521_at
24.7
17.2
731.3
12.4
42.2
beta-1,3-glucuronyltransferase 1 (glucuronosyltransferase
B3GAT1








P)



49111_at
242.1
150.9
1265
107.9
42.2
MRNA; cDNA DKFZp762M127 (from clone
—








DKFZp762M127)



206676_at
25.6
8.4
11672.8
2.9
42.2
carcinoembryonic antigen-related cell adhesion
CEACAM8








molecule 8



209970_x_at
558.3
425.2
3740.3
162.5
42.2
caspase 1, apoptosis-related cysteine peptidase
CASP1








(interleukin 1, beta, convertase)



216392_s_at
288.4
175.1
1390.9
40.1
42.2
SEC23 interacting protein
SEC23IP


201539_s_at
357.3
328.8
6236.3
98.9
42.2
four and a half LIM domains 1
FHL1


204066_s_at
99.5
53.6
13416.6
8.8
42.2
centaurin, gamma 2
CENTG2


202392_s_at
197.9
91.7
971.1
29.9
42.2
phosphatidylserine decarboxylase
PISD


204914_s_at
68
22.8
6617.3
4.2
42.2
SRY (sex determining region Y)-box 11
SOX11


213050_at
85.5
61.6
2104.7
18.4
42.2
cordon-bleu homolog (mouse)
COBL


202797_at
512.7
296.4
2519.2
230.9
41.9
SAC1 suppressor of actin mutations 1-like (yeast)
SACM1L


205844_at
44.7
3.2
2772.1
2.6
41.9
vanin 1 /// vanin 1
VNN1


221023_s_at
46.3
6
655.1
4.1
41.9
potassium voltage-gated channel, subfamily H (eag-
KCNH6








related), member 6 /// potassium voltage-gated channel,









subfamily H (eag-related), member 6



219799_s_at
198.1
82
2562.8
30.6
41.9
dehydrogenase/reductase (SDR family) member 9
DHRS9


202803_s_at
827.9
622.5
7958.6
236.1
41.9
integrin, beta 2 (antigen CD18 (p95), lymphocyte function-
ITGB2








associated antigen 1; macrophage antigen 1 (mac-1)









beta subunit)



221157_s_at
25.8
14.7
294.4
5
41.9
F-box protein 24
FBXO24


202411_at
184.7
70.5
20733
10.7
41.9
interferon, alpha-inducible protein 27
IFI27


206986_at
35.2
16.2
238.3
5.6
41.9
fibroblast growth factor 18
FGF18


203550_s_at
191
73.5
1361.8
46.2
41.5
chromosome 1 open reading frame 2
C1orf2


210586_x_at
69.6
27.6
8076.6
14
41.5
Rhesus blood group, D antigen
RHD


215874_at
144.7
31.8
1354
54.7
41.5
ST3 beta-galactoside alpha-2,3-sialyltransferase 1
ST3GAL1


219201_s_at
12.2
6.1
317.3
5.3
41.5
twisted gastrulation homolog 1 (Drosophila)
TWSG1


219363_s_at
245.9
138.9
938.5
70.7
41.5
MTERF domain containing 1
MTERFD1


222134_at
23.2
8.2
453.2
6.7
41.5
D-aspartate oxidase
DDO


202431_s_at
1088.3
130.1
8590.2
54.6
41.5
v-myc myelocytomatosis viral oncogene homolog (avian)
MYC


219913_s_at
297.8
220.7
1053.6
40.1
41.5
Cm, crooked neck-like 1 (Drosophila)
CRNKL1


202196_s_at
8.5
3.5
592.6
0.8
41.5
dickkopf homolog 3 (Xenopus laevis)
DKK3


217559_at
143.2
78.6
819.1
28.8
41.5
ribosomal protein L10-like
RPL10L


205442_at
23.3
7.8
1395.9
2.4
41.5
microfibrillar-associated protein 3-like
MFAP3L


212915_at
12
5.1
653.8
1
41.5
PDZ domain containing RING finger 3
PDZRN3


205424_at
91.1
72.1
711.9
20.3
41.5
ProSAPiP2 protein
ProSAPiP2


204288_s_at
30.9
16.4
1075.6
8.8
41.1
sorbin and SH3 domain containing 2
SORBS2


211250_s_at
123.7
10.2
1289.1
9.9
41.1
SH3-domain binding protein 2
SH3BP2


211565_at
111.6
8
1229.6
11.1
41.1
SH3-domain GRB2-like 3
SH3GL3


212759_s_at
50.3
20
1354.5
11.1
41.1
transcription factor 7-like 2 (T-cell specific, HMG-box)
TCF7L2


213269_at
161.6
26.4
990
13.7
41.1
zinc finger protein 248
ZNF248


202933_s_at
87.6
7.7
1307.2
3
41.1
v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1
YES1


204319_s_at
323.1
27
3182.8
9.5
41.1
regulator of G-protein signalling 10
RGS10


206179_s_at
33.8
13.5
280.9
6.4
41.1
brain-specific protein p25 alpha
TPPP


202694_at
23.1
10.3
411.9
4.7
41.1
serine/threonine kinase 17a (apoptosis-inducing)
STK17A


213317_at
62.8
11.5
4466.4
1.6
41.1
Chloride intracellular channel 5
CLIC5


221790_s_at
153.6
46.8
3617.7
12.9
41.1
low density lipoprotein receptor adaptor protein 1
LDLRAP1


209168_at
202.8
133.5
2043.8
18.8
41.1
glycoprotein M6B
GPM6B


204430_s_at
433.8
96.8
8380.8
16.8
41.1
solute carrier family 2 (facilitated glucose/fructose
SLC2A5








transporter), member 5



203111_s_at
266.2
23.4
2421.3
22.9
40.7
PTK2B protein tyrosine kinase 2 beta
PTK2B


204011_at
238.2
32.7
4642.4
23.3
40.7
sprouty homolog 2 (Drosophila)
SPRY2


206077_at
98.8
27.1
3637.6
19.7
40.7
Kell blood group
KEL


208460_at
116.9
25.4
674.9
13.3
40.7
gap junction protein, alpha 7, 45 kDa (connexin 45)
GJA7


210401_at
875.3
442.5
5542.9
273.2
40.7
purinergic receptor P2X, ligand-gated ion channel, 1
P2RX1


212186_at
66.1
36.6
986.1
28.3
40.7
acetyl-Coenzyme A carboxylase alpha
ACACA


212199_at
654.1
450.9
2384.1
261.7
40.7
Morf4 family associated protein 1-like 1
MRFAP1L1


201887_at
159.2
81.2
2829.5
30.4
40.7
interleukin 13 receptor, alpha 1
IL13RA1


205259_at
116.8
12.2
2391.5
4
40.7
nuclear receptor subfamily 3, group C, member 2
NR3C2


206150_at
440.2
65.5
5428.4
25.6
40.7
tumor necrosis factor receptor superfamily, member 7
TNFRSF7


214298_x_at
1264.2
1096.3
7522.7
184.1
40.7
septin 6
SEPT6


210390_s_at
39.8
11.9
314.9
3.3
40.7
chemokine (C-C motif) ligand 14 /// chemokine (C-C
CCL14 /// CCL15








motif) ligand 15



202746_at
186.5
152.4
9006.6
24.9
40.7
integral membrane protein 2A
ITM2A


211286_x_at
39.9
21.4
331.6
7.4
40.7
colony stimulating factor 2 receptor, alpha, low-affinity
CSF2RA








(granulocyte-macrophage)



220089_at
63.8
22.6
573.9
6
40.7
L-2-hydroxyglutarate dehydrogenase
L2HGDH


200736_s_at
2887.8
1921.6
31355.7
1488.8
40.4
glutathione peroxidase 1
GPX1


204468_s_at
12.2
5.1
736.9
3.6
40.4
tyrosine kinase with immunoglobulin-like and EGF-like
TIE1








domains 1



210094_s_at
165
41.8
1041.4
27.5
40.4
par-3 partitioning defective 3 homolog (C. elegans)
PARD3


217984_at
1991.8
1242.4
15329.1
851.9
40.4
ribonuclease T2
RNASET2


219829_at
31.7
12.6
379.4
9.6
40.4
integrin beta 1 binding protein (melusin) 2
ITGB1BP2


64064_at
439.2
266.2
4543.4
171.3
40.4
GTPase, IMAP family member 5
GIMAP5


208966_x_at
3288.9
1811.3
12809.7
786.3
40.4
interferon, gamma-inducible protein 16
IFI16


213888_s_at
336
144.1
2671.9
10.8
40.4
TRAF3 interacting protein 3
TRAF3IP3


203104_at
156.1
81.9
4853.9
20.2
40.4
colony stimulating factor 1 receptor, formerly McDonough
CSF1R








feline sarcoma viral (v-fms) oncogene homolog /// colony









stimulating factor 1 receptor, formerly McDonough feline









sarcoma viral (v-fms) oncogene homolog



202668_at
282.8
98.6
4724.3
7.1
40.4
ephrin-B2
EFNB2


203110_at
942.9
657.8
4194.4
419.8
40.0
PTK2B protein tyrosine kinase 2 beta
PTK2B


203688_at
756.1
258
5245.7
177
40.0
polycystic kidney disease 2 (autosomal dominant)
PKD2


207358_x_at
775.4
601.9
3134.2
315.2
40.0
microtubule-actin crosslinking factor 1
MACF1


209631_s_at
9.4
2.2
423.1
1.3
40.0
G protein-coupled receptor 37 (endothelin receptor type B-
GPR37








like)



210066_s_at
8.2
4.2
183.1
1.1
40.0
aquaporin 4
AQP4


213848_at
330.6
78.2
2652.2
24.4
40.0
Dual specificity phosphatase 7
DUSP7


220850_at
12.6
3.9
357.8
1.1
40.0
MORC family CW-type zinc finger 1
MORC1


218816_at
33.6
13.1
422.8
6.1
40.0
leucine rich repeat containing 1
LRRC1


203817_at
196.6
124
1401.8
10.1
40.0
—
—


204915_s_at
63
13.8
2637.5
4
40.0
SRY (sex determining region Y)-box 11
SOX11


218966_at
1090.3
549.8
4844.8
343.3
39.6
myosin VC
MYO5C


51146_at
86.5
10.7
414.5
8.2
39.6
phosphatidylinositol glycan, class V
PIGV


205528_s_at
17
3.2
436
1.4
39.6
runt-related transcription factor 1; translocated to, 1
RUNX1T1








(cyclin D-related)



215388_s_at
5.7
3.2
626
1.4
39.6
complement factor H /// complement factor H-related 1
CFH /// CFHL1


215672_s_at
114.2
49
643.7
18.7
39.6
KIAA0828 protein
KIAA0828


202178_at
49.4
16.9
9160.2
6.6
39.6
protein kinase C, zeta
PRKCZ


209670_at
561.5
298
15751.4
97.6
39.6
T cell receptor alpha constant /// T cell receptor alpha
TRAC








constant



200986_at
142.2
25.8
1035.7
8.5
39.6
serpin peptidase inhibitor, clade G (C1 inhibitor), member
SERPING1








1, (angioedema, hereditary)



217440_at
26.3
4
796.2
0.5
39.6
MRNA; cDNA DKFZp566A193 (from clone
—








DKFZp566A193)



213920_at
47.8
18.4
592.2
5.6
39.6
cut-like 2 (Drosophila)
CUTL2


212489_at
390.1
192
2846.1
5.9
39.6
collagen, type V, alpha 1
COL5A1


213831_at
519.5
80.8
9979.3
8.5
39.6
major histocompatibility complex, class II, DQ alpha 1
HLA-DQA1


201811_x_at
1176.8
559
14168.3
14
39.6
SH3-domain binding protein 5 (BTK-associated)
SH3BP5


203116_s_at
499.9
411.2
22232
218.8
39.3
ferrochelatase (protoporphyria)
FECH


213280_at
326
39.5
2453.6
21.7
39.3
GTPase activating Rap/RanGAP domain-like 4
GARNL4


213737_x_at
599.4
466
12405.3
237.8
39.3
hypothetical LOC283768 /// similar to hypothetical
LOC283768 ///








protein /// similar to hypothetical protein /// golgi
LOC388080 ///








autoantigen, golgin family member /// similar to
LOC388189 ///








hypothetical protein /// similar to hypothetical protein ///
LOC390535 ///








hypothetical protein DKFZp434P162
LOC400304 ///









LOC440234 ///









DKFZp434P162


218864_at
47.5
11.1
3993.7
10.3
39.3
tensin 1
TNS1


218980_at
24.5
6.5
632.6
5.8
39.3
formin homology 2 domain containing 3
FHOD3


208613_s_at
185.1
40.9
4202.2
15.4
39.3
filamin B, beta (actin binding protein 278)
FLNB


218536_at
202.7
131.6
826.2
7.1
39.3
MRS2-like, magnesium homeostasis factor (S. cerevisiae)
MRS2L


208303_s_at
47.2
25.1
2971.8
6.9
39.3
cytokine receptor-like factor 2
CRLF2


216620_s_at
192.7
27.7
3588.2
12.3
39.3
Rho guanine nucleotide exchange factor (GEF) 10
ARHGEF10


205715_at
26.5
18.8
1743.7
7.5
39.3
bone marrow stromal cell antigen 1
BST1


215017_s_at
148.3
71.4
866.3
2.2
39.3
formin binding protein 1-like
FNBP1L


207218_at
63
24.6
565.5
3.5
39.3
coagulation factor IX (plasma thromboplastic component,
F9








Christmas disease, hemophilia B)



208654_s_at
1274.4
754.9
15234.8
667.6
38.9
CD164 antigen, sialomucin
CD164


209638_x_at
41.2
3.4
532.9
1.8
38.9
regulator of G-protein signalling 12
RGS12


214049_x_at
38.7
15.3
2222.3
7.7
38.9
CD7 antigen (p41)
CD7


218965_s_at
75.9
13.5
397.8
9.5
38.9
RNA binding motif protein 21
RBM21


220751_s_at
52
19.2
4567.8
11.3
38.9
chromosome 5 open reading frame 4
C5orf4


202275_at
226.8
115
4046.1
45.6
38.9
glucose-6-phosphate dehydrogenase
G6PD


219191_s_at
67.1
28.6
1955.3
9.7
38.9
bridging integrator 2
BIN2


218328_at
119.6
97.9
861.5
16.1
38.9
coenzyme Q4 homolog (yeast)
COQ4


206622_at
58.4
45.3
3374
7.6
38.9
thyrotropin-releasing hormone
TRH


203854_at
56
18.2
406.4
12.2
38.5
I factor (complement)
IF


204462_s_at
207.7
42.5
1528.7
26.5
38.5
solute carrier family 16 (monocarboxylic acid
SLC16A2








transporters), member 2



218361_at
251.4
34.4
1506.7
22.1
38.5
golgi phosphoprotein 3-like
GOLPH3L


204187_at
133
21.5
10704.9
10.7
38.5
guanosine monophosphate reductase /// guanosine
GMPR








monophosphate reductase



209705_at
774.4
659.1
3152.7
307.1
38.5
metal response element binding transcription factor 2
MTF2


220232_at
570.7
370.1
6663.3
133
38.5
stearoyl-CoA desaturase 5
SCD5


222273_at
172.6
109.8
752.1
30.5
38.5
poly(A) polymerase gamma
PAPOLG


200885_at
301.6
195.1
1938.3
60.7
38.5
ras homolog gene family, member C
RHOC


205372_at
87.9
9.5
860
2.2
38.5
pleiomorphic adenoma gene 1
PLAG1


215702_s_at
19
9.1
222
2.4
38.5
cystic fibrosis transmembrane conductance regulator,
CFTR








ATP-binding cassette (sub-family C, member 7)



216123_x_at
78.6
43.1
655.2
4.4
38.5
CDNA FLJ14096 fis, clone MAMMA1000752
—


214745_at
214.1
99.5
2085.9
2.2
38.5
phospholipase C-like 3
PLCL3


206995_x_at
112.9
6.8
541.1
6.5
38.1
scavenger receptor class F, member 1
SCARF1


210644_s_at
2023.5
1311.6
9630.6
700
38.1
leukocyte-associated Ig-like receptor 1
LAIR1


213518_at
198.1
59.3
773.3
47.3
38.1
protein kinase C, iota
PRKCI


216407_at
61.4
13.9
526.8
8.7
38.1
Vac14 homolog (S. cerevisiae)
VAC14


204297_at
424.7
357.1
9590.8
156.3
38.1
phosphoinositide-3-kinase, class 3
PIK3C3


205174_s_at
23.2
5.3
712.9
1.9
38.1
glutaminyl-peptide cyclotransferase (glutaminyl cyclase)
QPCT


218989_x_at
175.4
115
603
19.2
38.1
solute carrier family 30 (zinc transporter), member 5
SLC30A5


204759_at
484.7
307
9086.3
34.2
38.1
regulator of chromosome condensation (RCC1) and BTB
RCBTB2








(POZ) domain containing protein 2



206479_at
17.1
5.8
214.2
1.8
38.1
transient receptor potential cation channel, subfamily M,
TRPM1








member 1



214012_at
126.4
71
1014.4
7.5
38.1
type 1 tumor necrosis factor receptor shedding
ARTS-1








aminopeptidase regulator



202451_at
260.2
193.2
861.3
16.8
38.1
general transcription factor IIH, polypeptide 1, 62 kDa
GTF2H1


219797_at
103.8
72.9
686.8
4.2
38.1
mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-
MGAT4A








acetylglucosaminyltransferase, isoenzyme A



206637_at
298.6
54.2
4668.9
1.6
38.1
purinergic receptor P2Y, G-protein coupled, 14
P2RY14


203585_at
219.3
174
2221.3
40.4
38.1
zinc finger protein 185 (LIM domain)
ZNF185


204700_x_at
158.8
78.3
747
43.7
37.8
chromosome 1 open reading frame 107
C1orf107


211924_s_at
184.9
27.2
2286.6
32.1
37.8
plasminogen activator, urokinase receptor ///
PLAUR








plasminogen activator, urokinase receptor



212977_at
93.2
5
1209.6
4.3
37.8
chemokine orphan receptor 1
CMKOR1


206177_s_at
130.3
68.7
3199
26.4
37.8
arginase, liver
ARG1


201302_at
300
203.7
2835.2
21.2
37.8
annexin A4
ANXA4


208343_s_at
7.2
3
2604.5
1.1
37.8
nuclear receptor subfamily 5, group A, member 2
NR5A2


209615_s_at
92.3
24.5
507.8
6.3
37.8
p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog,
PAK1








yeast)



220646_s_at
79.7
23
801.8
5
37.8
killer cell lectin-like receptor subfamily F, member 1
KLRF1


204811_s_at
112
50.8
1771.5
12.1
37.8
calcium channel, voltage-dependent, alpha 2/delta
CACNA2D2








subunit 2



205462_s_at
310.4
171.9
2565.1
18.5
37.8
hippocalcin-like 1
HPCAL1


213096_at
320.3
249.8
14744.6
27.6
37.8
transmembrane and coiled-coil domain family 2
TMCC2


217901_at
110.4
74.5
1631
5.4
37.8
Desmoglein 2
DSG2


204204_at
87.5
26.1
918.5
13.1
37.4
solute carrier family 31 (copper transporters), member 2
SLC31A2


208073_x_at
2070.2
1406.3
13227.3
1120.5
37.4
tetratricopeptide repeat domain 3
TTC3


208799_at
545.7
302.9
2235
353.8
37.4
proteasome (prosome, macropain) subunit, beta type, 5
PSMB5


214040_s_at
41.5
10.3
2140.6
9
37.4
gelsolin (amyloidosis, Finnish type)
GSN


218417_s_at
107.6
23.1
990.5
14.8
37.4
hypothetical protein FLJ20489
FLJ20489


218659_at
2636.3
1222.8
19916.5
736.9
37.4
additional sex combs like 2 (Drosophila)
ASXL2


220178_at
140.7
11.2
1510.2
11.3
37.4
chromosome 19 open reading frame 28
C19orf28


221350_at
53.8
15.1
917.6
11.3
37.4
homeo box C8
HOXC8


205945_at
97.8
7
1113.7
3.3
37.4
interleukin 6 receptor /// interleukin 6 receptor
IL6R


205614_x_at
85.9
47.3
694.9
20.6
37.4
macrophage stimulating 1 (hepatocyte growth factor-like)
MST1


202628_s_at
27.6
18.9
1056.7
8
37.4
serpin peptidase inhibitor, clade E (nexin, plasminogen
SERPINE1








activator inhibitor type 1), member 1



205952_at
88.1
19.7
2026.6
8.6
37.4
potassium channel, subfamily K, member 3
KCNK3


210504_at
181.5
109
11394.7
31.4
37.4
Kruppel-like factor 1 (erythroid)
KLF1


46665_at
83.8
45.2
1801.6
15.5
37.4
sema domain, immunoglobulin domain (Ig),
SEMA4C








transmembrane domain (TM) and short cytoplasmic









domain, (semaphorin) 4C



209543_s_at
704.3
328.5
11548
98.4
37.4
CD34 antigen
CD34


205821_at
457.5
243
9684.2
45.4
37.4
killer cell lectin-like receptor subfamily K, member 1
KLRK1


206233_at
245.2
162.6
1798.1
5.9
37.4
UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase,
B4GALT6








polypeptide 6



206574_s_at
244.7
135.8
2612.2
8.3
37.4
protein tyrosine phosphatase type IVA, member 3
PTP4A3


201363_s_at
313.2
120.7
1430.5
98.9
37.0
influenza virus NS1A binding protein
IVNS1ABP


203254_s_at
297.5
188.7
1554.2
131.8
37.0
talin 1
TLN1


206343_s_at
20.8
8.8
1783.2
5.1
37.0
neuregulin 1
NRG1


208594_x_at
398.6
305.3
3235.8
170.4
37.0
leukocyte immunoglobulin-like receptor, subfamily A (with
LILRA6








TM domain), member 6



210030_at
46.4
13.8
557.9
9.9
37.0
—
—


213854_at
323.8
36.7
1730.3
26
37.0
synaptogyrin 1
SYNGR1


215299_x_at
681.9
407.1
4249.4
370.6
37.0
sulfotransferase family, cytosolic, 1A, phenol-preferring,
SULT1A1








member 1



220285_at
932.1
658.1
4858.2
331.9
37.0
chromosome 9 open reading frame 77
C9orf77


220684_at
244.3
156.4
1550.4
83.4
37.0
T-box 21
TBX21


221747_at
332.6
46.9
5156.1
40.1
37.0
Tensin 1 /// Tensin 1
TNS1


204513_s_at
515.9
363
4569.4
120.1
37.0
engulfment and cell motility 1 (ced-12 homolog, C. elegans)
ELMO1


208109_s_at
57.6
9.4
790.8
4.4
37.0
chromosome 15 open reading frame 5 /// chromosome
C15orf5








15 open reading frame 5



213364_s_at
220.2
97.9
1125.3
36.8
37.0
sorting nexin 1
SNX1


203949_at
269.1
88
44296
25
37.0
myeloperoxidase
MPO


201109_s_at
26.2
13.5
1803
3.3
37.0
thrombospondin 1
THBS1


205983_at
581
207.2
7380
21.6
37.0
dipeptidase 1 (renal)
DPEP1


218742_at
406.8
167.4
2459.7
21.9
37.0
nuclear prelamin A recognition factor-like
NARFL


212828_at
257.9
134.8
2422.8
27.5
37.0
synaptojanin 2
SYNJ2


209576_at
205.7
169.9
1733.8
11.3
37.0
guanine nucleotide binding protein (G protein), alpha
GNAI1








inhibiting activity polypeptide 1



212526_at
62.9
14.9
996.9
3
37.0
spastic paraplegia 20, spartin (Troyer syndrome)
SPG20


205463_s_at
139.4
41.4
3342.1
5.5
37.0
platelet-derived growth factor alpha polypeptide
PDGFA


203988_s_at
226.8
20
1797.6
12.4
36.7
fucosyltransferase 8 (alpha (1,6) fucosyltransferase)
FUT8


212181_s_at
595.8
508.9
7196.3
373.3
36.7
nudix (nucleoside diphosphate linked moiety X)-type
NUDT4








motif 4



214255_at
161.3
24.5
2123.3
18.3
36.7
ATPase, Class V, type 10A
ATP10A


213063_at
305.7
237
1454.3
91.9
36.7
nuclear protein UKp68
FLJ11806


209210_s_at
88.1
16.6
1212.8
4.9
36.7
pleckstrin homology domain containing, family C (with
PLEKHC1








FERM domain) member 1



204401_at
175.2
51.2
2120.8
12
36.7
potassium intermediate/small conductance calcium-
KCNN4








activated channel, subfamily N, member 4



201848_s_at
151.7
93.2
778.4
7.9
36.7
BCL2/adenovirus E1B 19 kDa interacting protein 3
BNIP3


214453_s_at
296.5
109.3
6049.8
43.3
36.7
interferon-induced protein 44
IFI44


218892_at
149.5
36.5
863.8
12.8
36.7
dachsous 1 (Drosophila)
DCHS1


201324_at
94.7
14.1
3238.4
3.7
36.7
epithelial membrane protein 1
EMP1


201029_s_at
4746
2562.3
29103.9
689.6
36.7
CD99 antigen
CD99


203038_at
353
73.2
5596.8
6.7
36.7
protein tyrosine phosphatase, receptor type, K
PTPRK


218035_s_at
174.4
73.7
1360.7
16.9
36.7
RNA-binding protein
FLJ20273


203029_s_at
22.1
12.1
1684
9.2
36.3
protein tyrosine phosphatase, receptor type, N
PTPRN2








polypeptide 2



203040_s_at
462.5
424.8
20562.7
233.3
36.3
hydroxymethylbilane synthase
HMBS


211876_x_at
22.8
6
700.3
5.1
36.3
protocadherin gamma subfamily A, 12 /// protocadherin
PCDHGA12 ///








gamma subfamily A, 11 /// protocadherin gamma
PCDHGA11 ///








subfamily A, 10 /// protocadherin gamma subfamily A, 6
PCDHGA10 ///








/// protocadherin gamma subfamily A, 5 /// protocadherin
PCDHGA6 ///








gamma subfamily A, 3
PCDHGA5 ///









PCDHGA3


216298_at
85.4
4
508.1
3.8
36.3
T cell receptor gamma constant 2
LOC442535


219701_at
38.1
4.3
619.8
2.4
36.3
tropomodulin 2 (neuronal)
TMOD2


221081_s_at
358
48.4
2899.8
32.4
36.3
DENN/MADD domain containing 2D
DENND2D


209963_s_at
127.9
49.4
1950.4
17.8
36.3
erythropoietin receptor
EPOR


217096_at
43
9.2
442.9
3.5
36.3
piccolo (presynaptic cytomatrix protein)
PCLO


217820_s_at
138.3
13.4
1021.9
6.3
36.3
enabled homolog (Drosophila)
ENAH


205390_s_at
29.7
26.3
3939.1
9.5
36.3
ankyrin 1, erythrocytic /// ankyrin 1, erythrocytic
ANK1


206366_x_at
44
24.7
564.3
6
36.3
chemokine (C motif) ligand 2
XCL2


211568_at
19.9
3.1
728.8
1.5
36.3
brain-specific angiogenesis inhibitor 3
BAI3


213894_at
96
24.3
2885.9
6.1
36.3
KIAA0960 protein
KIAA0960


212314_at
339.9
155.7
7986.2
55.6
36.3
KIAA0746 protein
KIAA0746


222136_x_at
519.1
310.1
2538.9
98.6
36.3
zinc finger protein 43 (HTF6)
ZNF43


205159_at
439.5
343.6
2239.7
154.7
36.3
colony stimulating factor 2 receptor, beta, low-affinity
CSF2RB








(granulocyte-macrophage) /// colony stimulating factor 2









receptor, beta, low-affinity (granulocyte-macrophage)



220789_s_at
101.1
70.6
573.6
29
36.3
transforming growth factor beta regulator 4
TBRG4


204891_s_at
418.3
189
5581.2
30.7
36.3
lymphocyte-specific protein tyrosine kinase
LCK


212443_at
263.3
138.7
2162
17.1
36.3
neurobeachin-like 2
NBEAL2


202992_at
34.6
19.2
645.1
3.7
36.3
complement component 7
C7


210435_at
45.6
22.2
280.1
2.7
36.3
neighbor of BRCA1 gene 2
NBR2


202630_at
200.3
121.9
895.5
73
35.9
amyloid beta precursor protein (cytoplasmic tail) binding
APPBP2








protein 2



203381_s_at
29.3
10.4
1129.3
5.6
35.9
apolipoprotein E
APOE


212095_s_at
47.9
11
574.8
7.8
35.9
mitochondrial tumor suppressor 1
MTUS1


212151_at
114.4
30.4
10825.3
16.5
35.9
Pre-B-cell leukemia transcription factor 1
PBX1


213994_s_at
9.7
3.2
676
2.1
35.9
spondin 1, extracellular matrix protein
SPON1


218762_at
53.7
24.8
851.9
17.7
35.9
zinc finger protein 574
ZNF574


219149_x_at
129
42.5
571.6
38.9
35.9
debranching enzyme homolog 1 (S. cerevisiae)
DBR1


205862_at
23.7
2.3
422
1
35.9
GREB1 protein
GREB1


211450_s_at
1390
769.9
6721.5
168
35.9
mutS homolog 6 (E. coli)
MSH6


213882_at
117.5
19
636.6
5.8
35.9
TM2 domain containing 1
TM2D1


215842_s_at
43.1
5.5
1086.9
2.7
35.9
ATPase, Class VI, type 11A
ATP11A


216565_x_at
484.6
268.2
3433.7
128.6
35.9
similar to Interferon-induced transmembrane protein 3
LOC391020








(Interferon-inducible protein 1-8U)



220577_at
283.9
196.6
1308.8
83
35.9
GTPase, very large interferon inducible 1
GVIN1


207968_s_at
679.1
449.9
2961.8
79.5
35.9
MADS box transcription enhancer factor 2, polypeptide C
MEF2C








(myocyte enhancer factor 2C)



212761_at
621.5
511.4
4998.4
101.8
35.9
transcription factor 7-like 2 (T-cell specific, HMG-box)
TCF7L2


217067_s_at
20.2
4.4
741.1
1.9
35.9
dentin matrix acidic phosphoprotein
DMP1


212979_s_at
100.9
40.9
523.5
4.8
35.9
KIAA0738 gene product
KIAA0738


218402_s_at
945
647.2
5332.1
139.5
35.9
Hermansky-Pudlak syndrome 4
HPS4


219048_at
189.5
37.2
963.8
12.3
35.9
phosphatigylinositol glycan, class N
PIGN


221558_s_at
4751.5
2901.3
16261.4
242.4
35.9
lymphoid enhancer-binding factor 1
LEF1


201189_s_at
357.3
98
2314
12.8
35.9
inositol 1,4,5-triphosphate receptor, type 3
ITPR3


202540_s_at
165.2
26.9
835.4
20.7
35.6
3-hydroxy-3-methylglutaryl-Coenzyme A reductase
HMGCR


210655_s_at
89.9
21.2
6692.2
10.7
35.6
forkhead box O3A
FOXO3A


213395_at
126
7.5
1760
9.8
35.6
megalencephalic leukoencephalopathy with subcortical
MLC1








cysts 1



203574_at
307.6
223.4
9812.8
43.7
35.6
nuclear factor, interleukin 3 regulated
NFIL3


210615_at
40.3
12.7
335.3
3.2
35.6
neuropilin 1
NRP1


202833_s_at
107.1
24.3
1493.7
8.1
35.6
serpin peptidase inhibitor, clade A (alpha-1
SERPINA1








antiproteinase, antitrypsin), member 1



205098_at
220.8
141.3
2242.5
36.1
35.6
chemokine (C-C motif) receptor 1
CCR1


220922_s_at
43.1
19
1787.1
6.8
35.6
sperm protein associated with the nucleus, X-linked,
SPANXA1 ///








family member A1 /// SPANX family, member B1 ///
SPANXB1 ///








SPANX family, member A2 /// SPANX family, member C
SPANXA2 ///








/// SPANX family, member B2
SPANXC ///









SPANXB2


218656_s_at
124.8
34.5
1094.7
9.4
35.6
lipoma HMGIC fusion partner
LHFP


201341_at
245.6
58.5
1313.2
65.5
35.2
ectodermal-neural cortex (with BTB-like domain)
ENC1


202039_at
2536.6
1152.1
12225.9
882.4
35.2
TGFB1-induced anti-apoptotic factor 1 /// myosin XVIIIA
TIAF1 ///









MYO18A


202441_at
514.4
310.1
3817.2
227.7
35.2
SPFH domain family, member 1
SPFH1


204158_s_at
312.4
27.1
2026.7
13.6
35.2
T-cell, immune regulator 1, ATPase, H+ transporting,
TCIRG1








lysosomal V0 protein a isoform 3



204417_at
307.3
192.3
1291
152.9
35.2
galactosylceramidase (Krabbe disease)
GALC


205702_at
212.7
167
922.4
94.3
35.2
putative homeodomain transcription factor 1
PHTF1


208664_s_at
378.6
46.8
2577.1
15.2
35.2
tetratricopeptide repeat domain 3
TTC3


220024_s_at
202.4
25.4
3704.4
12.4
35.2
periaxin
PRX


204643_s_at
168.2
37.5
838.5
13.6
35.2
cytosolic ovarian carcinoma antigen 1
COVA1


213530_at
176.9
104.4
968.1
41
35.2
RAB3 GTPase activating protein subunit 1 (catalytic)
RAB3GAP1


216286_at
135.2
15.4
784.3
5.9
35.2
UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase,
B4GALT6








polypeptide 6



212641_at
243.9
104.7
1762.8
21.2
35.2
human immunodeficiency virus type I enhancer binding
HIVEP2








protein 2



214752_x_at
448.9
347.9
3063.9
126.4
35.2
filamin A, alpha (actin binding protein 280)
FLNA


206032_at
133.4
56
2028.8
4.8
35.2
desmocollin 3
DSC3


213663_s_at
23.4
8.2
259.6
1.8
35.2
hypothetical LOC389275
LOC389275


219211_at
152.2
33.4
1800.2
9.8
35.2
ubiquitin specific peptidase 18
USP18


213839_at
142
94.1
2828.6
11.4
35.2
KIAA0500 protein
KIAA0500


208818_s_at
1135.7
934.7
4507
488.8
34.8
catechol-O-methyltransferase
COMT


211434_s_at
60.3
16.5
825.4
10.2
34.8
chemokine (C-C motif) receptor-like 2
CCRL2


213715_s_at
28
9.2
404.3
5.2
34.8
ankyrin repeat domain 47
ANKRD47


217542_at
143
9.9
1123.1
8.2
34.8
Mdm2, transformed 3T3 cell double minute 2, p53 binding
MDM2








protein (mouse)



217753_s_at
5938.3
4006.8
25428.5
2076.8
34.8
ribosomal protein S26 /// 40S ribosomal protein S26-like
RPS26 ///








/// similar to 40S ribosomal protein S26
RPS26L ///









LOC440440


204467_s_at
171.2
51.3
13693.2
12.8
34.8
synuclein, alpha (non A4 component of amyloid
SNCA








precursor) /// synuclein, alpha (non A4 component of









amyloid precursor)



204712_at
14.4
5.4
195.8
1.3
34.8
WNT inhibitory factor 1
WIF1


213797_at
225.5
42.7
3486.1
14.5
34.8
radical S-adenosyl methionine domain containing 2
RSAD2


218311_at
138.3
67.8
1156.1
19.2
34.8
mitogen-activated protein kinase kinase kinase kinase 3
MAP4K3


203063_at
576.5
303.1
3994.1
63.5
34.8
protein phosphatase 1F (PP2C domain containing)
PPM1F


221221_s_at
240.4
149
1298.1
18.7
34.8
kelch-like 3 (Drosophila)
KLHL3


217110_s_at
36.7
7.1
2577.8
1.9
34.8
mucin 4, tracheobronchial
MUC4


201904_s_at
39.3
16.3
1431.6
8.9
34.4
CTD (carboxy-terminal domain, RNA polymerase II,
CTDSPL








polypeptide A) small phosphatase-like



202017_at
94.7
21
750.8
12.3
34.4
epoxide hydrolase 1, microsomal (xenobiotic)
EPHX1


203964_at
1081
748.9
3821.7
503
34.4
N-myc (and STAT) interactor
NMI


207100_s_at
251.9
14
2082.2
22.6
34.4
vesicle-associated membrane protein 1 (synaptobrevin 1)
VAMP1


207413_s_at
92.2
21.6
661.3
11.3
34.4
sodium channel, voltage-gated, type V, alpha (long QT
SCN5A








syndrome 3)



207734_at
261.8
151
1265.9
82.4
34.4
lymphocyte transmembrane adaptor 1
LAX1


221274_s_at
276.7
29
1206.4
24.3
34.4
lectin, mannose-binding 2-like /// lectin, mannose-binding
LMAN2L








2-like



208361_s_at
180.4
65.5
728.9
18.9
34.4
polymerase (RNA) III (DNA directed) polypeptide D,
POLR3D








44 kDa



210972_x_at
758.2
554.4
24206.5
214.3
34.4
T cell receptor alpha locus /// T cell receptor delta variable
TRA@ /// TRDV2








2 /// T cell receptor alpha variable 20 /// T cell receptor
/// TRAV20 ///








alpha joining 17 /// T cell receptor alpha constant
TRAJ17 /// TRAC


204849_at
810.8
215
11702.5
5.4
34.4
transcription factor-like 5 (basic helix-loop-helix)
TCFL5


206400_at
31.9
13.4
575.3
5
34.4
lectin, galactoside-binding, soluble, 7 (galectin 7)
LGALS7


214667_s_at
101.6
35
998
11.4
34.4
tumor protein p53 inducible protein 11
TP53I11


220532_s_at
54.2
13.7
777.4
3.8
34.4
LR8 protein
LR8


201616_s_at
22.8
6.6
1425.1
2.1
34.4
caldesmon 1
CALD1


203910_at
179.7
83.8
10198.4
9.4
34.4
Rho GTPase activating protein 29
ARHGAP29


215761_at
164
112
967.7
19.1
34.4
Dmx-like 2
DMXL2


201579_at
158.1
58.3
5413.2
7.1
34.4
FAT tumor suppressor homolog 1 (Drosophila)
FAT


212589_at
175.6
39.9
1058.4
5.8
34.4
Sterol carrier protein 2
SCP2


210765_at
39.6
13.3
346.5
12.3
34.1
CSE1 chromosome segregation 1-like (yeast)
CSE1L


214370_at
14.7
3.3
1290.2
3.3
34.1
S100 calcium binding protein A8 (calgranulin A)
S100A8


221900_at
24.3
10.2
428.4
6.6
34.1
collagen, type VIII, alpha 2
COL8A2


203115_at
130.9
23.7
5913.7
11.8
34.1
ferrochelatase (protoporphyria)
FECH


203335_at
364.4
171.5
12858.3
46.7
34.1
phytanoyl-CoA hydroxylase (Refsum disease)
PHYH


212959_s_at
740.4
459.9
6222
203
34.1
N-acetylglucosamine-1-phosphate transferase, alpha and
GNPTAB








beta subunits



221182_at
23.5
5.1
327.6
1.8
34.1
chromosome 1 open reading frame 129
C1orf129


202565_s_at
206.9
161
1008.3
92.6
33.7
supervillin
SVIL


205538_at
53.5
15.2
482.7
10.8
33.7
coronin, actin binding protein, 2A
CORO2A


210904_s_at
100.9
9.1
1814.7
17.2
33.7
interleukin 13 receptor, alpha 1
IL13RA1


214094_at
57.8
25.4
508.9
17.1
33.7
far upstream element (FUSE) binding protein 1
FUBP1


216737_at
26
2.1
239.6
1.4
33.7
CDNA: FLJ20872 fis, clone ADKA02604
—


219668_at
38.9
16.6
450
8.5
33.7
ganglioside-induced differentiation-associated protein 1-
GDAP1L1








like 1



202308_at
143
38
917.9
16.8
33.7
sterol regulatory element binding transcription factor 1
SREBF1


205264_at
213.8
47.3
1503.1
17.1
33.7
CD3E antigen, epsilon polypeptide associated protein
CD3EAP


207677_s_at
947.3
692.2
4262.2
272.6
33.7
neutrophil cytosolic factor 4, 40 kDa /// neutrophil cytosolic
NCF4








factor 4, 40 kDa



208949_s_at
310.6
81.7
38822.2
26
33.7
lectin, galactoside-binding, soluble, 3 (galectin 3) ///
LGALS3 ///








galectin-3 internal gene
GALIG


206145_at
149.5
39.7
9642.4
9.1
33.7
Rhesus blood group-associated glycoprotein
RHAG


209570_s_at
74.1
28.9
1641.8
6
33.7
DNA segment on chromosome 4 (unique) 234 expressed
D4S234E








sequence



212554_at
57.1
22.7
603.1
3.7
33.7
CAP, adenylate cyclase-associated protein, 2 (yeast)
CAP2


206650_at
41.2
15.7
306.3
8.6
33.3
IQ motif containing C
IQCC


219529_at
18.7
4.6
1679.1
3.4
33.3
chloride intracellular channel 3
CLIC3


211366_x_at
813.4
586.8
4143.1
273.4
33.3
caspase 1, apoptosis-related cysteine peptidase
CASP1








(interleukin 1, beta, convertase)



215648_at
103.5
27.2
615.5
9.1
33.3
—
—


202086_at
1340.7
562.8
24405.6
74.3
33.3
myxovirus (influenza virus) resistance 1, interferon-
MX1








inducible protein p78 (mouse) /// myxovirus (influenza









virus) resistance 1, interferon-inducible protein p78









(mouse)



205728_at
33.5
6.4
1607.1
2.1
33.3
CDNA clone IMAGE: 4811759
—


211902_x_at
419.5
303.6
8249.5
116.8
33.3
T cell receptor alpha locus
TRA@


213764_s_at
5.3
2.5
694.3
0.6
33.3
microfibrillar associated protein 5
MFAP5


211102_s_at
251.5
164.5
1535.4
6.7
33.3
leukocyte immunoglobulin-like receptor, subfamily A (with
LILRA2








TM domain), member 2



205573_s_at
53.1
8.9
1291.8
4.9
33.0
sorting nexin 7
SNX7


209407_s_at
339.6
126.1
1400.4
139.1
33.0
deformed epidermal autoregulatory factor 1 (Drosophila)
DEAF1


212264_s_at
284.9
94.7
1688.2
55.8
33.0
KIAA0261
KIAA0261


214567_s_at
14
5.7
436
5.5
33.0
chemokine (C motif) ligand 1 /// chemokine (C motif)
XCL1 /// XCL2








ligand 2



222216_s_at
311.4
48.4
1334.9
51.3
33.0
mitochondrial ribosomal protein L17
MRPL17


203757_s_at
220.7
22.3
7715.1
10.1
33.0
carcinoembryonic antigen-related cell adhesion
CEACAM6








molecule 6 (non-specific cross reacting antigen)



204039_at
129.9
49.4
2825.4
20.1
33.0
CCAAT/enhancer binding protein (C/EBP), alpha
CEBPA


220576_at
80.2
13.7
750.9
5.9
33.0
GPI deacylase
PGAP1


216747_at
70
20
562.1
9.1
33.0
amyloid beta (A4) precursor protein-binding, family B,
APBB2








member 2 (Fe65-like)



202273_at
43.6
22.7
1188.9
9
33.0
platelet-derived growth factor receptor, beta polypeptide
PDGFRB


203987_at
185.2
97.5
2062
29.6
33.0
frizzled homolog 6 (Drosophila)
FZD6


216280_s_at
47.4
17
349.9
3.5
33.0
Dicer1, Dcr-1 homolog (Drosophila)
DICER1


206831_s_at
67.5
18.8
520.8
5.7
33.0
arylsulfatase D
ARSD


200096_s_at
1044
670.1
3796
382.6
32.6
ATPase, H+ transporting, lysosomal 9 kDa, V0 subunit
ATP6V0E








e /// ATPase, H+ transporting, lysosomal 9 kDa, V0









subunit e



206067_s_at
24.2
4.9
1338.9
4
32.6
Wilms tumor 1
WT1


208056_s_at
1111.8
533.9
6352.1
315.6
32.6
core-bindirig factor, runt domain, alpha subunit 2;
CBFA2T3








translocated to, 3



209288_s_at
141.9
7.4
2379.5
6.1
32.6
CDC42 effector protein (Rho GTPase binding) 3
CDC42EP3


210915_x_at
669.4
434.1
13605.2
260.8
32.6
T cell receptor beta variable 19 /// T cell receptor beta
TRBV19 ///








constant 1
TRBC1


217758_s_at
636.8
342.6
3167.8
370.7
32.6
SM-11044 binding protein
SMBP


219593_at
40.1
12.7
419.5
8.4
32.6
solute carrier family 15, member 3
SLC15A3


203428_s_at
442.8
159.9
1857.4
70.3
32.6
ASF1 anti-silencing function 1 homolog A (S. cerevisiae)
ASF1A


208908_s_at
270.4
47.7
2051.6
23.8
32.6
calpastatin
CAST


218081_at
150.9
22.7
1249.2
6.8
32.6
chromosome 20 open reading frame 27
C20orf27


218660_at
151.5
37.7
2348.1
14.6
32.6
dysferlin, limb girdle muscular dystrophy 2B (autosomal
DYSF








recessive)



219869_s_at
393.7
317.3
2196.2
66.5
32.6
solute carrier family 39 (zinc transporter), member 8
SLC39A8


213558_at
225.6
48.5
22160
12.8
32.6
piccolo (presynaptic cytomatrix protein)
PCLO


220121_at
77.8
17.7
503.4
6.6
32.6
lines homolog 1 (Drosophila)
LINS1


65517_at
118.5
62.4
747
23.3
32.6
adaptor-related protein complex 1, mu 2 subunit
AP1M2


203450_at
161.7
73.9
561.9
19.6
32.6
PKD2 interactor, golgi and endoplasmic reticulum
PGEA1








associated 1



201849_at
125.2
45.5
920.7
9.2
32.6
BCL2/adenovirus E1B 19 kDa interacting protein 3
BNIP3


211626_x_at
395
173.7
1625.1
14.7
32.6
v-ets erythroblastosis virus E26 oncogene like (avian) /// v-
ERG








ets erythroblastosis virus E26 oncogene like (avian)



215382_x_at
41.6
31.4
920.6
6.9
32.6
tryptase alpha/beta 1
TPSAB1


214757_at
69.6
28.4
397.8
7.6
32.6
CDNA clone IMAGE: 3456494
—


202718_at
113.1
58.5
4105.7
4.9
32.6
insulin-like growth factor binding protein 2, 36 kDa
IGFBP2


200979_at
323.9
250.3
1611.6
244.2
32.2
Mitogen-activated protein kinase kinase kinase 15 ///
MAP3K15








CDNA FLJ34891 fis, clone NT2NE2017562



203739_at
583.5
248.5
2923
270.5
32.2
zinc finger protein 217
ZNF217


204411_at
64.1
24.9
654.9
17.7
32.2
kinesin family member 21B
KIF21B


212814_at
250.7
121.8
1055.7
132.4
32.2
KIAA0828 protein
KIAA0828


212830_at
423.1
227.3
2842.1
199.4
32.2
EGF-like-domain, multiple 5
EGFL5


217790_s_at
58.1
9
507.9
6.5
32.2
signal sequence receptor, gamma (translocon-associated
SSR3








protein gamma)



219684_at
196.8
23.5
1058.6
20.7
32.2
28 kD interferon responsive protein
IFRG28


221656_s_at
90.5
15.2
619
7.6
32.2
Rho guanine nucleotide exchange factor (GEF) 10-like
ARHGEF10L


221757_at
465.1
292.9
3099.8
216.1
32.2
HGFL gene /// HGFL gene
MGC17330


206127_at
356.6
70.3
1993.9
23.1
32.2
ELK3, ETS-domain protein (SRF accessory protein 2)
ELK3


216026_s_at
686
510.8
3365
21.1
32.2
polymerase (DNA directed), epsilon
POLE


220329_s_at
127.5
83.2
656.2
19.9
32.2
chromosome 6 open reading frame 96
C6orf96


202887_s_at
1419.6
658.6
11347.7
32.1
32.2
DNA-damage-inducible transcript 4
DDIT4


207621_s_at
159.4
62.9
2413.2
13.3
32.2
phosphatidylethanolamine N-methyltransferase
PEMT


209776_s_at
31
19.7
397.5
5.2
32.2
solute carrier family 19 (folate transporter), member 1
SLC19A1


204793_at
209.4
154.8
1899.3
12.8
32.2
G protein-coupled receptor associated sorting protein 1
GPRASP1


204115_at
371.9
300.5
4663.6
3.3
32.2
guanine nucleotide binding protein (G protein), gamma 11
GNG11


202948_at
47.7
6.3
591.8
3.8
31.9
interleukin 1 receptor, type I
IL1R1


205885_s_at
1000.2
455.9
5752.2
323.3
31.9
integrin, alpha 4 (antigen CD49D, alpha 4 subunit of
ITGA4








VLA4 receptor)



206359_at
21.1
7
299.7
7.2
31.9
suppressor of cytokine signaling 3
SOCS3


1438_at
111.7
31.1
746.6
15.3
31.9
EPH receptor B3
EPHB3


208637_x_at
505.3
198.4
3743.8
95.3
31.9
actinin, alpha 1
ACTN1


209167_at
150.4
12.8
2836
5.8
31.9
glycoprotein M6B
GPM6B


211657_at
313.7
63.9
10789
22.5
31.9
carcinoembryonic antigen-related cell adhesion
CEACAM6








molecule 6 (non-specific cross reacting antigen)



210705_s_at
189.1
119.2
849.2
12.6
31.9
tripartite motif-containing 5
TRIM5


221529_s_at
222
44.4
4666.8
13.3
31.9
plasmalemma vesicle associated protein
PLVAP


218806_s_at
287.1
204.7
1924.9
23.3
31.9
vav 3 oncogene
VAV3


202789_at
266.4
176.7
1223.4
20.9
31.9
phospholipase C, gamma 1
PLCG1


209170_s_at
197.8
44.6
3675.7
4.5
31.9
glycoprotein M6B
GPM6B


203726_s_at
56.5
18.7
2318.4
11.7
31.5
laminin, alpha 3
LAMA3


204006_s_at
166.9
19.8
2149.5
10.6
31.5
Fc fragment of IgG, low affinity IIIa, receptor (CD16a) ///
FCGR3A ///








Fc fragment of IgG, low affinity IIIb, receptor (CD16b)
FCGR3B


204232_at
313.8
222.3
4420.7
144.8
31.5
Fc fragment of IgE, high affinity I, receptor for; gamma
FCER1G








polypeptide



219120_at
180.4
15.2
667
26.2
31.5
hypothetical protein FLJ21945
FLJ21945


219354_at
92.7
35.5
482.9
27.5
31.5
hypothetical protein FLJ11078
FLJ11078


202888_s_at
63.4
11.5
749.5
5.1
31.5
alanyl (membrane) aminopeptidase (aminopeptidase N,
ANPEP








aminopeptidase M, microsomal aminopeptidase, CD13,









p150)



203650_at
49.3
6.5
324.9
2.7
31.5
protein C receptor, endothelial (EPCR)
PROCR


214353_at
50.1
16.6
321.3
8.2
31.5
Cadherin, EGF LAG seven-pass G-type receptor 1
CELSR1








(flamingo homolog, Drosophila)



212613_at
304.4
35
1511.8
8.7
31.5
butyrophilin, subfamily 3, member A2
BTN3A2


206762_at
115.6
25.7
4277.4
9.9
31.5
potassium voltage-gated channel, shaker-related
KCNA5








subfamily, member 5



213218_at
166.7
123.6
656.9
19.5
31.5
zinc finger protein 187
ZNF187


218087_s_at
47.4
9.3
1490.3
0.9
31.5
sorbin and SH3 domain containing 1
SORBS1


204174_at
1237
842
13270.9
119
31.5
arachidonate 5-lipoxygenase-activating protein
ALOX5AP


217022_s_at
1283.9
273.1
35058.2
6.6
31.5
immunoglobulin heavy constant alpha 1 ///
IGHA1 /// IGHA2








immunoglobulin heavy constant alpha 2 (A2m marker) ///
/// MGC27165








hypothetical protein MGC27165



203435_s_at
3792.8
2101.1
15156.8
14.9
31.5
membrane metallo-endopeptidase (neutral
MME








endopeptidase, enkephalinase, CALLA, CD10)



202219_at
30.5
13.8
7056.9
9.1
31.1
solute carrier family 6 (neurotransmitter transporter,
SLC6A8








creatine), member 8



202809_s_at
1265.5
710
7400.2
512
31.1
chromosome 1 open reading frame 60
C1orf60


203476_at
140.1
8.3
3079.9
12.4
31.1
trophoblast glycoprotein
TPBG


203662_s_at
44.7
19.3
3171.4
12.3
31.1
tropomodulin 1
TMOD1


213294_at
660.6
489.1
4962.7
346.1
31.1
Coiled-coil domain containing 75
CCDC75


209474_s_at
59.7
14.6
449.6
6.8
31.1
ectonucleoside triphosphate diphosphohydrolase 1
ENTPD1


211462_s_at
75.1
13.4
784.2
4.4
31.1
transducin (beta)-like 1Y-linked
TBL1Y


214277_at
21.5
2
356.2
0.5
31.1
COX11 homolog, cytochrome c oxidase assembly protein
COX11 ///








(yeast) /// COX11 homolog, cytochrome c oxidase
COX11P








assembly protein (yeast) pseudogene



217264_s_at
72.4
31.9
487.4
9.2
31.1
sodium channel, nonvoltage-gated 1 alpha
SCNN1A


214110_s_at
28.3
16.8
809.3
6.8
31.1
Similar to lymphocyte-specific protein 1
LOC440886


202125_s_at
447.1
312.2
8793.8
278.3
30.7
amyotrophic lateral sclerosis 2 (juvenile) chromosome
ALS2CR3








region, candidate 3



203972_s_at
257.9
191.8
834.8
107.8
30.7
peroxisomal biogenesis factor 3
PEX3


204655_at
243.8
157.3
2562.6
116.7
30.7
chemokine (C-C motif) ligand 5 /// chemokine (C-C motif)
CCL5








ligand 5



205565_s_at
178.6
49.2
911.6
28.9
30.7
frataxin
FXN


206135_at
9.3
4.6
1153
2.3
30.7
suppression of tumorigenicity 18 (breast carcinoma) (zinc
ST18








finger protein)



206488_s_at
109.2
11.5
6444.4
9.5
30.7
CD36 antigen (collagen type I receptor, thrombospondin
CD36








receptor)



210451_at
23.3
9.8
1635.2
7.6
30.7
pyruvate kinase, liver and RBC
PKLR


210703_at
51.1
8.6
287.8
8.2
30.7
—
—


212647_at
42.7
16.4
523.9
10.9
30.7
related RAS viral (r-ras) oncogene homolog
RRAS


213964_x_at
23.1
2.6
511.9
2.7
30.7
Chromosome 10 open reading frame 95
C10orf95


219360_s_at
13
7.5
2377.6
5.6
30.7
transient receptor potential cation channel, subfamily M,
TRPM4








member 4



221484_at
431
310.7
4031.7
189
30.7
UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase,
B4GALT5








polypeptide 5



222084_s_at
9.9
5.6
249.1
3.7
30.7
SET binding factor 1
SBF1


205926_at
294.3
150.8
1725.2
62.9
30.7
interleukin 27 receptor, alpha
IL27RA


206304_at
51.8
24.1.
1450.1
8.8
30.7
myosin binding protein H
MYBPH


210683_at
5.9
1.7
332.1
0.6
30.7
neurturin
NRTN


215650_at
92.7
20.3
695.3
8.3
30.7
—
—


217147_s_at
63.7
6
1595.6
2.4
30.7
T cell receptor associated transmembrane adaptor 1
TRAT1


202456_s_at
40.8
21
1242.7
9.6
30.7
zyg-11 homolog B (C. elegans)-like
ZYG11BL


213012_at
202.8
116
771.6
36.3
30.7
neural precursor cell expressed, developmentally down-
NEDD4








regulated 4



207513_s_at
241.5
181.8
833.3
84.5
30.7
zinc finger protein 189
ZNF189


204620_s_at
208.6
169.4
12708.4
18.5
30.7
chondroitin sulfate proteoglycan 2 (versican)
CSPG2


211574_s_at
383.8
195.8
1584.4
46.6
30.7
membrane cofactor protein (CD46, trophoblast-
MCP








lymphocyte cross-reactive antigen)



219683_at
56.8
24.9
707.8
2.2
30.7
frizzled homolog 3 (Drosophila)
FZD3


213005_s_at
177.3
116.5
6672.7
8.4
30.7
ankyrin repeat domain 15
ANKRD15


218468_s_at
105.2
33.7
4564
4.3
30.7
gremlin 1, cysteine knot superfamily, homolog (Xenopus
GREM1








laevis)



222154_s_at
275.4
128.6
13569
12.1
30.7
DNA polymerase-transactivated protein 6
DNAPTP6


210663_s_at
44.4
15.8
1257.6
8.7
30.4
kynureninase (L-kynurenine hydrolase)
KYNU


211600_at
5593.8
3335.9
31276.5
2421.9
30.4
—
—


212216_at
212.7
31.6
957.9
23.4
30.4
prolyl endopeptidase-like
PREPL


212848_s_at
64.8
19.9
2991.1
11.2
30.4
chromosome 9 open reading frame 3
C9orf3


213800_at
24.7
7.3
326.6
6
30.4
complement factor H
CFH


219540_at
137.6
17.3
531.1
11.2
30.4
zinc finger protein 267
ZNF267


203471_s_at
454.6
222.9
2688
73.5
30.4
pleckstrin
PLEK


204548_at
21.1
13.4
813.5
6.4
30.4
steroidogenic acute regulator
STAR


215064_at
76.1
17.5
473.1
8.3
30.4
Sterol-C5-desaturase (ERG3 delta-5-desaturase
SC5DL








homolog, fungal)-like



204439_at
215.3
10
10754
4.7
30.4
interferon-induced protein 44-like
IFI44L


210975_x_at
181.1
69.3
824.9
28.2
30.4
Fas-activated serine/threonine kinase
FASTK


213698_at
489.6
393.5
1567.9
83.7
30.4
zinc finger, MYM-type 6
ZMYM6


218469_at
139
97.9
4088.8
7.9
30.4
gremlin 1, cysteine knot superfamily, homolog (Xenopus
GREM1








laevis)



201655_s_at
49.3
8.6
641.1
6.8
30.0
heparan sulfate proteoglycan 2 (perlecan)
HSPG2


210074_at
63.6
7.6
303.9
8.1
30.0
cathepsin L2
CTSL2


212466_at
26.2
5.6
657.5
4
30.0
sprouty-related, EVH1 domain containing 2
SPRED2


213521_at
776.2
547.8
4117
383.4
30.0
Protein tyrosine phosphatase, non-receptor type 18 (brain-
PTPN18








derived)



218229_s_at
435
234.6
2198.6
176.2
30.0
pogo transposable element with KRAB domain
POGK


209663_s_at
23.6
14.4
324.8
6.9
30.0
integrin, alpha 7
ITGA7


219731_at
317.6
207.2
1712.3
61.6
30.0
weakly similar to zinc finger protein 195
FLJ34077


221195_at
36
8.2
262.1
3.5
30.0
PTD016 protein
LOC51136


204276_at
105.8
23.9
706.7
6.8
30.0
thymidine kinase 2, mitochondrial
TK2


206090_s_at
176.7
107.4
666.5
50.4
30.0
disrupted in schizophrenia 1
DISC1


206618_at
45
13.6
282.2
5.2
30.0
interleukin 18 receptor 1
IL18R1


214666_x_at
123.3
45.9
565.4
9.5
30.0
iron-responsive element binding protein 2
IREB2


204821_at
222.6
133.8
1084.6
32
30.0
butyrophilin, subfamily 3, member A3
BTN3A3


47560_at
204.3
86
991.2
25.8
30.0
latrophilin 1
LPHN1


209356_x_at
118
25.8
815.1
10.6
30.0
EGF-containing fibulin-like extracellular matrix protein 2
EFEMP2


216167_at
18.5
8.4
225.8
2.6
30.0
leucine rich repeat neuronal 5
LRRN5


32402_s_at
85.9
53.2
334.4
16.9
30.0
symplekin
SYMPK


213355_at
116.3
14.9
832.8
4.9
30.0
ST3 beta-galactoside alpha-2,3-sialyltransferase 6
ST3GAL6


37986_at
105.5
41.3
1787.6
5.1
30.0
erythropoietin receptor
EPOR


200994_at
616.5
375
2982.3
255.3
29.6
Importin 7
IPO7


202265_at
590.9
220.6
8430.4
244.1
29.6
polycomb group ring finger 4
PCGF4


211917_s_at
63.6
5.6
415.6
5.7
29.6
prolactin receptor /// prolactin receptor
PRLR


219470_x_at
154.2
87.6
1374.8
53.1
29.6
cyclin J
CCNJ


220676_at
52.2
7.7
313
4.8
29.6
ADAM metallopeptidase with thrombospondin type 1
ADAMTS8








motif, 8



200859_x_at
686.3
476.2
4868.3
194.6
29.6
filamin A, alpha (actin binding protein 280)
FLNA


200887_s_at
1051.4
588.9
8128.3
154.8
29.6
signal transducer and activator of transcription 1, 91 kDa
STAT1


204150_at
216.4
53
10597.1
14.1
29.6
stabilin 1
STAB1


220396_at
197.7
48.5
1749.4
19.2
29.6
—
—


221042_s_at
100.7
16
1322
7.4
29.6
calmin (calponin-like, transmembrane)
CLMN


218686_s_at
54.6
49.1
1557.5
19.7
29.6
rhomboid family 1 (Drosophila)
RHBDF1


206682_at
78.9
23.6
445.7
6.2
29.6
C-type lectin domain family 10, member A
CLEC10A


208273_at
128.8
65.6
524.1
11.5
29.6
zinc finger protein 695
ZNF695


208614_s_at
514.9
365.6
5706.7
64.1
29.6
filamin B, beta (actin binding protein 278)
FLNB


214735_at
167.4
65.5
2571
7
29.6
phosphoinositide-binding protein PIP3-E
PIP3-E


200659_s_at
472.5
151.4
4886.9
87
29.3
prohibitin
PHB


215222_x_at
1112.1
652.9
4103.4
671.1
29.3
microtubule-actin crosslinking factor 1
MACF1


203043_at
851.8
563
4757.6
206.9
29.3
zinc finger, BED-type containing 1
ZBED1


212739_s_at
663
261.3
3017
109.5
29.3
non-metastatic cells 4, protein expressed in
NME4


219767_s_at
305.3
259.4
1419.8
86.3
29.3
crystallin, zeta (quinone reductase)-like 1
CRYZL1


209671_x_at
641.5
291.3
22825.7
60.1
29.3
T cell receptor alpha locus /// T cell receptor alpha locus
TRA@ /// TRAC








/// T cell receptor alpha constant /// cell receptor alpha









constant



211597_s_at
176.8
29.1
5111.3
8.3
29.3
homeodomain-only protein /// homeodomain-only protein
HOP


221370_at
108.6
41.1
551.4
16.6
29.3
kruppel-like zinc finger factor X17
LOC377064


221641_s_at
343.8
229.3
2829.3
42.4
29.3
acyl-CoA thioesterase 9
ACOT9


212976_at
27.3
12
286.2
1.8
29.3
leucine rich repeat containing 8 family, member B
LRRC8B


207190_at
29.8
24.9
782.1
6.4
29.3
zinc finger, ZZ-type with EF-hand domain 1
ZZEF1


203434_s_at
3344.3
2134.2
13818.9
3.4
29.3
membrane metallo-endopeptidase (neutral
MME








endopeptidase, enkephalinase, CALLA, CD10)



206940_s_at
811.4
463.5
11867.2
33.2
29.3
POU domain, class 4, transcription factor 1
POU4F1


208454_s_at
166.5
23
1452.4
18.8
28.9
plasma glutamate carboxypeptidase
PGCP


211372_s_at
30.8
11.7
750.5
6.1
28.9
interleukin 1 receptor, type II
IL1R2


211743_s_at
96.8
14.7
29321.7
12.2
28.9
proteoglycan 2, bone marrow (natural killer cell activator,
PRG2








eosinophil granule major basic protein) /// proteoglycan 2,









bone marrow (natural killer cell activator, eosinophil









granule major basic protein)



216037_x_at
368.2
206.5
1613
120.8
28.9
transcription factor 7-like 2 (T-cell specific, HMG-box)
TCF7L2


218921_at
227.6
40.7
1358.9
53.8
28.9
single immunoglobulin and toll-interleukin 1 receptor
SIGIRR








(TIR) domain



38487_at
289.4
82.3
13184.4
50.7
28.9
stabilin 1
STAB1


200813_s_at
666.6
416.6
2386
63.5
28.9
platelet-activating factor acetylhydrolase, isoform Ib,
PAFAH1B1








alpha subunit 45 kDa



219864_s_at
22.3
4.3
294.6
2
28.9
Down syndrome critical region gene 1-like 2
DSCR1L2


208680_at
8265.5
6447.7
43425.5
1422
28.9
peroxiredoxin 1
PRDX1


219451_at
178.6
31
1373.2
5.9
28.9
methionine sulfoxide reductase B2
MSRB2


204007_at
195.7
116.9
1789.5
26.7
28.9
Fc fragment of IgG, low affinity IIIb, receptor (CD16b)
FCGR3B


216333_x_at
53
28.1
1476.8
6.4
28.9
tenascin XB
TNXB


215442_s_at
12
4.8
444.7
1.5
28.9
thyroid stimulating hormone receptor
TSHR


202838_at
653.7
432.9
3736.2
70.3
28.9
fucosidase, alpha-L-1, tissue
FUCA1


204505_s_at
315.2
265.2
13524
32.7
28.9
erythrocyte membrane protein band 4.9 (dematin)
EPB49


221912_s_at
199.3
117.4
734.2
19.8
28.9
coiled-coil domain containing 28B
CCDC28B


219564_at
103.3
17.6
1219.7
8.8
28.5
potassium inwardly-rectifying channel, subfamily J,
KCNJ16








member 16



204482_at
26.5
16.4
433.9
7.7
28.5
claudin 5 (transmembrane protein deleted in
CLDN5








velocardiofacial syndrome)



212486_s_at
139.3
14.3
766.1
4.1
28.5
FYN oncogene related to SRC, FGR, YES
FYN


215646_s_at
42.5
5.4
6886.2
2.5
28.5
chondroitin sulfate proteoglycan 2 (versican) ///
CSPG2








chondroitin sulfate proteoglycan 2 (versican) ///



216833_x_at
278.3
162.2
23091.1
19.7
28.5
glycophorin B (includes Ss blood group) /// glycophorin E
GYPB /// GYPE


214945_at
97.6
72.1
821.6
4.1
28.5
NY-REN-7 antigen /// similar to KIAA0752 protein
NY-REN-7 ///









LOC389347


202877_s_at
193.8
23.9
1033
19.1
28.1
complement component 1, q subcomponent, receptor 1
C1QR1








/// complement component 1, q subcomponent,









receptor 1



210340_s_at
34
4.5
280.4
3.5
28.1
colony stimulating factor 2 receptor, alpha, low-affinity
CSF2RA








(granulocyte-macrophage)



221059_s_at
276.9
165.1
3040.2
105.5
28.1
coactosin-like 1 (Dictyostelium)
COTL1


203482_at
349.4
302.5
1426.7
139.9
28.1
chromosome 10 open reading frame 6
C10orf6


206023_at
13.1
6.9
366.1
3.4
28.1
neuromedin U
NMU


43511_s_at
419
243.3
1829
96.1
28.1
MRNA; cDNA DKFZp762M127 (from clone
—








DKFZp762M127)



204689_at
917.2
831.8
4085.4
104.7
28.1
hematopoietically expressed homeobox
HHEX


213385_at
150.6
28.5
2256.5
8
28.1
Chimerin (chimaerin) 2
CHN2


201911_s_at
120.3
20
853.8
6.4
28.1
FERM, RhoGEF (ARHGEF) and pleckstrin domain
FARP1








protein 1 (chondrocyte-derived)



213856_at
84.7
15.7
403.4
5.1
28.1
CD47 antigen (Rh-related antigen, integrin-associated
CD47








signal transducer)



213953_at
49.5
15.7
693.1
3.2
28.1
keratin 20
KRT20


203139_at
746
321.6
4394
102.3
28.1
death-associated protein kinase 1
DAPK1


213451_x_at
52
41.4
1626
9
28.1
tenascin XB
TNXB


220530_at
49.1
17.1
414.9
3.7
28.1
—
—


220952_s_at
168
141.6
1240.3
6
28.1
pleckstrin homology domain containing, family A member 5
PLEKHA5


202671_s_at
203.5
102.2
2003.4
5.7
28.1
pyridoxal (pyridoxine, vitamin B6) kinase
PDXK


202665_s_at
835.1
582.7
3306.9
384.7
27.8
Wiskott-Aldrich syndrome protein interacting protein
WASPIP


204866_at
211.5
75.7
1149.8
72.8
27.8
PHD finger protein 16
PHF16


207063_at
34.8
6.4
444.4
3.7
27.8
chromosome Y open reading frame 14
CYorf14


207605_x_at
713.7
490.7
3210.3
279.1
27.8
zinc finger protein 117 (HPF9)
ZNF117


208805_at
6471.6
4957.8
25767.4
2603.4
27.8
proteasome (prosome, macropain) subunit, alpha type, 6
PSMA6


209135_at
56.4
3
536.8
2.4
27.8
aspartate beta-hydroxylase
ASPH


213696_s_at
144.5
47.7
666.6
30.8
27.8
mediator of RNA polymerase II transcription, subunit 8
MED8








homolog (yeast)



216071_x_at
702.9
347
2780
381.2
27.8
mediator of RNA polymerase II transcription, subunit 12
MED12








homolog (yeast)



218181_s_at
372
256.6
1267
170.4
27.8
mitogen-activated protein kinase kinase kinase kinase 4
MAP4K4


218781_at
767.9
476.7
4153.5
332.5
27.8
SMC6 structural maintenance of chromosomes 6-like 1
SMC6L1








(yeast)



220582_at
100.2
14.2
522.5
9.2
27.8
—
—


202018_s_at
36.7
13.7
38822.7
5.7
27.8
lactotransferrin
LTF


201162_at
751
32.6
11849.6
15.7
27.8
insulin-like growth factor binding protein 7
IGFBP7


207802_at
10.5
4.1
4963.3
0.9
27.8
cysteine-rich secretory protein 3
CRISP3


220798_x_at
85.6
13.9
721.7
4.1
27.8
plasticity-related gene 2
PRG2


203411_s_at
190.1
23.1
2250.7
8.1
27.8
lamin A/C
LMNA


208862_s_at
248.5
93.1
1480.8
35.8
27.8
catenin (cadherin-associated protein), delta 1
CTNND1


217257_at
37.2
4.5
228.7
1.9
27.8
Stathmin 1/oncoprotein 18
STMN1


221352_at
80.5
23.1
489.8
8.4
27.8
DNA binding protein for surfactant protein B
HUMBINDC


201701_s_at
152.7
104.7
748.9
9.5
27.8
progesterone receptor membrane component 2
PGRMC2


218141_at
151
82.4
5427.4
15.3
27.8
likely ortholog of mouse ubiquitin-conjugating enzyme E2-
E2-230K








230K



201188_s_at
243.2
136.8
1625
29.1
27.8
inositol 1,4,5-triphosphate receptor, type 3
ITPR3


208405_s_at
2539.4
1613.7
19923.7
888.6
27.4
CD164 antigen, sialomucin
CD164


211819_s_at
95
5
1000
3.4
27.4
sorbin and SH3 domain containing 1
SORBS1


213556_at
105
10.3
946.4
7.8
27.4
similar to R28379_1
LOC390940


208033_s_at
95.8
15.5
1150.3
6.3
27.4
AT-binding transcription factor 1
ATBF1


209272_at
284.7
193.5
1317.9
33.7
27.4
NGFI-A binding protein 1 (EGR1 binding protein 1)
NAB1


209604_s_at
296.1
106.9
5495.4
27.4
27.4
GATA binding protein 3
GATA3


220010_at
30.8
7.5
4146.7
3.3
27.4
KCNE1-like
KCNE1L


218017_s_at
210.9
40.1
1100.6
19.4
27.4
transmembrane protein 76
TMEM76


203398_s_at
72.1
24.1
553.6
6.4
27.4
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-
GALNT3








acetylgalactosaminyltransferase 3 (GalNAc-T3)



203577_at
89.1
17.9
472.5
5.5
27.4
general transcription factor IIH, polypeptide 4, 52 kDa
GTF2H4


220252_x_at
399.1
132.7
2976.4
33.6
27.4
chromosome X open reading frame 21
CXorf21


204882_at
679.5
332.4
3947.9
30.2
27.4
Rho GTPase activating protein 25
ARHGAP25


205557_at
40.4
29.5
14658
6.3
27.4
bactericidal/permeability-increasing protein
BPI


202966_at
51.1
20.6
440.5
3
27.4
calpain 6
CAPN6


206761_at
182.3
81.9
2348
11.1
27.4
CD96 antigen
CD96


200931_s_at
1317.9
900.8
6524.3
471.1
27.0
vinculin
VCL


203469_s_at
47.2
16.6
512.7
11.4
27.0
cyclin-dependent kinase (CDC2-like) 10
CDK10


205987_at
249.7
16
7020.6
9.7
27.0
CD1C antigen, c polypeptide
CD1C


207668_x_at
2269.9
1931.1
10249.1
1036.8
27.0
protein disulfide isomerase family A, member 6
PDIA6


208167_s_at
54.3
6.5
1014.3
4.6
27.0
matrix metallopeptidase 16 (membrane-inserted)
MMP16


216672_s_at
12.4
6.2
212.7
4.2
27.0
myelin transcription factor 1-like
MYT1L


218275_at
99.3
19.2
384
10.7
27.0
solute carrier family 25 (mitochondrial carrier,
SLC25A10








dicarboxylate transporter), member 10



202169_s_at
601.6
377.7
1966.2
166.7
27.0
aminoadipate-semialdehyde dehydrogenase-
AASDHPPT








phosphopantetheinyl transferase



204846_at
70.3
15.1
733.6
6.7
27.0
ceruloplasmin (ferroxidase)
CP


212623_at
414.1
261
1305.9
112.5
27.0
transmembrane protein 41B
TMEM41B


214582_at
252.1
143.6
1684.1
43.7
27.0
phosphodiesterase 3B, cGMP-inhibited
PDE3B


220030_at
20.9
3.5
364.3
1.5
27.0
serine/threonine/tyrosine kinase 1
STYK1


218454_at
207.2
52.4
12684.2
21.7
27.0
hypothetical protein FLJ22662
FLJ22662


219467_at
181.6
129.5
614.8
36.9
27.0
hypothetical protein FLJ20125
FLJ20125


209122_at
542.2
267.6
8508.3
60.5
27.0
adipose differentiation-related protein
ADFP


218019_s_at
483.5
320.9
4313.3
154.2
27.0
pyridoxal (pyridoxine, vitamin B6) kinase
PDXK


216174_at
178.7
87.5
794.2
18.1
27.0
hepatocellular carcinoma-related HCRP1
HCRP1


216033_s_at
503.1
258.6
2491.8
22
27.0
FYN oncogene related to SRC, FGR, YES
FYN


206785_s_at
46.3
11.1
345.9
2.3
27.0
killer cell lectin-like receptor subfamily C, member ///
KLRC1 ///








killer cell lectin-like receptor subfamily C, member 2
KLRC2


213712_at
86.4
15
1058.3
3
27.0
elongation of very long chain fatty acids (FEN1/Elo2,
ELOVL2








SUR4/Elo3, yeast)-like 2



204518_s_at
35.7
27.8
1300.7
8.2
27.0
peptidylprolyl isomerase C (cyclophilin C)
PPIC


203922_s_at
312.1
123.8
1877.8
77.6
26.7
cytochrome b-245, beta polypeptide (chronic
CYBB








granulomatous disease)



204669_s_at
173.3
18.2
2477.9
12
26.7
ring finger protein 24
RNF24


209081_s_at
26.6
7.7
800.2
5.9
26.7
collagen, type XVIII, alpha 1
COL18A1


212352_s_at
1654.9
932.1
8879.8
606.1
26.7
transmembrane ernp24-like trafficking protein 10 (yeast)
TMED10


214706_at
185.9
36.8
735.8
20.7
26.7
zinc finger protein 200
ZNF200


201703_s_at
679.9
445.1
2195.6
91.2
26.7
protein phosphatase 1, regulatory subunit 10
PPP1R10


203929_s_at
85.4
34.9
576.4
17.3
26.7
microtubule-associated protein tau
MAPT


209331_s_at
583.4
270.7
2420
106.1
26.7
MYC associated factor X
MAX


209879_at
211.8
114.5
2395.8
43.1
26.7
selectin P ligand
SELPLG


212230_at
128.2
40.7
1062.4
14.4
26.7
phosphatidic acid phosphatase type 2B
PPAP2B


218904_s_at
112.6
24
782.4
11.4
26.7
chromosome 9 open reading frame 40
C9orf40


208438_s_at
186.8
44.4
2461.2
11.1
26.7
Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene
FGR








homolog



210222_s_at
56.5
13.7
351.5
5.1
26.7
reticulon 1
RTN1


213157_s_at
62.7
32.2
547.2
9.7
26.7
KIAA0523 protein
KIAA0523


89476_r_at
210.9
132
981.1
48.9
26.7
aminopeptidase-like 1
NPEPL1


209434_s_at
143
85.4
597.2
12.4
26.7
phosphoribosyl pyrophosphate amidotransferase
PPAT


206235_at
669.4
314.9
4071.6
82
26.7
ligase IV, DNA, ATP-dependent
LIG4


204863_s_at
160.9
119.4
837.1
8.5
26.7
interleukin 6 signal transducer (gp130, oncostatin M
IL6ST








receptor)



206591_at
1526.9
1040
15016.2
19.7
26.7
recombination activating gene 1
RAG1


207339_s_at
2085.6
1712.7
24613.4
77.1
26.7
lymphotoxin beta (TNF superfamily, member 3)
LTB


202907_s_at
582.8
409.4
2160.4
481.3
26.3
nibrin
NBN


204725_s_at
425.6
347.8
1967.1
211.3
26.3
NCK adaptor protein 1
NCK1


206828_at
116.6
15.5
1426.5
10.7
26.3
TXK tyrosine kinase
TXK


209082_s_at
125.9
14.9
1409.2
12.6
26.3
collagen, type XVIII, alpha 1
COL18A1


210612_s_at
49.5
6.4
918.1
3.6
26.3
synaptojanin 2
SYNJ2


212179_at
1307.2
522
5366.7
338.9
26.3
chromosome 6 open reading frame 111
C6orf111


212268_at
550.5
299
11730.6
232.6
26.3
serpin peptidase inhibitor, clade B (ovalbumin), member 1
SERPINB1


213126_at
31.5
10.2
218.7
6.2
26.3
mediator of RNA polymerase II transcription, subunit 8
MEDS








homolog (yeast)



218446_s_at
129.4
15.8
573.3
14.2
26.3
family with sequence similarity 18, member B
FAM18B


220667_at
40.1
5.2
458.2
4
26.3
—
—


200827_at
111.6
46.7
675.1
21.4
26.3
procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1
PLOD1


203632_s_at
31
14.2
798.1
6.3
26.3
G protein-coupled receptor, family C, group 5, member B
GPRC5B


206302_s_at
441
298.4
9153.7
39.5
26.3
nudix (nucleoside diphosphate linked moiety X)-type
NUDT4 ///








motif 4 /// nudix (nucleoside diphosphate linked moiety X)-
NUDT4P1








type motif 4 pseudogene 1



207703_at
50.8
10.5
406.9
4
26.3
neuroligin 4, Y-linked
NLGN4Y


220405_at
89.5
32.1
556.7
6.6
26.3
syntrophin, gamma 1
SNTG1


216317_x_at
150
32.7
12972.6
12.5
26.3
Rhesus blood group, CcEe antigens
RHCE


207851_s_at
108.7
26.6
679.3
8.1
26.3
insulin receptor
INSR


208492_at
60.2
22.3
287.9
7.8
26.3
regulatory factor X-associated protein
RFXAP


218232_at
91.8
45.1
1938.4
8
26.3
complement component 1, q subcomponent, alpha
C1QA








polypeptide



209815_at
167.6
45
3201
3.4
26.3
patched homolog (Drosophila)
PTCH


200871_s_at
2085.5
1361.6
14505.4
683.1
25.9
prosaposin (variant Gaucher disease and variant
PSAP








metachromatic leukodystrophy)



200889_s_at
527.4
422
2478.5
212.3
25.9
signal sequence receptor, alpha (translocon-associated
SSR1








protein alpha)



207341_at
128.8
16.4
22403.2
11.7
25.9
proteinase 3 (serine proteinase, neutrophil, Wegener
PRTN3








granulomatosis autoantigen)



208420_x_at
347.2
224.8
1303.3
145.3
25.9
suppressor of Ty 6 homolog (S. cerevisiae)
SUPT6H


210016_at
148.8
7.3
3757.5
6.9
25.9
myelin transcription factor 1-like
MYT1L


213435_at
36.6
5.8
4632.2
5.3
25.9
SATB family member 2
SATB2


217367_s_at
127.2
38.5
675.7
33.7
25.9
zinc fingers and homeoboxes 3
ZHX3


219346_at
56.7
4.2
502.5
4.9
25.9
leucine rich repeat and fibronectin type III domain
LRFN3








containing 3



200816_s_at
1030.3
550.4
3684.2
240.8
25.9
platelet-activating factor acetylhydrolase, isoform Ib,
PAFAH1B1








alpha subunit 45 kDa



204858_s_at
143.8
32.9
992.8
16.2
25.9
endothelial cell growth factor 1 (platelet-derived)
ECGF1


214634_at
78.2
15.8
514.9
6.9
25.9
—
—


217695_x_at
114.1
25.5
1056.8
8.9
25.9
—
—


211071_s_at
904.7
682.7
4373.1
322.4
25.9
myeloid/lymphoid or mixed-lineage leukemia (trithorax
MLLT11








homolog, Drosophila); translocated to, 11 ///









myeloid/lymphoid or mixed-lineage leukemia (trithorax









homolog, Drosophila); translocated to, 11



212895_s_at
563.7
455.4
2422.8
191.8
25.9
active BCR-related gene
ABR


206165_s_at
89.7
34.9
467.2
7.9
25.9
chloride channel, calcium activated, family member 2
CLCA2


206914_at
45.4
11.4
322.1
3.4
25.9
class-I MHC-restricted T cell associated molecule
CRTAM


221246_x_at
217.6
148.6
2307.1
20
25.9
tensin 1 /// tensin 1
TNS1


201380_at
278.8
197.5
1221
150.2
25.6
cartilage associated protein
CRTAP


216633_s_at
45
7.7
306.4
4
25.6
phospholipase C-like 3
PLCL3


221501_x_at
3049
2089.6
13557
1205
25.6
hypothetical protein LOC339047
LOC339047


45297_at
130.3
38.8
1920.1
21.3
25.6
EH-domain containing 2
EHD2


202911_at
2201.5
1372.5
8710.3
645.7
25.6
mutS homolog 6 (E. coli)
MSH6


211342_x_at
784.7
489.5
3356.7
191.2
25.6
mediator of RNA polymerase II transcription, subunit 12
MED12








homolog (yeast)



218445_at
81.9
36.9
733.8
13.2
25.6
H2A histone family, member Y2
H2AFY2


202557_at
245.1
168.8
2210.8
33.3
25.6
stress 70 protein chaperone, microsome-associated,
STCH








60 kDa



200890_s_at
365.9
300.3
1698.2
54
25.6
signal sequence receptor, alpha (translocon-associated
SSR1








protein alpha)



215882_at
66.6
16.5
312.9
6.9
25.6
Centrosomal protein 152 kDa
CEP152


219602_s_at
160.6
75.9
1545.3
11.6
25.6
family with sequence similarity 38, member B
FAM38B


207402_at
77.6
19.7
440.4
4.3
25.6
zinc finger protein 132 (clone pHZ-12)
ZNF132


218346_s_at
682.6
523.1
11846.5
178.6
25.6
sestrin 1
SESN1


200952_s_at
210.9
49.5
3997.6
13
25.6
cyclin D2
CCND2


203608_at
957
649.2
5837.5
26.7
25.6
aldehyde dehydrogenase 5 family, member A1 (succinate-
ALDH5A1








semialdehyde dehydrogenase)



218862_at
291.5
69
2508.3
21.1
25.6
ankyrin repeat and SOCS box-containing 13
ASB13


218472_s_at
154.4
91.3
793.1
9.4
25.6
pelota homolog (Drosophila)
PELO


201743_at
67.2
16.5
1571.8
5.8
25.6
CD14 antigen /// CD14 antigen
CD14


202669_s_at
135.9
25.9
1724
10
25.6
ephrin-B2
EFNB2


218804_at
64.8
5.8
2319
0.7
25.6
transmembrane protein 16A
TMEM16A


202403_s_at
154.9
62.3
1745.3
9.2
25.6
collagen, type I, alpha 2
COL1A2


204014_at
10.9
7.3
504.9
2.6
25.6
dual specificity phosphatase 4
DUSP4


213959_s_at
69.6
41.5
719
2.8
25.6
KIAA1005 protein
KIAA1005


219759_at
415.7
208.8
3312.2
14.4
25.6
leukocyte-derived arginine aminopeptidase
LRAP


204445_s_at
613.4
374.9
3692.5
11.5
25.6
arachidonate 5-lipoxygenase
ALOX5


208542_x_at
25.5
8.2
342.1
5.1
25.2
zinc finger protein 208
ZNF208


212198_s_at
551.4
331.2
1856.6
315.1
25.2
transmembrane 9 superfamily protein member 4
TM9SF4


212203_x_at
2643.1
932.3
13245.4
931
25.2
interferon induced transmembrane protein 3 (1-8U)
IFITM3


216040_x_at
150.4
37.2
761.3
22
25.2
CDNA FLJ14073 fis, clone HEMBB1001812
—


218045_x_at
14.8
6.1
528.4
4.1
25.2
parathymosin
PTMS


218546_at
35.7
13.4
844.5
6.8
25.2
chromosome 1 open reading frame 115
C1orf115


219364_at
35.3
18
376.4
11.1
25.2
likely ortholog of mouse D11lgp2
LGP2


204413_at
67.7
31
410.9
13.9
25.2
TNF receptor-associated factor 2
TRAF2


205400_at
209.8
62.9
1064.9
26.4
25.2
Wiskott-Aldrich syndrome (eczema-thrombocytopenia)
WAS


209684_at
126.1
19.5
1033.7
9.4
25.2
Ras and Rab interactor 2
RIN2


213510_x_at
403.9
267.7
1583.6
42.9
25.2
TL132 protein
LOC220594


221584_s_at
75.5
27.7
536.4
6.7
25.2
potassium large conductance calcium-activated channel,
KCNMA1








subfamily M, alpha member 1



222078_at
51.2
19.6
743.7
7.2
25.2
Hyperpolarization activated cyclic nucleotide-gated
HCN3








potassium channel 3



202687_s_at
168.8
60.4
2096
16.1
25.2
tumor necrosis factor (ligand) superfamily, member 10 ///
TNFSF10








tumor necrosis factor (ligand) superfamily, member 10



203102_s_at
543.5
357
2600.5
61.1
25.2
mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-
MGAT2








acetylglucosaminyltransferase



207269_at
201.2
140.2
50844.5
26.2
25.2
defensin, alpha 4, corticostatin
DEFA4


214393_at
51.3
14.2
951.1
3.8
25.2
hypothetical protein LOC284062
LOC284062


220713_at
153.5
131.7
1002
27.8
25.2
Chromosome 11 open reading frame 49
C11orf49


206983_at
98.4
40.3
1311.9
4.3
25.2
chemokine (C-C motif) receptor 6
CCR6


220416_at
88.4
44.1
3159.1
3.4
25.2
ATPase, Class I, type 8B, member 4
ATP8B4


204349_at
108
6.7
412.9
6.6
24.8
cofactor required for Sp1 transcriptional activation,
CRSP9








subunit 9, 33 kDa



205718_at
208.5
12.1
3223.5
10.9
24.8
integrin, beta 7
ITGB7


210774_s_at
3772.2
3234.2
41868.2
1733.7
24.8
nuclear receptor coactivator 4
NCOA4


212552_at
1213.9
967.9
6135.2
553.6
24.8
hippocalcin-like 1
HPCAL1


202598_at
650
437.8
5525.2
129
24.8
S100 calcium binding protein A13
S100A13


204414_at
27.6
5
243.4
1.9
24.8
like-glycosyltransferase
LARGE


210128_s_at
183
38.2
1125.8
18.6
24.8
leukotriene B4 receptor
LTB4R


212217_at
273.7
155.4
836.9
60.3
24.8
prolyl endopeptidase-like
PREPL


210738_s_at
22.2
4.5
251.4
1.3
24.8
solute carrier family 4, sodium bicarbonate cotransporter,
SLC4A4








member 4



202599_s_at
2080.2
919.5
11117.1
95.4
24.8
nuclear receptor interacting protein 1
NRIP1


205795_at
30.2
14.8
1096.1
2.6
24.8
neurexin 3
NRXN3


206372_at
50
23.6
1704
5.3
24.8
myogenic factor 6 (herculin)
MYF6


206231_at
289.9
145.6
1890.7
37.6
24.8
potassium intermediate/small conductance calcium-
KCNN1








activated channel, subfamily N, member 1



209169_at
136.9
40.3
1283.6
3.5
24.8
glycoprotein M6B
GPM6B


208981_at
738.3
406.5
5037.4
25.6
24.8
platelet/endothelial cell adhesion molecule (CD31
PECAM1








antigen)
















TABLE 2







Probesets underexpressed in 25% of more of B-lineage ALL cases (n = 270) as compared to normal bone marrow CD19+CD10+ cells


from 4 healthy donors















CD10+
CD10+


% ALL





CD19+
CD19+
ALL
ALL
under




probe set ID
max
min
max
min
expressed
Title
Symbol

















202388_at
29835.8
25562.5
9759.4
10.9
100
regulator of G-protein signalling 2, 24 kDa
RGS2


204207_s_at
4433.5
3175.3
1223.2
332.7
100
RNA guanylyltransferase and 5′-phosphatase
RNGTT


204208_at
3110
1717.1
772.2
18.6
100
RNA guanylyltransferase and 5′-phosphatase
RNGTT


201853_s_at
12593.8
6539
3519.8
478.8
100
cell division cycle 25B
CDC25B


202626_s_at
5962.8
4459.4
4793.6
161.8
99
v-yes-1 Yamaguchi sarcoma viral related oncogene
LYN








homolog



205942_s_at
2204.8
1110.2
623.9
6.3
99
acyl-CoA synthetase medium-chain family member 3
ACSM3


207540_s_at
5984.8
4323.6
2507.6
34.6
99
spleen tyrosine kinase
SYK


206046_at
1778.2
1399.6
3305.2
24.2
99
ADAM metallopeptidase domain 23
ADAM23


210377_at
1677
767.9
656.8
6.9
99
acyl-CoA synthetase medium-chain family member 3
ACSM3


210754_s_at
6524.5
5533.3
5518.6
119.3
98
v-yes-1 Yamaguchi sarcoma viral related oncogene
LYN








homolog



201465_s_at
1499.1
591.2
823.4
6.2
98
v-jun sarcoma virus 17 oncogene homolog (avian)
JUN


203927_at
1369.3
1138.3
916.8
67.1
97
nuclear factor of kappa light polypeptide gene enhancer
NFKBIE








in B-cells inhibitor, epsilon



211639_x_at
3276
2582.8
14470.8
9.9
97
Isolate Black93 immunoglobulin heavy chain variable
—








region (IGVH) /// Isolate Black93 immunoglobulin heavy









chain variable region (IGVH)



216834_at
8959.4
2947.1
7948.4
3.6
97
regulator of G-protein signalling 1
RGS1


207574_s_at
6491.2
3330.7
5589.1
23.7
96
growth arrest and DNA-damage-inducible, beta
GADD45B


209305_s_at
7175.5
3216.3
4660.8
35.8
96
growth arrest and DNA-damage-inducible, beta
GADD45B


211633_x_at
3257.1
1593.6
1815.9
9.4
96
Immunoglobulin heavy constant gamma 1
IGHG1


213419_at
1983.8
877.8
809.5
4
96
amyloid beta (A4) precursor protein-binding, family B,
APBB2








member 2 (Fe65-like)



217168_s_at
6948.2
4299.7
9008.6
277
96
homocysteine-inducible, endoplasmic reticulum stress-
HERPUD1








inducible, ubiquitin-like domain member 1



213808_at
1370.8
704.8
6121.1
3.6
96
ADAM metallopeptidase domain 23
ADAM23


201044_x_at
4997.4
1908.8
4534.7
6.1
96
dual specificity phosphatase 1
DUSP1


201416_at
19683.9
13224.7
36012.1
314.4
96
SRY (sex determining region Y)-box 4
SOX4


205297_s_at
17637
11257.6
8701
19.1
96
CD79B antigen (immunoglobulin-associated beta)
CD79B


221986_s_at
1516.8
1088.1
1221.8
8.2
96
kelch-like 24 (Drosophila)
KLHL24


203036_s_at
377.2
246.6
424.5
7.5
96
metastasis suppressor 1
MTSS1


209304_x_at
5576.4
2633.1
4811.7
23.5
96
growth arrest and DNA-damage-inducible, beta
GADD45B


202191_s_at
5953.1
2637.8
2695.5
15.6
95
growth arrest-specific 7
GAS7


215949_x_at
2781.1
1745.5
3036.2
10.6
95
immunoglobulin heavy constant mu
IGHM


211650_x_at
3663.2
1700.3
18473.5
9.6
95
IgG heavy chain variable region (Vh26) /// IgG heavy
—








chain variable region (Vh26)



214623_at
1081.8
683.7
927
6.8
94
split hand/foot malformation (ectrodactyly) type 3
SHFM3P1








pseudogene 1



216491_x_at
7328.1
6235.1
10541.5
7.6
94
immunoglobulin heavy constant mu
IGHM


211637_x_at
68887
4946.8
11825.7
12.2
94
Immunoglobulin heavy chain variable region (VH IV
—








family) from IgM rheumatoid factor



214522_x_at
1124.3
1009.1
1334.7
7.2
94
histone 1, H3d
HIST1H3D


40148_at
1381.9
627.4
593.3
4.4
94
amyloid beta (A4) precursor protein-binding, family B,
APBB2








member 2 (Fe65-like)



220668_s_at
2345.6
1514.1
5694.5
21.5
94
DNA (cytosine-5-)-methyltransferase 3 beta
DNMT3B


204730_at
4967.4
2864
8362.2
16.1
93
regulating synaptic membrane exocytosis 3
RIMS3


214916_x_at
14343.8
6892.4
17677.2
82.3
93
immunoglobulin heavy locus
IGH@


218205_s_at
19891.4
12578.8
17879.7
801.3
93
MAP kinase interacting serine/threonine kinase 2
MKNK2


202988_s_at
2636.3
560.9
2173.7
2.9
93
regulator of G-protein signalling 1
RGS1


206864_s_at
1273.7
714.7
857.8
1.8
93
harakiri, BCL2 interacting protein (contains only BH3
HRK








domain)



210150_s_at
1324.2
1056
1372.4
5
93
laminin, alpha 5
LAMA5


214973_x_at
6122
2443.4
7633.2
10.1
93
immunoglobulin heavy constant delta
IGHD


217281_x_at
3751.2
1876.2
4004.5
5.9
93
Isolate Rice94 immunoglobulin heavy chain variable
—








region (IGVH)



214669_x_at
8995.8
5783
18674.6
159.4
93
Immunoglobulin kappa variable 1-5
IGKC


209062_x_at
1688.2
1275.6
1789.8
32.3
92
nuclear receptor coactivator 3
NCOA3


221496_s_at
1497.2
419.1
773.1
6.1
92
transducer of ERBB2, 2
TOB2


216510_x_at
3545
1371.3
10120.1
4.8
92
immunoglobulin heavy constant alpha 1 ///
IGHA1 ///








immunoglobulin heavy constant delta /// immunoglobulin
IGHD ///








heavy constant gamma 1
IGHG1 ///









IGHM


204562_at
17170.2
7589.8
8919.6
61.1
92
interferon regulatory factor 4
IRF4


201779_s_at
4113.5
2884
2079.7
439.5
91
ring finger protein 13
RNF13


211849_s_at
1289
694.5
544.9
13
91
RNA guanylyltransferase and 5′-phosphatase
RNGTT


216986_s_at
1767
1088.9
1045.9
26.5
91
interferon regulatory factor 4
IRF4


201303_at
11275.3
6684.6
4953
869.3
91
DEAD (Asp-Glu-Ala-Asp) box polypeptide 48
DDX48


211798_x_at
3202.8
1844.7
2570.4
13
91
immunoglobulin lambda joining 3
IGLJ3


212985_at
1998.5
948.9
1367.1
5
91
Hypothetical protein FLJ14001
FLJ14001


213593_s_at
2902.3
1697.1
1429.1
15
91
Transformer-2 alpha
TRA2A


216557_x_at
4084.7
1926.7
9300.4
89.7
91
immunoglobulin heavy constant alpha 1 ///
IGHA1 ///








immunoglobulin heavy constant gamma 1 ///
IGHG1 ///








immunoglobulin heavy constant gamma 3
IGHG3


210693_at
647
223.3
700.9
6.5
91
signal peptide peptidase-like 2B
SPPL2B


217360_x_at
679
447.1
853.8
5.2
91
immunoglobulin heavy constant alpha 1 ///
IGHA1 ///








immunoglobulin heavy constant gamma 1 ///
IGHG1 ///








immunoglobulin heavy constant gamma 3
IGHG3


204440_at
4557.9
1759.5
9729.2
47.8
91
CD83 antigen (activated B lymphocytes, immunoglobulin
CD83








superfamily)



203865_s_at
2572.5
1405.4
3163.5
7.1
90
adenosine deaminase, RNA-specific, B1 (RED1 homolog
ADARB1








rat)



215121_x_at
38082.2
24742.4
97827.3
411.9
90
immunoglobulin lambda locus
IGL@


212942_s_at
1062.1
467.7
871.1
6.3
90
KIAA1199
KIAA1199


204786_s_at
1394.1
633.2
626.5
7.3
90
interferon (alpha, beta and omega) receptor 2
IFNAR2


210172_at
2090.8
1430.9
2185.8
19.3
90
splicing factor 1
SF1


213511_s_at
8132.9
5082.3
4143.4
404.6
90
myotubularin related protein 1
MTMR1


221985_at
1969.6
1635.9
1694.5
229.7
90
kelch-like 24 (Drosophila)
KLHL24


203751_x_at
6801.2
2457.2
9483.9
3.2
89
jun D proto-oncogene
JUND


205466_s_at
456.1
371.8
864.3
2.5
89
heparan sulfate (glucosamine) 3-O-sulfotransferase 1
HS3ST1


207993_s_at
767.8
450
542.3
9
89
calcium binding protein P22
CHP


208553_at
538.7
230
415.9
5.2
89
histone 1, H1e
HIST1H1E


213638_at
2518.5
972.3
1773.4
7.5
89
phosphatase and actin regulator 1
PHACTR1


202779_s_at
4064.5
2660.1
7091.4
94
89
ubiquitin-conjugating enzyme E2S
UBE2S


212350_at
4326.3
3443.9
2686.8
395.3
89
TBC1 (tre-2/USP6, BUB2, cdc16) domain family,
TBC1D1








member 1



214777_at
2535.8
914.1
3431.5
11
88
Ig rearranged kappa-chain mRNA V-J1-region,
—








hybridoma AE6-5, 5′ end



221909_at
512.9
332.3
781.3
8.1
88
hypothetical protein FLJ14627
FLJ14627


216401_x_at
2337.3
950.1
2657.3
16.9
87
Ig rearranged kappa-chain mRNA V-J1-region,
LOC400969








hybridoma AE6-5, 5′ end /// Immunoglobulin kappa
/// IGKC








constant



219878_s_at
867.1
176.2
962.9
4.9
87
Kruppel-like factor 13
KLF13


221807_s_at
2186.5
1302.7
2491.7
10.9
87
hypothetical protein PP2447
PP2447


201668_x_at
1020.2
570.7
1370.6
10.9
87
myristoylated alanine-rich protein kinase C substrate
MARCKS


203589_s_at
901
779.9
1067.2
30.8
87
transcription factor Dp-2 (E2F dimerization partner 2)
TFDP2


219202_at
1964.6
1420.8
1763.9
17
87
rhomboid, veinlet-like 6 (Drosophila)
RHBDL6


221969_at
13313.2
10083.4
9494.5
125.3
87
Paired box gene 5 (B-cell lineage specific activator)
PAX5


211649_x_at
1586.1
762.4
1034
13.7
86
Immunoglobulin heavy constant mu /// Immunoglobulin
IGHM








heavy constant mu



216095_x_at
7254.6
3992.8
3149.7
298
86
myotubularin related protein 1
MTMR1


215379_x_at
14893.2
7687.7
37246.9
354.3
86
immunoglobulin lambda locus
IGL@


214326_x_at
5238.4
1687
6719.1
4.4
86
jun D proto-oncogene
JUND


215907_at
3754.8
2954.9
4524.6
76.9
86
BTB and CNC homology 1, basic leucine zipper
BACH2








transcription factor 2



202409_at
2262.9
492.3
35487.2
16.3
86
putative insulin-like growth factor II associated protein
LOC492304


216560_x_at
683.9
251.9
19290.6
10.3
86
Immunoglobulin lambda constant 1 (Mcg marker) ///
IGLC1 ///








Immunoglobulin lambda joining 3
IGLC2


204255_s_at
1219.3
464.5
772
11.8
86
vitamin D (1,25-dihydroxyvitamin D3) receptor
VDR


205861_at
6899.6
4313.1
13176.4
51.1
86
Spi-B transcription factor (Spi-1/PU.1 related) /// Spi-B
SPIB








transcription factor (Spi-1/PU.1 related)



212451_at
1861.4
829.1
774.2
27.7
86
KIAA0256 gene product
KIAA0256


213998_s_at
1316.7
735.7
2193
5.7
86
DEAD (Asp-Glu-Ala-Asp) box polypeptide 17
DDX17


214455_at
1162.4
460.7
831.8
4.9
86
histone 1, H2bc
HIST1H2BC


213668_s_at
1789.5
1185.1
4590.5
11.1
86
SRY (sex determining region Y)-box 4
SOX4


213575_at
2193.8
846.7
1062.3
9.6
85
Transformer-2 alpha
TRA2A


216430_x_at
248.7
105
730.6
7.1
85
Immunoglobulin lambda chain variable region (IGVL
IGLV3-25 ///








gene)region, (IGL)
IGLC2


206641_at
318.9
157
1268
4.5
85
tumor necrosis factor receptor superfamily, member 17
TNFRSF17


220319_s_at
3796.9
2721.7
24534.1
150.8
85
myosin regulatory light chain interacting protein
MYLIP


201473_at
5254.1
1979.2
4775.3
52
84
jun B proto-oncogene
JUNB


205805_s_at
916.2
495.5
1461.5
5.1
84
receptor tyrosine kinase-like orphan receptor 1
ROR1


207521_s_at
1861
1427.3
2469.7
5.6
84
ATPase, Ca++ transporting, ubiquitous
ATP2A3


214911_s_at
5800.8
3632.4
5237.4
190.2
84
bromodomain containing 2
BRD2


219752_at
2390.6
1237.6
1756
18.2
84
RAS protein activator like 1 (GAP1 like)
RASAL1


44790_s_at
8505.4
3748.8
8257.3
6
84
chromosome 13 open reading frame 18
C13orf18


206478_at
2360.6
1769.8
5876.1
86.6
84
KIAA0125
KIAA0125


210180_s_at
2174.2
823.3
3334.9
9.1
84
splicing factor, arginine/serine-rich 10 (transformer 2
SFRS10








homolog, Drosophila)



217677_at
3478.3
922.5
920
20.2
84
pleckstrin homology domain containing, family A
PLEKHA2








(phosphoinositide binding specific) member 2



221671_x_at
31680.7
22551
62604.2
824.8
84
immunoglobulin kappa constant /// immunoglobulin kappa
IGKC ///








variable 1-5
IGKV1-5


211644_x_at
3855.6
1621.8
10586.8
15.6
84
immunoglobulin kappa constant /// immunoglobulin kappa
IGKC








constant



203796_s_at
1878.7
1512.3
1760.6
15
83
B-cell CLL/lymphoma 7A
BCL7A


209398_at
16587.4
5879.3
9073.2
152.8
83
histone 1, H1c
HIST1H1C


214975_s_at
2134.4
976.2
807.9
12.8
83
myotubularin related protein 1
MTMR1


216984_x_at
2571.9
1074.1
61397.8
14.5
83
Immunoglobulin lambda joining 3
IGLC2


213811_x_at
9733.6
8324.7
8071.1
756.7
83
transcription factor 3 (E2A immunoglobulin enhancer
TCF3








binding factors E12/E47)



214472_at
2531.2
829.1
2678.5
4.6
83
histone 1, H3d
HIST1H3D


209457_at
1335.3
711.6
3666.5
15.2
83
dual specificity phosphatase 5
DUSP5


203588_s_at
1599.5
1292.4
3992.3
37.4
83
transcription factor Dp-2 (E2F dimerization partner 2)
TFDP2


201022_s_at
2376.3
1884.5
4537.8
55.5
83
destrin (actin depolymerizing factor)
DSTN


204642_at
1707.9
798.1
1750.6
10.6
83
endothelial differentiation, sphingolipid G-protein-coupled
EDG1








receptor, 1



221651_x_at
33345.6
22787.2
65363
833.2
83
immunoglobulin kappa constant /// immunoglobulin kappa
IGKC ///








variable 1-5
IGKV1-5


205967_at
35751.3
3512.1
6722.1
343.1
82
histone 1, H4c
HIST1H4C


209138_x_at
29357.3
20677.1
73861.4
288.6
82
Immunoglobulin lambda constant 1 (Mcg marker) ///
IGLV3-25 ///








Dehydrogenase/reductase (SDR family) member 4 like 2
DHRS4 ///








/// Immunoglobulin lambda joining 3
IGLC2


220377_at
1115.8
527
2828.2
5.7
82
chromosome 14 open reading frame 110
C14orf110


201464_x_at
6805.8
3623.7
8372.6
35.1
82
v-jun sarcoma virus 17 oncogene homolog (avian)
JUN


209558_s_at
2068
1613.9
2686.7
18.5
82
huntingtin interacting protein-1-related
HIP1R


204254_s_at
659.8
405.3
772.8
11.3
81
vitamin D (1,25-dihydroxyvitamin D3) receptor
VDR


217783_s_at
13626.2
9959.4
22889.8
1046.7
81
yippee-like 5 (Drosophila)
YPEL5


218611_at
3234.4
2084.7
3865.3
198.3
81
immediate early response 5
IER5


201670_s_at
1189.3
856.9
1989.8
3.5
81
myristoylated alanine-rich protein kinase C substrate
MARCKS


211641_x_at
3555.3
1451.3
3293
36.3
81
Isolate Middle91 immunoglobulin heavy chain variable
—








region (IGVH) /// Isolate Middle91 immunoglobulin heavy









chain variable region (IGVH)



211643_x_at
1996.9
1433.2
2681
50.1
81
Immunoglobulin kappa variable 1-5 /// Immunoglobulin
IGKC








kappa variable 1-5



211881_x_at
2614.2
1336
2124.8
29.4
81
immunoglobulin lambda joining 3
IGLJ3


216365_x_at
631.9
215.9
904.6
7.3
81
Immunoglobulin lambda constant 1 (Mcg marker)
IGLV3-25


208995_at
1294.9
882
2851.1
26.5
81
titin
TTN


214768_x_at
1795.5
1077.9
8676.1
16.2
81
(clone TR1.6VL) anti-thyroid peroxidase monoclonal
—








autoantibody IgK chain, V region



201466_s_at
921.5
787.4
2738.4
9.6
81
v-jun sarcoma virus 17 oncogene homolog (avian)
JUN


221841_s_at
2789.2
1790.2
11750.7
11.4
81
Kruppel-like factor 4 (gut)
KLF4


216576_x_at
1975.4
979.2
3352.2
16.5
81
Immunoglobulin kappa light chain variable region (IGKV
—








gene), clone 25



211655_at
212
201.8
745.9
3.1
81
Immunoglobulin lambda joining 3
IGLC2


203973_s_at
1408.8
859.5
4658
6.9
81
CCAAT/enhancer binding protein (C/EBP), delta
CEBPD


204315_s_at
946.5
492.1
525.7
8.3
80
G-2 and S-phase expressed 1
GTSE1


222045_s_at
857.3
586.8
1247.2
11.5
80
chromosome 20 open reading frame 67
C20orf67


201462_at
414.5
295.2
1052.3
7.3
80
secernin 1
SCRN1


221766_s_at
790.1
490.7
5906.8
5
80
family with sequence similarity 46, member A
FAM46A


208937_s_at
968.9
404.1
1480.6
6.7
80
inhibitor of DNA binding 1, dominant negative helix-loop-
ID1








helix protein



209374_s_at
37136
23220
48689.7
660.5
80
immunoglobulin heavy constant mu
IGHM


219517_at
1979.2
948.8
1150.7
14.8
80
elongation factor RNA polymerase II-like 3
ELL3


214677_x_at
32140.2
22901.4
67468.9
346.5
80
immunoglobulin lambda locus
IGL@


211199_s_at
334.7
174.5
751.5
5.8
80
inducible T-cell co-stimulator ligand
ICOSLG


210776_x_at
13331.7
9144.1
9907.6
669.1
80
transcription factor 3 (E2A immunoglobulin enhancer
TCF3








binding factors E12/E47)



218473_s_at
5608.8
4109.8
8071.8
522.8
80
glycosyltransferase 25 domain containing 1
GLT25D1


221239_s_at
1531.7
693
3556
18
80
Fc receptor-like 2 /// Fc receptor-like 2
FCRL2


217258_x_at
1046.5
523.9
4342.2
8.9
80
Clone ds1-1 immunoglobulin lambda chain VJ region,
—








(IGL)



205148_s_at
385.7
200.8
687.1
7
79
chloride channel 4
CLCN4


219463_at
3214.4
1350.9
13373
14.1
79
chromosome 20 open reading frame 103
C20orf103


200920_s_at
38532.8
16690.7
33740.6
861.8
79
B-cell translocation gene 1, anti-proliferative
BTG1


216356_x_at
631.4
390.7
536.4
12.7
79
BAl1-associated protein 3
BAIAP3


222044_at
1249.2
664
2083.4
26.9
79
—
—


202946_s_at
2248.1
1707.1
6129.4
60.2
79
BTB (POZ) domain containing 3
BTBD3


207038_at
281.4
238.9
300.4
6.2
79
solute carrier family 16 (monocarboxylic acid
SLC16A6








transporters), member 6



207237_at
956.6
465.4
1294
12.3
79
potassium voltage-gated channel, shaker-related
KCNA3








subfamily, member 3



217384_x_at
612.4
304.7
911.3
4.8
79
similar to immunoglobulin M chain
LOC388255


209324_s_at
2041.9
708.8
6688.9
12.5
79
regulator of G-protein signalling 16
RGS16


204121_at
408.3
367.7
1061.5
6
79
growth arrest and DNA-damage-inducible, gamma
GADD45G


203942_s_at
361
171.6
475.7
4.3
78
MAP/microtubule affinity-regulating kinase 2
MARK2


222313_at
349.6
202.6
841.7
2.6
78
CCR4-NOT transcription complex, subunit 2
CNOT2


219978_s_at
4662.1
2406.5
3581.7
46.1
78
nucleolar and spindle associated protein 1
NUSAP1


213931_at
1964.2
1049.6
5069
8.8
78
inhibitor of DNA binding 2, dominant negative helix-loop-
ID2 /// ID2B








helix protein /// inhibitor of DNA binding 2B, dominant









negative helix-loop-helix protein



206394_at
389.7
292.1
888.7
5.1
78
myosin binding protein C, fast type
MYBPC2


202625_at
2660.4
1441.8
2664.1
42.3
77
v-yes-1 Yamaguchi sarcoma viral related oncogene
LYN








homolog /// v-yes-1 Yamaguchi sarcoma viral related









oncogene homolog



209795_at
7502.8
6458.6
16301.1
31.6
77
CD69 antigen (p60, early T-cell activation antigen)
CD69


204165_at
4862.1
2495.5
6203
70.3
77
WAS protein family, member 1
WASF1


219041_s_at
5504.4
3685.5
4616.5
468.6
77
replication initiator 1
REPIN1


219471_at
12565.2
5971.3
13508.4
33.2
77
chromosome 13 open reading frame 18
C13orf18


220066_at
375.4
86.3
382.2
2.5
77
caspase recruitment domain family, member 15
CARD15


212575_at
144.6
44.4
292.7
3.8
77
chromosome 19 open reading frame 6
C19orf6


212970_at
2128.3
1091.9
1609.5
75.3
77
Hypothetical protein FLJ14001
FLJ14001


219518_s_at
1488.3
893.3
1512
9.8
77
elongation factor RNA polymerase II-like 3
ELL3


222015_at
633
193.6
914.6
21.6
77
Casein kinase 1, epsilon
CSNK1E


209579_s_at
3990.3
2660.8
3384
170.6
76
methyl-CpG binding domain protein 4
MBD4


210024_s_at
2119.7
1680.2
3640.3
12.3
76
ubiquitin-conjugating enzyme E2E 3 (UBC415 homolog,
UBE2E3








yeast)



216542_x_at
2645.8
1678.4
2673.3
163.1
76
immunoglobulin heavy constant gamma 1 (G1m marker)
IGHG1 ///








/// hypothetical protein MGC27165
MGC27165


219396_s_at
5460.4
2755.9
13298.1
16.4
76
nei endonuclease VIII-like 1 (E. coli)
NEIL1


205413_at
743.7
198.2
2539.4
1.6
76
metallophosphoesterase domain containing 2
MPPED2


204936_at
372.7
152.6
479
8.4
76
mitogen-activated protein kinase kinase kinase kinase 2
MAP4K2


211640_x_at
1068.2
595
957.6
5.2
76
Immunoglobulin heavy variable 1-69 /// Immunoglobulin
IGHV1-69








heavy variable 1-69



219474_at
738.5
237.1
669.4
4.3
76
TPA-induced transmembrane protein
TTMP


215918_s_at
559.5
394.8
1953.4
7
76
spectrin, beta, non-erythrocytic 1
SPTBN1


208549_x_at
18830.4
15231.4
27927.9
3006.9
75
prothymosin, alpha
PTMA


204004_at
706.5
501.8
1864.2
8.2
75
PRKC, apoptosis, WT1, regulator
PAWR


212225_at
5240.5
2651.9
5996.8
16.3
75
eukaryotic translation initiation factor 1
EIF1


209994_s_at
625.3
379
769.6
6.1
74
ATP-binding cassette, sub-family B (MDR/TAP), member
ABCB1 ///








1 /// ATP-binding cassette, sub-family B (MDR/TAP),
ABCB4








member 4



204621_s_at
690.7
254.2
6807.8
3.7
74
nuclear receptor subfamily 4, group A, member 2
NR4A2


203749_s_at
1201.3
388.8
736.1
6.7
74
retinoic acid receptor, alpha
RARA


208610_s_at
3729.1
1815
3999.5
60.7
74
serine/arginine repetitive matrix 2
SRRM2


210282_at
261.2
213.2
366.3
1
74
zinc finger protein 198
ZNF198


214860_at
430.9
222.1
490
4.6
74
solute carrier family 9 (sodium/hydrogen exchanger),
SLC9A7








member 7



217227_x_at
1602.6
756.2
2441.6
23
74
Rearranged Humigla1L1 gene encoding IgG light chain
—


201951_at
279.8
226.8
738.3
2.9
74
activated leukocyte cell adhesion molecule
ALCAM


205692_s_at
4324.2
2887.3
3686
27.6
74
CD38 antigen (p45)
CD38


213986_s_at
841.4
593.5
1076.9
4.5
74
chromosome 19 open reading frame 6
C19orf6


211634_x_at
5224.7
1694.7
4720.7
20.3
73
immunoglobulin heavy constant mu /// immunoglobulin
IGHM








heavy constant mu



81737_at
646.3
446.2
770.6
7.4
73
SLC7A5 pseudogene /// Hypothetical protein
LOC388221








LOC440345 /// Homo sapiens, clone IMAGE: 4271781
///









LOC440345


202083_s_at
317.7
183.4
1605
2.4
73
SEC14-like 1 (S. cerevisiae)
SEC14L1


219737_s_at
11684.4
7378.4
14726.6
16.7
73
protocadherin 9
PCDH9


220719_at
1481
469.5
797
6.9
73
hypothetical protein FLJ13769
FLJ13769


208785_s_at
4134.8
3677.7
13593.6
594.9
73
microtubule-associated protein 1 light chain 3 beta
MAP1LC3B


209191_at
2880.1
1467.9
6610.5
8.6
73
tubulin, beta 6
TUBB6


217148_x_at
4052.1
2173.6
58163.1
58
73
immunoglobulin lambda variable 2-14
IGLV2-14


210130_s_at
974.7
577.8
889.6
18.4
73
transmembrane 7 superfamily member 2
TM7SF2


213311_s_at
1408
1130.2
1200.8
15.6
73
KIAA1049 protein
KIAA1049


205484_at
938.8
533
2842.4
25
73
signaling threshold regulating transmembrane adaptor 1
SIT1


218857_s_at
1156.2
560.9
1331.2
15.2
72
asparaginase like 1
ASRGL1


219692_at
551
246
718.4
9.5
72
kringle containing transmembrane protein 2
KREMEN2


201041_s_at
31896.4
27090.3
35352.9
639.6
72
dual specificity phosphatase 1
DUSP1


201353_s_at
1792.5
1125.4
1363.6
42.7
72
bromodomain adjacent to zinc finger domain, 2A
BAZ2A


209876_at
1164.7
741.6
933.9
25.3
72
G protein-coupled receptor kinase interactor 2
GIT2


211908_x_at
840.4
383.1
1279.8
10.5
72
IgG heavy chain variable region (Vh26) /// IgG heavy
—








chain variable region (Vh26)



213309_at
2887.6
2012.8
3909
51.6
72
phospholipase C-like 2
PLCL2


215176_x_at
5352.9
2060.8
9753.4
29.7
72
Immunoglobulin kappa light chain variable region (IGKV
—








gene), clone 25



222158_s_at
1538.1
1024.4
8371.1
33.7
72
chromosome 1 open reading frame 121
C1orf121


214696_at
673.2
368
3256.6
4.3
72
hypothetical protein MGC14376
MGC14376


212886_at
3206.4
1651.1
5457.4
89.7
71
DKFZP434C171 protein
DKFZP434C171


222145_at
925.4
605.5
1445
7.4
71
Hypothetical protein LOC440345
LOC440345


215692_s_at
715.3
222.9
1591.7
3.7
71
metallophosphoesterase domain containing 2
MPPED2


218319_at
1039.6
480.7
2475.8
2.4
71
pellino homolog 1 (Drosophila)
PELI1


201738_at
4836.6
3578.5
6966.7
648.1
71
translation factor sui1 homolog
GC20


202165_at
1200.4
799.6
1456
40.8
71
protein phosphatase 1, regulatory (inhibitor) subunit 2
PPP1R2


202283_at
2098.9
1138.5
3262.7
13.2
71
serpin peptidase inhibitor, clade F (alpha-2 antiplasmin,
SERPINF1








pigment epithelium derived factor), member 1



208621_s_at
4972.8
2805.7
15342.9
32.8
71
villin 2 (ezrin)
VIL2


213394_at
1188.9
875
6923.8
15.5
71
mitogen activated protein kinase binding protein 1
MAPKBP1


213718_at
834.5
527.1
1336.4
14.3
70
RNA binding motif protein 4
RBM4


222258_s_at
686
179
908.7
4.5
70
SH3-domain binding protein 4
SH3BP4


202241_at
1454.6
748.6
2493.8
15.4
70
tribbles homolog 1 (Drosophila)
TRIB1


208616_s_at
10243.9
8059.5
9030.6
2120.1
70
protein tyrosine phosphatase type IVA, member 2
PTP4A2


210281_s_at
603
419.9
1173.4
10.5
70
zinc finger protein 198
ZNF198


221755_at
619.1
525.1
1257
7.8
70
EH domain binding protein 1-like 1
EHBP1L1


222315_at
717.8
189.5
3569.7
7.5
70
Potassium inwardly-rectifying channel, subfamily J,
KCNJ15








member 15



201961_s_at
409.1
306.2
506
10.4
70
ring finger protein 41
RNF41


202864_s_at
2177.6
1438.3
2327.6
71.3
70
nuclear antigen Sp100
SP100


204681_s_at
1024.3
453.5
1395.2
8.1
70
Rap guanine nucleotide exchange factor (GEF) 5
RAPGEF5


208018_s_at
4580.1
1787.4
3725.6
34.5
70
hemopoietic cell kinase
HCK


208078_s_at
7552.5
1852.9
12086.4
22
70
SNF1-like kinase /// SNF1-like kinase
SNF1LK


211635_x_at
5284
1353.9
4018.2
17.2
70
Immunoglobulin heavy variable 1-69 /// Immunoglobulin
IGHV1-69








heavy variable 1-69



212827_at
26342.6
20722.2
42899.7
451.6
70
immunoglobulin heavy constant mu /// immunoglobulin
IGHM








heavy constant mu



91703_at
987.4
806.9
1421.1
18.6
70
EH domain binding protein 1-like 1
EHBP1L1


202082_s_at
736.6
531.1
1740.6
7.7
70
SEC14-like 1 (S. cerevisiae)
SEC14L1


209711_at
2282.7
1650.5
4802
123.6
70
solute carrier family 35 (UDP-glucuronic acid/UDP-N-
SLC35D1








acetylgalactosamine dual transporter), member D1



209765_at
1649
1006.1
1671.7
25
69
ADAM metallopeptidase domain 19 (meltrin beta)
ADAM19


209189_at
18298
8625.6
23154.4
27.1
69
v-fos FBJ murine osteosarcoma viral oncogene homolog
FOS


214836_x_at
6042.5
2307.2
9640.9
95.8
69
immunoglobulin kappa constant /// immunoglobulin kappa
IGKC ///








variable 1-5
IGKV1-5


211645_x_at
4806.7
1366.1
6733.2
32.1
69
Immunoglobulin kappa light chain (IGKV) mRNA variable
—








region, joining region, and constant region ///









Immunoglobulin kappa light chain (IGKV) mRNA variable









region, joining region, and constant region



220046_s_at
9791.7
5330.2
18566.8
700.8
69
cyclin L1
CCNL1


222067_x_at
5113.8
2281.1
5150.2
71
69
histone 1, H2bd
HIST1H2BD


201739_at
1031.8
566.7
15238.3
9.4
69
serum/glucocorticoid regulated kinase
SGK


201792_at
3894.1
2225.8
6769.2
32.7
68
AE binding protein 1
AEBP1


213476_x_at
4760.7
3613.7
8249
538.4
68
tubulin, beta 3
TUBB3


214290_s_at
37691.1
15264.6
33965.1
608.2
68
histone 2, H2aa
HIST2H2AA


214708_at
244.2
114.9
451.8
4.4
68
syntrophin, beta 1 (dystrophin-associated protein A1,
SNTB1








59 kDa, basic component 1)



218612_s_at
1028.2
575
970.5
27.3
68
tumor suppressing subtransferable candidate 4
TSSC4


218696_at
3446.9
3255.1
8935
148.1
68
eukaryotic translation initiation factor 2-alpha kinase 3
EIF2AK3


200846_s_at
6661.4
5681.8
8018
491.9
68
protein phosphatase 1, catalytic subunit, alpha isoform
PPP1CA


201392_s_at
1306
739.6
1220.5
7
68
insulin-like growth factor 2 receptor
IGF2R


208576_s_at
282.8
114.3
298.8
3.6
68
histone 1, H3b
HIST1H3B


204192_at
13251.7
5624.7
10302.9
225.6
67
CD37 antigen
CD37


208091_s_at
4116.6
2073.2
3069.3
124.4
67
EGFR-coamplified and overexpressed protein /// EGFR-
ECOP








coamplified and overexpressed protein



215214_at
1058.7
400.8
17480.7
5
67
Immunoglobulin lambda constant 1 (Mcg marker) ///
IGLV3-25 ///








Immunoglobulin lambda joining 3
IGLC2


217378_x_at
2616.1
1178.5
7662.5
21
67
similar to Ig kappa chain precursor V region (orphon
LOC391427








V108) - human (fragment)



207704_s_at
1084.8
780.1
1241.6
15.7
67
growth arrest-specific 7
GAS7


218100_s_at
1189.7
690.8
2508
51.4
67
estrogen-related receptor beta like 1
ESRRBL1


202147_s_at
1318.9
508.9
1610.5
9.8
67
interferon-related developmental regulator 1
IFRD1


208727_s_at
9260.1
1361
4138.1
45.2
67
cell division cycle 42 (GTP binding protein, 25 kDa)
CDC42


216706_x_at
207
79.7
368.5
6.9
67
Active Ig mu-chain mRNA V-region (VDJ), 5′ end, clone
—








mu-11-8



219751_at
310.6
231.6
420.2
5.3
67
hypothetical protein FLJ21148
FLJ21148


215092_s_at
361.3
186.8
1137.8
11.4
67
nuclear factor of activated T-cells 5, tonicity-responsive
NFAT5


219577_s_at
1163.9
833.6
3119.6
54.9
67
ATP-binding cassette, sub-family A (ABC1), member 7
ABCA7


202733_at
4530.6
1589.5
2513.1
12.8
66
procollagen-proline, 2-oxoglutarate 4-dioxygenase
P4HA2








(proline 4-hydroxylase), alpha polypeptide II



207819_s_at
806.5
550.4
1100.7
8
66
ATP-binding cassette, sub-family B (MDR/TAP), member 4
ABCB4


211944_at
1418.4
805
1310.1
17.6
66
BAT2 domain containing 1
BAT2D1


200702_s_at
1386.6
561.8
1982.9
16.2
66
DEAD (Asp-Glu-Ala-Asp) box polypeptide 24
DDX24


203752_s_at
21461.8
16988.4
36043.8
2627.2
66
jun D proto-oncogene
JUND


210640_s_at
260.5
106.6
2653.6
8.5
66
G protein-coupled receptor 30
GPR30


217320_at
311.9
147.1
738.6
3.4
66
Ig rearranged gamma-chain mRNA V-region, 5′ end of
—








cds (from clone S9P16)



205780_at
605.3
143
1884.3
6.7
66
BCL2-interacting killer (apoptosis-inducing)
BIK


202844_s_at
853.6
453
685.1
11.7
66
ralA binding protein 1
RALBP1


217198_x_at
779.9
452.7
1188.6
8.5
66
immunoglobulin heavy locus /// immunoglobulin heavy
IGH@ ///








constant delta /// immunoglobulin heavy constant gamma
IGHD ///








1 (G1m marker)
IGHG1


218404_at
346
122.8
533.2
7.7
66
sorting nexin 10
SNX10


209372_x_at
576.3
131.3
1377.7
9.4
66
tubulin, beta 2
TUBB2


202719_s_at
545
356.5
1245.4
9.5
66
testis derived transcript (3 LIM domains)
TES


207535_s_at
658.4
446.7
721.3
6.6
65
nuclear factor of kappa light polypeptide gene enhancer
NFKB2








in B-cells 2 (p49/p100)



208523_x_at
1864.9
1135.7
2759
62.3
65
histone 1, H2bi
HIST1H2BI


210240_s_at
3675.6
1394.4
1846.6
53.4
65
cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)
CDKN2D



739.8
222
515.3
5.6
65
immunoglobulin kappa constant /// similar to Ig kappa
IGKC ///








chain
LOC339562


216066_at
391.6
229.2
542.8
11.9
65
ATP-binding cassette, sub-family A (ABC1), member 1
ABCA1


211226_at
100.1
57.9
246.2
3.5
65
galanin receptor 2
GALR2


204215_at
4073.8
3830.3
3926.3
401.2
64
chromosome 7 open reading frame 23
C7orf23


219341_at
430.1
138.9
707.8
4.9
64
ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive
CLN8








with mental retardation)



220603_s_at
1196.8
787.4
1233.3
44.1
64
multiple C2-domains with two transmembrane regions 2
MCTP2


201669_s_at
1969.4
891
4075.8
3.3
64
myristoylated alanine-rich protein kinase C substrate
MARCKS


202819_s_at
986.9
863.2
2552.4
30.6
64
transcription elongation factor B (SIII), polypeptide 3
TCEB3








(110 kDa, elongin A)



201243_s_at
300.7
171.1
474.3
8.1
64
ATPase, Na+/K+ transporting, beta 1 polypeptide
ATP1B1


209154_at
4487.1
1728.6
2541.9
178.4
64
Tax1 (human T-cell leukemia virus type I) binding
TAX1BP3








protein 3



215946_x_at
8832.4
6771.2
13320.6
297.3
64
similar to omega protein
LOC91353


217179_x_at
1514.4
959
1819.1
28.8
64
(clone 9F2L) Ig rearranged L-chain mRNA V-region, 5′
—








end



201021_s_at
1894.7
1359.4
4252.5
62.6
64
destrin (actin depolymerizing factor)
DSTN


204005_s_at
231.6
143.2
471.2
1.6
64
PRKC, apoptosis, WT1, regulator
PAWR


217963_s_at
1003.1
479
7490.1
17.3
64
nerve growth factor receptor (TNFRSF16) associated
NGFRAP1








protein 1



201917_s_at
2035.5
1564.9
2933.3
216.1
64
solute carrier family 25, member 36
SLC25A36


208490_x_at
2965.2
2315
4156.3
66.3
64
histone 1, H2bf
HIST1H2BF


211868_x_at
1153.8
685.2
2705.6
16.7
64
immunoglobulin heavy constant alpha 1 ///
IGHA1 ///








immunoglobulin heavy constant gamma 1 (G1m marker)
IGHG1 ///








/// immunoglobulin heavy constant gamma 3 (G3m
IGHG3








marker)



206865_at
544.2
280.4
1736.8
8.4
64
Harakiri, BCL2 interacting protein (contains only BH3
HRK








domain)



202354_s_at
635.7
559.8
888.1
10.2
63
general transcription factor IIF, polypeptide 1, 74 kDa
GTF2F1


203505_at
2678.1
1046.2
2299.6
7.7
63
ATP-binding cassette, sub-family A (ABC1), member 1
ABCA1


212574_x_at
1371.7
942.4
1732.6
23.8
63
chromosome 19 open reading frame 6
C19orf6


212826_s_at
19729.1
15012.9
19642.3
1648.1
63
solute carrier family 25 (mitochondrial carrier; adenine
SLC25A6








nucleotide translocator), member 6



222024_s_at
1582.5
1143.2
5119
28.3
63
A kinase (PRKA) anchor protein 13
AKAP13


202166_s_at
2057.9
1473.3
1443
170.4
63
protein phosphatase 1, regulatory (inhibitor) subunit 2
PPP1R2


207492_at
1232.9
853.9
975.7
44.3
63
N-glycanase 1
NGLY1


215777_at
634.9
229.3
19107.3
4.6
63
IgV lambda [human, chronic lymphocytic leukemia case
—








P87, mRNA Partial Mutant, 237 nt]



205734_s_at
1450.1
47.1
593
2.8
62
AF4/FMR2 family, member 3
AFF3


208244_at
651
427.8
885.3
13.6
62
bone morphogenetic protein 3 (osteogenic)
BMP3


208685_x_at
5013.2
3634.6
4652.7
168.3
62
bromodomain containing 2
BRD2


209020_at
3058.3
1661.5
4878.3
377.5
62
chromosome 20 open reading frame 111
C20orf111


209761_s_at
4503.7
3048.2
3929.8
514.6
62
SP110 nuclear body protein
SP110


213002_at
730.9
613.7
1010.8
24.9
62
Myristoylated alanine-rich protein kinase C substrate
MARCKS


215785_s_at
6233.1
4436.7
6694.4
199.8
62
cytoplasmic FMR1 interacting protein 2
CYFIP2


216971_s_at
371.8
154.2
741.3
4.4
62
plectin 1, intermediate filament binding protein 500 kDa
PLEC1


38340_at
3343.8
2368.3
4903.3
346.7
62
huntingtin interacting protein-1-related
HIP1R


202723_s_at
6466.6
4219.6
17277.3
134
62
forkhead box O1A (rhabdomyosarcoma)
FOXO1A


201235_s_at
2025.4
1288.6
2444
15.1
62
BTG family, member 2
BTG2


205655_at
403.5
276.4
727.1
3.4
62
Mdm4, transformed 3T3 cell double minute 4, p53 binding
MDM4








protein (mouse)



219505_at
2737.3
2243.7
4093.5
42.1
62
cat eye syndrome chromosome region, candidate 1
CECR1


215621_s_at
1006.6
621.9
5610.5
9.2
62
immunoglobulin heavy constant delta
IGHD


200790_at
8522.6
5203
11216.3
281.2
61
ornithine decarboxylase 1
ODC1


216541_x_at
892.6
313.8
927.6
7
61
immunoglobulin heavy constant gamma 1 ///
IGHG1 ///








immunoglobulin heavy constant gamma 3
IGHG3


202503_s_at
11012.2
8769.1
10879.3
475.6
61
KIAA0101
KIAA0101


204081_at
717.2
168.4
1091.9
14.4
61
neurogranin (protein kinase C substrate, RC3)
NRGN


207838_x_at
981.8
649.4
1635
10.6
61
pre-B-cell leukemia transcription factor interacting protein 1
PBXIP1


209682_at
2478.1
1025.2
2193.7
129.8
61
Cas-Br-M (murine) ecotropic retroviral transforming
CBLB








sequence b



202773_s_at
431.4
216.8
451.7
5.7
61
splicing factor, arginine/serine-rich 8 (suppressor-of-white-
SFRS8








apricot homolog, Drosophila)



214469_at
1051.2
408.8
2077.8
6.9
61
histone 1, H2ae
HIST1H2AE


218302_at
925.2
657.8
1130.3
10.9
61
presenilin enhancer 2 homolog (C. elegans)
PSENEN


201688_s_at
2138.1
1206.6
7186
9
61
tumor protein D52
TPD52


204961_s_at
2274
1590.8
2420.1
6.6
60
neutrophil cytosolic factor 1 (47 kDa, chronic
NCF1








granulomatous disease, autosomal 1)



208527_x_at
2428.2
1698.4
3233.1
139.5
60
histone 1, H2be
HIST1H2BE


218280_x_at
14912.4
4785.1
11736.4
394.9
60
histone 2, H2aa
HIST2H2AA


220085_at
1071.5
318.2
880.2
5.2
60
helicase, lymphoid-specific
HELLS


215498_s_at
5844.5
3004.3
21628.8
326.9
60
mitogen-activated protein kinase kinase 3 /// mitogen-
MAP2K3








activated protein kinase kinase 3



204152_s_at
1746.6
983.2
1317.7
9.3
60
manic fringe homolog (Drosophila)
MFNG


204790_at
1686.5
945.9
2070.3
17.7
60
SMAD, mothers against DPP homolog 7 (Drosophila)
SMAD7


210594_x_at
1508.6
819.7
1369.8
61
60
myelin protein zero-like 1
MPZL1


212587_s_at
7477.2
2952.5
8415.8
35.6
60
protein tyrosine phosphatase, receptor type, C
PTPRC


213015_at
2233.4
966.7
1632.3
119.4
60
Bobby sox homolog (Drosophila)
BBX


215908_at
637.4
160.6
619
6.2
60
Membrane-associated ring finger (C3HC4) 6
MARCH6


205666_at
525.6
174.3
567.5
9.9
60
flavin containing monooxygenase 1
FMO1


209760_at
6164.9
4460.5
9469.1
632
60
KIAA0922 protein
KIAA0922


212487_at
1468.3
1046.3
1280
61.7
60
KIAA0553 protein
KIAA0553


214084_x_at
2283.5
1604.9
2794.8
21.7
60
neutrophil cytosolic factor 1 (47 kDa, chronic
NCF1








granulomatous disease, autosomal 1)



216300_x_at
400.9
157
421
6.3
60
retinoic acid receptor, alpha
RARA


216503_s_at
373
304.1
446.9
10
60
myeloid/lymphoid or mixed-lineage leukemia (trithorax
MLLT10








homolog, Drosophila); translocated to, 10



220369_at
473.2
186.1
566.3
18.4
60
KIAA2010
KIAA2010


216853_x_at
771.7
402.8
3033.3
17.9
60
Immunoglobulin lambda joining 3
IGLJ3


209318_x_at
773.2
451.5
845.6
6.2
59
pleiomorphic adenoma gene-like 1
PLAGL1


217184_s_at
719.1
381.7
1070.9
10.8
59
leukocyte tyrosine kinase
LTK


217975_at
407.1
252.5
1308.6
5
59
WW domain binding protein 5
WBP5


201291_s_at
4378.2
1215.3
2993.2
12.6
59
topoisomerase (DNA) II alpha 170 kDa
TOP2A


208900_s_at
2917.2
890.6
2375.6
13.1
59
topoisomerase (DNA) I
TOP1


215224_at
345.8
184.4
398.1
7
59
ribosomal protein L23
RPL23


216027_at
257.2
92.1
269.6
2.5
59
thioredoxin domain containing 13
TXNDC13


202768_at
5278.9
656.8
12292.3
16
59
FBJ murine osteosarcoma viral oncogene homolog B
FOSB


201216_at
10786
7362.1
9271.5
913.1
59
endoplasmic reticulum protein 29
ERP29


209715_at
658.5
505.7
607
27
59
chromobox homolog 5 (HP1 alpha homolog, Drosophila)
CBX5


221520_s_at
1580.8
714
2876.9
23.1
59
cell division cycle associated 8
CDCA8


201690_s_at
1828.9
1315
5834.8
18.5
59
tumor protein D52
TPD52


201890_at
3517.3
1900
4008
18.4
58
ribonucleotide reductase M2 polypeptide
RRM2


209204_at
276.6
190.6
497.6
7
58
LIM domain only 4
LMO4


215589_at
174.9
104.6
490.4
2.4
58
SMAD specific E3 ubiquitin protein ligase 1
SMURF1


216054_x_at
1967
1230.6
11056.3
205
58
myosin, light polypeptide 4, alkali; atrial, embryonic
MYL4


200917_s_at
548.2
419.2
713
5.3
58
signal recognition particle receptor (‘docking protein’)
SRPR


202332_at
2393.6
1053.4
1876.3
54.6
58
casein kinase 1, epsilon
CSNK1E


205548_s_at
1716.9
1128.9
3271.5
10.1
58
BTG family, member 3
BTG3


205511_at
431.6
250.6
588.5
4
57
hypothetical protein FLJ10038
FLJ10038


205735_s_at
350.5
129.7
531.1
5.4
57
AF4/FMR2 family, member 3
AFF3


221234_s_at
7856.5
4916.3
9481.1
67.1
57
BTB and CNC homology 1, basic leucine zipper
BACH2








transcription factor 2 /// BTB and CNC homology 1, basic









leucine zipper transcription factor 2



216905_s_at
170.4
52.4
353.3
2.2
57
suppression of tumorigenicity 14 (colon carcinoma,
ST14








matriptase, epithin)



202340_x_at
1678.5
281.2
5316.6
16.4
57
nuclear receptor subfamily 4, group A, member 1
NR4A1


215108_x_at
104.7
27.2
980.8
1
57
trinucleotide repeat containing 9
TNRC9


220331_at
469.3
340.8
1727.5
10.2
57
cytochrome P450, family 46, subfamily A, polypeptide 1
CYP46A1


210656_at
195.3
105.3
313
2.4
57
embryonic ectoderm development
EED


210872_x_at
1054.2
636.6
910.4
15.6
57
growth arrest-specific 7
GAS7


212430_at
3874.3
2227.6
7014.2
368
57
RNA-binding region (RNP1, RRM) containing 1 /// RNA-
RNPC1








binding region (RNP1, RRM) containing 1



213517_at
1773.3
845.4
1174.7
110.1
57
Poly(rC) binding protein 2
PCBP2


215925_s_at
4238.1
1888.1
4968.5
9.1
57
CD72 antigen
CD72


203725_at
1583.5
1262.3
6711.6
30.6
57
growth arrest and DNA-damage-inducible, alpha
GADD45A


212113_at
899.1
423.6
830.4
18.9
56
hypothetical LOC552889
LOC552889


213502_x_at
10063.7
7408.9
8939.7
480.7
56
similar to bK246H3.1 (immunoglobulin lambda-like
LOC91316








polypeptide 1, pre-B-cell specific)



215078_at
455.7
188.4
853.5
4.3
56
superoxide dismutase 2, mitochondrial
SOD2


216969_s_at
816.1
494
706.4
7.2
56
kinesin family member 22
KIF22


203290_at
583.9
388.9
21095.6
8.8
56
major histocompatibility complex, class II, DQ alpha 1 ///
HLA-DQA1








major histocompatibility complex, class II, DQ alpha 1



218002_s_at
198.9
94
1519.6
3.1
56
chemokine (C—X—C motif) ligand 14
CXCL14


212130_x_at
31870.8
22675.5
92658.7
4959.1
56
eukaryotic translation initiation factor 1
EIF1


212016_s_at
2144.1
2025.9
3775
76.9
56
polypyrimidine tract binding protein 1
PTBP1


216997_x_at
1772.9
1068.2
5808.1
4.3
56
transducin-like enhancer of split 4 (E(sp1) homolog,
TLE4








Drosophila)



210088_x_at
1798.2
1214.4
12113
204
56
myosin, light polypeptide 4, alkali; atrial, embryonic
MYL4


205347_s_at
1244.6
606
5245.4
39.6
56
thymosin-like 8
TMSL8


201876_at
484.2
398.4
5375.3
7.9
56
paraoxonase 2
PON2


206459_s_at
211.3
121.1
330.1
8.5
55
wingless-type MMTV integration site family, member 2B
WNT2B


206555_s_at
2931.4
1311.7
1416.1
161.1
55
THUMP domain containing 1
THUMPD1


208702_x_at
2780.2
2063.1
4542.2
112.7
55
amyloid beta (A4) precursor-like protein 2
APLP2


215513_at
257.1
198.6
438.5
9
55
hydatidiform mole associated and imprinted
HYMAI


215635_at
149.7
90.2
256.5
1.1
55
Phosphodiesterase 8A
PDE8A


219437_s_at
1153.5
478.4
1406
14.9
55
ankyrin repeat domain 11
ANKRD11


208960_s_at
3772.2
1315.2
23071.2
15.1
55
Kruppel-like factor 6
KLF6


203037_s_at
3407.9
1492.7
5965.9
63.7
55
metastasis suppressor 1
MTSS1


205449_at
708.6
491.4
845.1
8
55
SAC3 domain containing 1
SAC3D1


208615_s_at
4008.2
2618.2
3219.2
469.2
55
protein tyrosine phosphatase type IVA, member 2
PTP4A2


217591_at
922.4
388
1491
11.9
55
SKI-like
SKIL


222238_s_at
700.1
271.8
1836.4
12.1
55
polymerase (DNA directed), mu
POLM


218856_at
2635.9
933.8
6067.9
16.2
55
tumor necrosis factor receptor superfamily, member 21
TNFRSF21


201996_s_at
1068.9
397.4
809.9
12.1
54
spen homolog, transcriptional regulator (Drosophila)
SPEN


209069_s_at
36623.3
24646.6
44984.8
3477.8
54
H3 histone, family 3B (H3.3B)
H3F3B


209262_s_at
502.8
224.7
533.8
9.3
54
nuclear receptor subfamily 2, group F, member 6
NR2F6


213730_x_at
5090.4
3880.5
4655.5
407.8
54
transcription factor 3 (E2A immunoglobulin enhancer
TCF3








binding factors E12/E47)



213742_at
887.4
515.1
1080.7
24.7
54
splicing factor, arginine/serine-rich 11
SFRS11


221586_s_at
766.3
451.4
862.6
4.3
54
E2F transcription factor 5, p130-binding
E2F5


209773_s_at
4102.1
2963.2
9386.6
273.9
54
ribonucleotide reductase M2 polypeptide
RRM2


205931_s_at
126.3
78.6
567.7
5.1
54
cAMP responsive element binding protein 5
CREB5


215223_s_at
1802.3
683.2
13374.5
24.7
54
superoxide dismutase 2, mitochondrial
SOD2


212094_at
298.8
175.7
14501.7
3.3
54
paternally expressed 10
PEG10


204794_at
978.6
131
765.5
9.1
54
dual specificity phosphatase 2
DUSP2


207186_s_at
3198.9
2048.3
3694.6
175.4
54
fetal Alzheimer antigen
FALZ


208515_at
273.2
147.1
314.1
2.7
54
histone 1, H2bm
HIST1H2BM


216278_at
693.4
224.7
773.7
8.1
54
KIAA0256 gene product
KIAA0256


201689_s_at
1240
836.8
3977.5
5.6
54
tumor protein D52
TPD52


208547_at
214.9
70.7
717.9
4.1
54
histone 1, H2bb
HIST1H2BB


202021_x_at
31691.4
21494.7
85265.8
4111
54
eukaryotic translation initiation factor 1
EIF1


211789_s_at
1245.2
392.4
2084.4
3.9
54
MondoA
MONDOA


216211_at
706.9
446.7
969.5
4.1
54
Chromosome 10 open reading frame 18
C10orf18


216855_s_at
762.9
453.7
745.5
9.6
54
heterogeneous nuclear ribonucleoprotein U (scaffold
HNRPU








attachment factor A)



217729_s_at
4929.7
2647.3
3119.9
82.2
54
amino-terminal enhancer of split
AES


205398_s_at
853.6
471.2
2255.6
15.6
54
SMAD, mothers against DPP homolog 3 (Drosophila)
SMAD3


219582_at
1125.1
657.8
2626.9
26
54
opioid growth factor receptor-like 1
OGFRL1


221658_s_at
346.4
188.1
872.7
10.9
54
interleukin 21 receptor
IL21R


201101_s_at
3208.5
2063.6
5635
67
53
BCL2-associated transcription factor 1
BCLAF1


209759_s_at
615.2
547.2
916.5
19.2
53
dodecenoyl-Coenzyme A delta isomerase (3,2 trans-
DCI








enoyl-Coenzyme A isomerase)



213134_x_at
2196
1367.7
3628.9
34.2
53
BTG family, member 3
BTG3


213973_at
550.6
326.5
905.3
23
53
ribosome binding protein 1 homolog 180 kDa (dog)
RRBP1


218247_s_at
1742.4
1256.3
2236.9
23.3
53
ring finger and KH domain containing 2
RKHD2


220084_at
64.6
18.9
377.2
0.9
53
chromosome 14 open reading frame 105
C14orf105


205020_s_at
673.7
395.9
7567.1
10.8
53
ADP-ribosylation factor-like 4
ARL4


203431_s_at
811.1
664
1444.9
5
53
Rho GTPase-activating protein
RICS


203647_s_at
1905.8
1751.4
2621.7
99.7
53
ferredoxin 1
FDX1


206967_at
509.1
418.5
824.2
16.3
53
cyclin T1
CCNT1


211067_s_at
1610.4
1150.4
2029.1
14.7
53
growth arrest-specific 7 /// growth arrest-specific 7
GAS7


219079_at
1986.5
1349.2
2656.5
282.9
53
cytochrome b5 reductase 4
CYB5R4


200796_s_at
824.2
351.7
2316.3
7.2
53
myeloid cell leukemia sequence 1 (BCL2-related)
MCL1


206885_x_at
754.9
476.8
2066.3
16.3
53
growth hormone 1
GH1


215499_at
3466.8
2239.5
12058.5
356.5
53
mitogen-activated protein kinase kinase 3 /// mitogen-
MAP2K3








activated protein kinase kinase 3



209774_x_at
167.5
75.2
481.9
5.5
53
chemokine (C—X—C motif) ligand 2
CXCL2


210830_s_at
331
242.4
5046.2
7.2
53
paraoxonase 2
HIST4PON2


208580_x_at
822
213.3
1069.5
7.8
53
histone 1, H4k /// histone 1, H4j
HIST1H4J


210450_at
1833.4
612.6
1191.4
5.2
53
hypothetical protein LOC90925
LOC90925


213649_at
5388.1
2999.2
6475.2
472.9
53
splicing factor, arginine/serine-rich 7, 35 kDa
SFRS7


220012_at
781.5
388.1
895
12.3
53
ERO1-like beta (S. cerevisiae)
ERO1LB


201502_s_at
17163.8
10773.5
46569.3
853.9
53
nuclear factor of kappa light polypeptide gene enhancer
NFKBIA








in B-cells inhibitor, alpha



202818_s_at
1643
1085.6
4783.7
230.2
53
transcription elongation factor B (SIII), polypeptide 3
TCEB3








(110 kDa, elongin A)



214007_s_at
517.6
394.4
1224.7
16.4
53
PTK9 protein tyrosine kinase 9
PTK9


219057_at
364
227.5
767.7
21.2
53
rabaptin, RAB GTPase binding effector protein 2
RABEP2


213566_at
684.1
410.2
4352.6
6.8
53
ribonuclease, RNase A family, k6 /// ribonuclease,
RNASE6








RNase A family, k6



201242_s_at
194.3
113.3
318.9
2
52
ATPase, Na+/K+ transporting, beta 1 polypeptide
ATP1B1


213042_s_at
1042.3
539.7
1179.2
4.5
52
ATPase, Ca++ transporting, ubiquitous
ATP2A3


214095_at
257.5
138.9
356.9
7.2
52
serine hydroxymethyltransferase 2 (mitochondrial)
SHMT2


219555_s_at
830
381.5
1573.2
14
52
uncharacterized bone marrow protein BM039
BM039


217276_x_at
863.2
308.8
1969.2
9.4
52
serine hydrolase-like 2
SERHL2


204141_at
1257.3
269.4
15893
2.8
52
tubulin, beta 2
TUBB2


203504_s_at
1918.4
1199.3
2847.2
124.2
52
ATP-binding cassette, sub-family A (ABC1), member 1
ABCA1


208930_s_at
2787.7
728.6
3337.9
10.9
52
interleukin enhancer binding factor 3, 90 kDa
ILF3


209088_s_at
1844.7
948.9
2377.1
140.9
52
ubinuclein 1
UBN1


211899_s_at
588.9
278.8
1062.4
11.9
52
TNF receptor-associated factor 4
TRAF4


214308_s_at
241.8
183.2
350.9
11.2
52
homogentisate 1,2-dioxygenase (homogentisate oxidase)
HGD


219179_at
562.2
418
933.6
4.7
52
dapper, antagonist of beta-catenin, homolog 1 (Xenopus
DACT1








laevis)



213345_at
540.7
335.9
1086.5
12.4
52
nuclear factor of activated T-cells, cytoplasmic,
NFATC4








calcineurin-dependent 4



216248_s_at
910.5
287.2
10463.2
5
52
nuclear receptor subfamily 4, group A, member 2
NR4A2


210395_x_at
2016.7
1139
13375.5
213.8
52
myosin, light polypeptide 4, alkali; atrial, embryonic
MYL4


211138_s_at
1347.3
650.6
2154.6
40.2
51
kynurenine 3-monooxygenase (kynurenine 3-
KMO








hydroxylase)



215392_at
411.6
224.1
466
1.2
51
Multiple inositol polyphosphate histidine phosphatase, 1
MINPP1


215623_x_at
607.6
323.7
813.1
5.5
51
SMC4 structural maintenance of chromosomes 4-like 1
SMC4L1








(yeast)



218033_s_at
461.4
291.7
498.6
14.3
51
stannin
SNN


214464_at
199.1
35.8
733.4
2.9
51
CDC42 binding protein kinase alpha (DMPK-like)
CDC42BPA


216373_at
190.6
96.3
404.2
1.2
51
Hypothetical protein FLJ90013
FLJ90013


200712_s_at
2609.1
2080.3
3286.1
434.4
51
microtubule-associated protein, RP/EB family, member 1
MAPRE1


203919_at
814.8
488.1
776.7
5.8
51
transcription elongation factor A (SII), 2
TCEA2


209750_at
673.3
407.6
807.5
22.5
51
nuclear receptor subfamily 1, group D, member 2
NR1D2


212774_at
5871.1
4225.9
6384.8
284.6
51
zinc finger protein 238
ZNF238


218260_at
865.6
711.8
2892
20.5
51
cross-immune reaction antigen PCIA1
PCIA1


205671_s_at
689
503.6
2229.6
8.3
51
major histocompatibility complex, class II, DO beta
HLA-DOB


201846_s_at
2714
1876.5
4890.4
179.1
51
RING1 and YY1 binding protein
RYBP


202076_at
2724
2258.9
4525.3
417.2
51
baculoviral IAP repeat-containing 2
BIRC2


202782_s_at
2320.6
1102
1432.9
118.5
51
skeletal muscle and kidney enriched inositol phosphatase
SKIP


208077_at
930.8
569.3
1293.3
14.6
51
chromosome 9 open reading frame 38
C9orf38


215188_at
589.7
221
424.2
4.9
51
serine/threonine kinase 24 (STE20 homolog, yeast)
STK24


218811_at
699.2
349.3
916.1
7.5
51
chromosome 7 open reading frame 19
C7orf19


220937_s_at
1450
620.9
2138.9
14.3
51
ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-
ST6GALNAC4








N-acetylgalactosaminide alpha-2,6-sialyltransferase 4



203243_s_at
262.6
108.2
615.8
1.5
51
PDZ and LIM domain 5
PDLIM5


221551_x_at
987.7
682.4
2015.3
21.6
51
ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-
ST6GALNAC4








N-acetylgalactosaminide alpha-2,6-sialyltransferase 4



217234_s_at
7979
3102
19092.8
29.1
51
villin 2 (ezrin)
VIL2


208069_x_at
577.9
384.2
1644.2
10.1
51
chorionic somatomammotropin hormone 1 (placental
CSH1 ///








lactogen) /// chorionic somatomammotropin hormone 2 ///
CSH2 ///








chorionic somatomammotropin hormone-like 1 /// growth
CSHL1 ///








hormone 1 /// growth hormone 2
GH1 /// GH2


200648_s_at
1761.8
951.5
5262.9
3
51
glutamate-ammonia ligase (glutamine synthetase)
GLUL


210889_s_at
343.6
180
1849.1
7.1
51
Fc fragment of IgG, low affinity IIb, receptor (CD32)
FCGR2B


203628_at
410.3
208.3
1386.3
5.2
51
insulin-like growth factor 1 receptor
IGF1R


201793_x_at
690.1
311.4
855.6
12.2
50
chromosome 1 open reading frame 16
C1orf16


215357_s_at
706.9
619
983.5
23.8
50
polymerase (DNA-directed), delta interacting protein 3
POLDIP3


201925_s_at
1190.3
834.1
2621.5
29
50
decay accelerating factor for complement (CD55, Cromer
DAF








blood group system)



213747_at
217.4
155.9
505.8
5.6
50
—
—


213122_at
1063.7
507
4660.5
12.5
50
TSPY-like 5
TSPYL5


200783_s_at
3283.3
2555.7
3636.6
276.3
50
stathmin 1/oncoprotein 18
STMN1


209713_s_at
309.2
247.8
624.8
8.5
50
solute carrier family 35 (UDP-glucuronic acid/UDP-N-
SLC35D1








acetylgalactosamine dual transporter), member D1



206675_s_at
117.8
82.7
259.1
2
50
SKI-like
SKIL


205397_x_at
380.7
98.7
1241
10.8
50
SMAD, mothers against DPP homolog 3 (Drosophila)
SMAD3


209151_x_at
1522.5
934.4
1986
8
50
transcription factor 3 (E2A immunoglobulin enhancer
TCF3








binding factors E12/E47)



218724_s_at
1079.1
581.3
1009.7
20.5
50
TGFB-induced factor 2 (TALE family homeobox)
TGIF2


219990_at
521.6
393.4
1001
5.4
50
E2F transcription factor 8
E2F8


216412_x_at
475
198.6
1291.7
9.7
50
Clone ds1-1 immunoglobulin lambda chain VJ region,
—








(IGL)



202393_s_at
3382
1512.9
8593.5
160.2
50
Kruppel-like factor 10
KLF10


214826_at
216.5
166.3
473.3
6
50
2′-phosphodiesterase
2′-PDE


202464_s_at
625.6
494.3
4013.6
9
50
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
PFKFB3


206195_x_at
230
164.5
436.5
8.5
49
growth hormone 2
GH2


210448_s_at
6937.5
1830
13603.4
33.3
49
purinergic receptor P2X, ligand-gated ion channel, 5
P2RX5


214516_at
260
99.8
440.2
4.6
49
histone 1, H4b
HIST1H4B


207106_s_at
519.4
285.3
1063.1
6.8
49
leukocyte tyrosine kinase
LTK


208046_at
274
104.8
701.7
7.9
49
histone 1, H4a
HIST1H4A


215284_at
406.3
296.3
1224.3
7.9
49
Sorting nexin 9
SNX9


204285_s_at
3741
3031.1
25815.9
127.7
49
phorbol-12-myristate-13-acetate-induced protein 1
PMAIP1


201499_s_at
6299
4419.1
7502.7
892.6
49
ubiquitin specific peptidase 7 (herpes virus-associated)
USP7


202240_at
964.4
607.7
1358.9
23.8
49
polo-like kinase 1 (Drosophila)
PLK1


213887_s_at
1776
1213.9
1430.7
56.8
49
polymerase (RNA) II (DNA directed) polypeptide E,
POLR2E








25 kDa



214056_at
550.7
294.7
690.3
7.3
49
Myeloid cell leukemia sequence 1 (BCL2-related)
MCL1


217230_at
471.6
59.2
695.4
7
49
villin 2 (ezrin)
VIL2


203391_at
497.4
170.6
1012.4
17.2
49
FK506 binding protein 2, 13 kDa
FKBP2


219681_s_at
487.9
328.9
1101
4.4
49
RAB11 family interacting protein 1 (class I)
RAB11FIP1


210387_at
3080.5
1587.3
7883.1
12.2
49
histone 1, H2bg
HIST1H2BG


219839_x_at
442.9
211.3
1486.8
7.6
49
T-cell leukemia/lymphoma 1B /// T-cell
TCL1B ///








leukemia/lymphoma 6
TCL6


206413_s_at
1611.3
892.6
34444.7
23.8
49
T-cell leukemia/lymphoma 1B /// T-cell
TCL1B ///








leukemia/lymphoma 6
TCL6


208546_x_at
1652.9
954.3
1981.3
32.4
49
histone 1, H2bh
HIST1H2BH


209753_s_at
1802.8
1211.1
2265.4
188.5
49
thymopoietin
TMPO


214712_at
364
86.8
327.1
1.6
49
—
—


216207_x_at
4775.2
3222.6
9161.2
398.9
49
immunoglobulin kappa variable 1D-13
IGKV1D-13


219961_s_at
434.9
261.5
641.1
16.1
49
chromosome 20 open reading frame 19
C20orf19


220987_s_at
1908.9
838.2
1462.1
109.5
49
chromosome 11 open reading frame 17 /// chromosome
C11orf17 ///








11 open reading frame 17 /// NUAK family, SNF1-like
NUAK2








kinase, 2 /// NUAK family, SNF1-like kinase, 2



219659_at
126.6
72.7
996.1
5.9
49
ATPase, aminophospholipid transporter-like, Class I, type
ATP8A2








8A, member 2



202379_s_at
5195.1
2436.4
4839.2
148.8
48
natural killer-tumor recognition sequence
NKTR


210791_s_at
793
342.6
1070.1
8.1
48
Rho GTPase-activating protein
RICS


212665_at
1742.4
925.9
2080.5
229.1
48
TCDD-inducible poly(ADP-ribose) polymerase
TIPARP


206660_at
14361.7
8315
29213.3
26.9
48
immunoglobulin lambda-like polypeptide 1
IGLL1


220400_at
220.9
123.3
457.5
5.5
48
vacuolar protein sorting 13B (yeast)
VPS13B


202014_at
2765
1272.3
17225.8
37.9
48
protein phosphatase 1, regulatory (inhibitor) subunit 15A
PPP1R15A


212611_at
1669.7
1156.8
8728.6
150.2
48
deltex 4 homolog (Drosophila)
DTX4


205769_at
310.3
192.6
1536.6
4.7
48
solute carrier family 27 (fatty acid transporter), member 2
SLC27A2


209269_s_at
1196.2
890
1180.9
131.4
48
Spleen tyrosine kinase
SYK


209469_at
217.3
34
256.4
2.1
48
glycoprotein M6A
GPM6A


213939_s_at
619.7
451.4
1008
6.7
48
rap2 interacting protein x
RIPX


215338_s_at
1640.9
956.8
1577.3
16.6
48
natural killer-tumor recognition sequence
NKTR


216645_at
600.6
427.4
745.3
24.2
48
—
—


219340_s_at
689.7
323.6
994.5
9.6
48
ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive
CLN8








with mental retardation)



221004_s_at
3633.1
1929.3
6469.8
15.2
48
integral membrane protein 2C /// integral membrane
ITM2C








protein 2C



206665_s_at
477.7
197.9
4662.1
3A
48
BCL2-like 1
BCL2L1


206255_at
1042.3
700
3332.5
7.8
48
B lymphoid tyrosine kinase
BLK


202208_s_at
548.3
385.1
2457.6
10.6
48
ADP-ribosylation factor-like 7
ARL7


201236_s_at
5477.4
4515.7
4123.8
551.1
47
BTG family, member 2
BTG2


207002_s_at
378.3
188.2
433.3
2
47
pleiomorphic adenoma gene-like 1
PLAGL1


207798_s_at
201.9
76
526.5
2.7
47
ataxin 2-like
ATXN2L


214554_at
396.1
163.7
871.2
3.2
47
histone 1, H2al
HIST1H2AL


220001_at
284.9
175.2
4940.2
8
47
peptidyl arginine deiminase, type IV
PADI4


212457_at
667.9
310.9
1110
18.1
47
transcription factor binding to IGHM enhancer 3
TFE3


213061_s_at
953.9
821.8
1418.2
114.7
47
N-terminal asparagine amidase
NTAN1


218529_at
515.8
310.3
522.9
27.8
47
CD320 antigen
CD320


202871_at
481.2
246.6
1360.7
14.4
47
TNF receptor-associated factor 4
TRAF4


215891_s_at
318.1
138.6
781.1
5.9
47
GM2 ganglioside activator
GM2A


215200_x_at
1026.2
273.1
4081.9
12.7
47
Villin 2 (ezrin)
VIL2


206342_x_at
481.2
311.1
3521.6
8.3
47
iduronate 2-sulfatase (Hunter syndrome)
IDS


202479_s_at
707.8
486.7
5353.1
9.3
47
tribbles homolog 2 (Drosophila)
TRIB2


217849_s_at
141.2
44
919.4
3.9
47
CDC42 binding protein kinase beta (DMPK-like)
CDC42BPB


210506_at
134.1
84.3
855.2
5.1
47
fucosyltransferase 7 (alpha (1,3) fucosyltransferase)
FUT7


205023_at
205.3
58.5
370.3
4.3
47
RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)
RAD51


206632_s_at
937.4
353
856.9
2.9
47
apolipoprotein B mRNA editing enzyme, catalytic
APOBEC3B








polypeptide-like 3B



211947_s_at
1169
170.5
1508.8
10.9
47
BAT2 domain containing 1
BAT2D1


206314_at
158.9
90
323.8
4.4
47
zinc finger protein 167
ZNF167


219313_at
154.4
116.7
380.8
4.8
47
hypothetical protein DKFZp434C0328
DKFZp434C0328


205544_s_at
215.9
129
5833.9
10.1
47
complement component (3d/Epstein Barr virus) receptor 2
CR2


206951_at
606.2
340.8
663.5
12.3
46
histone 1, H4e
HIST1H4E


212620_at
509.8
199.8
1165.4
15
46
zinc finger protein 609
ZNF609


212240_s_at
2426.9
1923.9
8975.2
277.2
46
phosphoinositide-3-kinase, regulatory subunit 1 (p85
PIK3R1








alpha)



205425_at
861.5
365.5
1018.8
4.3
46
huntingtin interacting protein 1
HIP1


217390_x_at
755
553.5
779.3
23.7
46
—
—


220609_at
617
260.1
601.4
4.7
46
hypothetical protein LOC202181
LOC202181


221491_x_at
1553.3
699.6
2570
2.5
46
major histocompatibility complex, class II, DR beta 1 ///
HLA-DRB1 ///








major histocompatibility complex, class II, DR beta 1 ///
HLA-DRB3 ///








major histocompatibility complex, class II, DR beta 3 ///
HLA-DRB4








major histocompatibility complex, class II, DR beta 3 ///









major histocompatibility complex, class II, DR beta 4 ///









major histocompatibility complex, class II, DR beta 4



217536_x_at
136.5
46.7
276.9
0.9
46
—
—


212227_x_at
30362
21224.4
93725.6
4332.2
46
eukaryotic translation initiation factor 1
EIF1


205922_at
313.3
65.8
1335.5
6.8
46
vanin 2 /// vanin 2
VNN2


204684_at
476.7
190.9
3423.4
8.5
46
neuronal pentraxin I
NPTX1


214786_at
427.6
294.4
1480.2
7.1
46
mitogen-activated protein kinase kinase kinase 1
MAP3K1


215721_at
375.9
288.8
1301.2
5.2
46
immunoglobulin heavy constant gamma 1 (G1m marker)
IGHG1


205768_s_at
175.3
98.1
836.9
3.6
46
solute carrier family 27 (fatty acid transporter), member 2
SLC27A2


201397_at
1061.9
740.9
1765.5
23.8
46
phosphoglycerate dehydrogenase
PHGDH


211022_s_at
375.1
227.3
427.8
6.7
46
alpha thalassemia/mental retardation syndrome X-linked
ATRX








(RAD54 homolog, S. cerevisiae)



220797_at
216.3
169.9
429.9
3.8
46
hypothetical protein MGC3329
MGC3329


208705_s_at
6796.1
6040.4
20022
1065.6
46
eukaryotic translation initiation factor 5
EIF5


213780_at
134.2
77.1
476.5
5.7
46
Full-length cDNA clone CS0DI027YJ05 of Placenta Cot
—








25-normalized of Homo sapiens (human)



216456_at
667.5
279
2544.7
3.1
46
Protocadherin 9
PCDH9


37028_at
5364.5
1966.1
20132.4
281
46
protein phosphatase 1, regulatory (inhibitor) subunit 15A
PPP1R15A


219855_at
691.1
115.1
1950.7
15
46
nudix (nucleoside diphosphate linked moiety X)-type motif
NUDT11








11



201411_s_at
805.9
399.3
863.9
7.5
45
pleckstrin homology domain containing, family B
PLEKHB2








(evectins) member 2



201926_s_at
1353.7
877.4
2551.7
26.8
45
decay accelerating factor for complement (CD55, Cromer
DAF








blood group system)



202095_s_at
1357.7
1007.1
2523.9
21.7
45
baculoviral IAP repeat-containing 5 (survivin)
BIRC5


207904_s_at
448.8
304.7
583.5
9.7
45
leucyl/cystinyl aminopeptidase
LNPEP


211865_s_at
349.3
223.2
651.6
6.6
45
fizzy/cell division cycle 20 related 1 (Drosophila)
FZR1


213281_at
841.7
540.7
984.3
28.2
45
—
—


214108_at
510.5
345.5
990.6
23.5
45
MYC associated factor X
MAX


219709_x_at
423
326.4
666.2
6.8
45
chromosome 16 open reading frame 24
C16orf24


219996_at
424
247.1
427.5
7.9
45
ankyrin repeat and SOCS box-containing 7
ASB7


220220_at
321.7
221.7
595.8
3.4
45
hypothetical protein FLJ10120
FLJ10120


222263_at
512.1
304.2
770.4
17.1
45
solute carrier family 35, member E1
SLC35E1


209193_at
3851.9
2313.1
9601.8
305.9
45
pim-1 oncogene /// pim-1 oncogene
PIM1


208786_s_at
5397.9
3573.9
16076.1
661.2
45
microtubule-associated protein 1 light chain 3 beta
MAP1LC3B


209325_s_at
875.7
433.6
2078.9
10.7
45
regulator of G-protein signalling 16
RGS16


221054_s_at
405.2
125.6
890.2
2.4
45
T-cell leukemia/lymphoma 6
TCL6


203954_x_at
112.4
104
394.1
9.6
45
claudin 3
CLDN3


205214_at
696.7
515.9
3489
16.2
45
serine/threonine kinase 17b (apoptosis-inducing)
STK17B


201393_s_at
1577.7
1059.6
1740.6
12.7
45
insulin-like growth factor 2 receptor
IGF2R


212027_at
1333
485.9
996.2
18.9
45
RNA binding motif protein 25
RBM25


213669_at
844.5
573.2
991
8.8
45
FCH domain only 1
FCHO1


214542_x_at
506.2
283.5
898.1
10.8
45
histone 1, H2ai
HIST1H2AI


217236_x_at
710.2
459.7
761.3
23.6
45
Immunoglobulin heavy constant gamma 1 (G1m marker)
IGHG1


205901_at
667.9
295.2
1655.3
15.2
45
prepronociceptin
PNOC


212291_at
925.7
468.1
1971.1
11.8
45
homeodomain interacting protein kinase 1
HIPK1


205803_s_at
161.9
108.6
503.3
2.2
45
transient receptor potential cation channel, subfamily C,
TRPC1








member 1



220266_s_at
900.9
355.1
6496.8
11.3
45
Kruppel-like factor 4 (gut)
KLF4


215330_at
211.7
109.6
776.5
5.7
45
Hypothetical protein FLJ43663
FLJ43663


214043_at
266.7
154.3
3097.2
5.6
45
Protein tyrosine phosphatase, receptor type, D
PTPRD


201979_s_at
812.1
513.7
906.9
9.9
44
protein phosphatase 5, catalytic subunit
PPP5C


203479_s_at
588.2
244.4
715.9
15.1
44
OTU domain containing 4
OTUD4


204908_s_at
1879.3
431.4
2716.8
7.4
44
B-cell CLL/lymphoma 3
BCL3


209559_at
347.6
145.1
483.7
8.8
44
huntingtin interacting protein-1-related
HIP1R


209718_at
483
361.1
707.2
9.7
44
kleisin beta
hCAP-H2


212588_at
3482.7
2298.1
6552
94.9
44
protein tyrosine phosphatase, receptor type, C
PTPRC


218434_s_at
956.1
383.5
3026.3
9.4
44
acetoacetyl-CoA synthetase
AACS


214581_x_at
729.6
320.5
3228.7
3.1
44
tumor necrosis factor receptor superfamily, member 21
TNFRSF21


213172_at
108.6
53.6
428.6
3.8
44
tetratricopeptide repeat domain 9
TTC9


202478_at
1685.6
710.2
14010.6
14.2
44
tribbles homolog 2 (Drosophila)
TRIB2


218523_at
1581.8
585.8
2999.4
34.4
44
phospholysine phosphohistidine inorganic pyrophosphate
LHPP








phosphatase



220324_at
121.8
96.4
227.5
2.6
44
chromosome 6 open reading frame 155
C6orf155


203320_at
2769.4
1553.3
5905.3
148.9
44
lymphocyte adaptor protein
LNK


216518_at
205.1
116.7
515.1
4.4
44
MRNA; cDNA DKFZp564E233 (from clone
—








DKFZp564E233)



220809_at
135.3
66.2
449.4
3.5
44
hypothetical protein FLJ14327
FLJ14327


206802_at
233.8
138.6
478
10.2
44
paired box gene 5 (B-cell lineage specific activator)
PAX5


212478_at
661.4
318.8
1868.1
9.3
44
hypothetical protein FLJ13910
FLJ13910


217209_at
165.2
118.6
446.2
12.2
44
—
—


204719_at
102.2
52.9
338
1.8
44
ATP-binding cassette, sub-family A (ABC1), member 8
ABCA8


209982_s_at
155.3
109.2
1350.3
4.7
44
neurexin 2
NRXN2


201780_s_at
1014
631.5
772.5
40.1
44
ring finger protein 13
RNF13


209153_s_at
12253.8
5691
8812.5
552.7
44
transcription factor 3 (E2A immunoglobulin enhancer
TCF3








binding factors E12/E47)



209754_s_at
1401.8
705.4
1593.9
16.7
44
thymopoietin
TMPO


211404_s_at
1362.9
833
2347.3
22.9
44
amyloid beta (A4) precursor-like protein 2
APLP2


212073_at
730.4
433.9
766.1
8.7
44
casein kinase 2, alpha 1 polypeptide
CSNK2A1


214190_x_at
591
240.2
730.7
5.6
44
golgi associated, gamma adaptin ear containing, ARF
GGA2








binding protein 2



214422_at
250.7
58.5
306.9
2.1
44
RAD23 homolog B (S. cerevisiae)
RAD23B


215083_at
681.3
386.7
923.9
9.7
44
Paraspeckle component 1
PSPC1


216067_at
321.2
122
372.9
4.1
44
—
—


216218_s_at
1014.3
670.8
1657.5
30.6
44
phospholipase C-like 2
PLCL2


222309_at
281.3
147
1126.8
2.9
44
Chromosome 6 open reading frame 62
C6orf62


210993_s_at
4684
2723.7
16961
7.3
44
SMAD, mothers against DPP homolog 1 (Drosophila)
SMAD1


200916_at
5108.1
1744.3
6584.8
62.5
43
transgelin 2
TAGLN2


208947_s_at
452.8
239.9
528.5
9.1
43
regulator of nonsense transcripts 1
RENT1


210717_at
366.1
204.6
486.9
4.4
43
Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog,
UBE2D2








yeast)



217284_x_at
1056.8
484.7
2082.6
16.8
43
serine hydrolase-like
SERHL


217684_at
311.6
169.8
536.7
12.3
43
thymidylate synthetase
TYMS


218435_at
1320.3
790.5
1286.5
9.1
43
DnaJ (Hsp40) homolog, subfamily C, member 15
DNAJC15


219279_at
952.4
771.3
2004.7
24.3
43
dedicator of cytokinesis 10
DOCK10


222337_at
144.1
74.4
405.1
7.2
43
Nardilysin (N-arginine dibasic convertase)
NRD1


203896_s_at
116.5
34.3
890.2
2.2
43
phospholipase C, beta 4
PLCB4


201072_s_at
973.3
734.6
1263
53.5
43
SWI/SNF related, matrix associated, actin dependent
SMARCC1








regulator of chromatin, subfamily c, member 1



204269_at
1830.9
1064.3
3312.7
151.8
43
pim-2 oncogene
PIM2


208795_s_at
4268.9
3568.4
4893.9
592.1
43
MCM7 minichromosome maintenance deficient 7
MCM7








(S. cerevisiae)



212345_s_at
2299.8
1709.5
2604.3
251.9
43
cAMP responsive element binding protein 3-like 2
CREB3L2


215164_at
965.1
508.4
1611.4
4.7
43
Transcription factor 4
TCF4


218927_s_at
1032.4
762.2
1817.1
17.2
43
carbohydrate (chondroitin 4) sulfotransferase 12
CHST12


217274_x_at
1238.9
796.9
3380
97.2
43
myosin, light polypeptide 4, alkali; atrial, embryonic
MYL4


205620_at
173.8
72.8
322.8
6.7
43
coagulation factor X
F10


208583_x_at
1234.3
766.5
1297.9
37.6
43
histone 1, H2aj
HIST1H2AJ


211921_x_at
47312.2
33664.3
58378.1
7053.1
43
prothymosin, alpha (gene sequence 28) /// prothymosin,
PTMA








alpha (gene sequence 28)



219072_at
480.8
422.9
746.5
26
43
B-cell CLL/lymphoma 7C
BCL7C


216466_at
87.7
47.4
333.5
1.6
43
neuron navigator 3
NAV3


214774_x_at
114.6
17.3
1325.4
0.6
43
trinucleotide repeat containing 9
TNRC9


200681_at
5619.1
3222.4
4088.7
914.8
42
glyoxalase I
GLO1


202825_at
566.4
326.3
1090.4
12.8
42
solute carrier family 25 (mitochondrial carrier; adenine
SLC25A4








nucleotide translocator), member 4



216508_x_at
5910.3
3567.4
6310.2
494.6
42
high-mobility group box 1
HMGB1


220764_at
195.7
132.2
293.8
6.7
42
protein phosphatase 4, regulatory subunit 2
PPP4R2


212420_at
2900.9
2182.6
6708
168.7
42
E74-like factor 1 (ets domain transcription factor)
ELF1


212758_s_at
646.9
184.1
1585.5
9
42
transcription factor 8 (represses interleukin 2 expression)
TCF8


220374_at
339.7
241.8
682.4
12.6
42
BTB (POZ) domain containing 5
BTBD5


200616_s_at
946
343.2
927.7
12.4
42
KIAA0152
KIAA0152


205205_at
982.8
305.4
1182.4
10.7
42
v-rel reticuloendotheliosis viral oncogene homolog B,
RELB








nuclear factor of kappa light polypeptide gene enhancer









in B-cells 3 (avian)



207943_x_at
543
330.3
625.4
8.5
42
pleiomorphic adenoma gene-like 1
PLAGL1


209038_s_at
345
152.6
668
8.1
42
EH-domain containing 1
EHD1


210666_at
372.9
43.1
289.3
10.2
42
iduronate 2-sulfatase (Hunter syndrome)
IDS


212122_at
182.5
81.3
264
3
42
ras homolog gene family, member Q
RHOQ


212684_at
397
337.6
629.4
14.1
42
zinc finger protein 3 (A8-51)
ZNF3


215269_at
990.5
519.8
1185.3
15.4
42
transmembrane protein 1
TMEM1


216422_at
274
122.3
399.5
6.9
42
proliferation-associated 2G4, 38 kDa
PA2G4


221043_at
524.2
318.4
711.7
12.9
42
—
—


221952_x_at
17836.4
16373.5
17116.4
2216.8
42
TRM5 tRNA methyltransferase 5 homolog (S. cerevisiae)
TRMT5


203590_at
680.5
506.9
1718.3
21.6
42
dynein, cytoplasmic, light intermediate polypeptide 2
DNCLI2


208703_s_at
1557.7
1261.2
3450.2
133.7
42
amyloid beta (A4) precursor-like protein 2
APLP2


210362_x_at
328.4
126.9
723.2
5.6
42
promyelocytic leukemia
PML


214852_x_at
154.4
107.8
362.4
6
42
vacuolar protein sorting 13A (yeast)
VPS13A


217418_x_at
4552.9
1979.4
25689
63.2
42
membrane-spanning 4-domains, subfamily A, member 1
MS4A1


202192_s_at
3906.7
2433.3
4114.9
274.1
41
growth arrest-specific 7
GAS7


203376_at
3692.7
2663
3142.2
506
41
cell division cycle 40 homolog (yeast)
CDC40


209470_s_at
212.6
93.7
341.2
1.4
41
glycoprotein M6A
GPM6A


212529_at
297.1
117
559.5
8.7
41
hypothetical protein FLJ30656
FLJ30656


215159_s_at
466
342.8
742.5
6.5
41
NAD kinase
NADK


201565_s_at
5880.2
1727.4
19822.8
47.1
41
inhibitor of DNA binding 2, dominant negative helix-loop-
ID2








helix protein



213299_at
179.6
60.8
529.2
4.1
41
zinc finger and BTB domain containing 7A
ZBTB7A


208245_at
104.5
67
842.3
1.6
41
RAB9, member RAS oncogene family, pseudogene 1
RAB9P1


204346_s_at
1584.9
1272.1
2423.3
129.2
41
Ras association (RalGDS/AF-6) domain family 1
RASSF1


209478_at
1031.7
918
1260.3
41.6
41
stimulated by retinoic acid 13 homolog (mouse)
STRA13


210115_at
633.5
354.8
928.7
9
41
ribosomal protein L39-like
RPL39L


210218_s_at
510.7
252.4
430.8
8.7
41
nuclear antigen Sp100
SP100


210407_at
483.2
237.4
667
4.8
41
protein phosphatase 1A (formerly 2C), magnesium-
PPM1A








dependent, alpha isoform



212026_s_at
384.9
198.5
582.4
10.9
41
exocyst complex component 7
EXOC7


218401_s_at
959
552.1
927.4
73.5
41
zinc finger protein 281
ZNF281


222378_at
210.6
121.7
441.6
5.2
41
Hypothetical protein FLJ43663
FLJ43663


207631_at
165.8
85.7
337
7.7
41
neighbor of BRCA1 gene 2
NBR2


211151_x_at
667.6
384.3
2032.1
6
41
growth hormone 1
GH1


43427_at
201.2
143.7
621.5
9.3
41
acetyl-Coenzyme A carboxylase beta
ACACB


216361_s_at
279.2
87.6
690.4
2
41
MYST histone acetyltransferase (monocytic leukemia) 3
MYST3


219135_s_at
356.2
262.9
1031.1
9.5
41
hypothetical protein FLJ12681
FLJ12681


208476_s_at
185.2
147.7
735.6
6.5
41
FERM domain containing 4A
FRMD4A


213954_at
101
74.4
325.1
3.3
41
KIAA0888 protein
KIAA0888


212592_at
806.3
485.3
15583.5
8.7
41
Immunoglobulin J polypeptide, linker protein for
IGJ








immunoglobulin alpha and mu polypeptides



202005_at
443.9
239.8
814
25.5
41
suppression of tumorigenicity 14 (colon carcinoma,
ST14








matriptase, epithin)



202487_s_at
9563.8
8094.3
9690.7
1623.9
41
H2A histone family, member V
H2AFV


204484_at
3918.2
2035.4
3075.3
59.7
41
phosphoinositide-3-kinase, class 2, beta polypeptide
PIK3C2B


206707_x_at
3161.2
1759
4423.4
183.3
41
chromosome 6 open reading frame 32
C6orf32


214243_s_at
993.5
280.2
1457.1
10
41
serine hydrolase-like
SERHL


214481_at
430
143.5
665.5
3.9
41
histone 1, H2am
HIST1H2AM


217576_x_at
630.6
373
947.5
13.1
41
son of sevenless homolog 2 (Drosophila)
SOS2


222322_at
254.5
79.2
429.9
1.6
41
Transcribed locus
—


203833_s_at
873.1
695.6
1838
91.8
41
trans-golgi network protein 2
TGOLN2


200719_at
1366.7
1017.2
3859
22.4
41
S-phase kinase-associated protein 1A (p19A)
SKP1A


216277_at
135.1
67.5
619.8
5
41
BUB1 budding uninhibited by benzimidazoles 1 homolog
BUB1








(yeast)



200772_x_at
41243
33563.5
53587.8
7692.7
40
prothymosin, alpha (gene sequence 28)
PTMA


204048_s_at
369
251.6
684.4
6.3
40
phosphatase and actin regulator 2
PHACTR2


204074_s_at
1098.2
494.2
737.2
17.2
40
glycine-, glutamate-, thienylcyclohexylpiperidine-binding
GlyBP








protein



208719_s_at
2411.4
187.5
3784
6.1
40
DEAD (Asp-Glu-Ala-Asp) box polypeptide 17
DDX17


214743_at
2864.9
2185.8
3477.7
461.9
40
cut-like 1, CCAAT displacement protein (Drosophila)
CUTL1


214834_at
152.8
61.7
287.8
2.7
40
HBII-437 C/D box snoRNA /// HBII-13 snoRNA
HBII-437 ///









HBII-13


215802_at
699.1
240.8
742.6
5
40
Transducin-like enhancer of split 1 (E(sp1) homolog,
TLE1








Drosophila)



203233_at
1017
703
2086.3
21.8
40
interleukin 4 receptor
IL4R


220879_at
356.5
218.2
837.1
28.7
40
—
—


201283_s_at
289.1
87.5
329
6.7
40
OGT(O-Glc-NAc transferase)-interacting protein 106 KDa
OIP106


203395_s_at
309
220.9
380.9
8.2
40
hairy and enhancer of split 1, (Drosophila)
HES1


204524_at
692.2
215.4
649.7
9.2
40
3-phosphoinositide dependent protein kinase-1
PDPK1


215615_x_at
217.3
119
406.9
4.4
40
—
—


217650_x_at
526.7
320
665.4
16.1
40
ST3 beta-galactoside alpha-2,3-sialyltransferase 2
ST3GAL2


218039_at
4736
3722.1
7499
402.9
40
nucleolar and spindle associated protein 1
NUSAP1


221654_s_at
2225.9
1866.2
3238.5
454.2
40
ubiquitin specific peptidase 3
USP3


205193_at
417.5
181
1462.3
21.6
40
v-maf musculoaponeurotic fibrosarcoma oncogene
MAFF








homolog F (avian)



206100_at
490.7
264.8
1235.7
8.9
40
carboxypeptidase M
CPM


219703_at
211.4
170.9
493.9
3.6
40
meiosis-specific nuclear structural 1
MNS1


206204_at
74.9
46.7
814.1
1.8
40
growth factor receptor-bound protein 14
GRB14


204115_at
371.9
300.5
4663.6
3.3
40
guanine nucleotide binding protein (G protein), gamma 11
GNG11


202879_s_at
768.3
396.1
815.9
10.9
40
pleckstrin homology, Sec7 and coiled-coil domains
PSCD1








1(cytohesin 1)



205346_at
310.7
138.4
420.8
8.9
40
ST3 beta-galactoside alpha-2,3-sialyltransferase 2
ST3GAL2


213940_s_at
1325.5
781.7
2148.6
5.4
40
formin binding protein 1
FNBP1


214030_at
552.5
218.8
766.3
9.2
40
hypothetical protein DKFZp667G2110
DKFZp667G2110


219312_s_at
287.3
230
531.5
5.7
40
zinc finger and BTB domain containing 10
ZBTB10


219534_x_at
307.9
42
561.3
3.2
40
cyclin-dependent kinase inhibitor 1C (p57, Kip2)
CDKN1C


221848_at
429.1
362.1
661.7
24.7
40
zinc finger, CCCH-type with G patch domain
ZGPAT


203467_at
368
154.2
751.9
8
40
phosphomannomutase 1
PMM1


205024_s_at
1179.4
755.8
1567.1
28.5
39
RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)
RAD51


208808_s_at
14054.5
11679.2
14451.9
1436.6
39
high-mobility group box 2
HMGB2


208928_at
387.9
161.8
547.1
9.6
39
P450 (cytochrome) oxidoreductase
POR


209447_at
1248.8
638.5
1546.1
14.3
39
spectrin repeat containing, nuclear envelope 1
SYNE1


212105_s_at
1088.6
498.6
1463.7
13.4
39
DEAH (Asp-Glu-Ala-His) box polypeptide 9
DHX9


214665_s_at
3166
2307.8
3142.1
334.7
39
calcium binding protein P22
CHP


221628_s_at
326.8
98.4
548.3
8.3
39
cytokine-like nuclear factor n-pac
N-PAC


204646_at
418.5
299.3
1102.6
6.2
39
dihydropyrimidine dehydrogenase
DPYD


205081_at
1999.9
1137.4
6452.3
8.4
39
cysteine-rich protein 1 (intestinal)
CRIP1


206877_at
122
40.9
918.6
6
39
MAX dimerization protein 1
MXD1


212651_at
285.2
84.9
1297.4
4.8
39
Rho-related BTB domain containing 1
RHOBTB1


214251_s_at
603.2
285.5
1741.8
4.1
39
nuclear mitotic apparatus protein 1
NUMA1


201962_s_at
1277.2
637.4
1078.3
24.4
39
ring finger protein 41
RNF41


204183_s_at
383.8
245.7
428
9.8
39
adrenergic, beta, receptor kinase 2
ADRBK2


205267_at
12559.7
5949
10129.5
195.1
39
POU domain, class 2, associating factor 1
POU2AF1


209501_at
706.2
547.4
1404.7
21.9
39
cerebellar degeneration-related protein 2, 62 kDa
CDR2


215779_s_at
1882.7
716.6
3292.8
15.4
39
histone 1, H2bg
HIST1H2BG


219507_at
748.8
521.7
755.7
23
39
arginine/serine-rich coiled-coil 1
RSRC1


221908_at
523.4
234.3
943.1
13.8
39
Transmembrane protein 118
TMEM118


208325_s_at
664.6
384.2
1413.3
12.8
39
A kinase (PRKA) anchor protein 13
AKAP13


209803_s_at
109.2
47.7
258.5
1.7
39
pleckstrin homology-like domain, family A, member 2
PHLDA2


7592_s_at
106
47.9
252.5
4.4
39
hyperpolarization activated cyclic nucleotide-gated
HCN2








potassium channel 2



205489_at
1211.9
581.2
3410.5
45.9
39
crystallin, mu
CRYM


202102_s_at
4917.3
2139.9
4161.3
206.4
39
bromodomain containing 4
BRD4


209461_x_at
392
219.8
510.5
10.2
39
WD repeat domain 18
WDR18


210778_s_at
746.7
571.2
1009.9
9.4
39
MAX dimerization protein 4
MXD4


213062_at
944.9
662
1245.4
21.2
39
N-terminal asparagine amidase
NTAN1


213996_at
1935.9
1006.9
1599.5
31.4
39
yippee-like 1 (Drosophila)
YPEL1


55583_at
356.5
228.2
491.2
34.9
39
dedicator of cytokinesis 6
DOCK6


217626_at
183.5
73.9
598.9
8.1
39
aldo-keto reductase family 1, member C1 /// aldo-keto
AKR1C1 ///








reductase family 1, member C2
AKR1C2


219951_s_at
175.7
117.5
603
6.9
39
chromosome 20 open reading frame 12
C20orf12


205830_at
121.3
64
421.7
2.2
39
calmegin
CLGN


213156_at
498.5
259.4
517.5
4
38
MRNA; cDNA DKFZp586B211 (from clone
—








DKFZp586B211) /// Homo sapiens, clone









IMAGE: 4214654, mRNA



216621_at
567.5
296.2
664.1
12.4
38
Rho-associated, coiled-coil containing protein kinase 1
ROCK1


217268_at
92.9
29
371.7
0.8
38
RAB7, member RAS oncogene family
RAB7


210491_at
137.5
98.5
538.1
3.2
38
—
—


203126_at
439.7
366.7
1524.8
6
38
inositol(myo)-1(or 4)-monophosphatase 2
IMPA2


212254_s_at
162
121.3
552.2
4.5
38
dystonin
DST


202146_at
882.7
430.7
853.4
27.8
38
interferon-related developmental regulator 1
IFRD1


204975_at
1069.6
427.3
1016.3
13
38
epithelial membrane protein 2
EMP2


205426_s_at
453.2
267.2
650.8
11.7
38
huntingtin interacting protein 1
HIP1


209182_s_at
993.6
330.7
1620.7
9.7
38
chromosome 10 open reading frame 10
C10orf10


218194_at
5628.1
2372.6
5536
376.4
38
REX2, RNA exonuclease 2 homolog (S. cerevisiae)
REXO2


217204_at
190.3
82.6
408.3
2.2
38
Mitochondrial translational release factor 1-like
MTRF1L


219922_s_at
331
157.2
854.4
3.2
38
latent transforming growth factor beta binding protein 3
LTBP3


213537_at
2955.4
1564.6
10603.5
32.8
38
major histocompatibility complex, class II, DP alpha 1
HLA-DPA1


214230_at
333.3
172.9
3101.8
6.6
38
cell division cycle 42 (GTP binding protein, 25 kDa)
CDC42


209156_s_at
133.3
51.3
605.9
4.2
38
collagen, type VI, alpha 2
COL6A2


205306_x_at
1281.1
521.1
1837.7
62.9
37
kynurenine 3-monooxygenase (kynurenine 3-
KMO








hydroxylase)



208184_s_at
1225.2
677
1209.5
24.7
37
transmembrane protein 1
TMEM1


212492_s_at
1554.5
674.1
1671.1
79.6
37
jumonji domain containing 2B
JMJD2B


213106_at
1975.6
946.3
1743.3
150.2
37
ATPase, aminophospholipid transporter (APLT), Class I,
ATP8A1








type 8A, member 1



219286_s_at
1929.7
1420.7
2353.4
39
37
RNA binding motif protein 15
RBM15


204840_s_at
116.6
22.2
405.6
0.4
37
early endosome antigen 1, 162 kD
EEA1


219651_at
158
50.8
472.4
3.7
37
developmental pluripotency associated 4
DPPA4


210356_x_at
4859.8
2065.7
27465.2
118.8
37
membrane-spanning 4-domains, subfamily A, member 1
MS4A1


201367_s_at
3841.3
440.5
3294.3
4.4
37
zinc finger protein 36, C3H type-like 2
ZFP36L2


205436_s_at
5772.5
3401.4
8416.8
129.1
37
H2A histone family, member X
H2AFX


211672_s_at
1173.9
986.1
1802.1
18.1
37
actin related protein 2/3 complex, subunit 4, 20 kDa ///
ARPC4








actin related protein 2/3 complex, subunit 4, 20 kDa



212459_x_at
788.8
562.7
1530.9
53.5
37
succinate-CoA ligase, GDP-forming, beta subunit
SUCLG2


212520_s_at
2137.8
1356.8
2927.7
140.6
37
SWI/SNF related, matrix associated, actin dependent
SMARCA4








regulator of chromatin, subfamily a, member 4



215169_at
403.8
77.6
459.2
3.4
37
solute carrier family 35, member E2
SLC35E2


215781_s_at
303.2
111.1
458.5
4.7
37
topoisomerase (DNA) III beta
TOP3B


220589_s_at
302.3
168.9
504.6
10.4
37
uncharacterized hematopoietic stem/progenitor cells
MDS028








protein MDS028



222001_x_at
1020.4
723
2006.4
11
37
LOC440669
LOC440669


205423_at
1750.2
1333.8
3693.6
144.7
37
adaptor-related protein complex 1, beta 1 subunit
AP1B1


219371_s_at
8724.6
5051.9
18217
451.6
37
Kruppel-like factor 2 (lung)
KLF2


205471_s_at
235.8
104.3
1645.6
3.7
37
dachshund homolog 1 (Drosophila)
DACH1


36711_at
454.5
125.8
4719.8
2.7
37
v-maf musculoaponeurotic fibrosarcoma oncogene
MAFF








homolog F (avian)



209184_s_at
3447.1
1380.2
19735.9
1851
37
insulin receptor substrate 2
IRS2


216080_s_at
1763.4
1541.1
12130.1
26.7
37
fatty acid desaturase 3
FADS3


206551_x_at
1941.3
1090.3
1840.1
94.2
37
kelch-like 24 (Drosophila)
KLHL24


209118_s_at
6782.7
4027.8
10974.1
496.1
37
tubulin, alpha 3
TUBA3


209592_s_at
1061.5
830.1
1149.1
63.4
37
WD repeat domain 68
WDR68


211997_x_at
55066.4
40842.6
74824.4
4914.8
37
H3 histone, family 3B (H3.3B)
H3F3B


204680_s_at
531.6
492.2
1100
70.2
37
Rap guanine nucleotide exchange factor (GEF) 5
RAPGEF5


210360_s_at
351.1
241.1
706
6
37
metastasis suppressor 1
MTSS1


219995_s_at
67.8
22.6
234.6
0.4
37
hypothetical protein FLJ13841
FLJ13841


211141_s_at
113.6
76.1
433.7
4
37
CCR4-NOT transcription complex, subunit 3
CNOT3


204244_s_at
989.7
431.6
816
5.8
36
activator of S phase kinase
ASK


207740_s_at
1081.5
677
1204.7
20.3
36
nucleoporin 62 kDa
NUP62


209235_at
934.8
339.2
1405.7
21.7
36
chloride channel 7
CLCN7


214829_at
520.5
150.3
618.9
2
36
aminoadipate-semialdehyde synthase
AASS


216012_at
3285.1
822.5
2116.6
164.8
36
Unidentified mRNA, partial sequence
—


208579_x_at
6232.3
2992.5
13423.9
240.5
36
H2B histone family, member S
H2BFS


212609_s_at
309.3
116.3
677.5
5.3
36
V-akt murine thymoma viral oncogene homolog 3 (protein
AKT3








kinase B, gamma)



215768_at
206.3
134.9
520.2
5.6
36
SRY (sex determining region Y)-box 5
SOX5


216224_s_at
227.1
178.7
506
12.9
36
histone deacetylase 6
HDAC6


220297_at
133.8
90.5
314
8.7
36
BTB (POZ) domain containing 7
BTBD7


218785_s_at
120.6
74.9
459.4
3.1
36
RAB, member RAS oncogene family-like 5
RABL5


217263_x_at
190
129.4
767.3
9.1
36
runt-related transcription factor 1 (acute myeloid leukemia
RUNX1








1; aml1 oncogene)



201629_s_at
1512.1
1043.6
2486.8
52.9
36
acid phosphatase 1, soluble
ACP1


201679_at
514.4
351.2
759.1
8.6
36
arsenate resistance protein ARS2
ARS2


201745_at
908.2
601.1
1718.6
130.1
36
PTK9 protein tyrosine kinase 9
PTK9


202870_s_at
2228.1
1100.3
4341.3
56.3
36
CDC20 cell division cycle 20 homolog (S. cerevisiae)
CDC20


208107_s_at
594.2
283.2
834.1
11.6
36
exonuclease NEF-sp /// exonuclease NEF-sp
LOC81691


209257_s_at
2342.4
961.4
2637.3
83.1
36
chondroitin sulfate proteoglycan 6 (bamacan)
CSPG6


213810_s_at
392.9
168.6
563.2
11
36
Chromosome 6 open reading frame 166
C6orf166


213947_s_at
1435.9
1019.4
2459.7
55.1
36
nucleoporin 210 kDa
NUP210


214160_at
213.7
108.9
377.8
7
36
—
—


215720_s_at
432.1
288.8
825
6.5
36
nuclear transcription factor Y, alpha
NFYA


217785_s_at
386.1
113.6
458.8
7
36
SNARE protein Ykt6
YKT6


207057_at
275.7
163.6
909.8
5.2
36
solute carrier family 16 (monocarboxylic acid
SLC16A7








transporters), member 7



209446_s_at
190
110.3
394.6
4.8
36
—
—


201482_at
401
314.2
1198.1
30.8
36
quiescin Q6
QSCN6


214242_at
128.5
56.6
458
4.8
36
Mannosidase, alpha, class 1A, member 2
MAN1A2


219208_at
114.6
37.6
281
3.8
36
F-box protein 11
FBXO11


221125_s_at
479.4
282.6
2029.4
22.5
36
potassium large conductance calcium-activated channel,
KCNMB3








subfamily M beta member 3



211884_s_at
433.9
339.7
719.6
10
36
class II, major histocompatibility complex, transactivator
CIITA


219646_at
607
193.7
653.3
10
36
hypothetical protein FLJ20186
FLJ20186


204198_s_at
1516.7
621.8
4598.1
16
36
runt-related transcription factor 3
RUNX3


220958_at
245.4
213.8
499
8.5
36
unc-51-like kinase 4 (C. elegans)
ULK4


222179_at
238.6
189
550.6
10.6
36
—
—


212249_at
431.4
395.5
1226.3
13.1
36
phosphoinositide-3-kinase, regulatory subunit 1 (p85
PIK3R1








alpha)



208518_s_at
126.8
86.6
604.3
7.5
36
period homolog 2 (Drosophila)
PER2


211238_at
102.8
72.7
447
3.6
36
ADAM metallopeptidase domain 7
ADAM7


200706_s_at
2637
1168.1
2666
19.5
35
lipopolysaccharide-induced TNF factor
LITAF


200921_s_at
12107.4
6043.1
18371.2
274.8
35
B-cell translocation gene 1, anti-proliferative
BTG1


202705_at
2491.5
1661.2
4425.3
26.5
35
cyclin B2
CCNB2


207078_at
466.5
233.5
708.3
4.5
35
mediator of RNA polymerase II transcription, subunit 6
MED6








homolog (yeast)



207522_s_at
6423.6
2981.6
5910.6
75.5
35
ATPase, Ca++ transporting, ubiquitous
ATP2A3


209464_at
1253.5
825.7
1454.9
84.5
35
aurora kinase B
AURKB


211647_x_at
501.3
285.6
536.8
8.4
35
Immunoglobulin heavy constant mu /// Immunoglobulin
IGHM








heavy constant mu



211998_at
10496.3
4591.7
15151.5
702.8
35
H3 histone, family 3B (H3.3B)
H3F3B


212142_at
1054.9
612.5
1543.4
69.3
35
MCM4 minichromosome maintenance deficient 4
MCM4








(S. cerevisiae)



213691_at
365.7
283.3
623.9
24.4
35
—
—


200810_s_at
4607
3204.4
9656.1
380.4
35
cold inducible RNA binding protein
CIRBP


201006_at
375.3
235.7
940.5
8.9
35
peroxiredoxin 2
PRDX2


208704_x_at
3138
2390.2
6336.7
329
35
amyloid beta (A4) precursor-like protein 2
APLP2


214970_s_at
151.6
83.9
396.6
3.1
35
ST6 beta-galactosamide alpha-2,6-sialyltranferase 1
ST6GAL1


41577_at
756.4
535.7
4896.8
15.2
35
protein phosphatase 1, regulatory (inhibitor) subunit 16B
PPP1R16B


200853_at
11838.3
7861.6
13501
1153
35
H2A histone family, member Z
H2AFZ


204612_at
578.4
413.9
864.9
14.9
35
protein kinase (cAMP-dependent, catalytic) inhibitor alpha
PKIA


205406_s_at
280.5
215.1
477.6
4.1
35
sperm autoantigenic protein 17
SPA17


208918_s_at
1625.2
1160.2
1821
66.2
35
NAD kinase
NADK


212700_x_at
382.6
287.1
543.5
19.2
35
pleckstrin homology domain containing, family M (with
PLEKHM1








RUN domain) member 1



213229_at
1470.2
945.1
2296.5
38.7
35
Dicer1, Dcr-1 homolog (Drosophila)
DICER1


214405_at
299.6
112.6
432.8
3.9
35
CUG triplet repeat, RNA binding protein 2
CUGBP2


215984_s_at
360.6
181.1
484.1
9.6
35
ADP-ribosylation factor related protein 1
ARFRP1


216101_at
338.3
223.6
553.7
12.7
35
Hypothetical protein LOC283755
LOC283755


222366_at
1123.1
633.7
1108.5
107.5
35
Activity-dependent neuroprotector
ADNP


209053_s_at
1604.8
927.6
3584.9
27.4
35
Wolf-Hirschhorn syndrome candidate 1
WHSC1


217784_at
442.5
209.6
2269.5
16.8
35
SNARE protein Ykt6
YKT6


210279_at
1545.9
595.5
3675
9.7
35
G protein-coupled receptor 18
GPR18


219785_s_at
152.6
84.4
584.7
3.9
35
F-box protein 31
FBXO31


41397_at
321.1
264.6
939.1
12.2
35
hypothetical protein LOC55565
LOC55565


220799_at
139.2
44.1
500.8
2.7
35
glial cells missing homolog 2 (Drosophila)
GCM2


208072_s_at
4341.9
2975.7
14061.5
145.3
35
diacylglycerol kinase, delta 130 kDa
DGKD


213580_at
96
72.6
341.5
3
35
—
—


220842_at
104.2
82.3
458.1
4.6
35
Abelson helper integration site
AHI1


220450_at
706.7
410.9
2373.9
13
35
—
—


210932_s_at
157.8
61.9
314.6
3
34
ring finger protein (C3H2C3 type) 6
RNF6


212079_s_at
714.5
393.5
900.7
6.9
34
myeloid/lymphoid or mixed-lineage leukemia (trithorax
MLL








homolog, Drosophila)



213036_x_at
6399.2
4049.5
6841.1
79.3
34
ATPase, Ca++ transporting, ubiquitous
ATP2A3


213726_x_at
7796.1
5120
13306.9
910.2
34
tubulin, beta, 2
TUBB2


214041_x_at
6122.7
1995.5
4462.5
365.8
34
Ribosomal protein L37a
RPL37A


214463_x_at
1049.2
311
1545.7
16.6
34
histone 1, H4k /// histone 1, H4j
HIST1H4K ///









HIST1H4J


214557_at
170.5
55.5
277.9
2.4
34
pituitary tumor-transforming 2
PTTG2


215339_at
149.9
25.5
249.9
1.4
34
natural killer-tumor recognition sequence
NKTR


222352_at
327.4
242.8
480.9
12.4
34
F-box protein 31
FBXO31


205003_at
222.6
145.7
554.2
3.2
34
dedicator of cytokinesis 4
DOCK4


210610_at
235.6
157
554.7
15.4
34
carcinoembryonic antigen-related cell adhesion
CEACAM1








molecule 1 (biliary glycoprotein)



212019_at
180.4
108.3
415.5
2.8
34
ribosomal L1 domain containing 1
RSL1D1


213674_x_at
2559.9
1457.1
7346.2
20.9
34
immunoglobulin heavy constant delta
IGHD


217697_at
169
105.4
535.4
2.7
34
FYN oncogene related to SRC, FGR, YES
FYN


205301_s_at
112.2
99.8
329.2
6.8
34
8-oxoguanine DNA glycosylase
OGG1


218949_s_at
3172.1
2003.8
7319.2
179.9
34
glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1
QRSL1


201498_at
2576.2
1649.1
2581.9
338
34
Unknown protein
USP7


201678_s_at
3884.7
2665.8
3904
398.1
34
DC12 protein
DC12


215581_s_at
554.5
340.7
728.1
5.6
34
MCM3 minichromosome maintenance deficient 3
MCM3AP








(S. cerevisiae) associated protein



220018_at
412.3
263.1
462.6
4.9
34
Cas-Br-M (murine) ecotropic retroviral transforming
CBLL1








sequence-like 1



220286_at
354.5
271
686.7
18.3
34
myotubularin related protein 10
MTMR10


222150_s_at
3354
1546.8
3922.1
23.6
34
hypothetical protein LOC54103
LOC54103


66053_at
271.2
83.3
409.2
4.2
34
heterogeneous nuclear ribonucleoprotein U-like 2
HNRPUL2


204947_at
723.2
647
1959.6
45.5
34
E2F transcription factor 1
E2F1


215006_at
1050.5
675.3
2162
55.9
34
—
—


220328_at
168.9
122.6
339.6
4.4
34
polyhomeotic like 3 (Drosophila)
PHC3


221976_s_at
149.4
108.1
825.1
5.5
34
Hepatoma-derived growth factor, related protein 3
HDGFRP3


202387_at
1578.7
1163.7
8122.2
230.8
34
BCL2-associated athanogene /// BCL2-associated
BAG1








athanogene



203760_s_at
923.5
364.7
2249.3
14.1
34
Src-like-adaptor /// Src-like-adaptor
SLA


204324_s_at
181.4
92.4
623
7.3
34
golgi phosphoprotein 4
GOLPH4


221276_s_at
163.9
135.8
455.1
4.3
34
syncoilin, intermediate filament 1 /// syncoilin,
SYNC1








intermediate filament 1



215407_s_at
96.3
67.7
288.5
4.4
34
astrotactin 2
ASTN2


210393_at
418.7
136.2
3640.2
12.5
34
leucine-rich repeat-containing G protein-coupled receptor 5
LGR5


200671_s_at
1392.9
702.6
2278.6
8.7
34
spectrin, beta, non-erythrocytic 1
SPTBN1


202589_at
17240.3
13462.3
20596.6
380.9
34
thymidylate synthetase
TYMS


203742_s_at
743
677.9
1213.6
7
34
thymine-DNA glycosylase
TDG


219624_at
223.1
129.3
345.4
5.6
34
BCL2-associated athanogene 4
BAG4


76897_s_at
236.7
80.5
371.7
3.4
34
KIAA0674
KIAA0674


204826_at
534.2
443.9
1446.3
37.3
34
cyclin F
CCNF


210517_s_at
3300.7
1353.1
9242.7
11
34
A kinase (PRKA) anchor protein (gravin) 12
AKAP12


211039_at
168.1
70.9
868.7
7
34
cholinergic receptor, nicotinic, alpha polypeptide 1
CHRNA1








(muscle) /// cholinergic receptor, nicotinic, alpha









polypeptide 1 (muscle)



219778_at
102.8
76.6
310.6
2.8
34
zinc finger protein, multitype 2
ZFPM2


207573_x_at
11632.8
10131.6
12633.1
2167.8
33
ATP synthase, H+ transporting, mitochondrial F0
ATP5L








complex, subunit g



211919_s_at
29614.3
23208.6
54252.2
1497.1
33
chemokine (C—X—C motif) receptor 4 ///
CXCR4








chemokine (C—X—C motif) receptor 4



211936_at
9520.1
4084.9
9404.7
325.9
33
heat shock 70 kDa protein 5 (glucose-regulated protein,
HSPA5








78 kDa)



219876_s_at
314.1
140
513.2
9
33
hypotheticalprotein DKFZp434M0331
DKFZp434M0331


221557_s_at
728.3
173.4
1429.9
6.4
33
lymphoid enhancer-binding factor 1
LEF1


201085_s_at
3189.8
1357.3
13637.2
73
33
SON DNA binding protein
SON


201586_s_at
8569.9
5652.5
17622.8
1201.6
33
splicing factor proline/glutamine-rich (polypyrimidine tract
SFPQ








binding protein associated)



212733_at
2061.3
1548.7
5477
216.4
33
KIAA0226
KIAA0226


217930_s_at
284.2
214.8
636.1
9.5
33
toll interacting protein
TOLLIP


202509_s_at
258
105.5
790.5
11.1
33
tumor necrosis factor, alpha-induced protein 2
TNFAIP2


209936_at
357.6
274.7
869.6
6.4
33
RNA binding motif protein 5
RBM5


214284_s_at
193
132
753.1
5.6
33
Fibroblast growth factor 18
FGF18


215820_x_at
210.4
160
460.9
5.9
33
sorting nexin 13
SNX13


206700_s_at
1479.6
229
4109.1
15.1
33
Smcy homolog, Y-linked (mouse)
SMCY


204262_s_at
194
123.5
506.5
7.3
33
presenilin 2 (Alzheimer disease 4)
PSEN2


204049_s_at
168.2
135.5
479.6
7.5
33
phosphatase and actin regulator 2
PHACTR2


207781_s_at
194.5
118.1
751
1.1
33
zinc finger protein 6 (CMPX1)
ZNF6


205712_at
235.6
181
1105.9
6.4
33
protein tyrosine phosphatase, receptor type, D
PTPRD


204114_at
864.4
304.3
4631.7
12
33
nidogen 2 (osteonidogen)
NID2


202412_s_at
2463.6
945.5
1998.4
58.6
33
ubiquitin specific peptidase 1
USP1


202575_at
280.6
207.3
482
13.4
33
cellular retinoic acid binding protein 2
CRABP2


205249_at
225.3
75.4
367.7
11.7
33
early growth response 2 (Krox-20 homolog, Drosophila)
EGR2


219237_s_at
509.8
349.6
583.8
10
33
DnaJ (Hsp40) homolog, subfamily B, member 14
DNAJB14


203331_s_at
1079.1
847.9
2665.7
30.2
33
inositol polyphosphate-5-phosphatase, 145 kDa
INPP5D


214615_at
257.5
190.8
516.5
7.4
33
purinergic receptor P2Y, G-protein coupled, 10
P2RY10


205632_s_at
1124.2
750.9
2645.1
88.4
33
phosphatidylinositol-4-phosphate 5-kinase, type I, beta
PIP5K1B


214984_at
147.5
93.4
521.2
2
33
PI-3-kinase-related kinase SMG-1
SMG1


202732_at
876.3
589.3
2260.7
28.7
33
protein kinase (cAMP-dependent, catalytic) inhibitor
PKIG








gamma



213538_at
2967.3
1774.4
9703.8
472.3
33
SON DNA binding protein
SON


210592_s_at
4102.2
3018.5
15575.9
276.3
33
spermidine/spermine N1-acetyltransferase
SAT


214254_at
118.5
73.8
391.7
4.1
33
melanoma antigen family A, 4
MAGEA4


209465_x_at
88.2
60.5
352.3
3.3
33
pleiotrophin (heparin binding growth factor 8, neurite
PTN








growth-promoting factor 1)



221980_at
140
114.6
428.9
12.9
33
Elastin microfibril interfacer 2
EMILIN2


205617_at
348.8
147.5
454.9
6.4
33
proline rich Gla (G-carboxyglutamic acid) 2
PRRG2


212382_at
4841.3
2575.4
7602.8
80.3
33
Transcription factor 4
TCF4


213146_at
580.7
260.3
1033.7
9.3
33
—
—


215016_x_at
293
100.3
581.8
4.1
33
dystonin
DST


215464_s_at
1495.7
546
891
15.1
33
Tax1 (human T-cell leukemia virus type I) binding
TAX1BP3








protein 3



219233_s_at
742.2
542
1209.2
18.8
33
gasdermin-like
GSDML


220843_s_at
286.7
139.9
402.3
5.6
33
WD repeats and SOF1 domain containing
WDSOF1


206566_at
139.4
84.4
328.6
3.9
33
solute carrier family 7 (cationic amino acid transporter, y+
SLC7A1








system), member 1



209037_s_at
441.2
245.2
1038.9
9.6
33
EH-domain containing 1
EHD1


204525_at
119.9
94.7
373.2
1.3
33
PHD finger protein 14
PHF14


207604_s_at
498.4
299.6
1302.9
6
33
solute carrier family 4, sodium bicarbonate cotransporter,
SLC4A7








member 7



218480_at
322.2
291.5
680.8
22.7
33
hypothetical protein FLJ21839
FLJ21839


215112_x_at
62.4
14.6
597.2
0.3
33
MCF.2 cell line derived transforming sequence-like 2
MCF2L2


207462_at
263
165.5
1053.3
5.7
33
glycine receptor, alpha 2
GLRA2


207334_s_at
239.9
113.8
971.7
5.8
33
transforming growth factor, beta receptor II (70/80 kDa)
TGFBR2


220570_at
180.4
89.6
3075.1
7
33
resistin
RETN


213745_at
87.6
50.3
363.4
2.4
33
attractin-like 1
ATRNL1


202533_s_at
711
317.8
704.1
12.5
32
dihydrofolate reductase
DHFR


203795_s_at
3293
2438.1
5241.7
239.2
32
B-cell CLL/lymphoma 7A
BCL7A


211200_s_at
374.4
97.7
390.5
4.4
32
EF-hand calcium binding domain 2
EFCAB2


212629_s_at
983.6
762.4
1470.6
49.1
32
protein kinase N2
PKN2


218262_at
765.3
563.6
1191.6
48.3
32
hypothetical protein FLJ22318
FLJ22318


218802_at
2316.7
1822.3
2483.5
42.4
32
hypothetical protein FLJ20647
FLJ20647


222032_s_at
461.1
241.6
508.1
13.7
32
Unknown protein
USP7


206997_s_at
210.7
71.6
498.5
7.4
32
heparan sulfate 6-O-sulfotransferase 1
HS6ST1


213922_at
481.2
199.2
1028.1
2.3
32
tau tubulin kinase 2
TTBK2


60084_at
281
130
624.4
5
3
cylindromatosis (turban tumor syndrome)
CYLD


207712_at
163
88
395.3
4
3
B melanoma antigen
BAGE


216709_at
153.8
103.2
482.7
6.5
3
Hypothetical gene supported by BC013370; BC034583
LOC400655


205385_at
124.8
79.1
691.4
8.7
3
Mdm2, transformed 3T3 cell double minute 2, p53 binding
MDM2








protein (mouse)



209524_at
432.4
154.3
1100.3
3.9
3
hepatoma-derived growth factor, related protein 3
HDGFRP3


204688_at
283.8
139.5
1709.8
5.6
3
sarcoglycan, epsilon
SGCE


212092_at
323.4
177.7
27725.6
6.4
3
paternally expressed 10
PEG10


203317_at
1832.1
859.6
1426.6
133.2
3
pleckstrin and Sec7 domain containing 4
PSD4


204335_at
487.2
62.9
856
8.4
3
hypothetical protein FLJ10374
FLJ10374


208548_at
162.5
66.9
324.4
3.4
3
interferon, alpha 6
IFNA6


208608_s_at
337.6
133.3
587.1
10.4
3
syntrophin, beta 1 (dystrophin-associated protein A1,
SNTB1








59 kDa, basic component 1)



214305_s_at
4659
3426.8
5099.6
498.5
3
splicing factor 3b, subunit 1, 155 kDa
SF3B1


214744_s_at
279.8
117.4
349.2
7.6
3
Similar to Zgc: 73149 protein
LOC442209


219814_at
450.4
149.4
788.7
10
3
muscleblind-like 3 (Drosophila)
MBNL3


205840_x_at
798.1
421.9
2064.1
14.2
3
growth hormone 1
GH1


210961_s_at
171.3
91.8
415.9
3.7
3
adrenergic, alpha-1D-, receptor
ADRA1D


211192_s_at
431
237.8
881.3
8.3
3
CD84 antigen (leukocyte antigen)
CD84


213799_s_at
370.5
198.3
755
14.3
3
protein tyrosine phosphatase, receptor type, A
PTPRA


220729_at
151.5
60.7
336.3
2.6
3
—
—


207238_s_at
2281.5
1823
5647.1
43.2
3
protein tyrosine phosphatase, receptor type, C
PTPRC


214971_s_at
275.6
125.8
787.6
7.8
3
ST6 beta-galactosamide alpha-2,6-sialyltranferase 1
ST6GAL1


213988_s_at
943.7
577.2
4736.9
24.4
3
spermidine/spermine N1-acetyltransferase
SAT


201584_s_at
5701.3
3803.1
5988.4
552.8
3
DEAD (Asp-Glu-Ala-Asp) box polypeptide 39
DDX39


205308_at
426.6
135.5
505.4
3.9
3
chromosome 8 open reading frame 70
C8orf70


208977_x_at
9681.2
5369.7
14888.5
972
3
tubulin, beta, 2
TUBB2


210466_s_at
5244.2
3388
6177
820.6
3
SERPINE1 mRNA binding protein 1
SERBP1


213725_x_at
1418.9
780.6
1815.3
69.9
3
hypothetical protein LOC283824
LOC283824


218176_at
1009.6
548.2
1460.3
10.6
3
melanoma antigen family F, 1
MAGEF1


41037_at
189.6
101.1
356.3
6.6
3
TEA domain family member 4
TEAD4


207470_at
181.1
83.8
435.3
3.2
3
hypothetical protein DKFZp566H0824
DKFZp566H0824


209083_at
3910.9
3369.5
9674.6
516.6
3
coronin, actin binding protein, 1A
CORO1A


210741_at
116
54.2
258.8
2.9
3
Rho guanine nucleotide exchange factor (GEF) 12
ARHGEF12


219106_s_at
83.2
24.4
781.6
1.2
3
kelch repeat and BTB (POZ) domain containing 10
KBTBD10


33646_g_at
325.7
251.1
1119.4
4.5
3
GM2 ganglioside activator
GM2A


215002_at
116.2
32
583.2
2
31
KIAA0220-like protein /// hypothetical gene LOC283846 ///
LOC23117 ///








hypothetical protein 348162 /// NPIP-like locus ///
DKFZp547E087








hypothetical protein LOC440345 /// PI-3-kinase-related
///








kinase SMG-1 pseudogene
LOC348162









///









LOC388221









///









LOC440345









///









LOC440354


209526_s_at
622.2
426.6
1995
9.3
31
hepatoma-derived growth factor, related protein 3
HDGFRP3


201005_at
6598.1
4694.1
25569.7
11.4
31
CD9 antigen (p24)
CD9


206247_at
1394.4
1038.9
1334.3
166.5
31
MHC class I polypeptide-related sequence B
MICB


212315_s_at
453.7
257.2
856.9
11.4
31
nucleoporin 210 kDa
NUP210


215855_s_at
732.8
504.4
1338.6
36.5
31
TATA element modulatory factor 1
TMF1


218992_at
547.1
338.7
925.8
19.4
31
chromosome 9 open reading frame 46
C9or146


222023_at
270
146.6
382
3.6
31
A kinase (PRKA) anchor protein 13
AKAP13


207829_s_at
305.8
252.4
665.6
31.3
31
BCL2/adenovirus E1B 19 kDa interacting protein 1
BNIP1


215728_s_at
353.9
258.2
713.1
16.8
31
acyl-CoA thioesterase 7
ACOT7


218279_s_at
217.1
138.9
700.8
3.3
31
histone 2, H2aa
HIST2H2AA


220623_s_at
152.1
108.2
339.2
4.7
31
testis specific, 10
TSGA10


203245_s_at
253.2
176
590.9
10.2
31
FLJ35348
FLJ35348


203298_s_at
2224.3
1657
4931.3
308.5
31
Jumonji, AT rich interactive domain 2
JARID2


208622_s_at
8534.4
2241.9
17271.3
137.7
31
villin 2 (ezrin)
VIL2


209388_at
861.1
717.7
2495.3
65.9
31
poly(A) polymerase alpha
PAPOLA


222074_at
197.2
71.6
1101.8
2.2
31
uroporphyrinogen decarboxylase
UROD


211299_s_at
235.5
221.3
561.1
9.5
31
flotillin 2
FLOT2


214240_at
152.7
133.8
416.1
9.6
31
galanin
GAL


215037_s_at
900.5
530.2
6759
19.6
31
BCL2-like 1
BCL2L1


215163_at
177.2
41.2
971.9
4.6
31
—
—


215694_at
113.4
92.2
345
3.2
31
spermatogenesis associated 5-like 1
SPATA5L1


219073_s_at
282.2
200.3
1001.9
3.4
31
oxysterol binding protein-like 10
OSBPL10


214337_at
63.6
30.2
363.5
1.6
31
coatomer protein complex, subunit alpha
COPA


207339_s_at
2085.6
1712.7
24613.4
77.1
31
lymphotoxin beta (TNF superfamily, member 3)
LTB


201580_s_at
1692.5
1189.9
1675.7
160.3
31
thioredoxin domain containing 13
TXNDC13


201694_s_at
2112.8
467.7
3888.6
23.7
31
early growth response 1
EGR1


207999_s_at
667.3
514.6
836
69.8
31
adenosine deaminase, RNA-specific, B1 (RED1 homolog
ADARB1








rat)



212744_at
279.5
267
498.4
11
31
Bardet-Biedl syndrome 4
BBS4


212810_s_at
873.7
577.3
931.9
28.4
31
solute carrier family 1 (glutamate/neutral amino acid
SLC1A4








transporter), member 4



217203_at
192.4
68.4
327.3
3.5
31
—
—


217893_s_at
1798.4
767.9
2805.8
20.5
31
chromosome 1 open reading frame 108
C1orf108


220529_at
580.9
275.3
598.2
22.9
31
hypothetical protein FLJ11710
FLJ11710


221436_s_at
693.1
377.3
1276.4
10
31
cell division cycle associated 3 /// cell division cycle
CDCA3








associated 3



206919_at
185.6
109.2
552.5
3
31
ELK4, ETS-domain protein (SRF accessory protein 1)
ELK4


210928_at
179.2
64.4
491.1
6.8
31
CCR4-NOT transcription complex, subunit 2
CNOT2


217602_at
183
98.6
704.3
3.7
31
peptidylprolyl isomerase A (cyclophilin A)
PPIA


213523_at
555.5
373.4
1967.5
13.8
31
cyclin E1
CCNE1


204362_at
872
628.3
3033.3
9.9
31
src family associated phosphoprotein 2
SCAP2


204686_at
255
163.7
1166.5
5.3
31
insulin receptor substrate 1
IRS1


214627_at
398
173.9
5293.7
16.9
31
eosinophil peroxidase
EPX


215139_at
95.2
54.9
314.1
3.6
31
Rho guanine nucleotide exchange factor (GEF) 10
ARHGEF10


215767_at
119
73.9
582.8
4.6
31
chromosome 2 open reading frame 10
C2orf10


203827_at
148.4
66.5
727
3.9
31
WD40 repeat protein Interacting with phosphoInositides
WIPI49








of 49 kDa



201364_s_at
1746.5
1321.7
2921.9
120.9
30
ornithine decarboxylase antizyme 2
OAZ2


202413_s_at
4532.3
3194.3
4483.5
763.6
30
ubiquitin specific peptidase 1
USP1


202971_s_at
851
538
1188.6
8.7
30
dual-specificity tyrosine-(Y)-phosphorylation regulated
DYRK2








kinase 2



205367_at
2237.6
1328.9
3421.3
68.2
30
adaptor protein with pleckstrin homology and src
APS








homology 2 domains



208076_at
558.8
407.3
705.1
12.5
30
histone 1, H4d
HIST1H4D


209152_s_at
3493.2
1505.9
2674.6
248.4
30
transcription factor 3 (E2A immunoglobulin enhancer
TCF3








binding factors E12/E47)



212525_s_at
908.7
543.6
1204.8
13.5
30
H2A histone family, member X
H2AFX


215024_at
355.8
228.8
464.7
9
30
chromosome 7 open reading frame 28B
C7orf28B


219426_at
570
329.1
586.4
42.2
30
eukaryotic translation initiation factor 2C, 3
EIF2C3


222349_x_at
185.8
110.7
350.5
8.6
30
ring finger protein 126 pseudogene 1
RNF126P1


204935_at
112.6
32.6
258.5
1.9
30
protein tyrosine phosphatase, non-receptor type 2
PTPN2


215992_s_at
226.5
128.2
899.5
7.8
30
Rap guanine nucleotide exchange factor (GEF) 2
RAPGEF2


209967_s_at
134.8
43
415.7
5.5
30
cAMP responsive element modulator
CREM


204286_s_at
1054.4
645.4
6785.1
27
30
phorbol-12-myristate-13-acetate-induced protein 1
PMAIP1


206390_x_at
349.1
275
5566.7
21.4
30
platelet factor 4 (chemokine (C—X—C motif) ligand 4)
PF4


220270_at
142.4
102.5
516.2
5.9
30
tudor domain containing 4
TDRD4


204396_s_at
363.5
249.8
3619.7
4.4
30
G protein-coupled receptor kinase 5
GRK5


202305_s_at
1106
859.8
1483.6
59.9
30
fasciculation and elongation protein zeta 2 (zygin II)
FEZ2


203297_s_at
3578.4
2269.2
4416
249.5
30
Jumonji, AT rich interactive domain 2
JARID2


203311_s_at
1645.4
1021.3
3135
78.6
30
ADP-ribosylation factor 6
ARF6


206965_at
214.2
122.3
370.6
3.3
30
Kruppel-like factor 12
KLF12


208903_at
848.2
783.6
1237.4
131.2
30
Ribosomal protein S28
RPS28


210050_at
282.7
138
358.7
6.7
30
triosephosphate isomerase 1
TPI1


214656_x_at
1723.7
865.9
1324.6
76.4
30
myosin IC
MYO1C


218913_s_at
1248
564.4
1373.8
39.5
30
GEM interacting protein
GMIP


219840_s_at
837.2
186.2
1234.8
8
30
T-cell leukemia/lymphoma 6
TCL6


205350_at
194.6
78.9
417.2
8.8
30
cellular retinoic acid binding protein 1
CRABP1


206886_x_at
816.4
315.5
2779.8
7.6
30
growth hormone 1
GH1


218851_s_at
212
137
784.1
12.2
30
WD repeat domain 33
WDR33


201593_s_at
2313.4
2053.5
5467.5
439.2
30
likely ortholog of mouse immediate early response,
LEREPO4








erythropoietin 4



215212_at
272
129.7
714.5
3.1
30
CDNA FLJ12091 fis, clone HEMBB1002582
—


206361_at
220.1
126
661.1
13
30
G protein-coupled receptor 44
GPR44


206489_s_at
121.6
61.4
543.2
4.5
30
discs, large (Drosophila) homolog-associated protein 1
DLGAP1


202576_s_at
828.5
524.2
1222.5
32.9
30
DEAD (Asp-Glu-Ala-As) box polypeptide 19B /// DEAD
DDX19B ///








(Asp-Glu-Ala-As) box polypeptide 19A /// DDX19-DDX19L
DDX19A ///








protein
DDX19-









DDX19L


204982_at
759.2
306.6
1312
18.5
30
G protein-coupled receptor kinase interactor 2
GIT2


209181_s_at
2471.5
1445.1
3301
370.2
30
Rab geranylgeranyltransferase, beta subunit
RABGGTB


212119_at
1486.3
1058.8
1840.8
181.7
30
ras homolog gene family, member Q
RHOQ


213971_s_at
1705.5
1190
1646.9
278
30
suppressor of zeste 12 homolog (Drosophila)
SUZ12


214314_s_at
247.2
109.9
261.2
1.5
30
eukaryotic translation initiation factor 5B
EIF5B


217914_at
795.6
473.5
1574.4
36.4
30
two pore segment channel 1
TPCN1


219537_x_at
612.7
151.4
710.1
10.7
30
delta-like 3 (Drosophila)
DLL3


219892_at
406.1
301.3
693.9
12.7
30
transmembrane 6 superfamily member 1
TM6SF1


200906_s_at
196.9
84.1
443.8
5.7
30
palladin
KIAA0992


213963_s_at
296.6
119.6
722.2
9.6
30
Sin3A-associated protein, 30 kDa
SAP30


33148_at
202.2
153.4
456.9
5.9
30
zinc finger RNA binding protein
ZFR


212715_s_at
313
179.1
744.1
6.8
30
microtubule associated monoxygenase, calponin and LIM
MICAL3








domain containing 3



203845_at
1062.2
644.3
5682
75.2
30
p300/CBP-associated factor
PCAF


216961_s_at
162.2
126
401
11.5
30
RPA interacting protein
RIP


219841_at
178.9
78.2
389.7
4.2
30
activation-induced cytidine deaminase
AICDA


216065_at
170.2
63.4
574.6
4.9
30
—
—


220602_s_at
180
97.5
579.2
6.4
30
hypothetical protein FLJ22795 /// hypothetical protein
FLJ22795 ///








FLJ90297 /// LOC388161
LOC388152









///









LOC388161


202391_at
2179.6
964.3
13386.3
154.3
30
brain abundant, membrane attached signal protein 1
BASP1


216260_at
100.5
73.4
440.8
4.9
30
Dicer1, Dcr-1 homolog (Drosophila)
DICER1


200675_at
12263.9
7362.2
14130.7
1142.6
29
CD81 antigen (target of antiproliferative antibody 1)
CD81


209041_s_at
876.8
610.3
1024.8
15
29
ubiquitin-conjugating enzyme E2G 2 (UBC7 homolog,
UBE2G2








yeast)



209060_x_at
1380
753.8
1224.4
112.6
29
nuclear receptor coactivator 3
NCOA3


211279_at
287.2
194.6
367.2
11
29
nuclear respiratory factor 1
NRF1


212680_x_at
2180.1
1447
3705
43.5
29
protein phosphatase 1, regulatory (inhibitor) subunit 14B
PPP1R14B


214338_at
292.1
245.2
539.1
11.6
29
DnaJ (Hsp40) homolog, subfamily B, member 12
DNAJB12


214838_at
911.6
592.2
1570.7
30.9
29
SFT2 domain containing 2
SFT2D2


216350_s_at
654.8
237.3
1216.9
11.5
29
zinc finger protein 10
ZNF10


78330_at
539.8
377.5
856.9
42
29
zinc finger protein 335
ZNF335


211996_s_at
8974.6
6702.7
21416.6
985.7
29
KIAA0220-like protein /// hypothetical gene LOC283846 ///
LOC23117 ///








hypothetical protein 348162 /// PI-3-kinase-related kinase
DKFZp547E087








SMG-1 pseudogene /// similar to the PI-3-kinase-related
///








kinase SMG-1 family pseudogene 2
LOC348162









///









LOC440354









///









LOC613037


215554_at
111.1
48.1
454.1
2.4
29
glycosylphosphatidylinositol specific phospholipase D1
GPLD1


208348_s_at
116.4
38
303.5
3.3
29
Cas-Br-M (murine) ecotropic retroviral transforming
CBLB








sequence b



222205_x_at
137.1
109.4
502.2
5.7
29
Similar to hypothetical protein FLJ38374
LOC400840


212750_at
930.6
632
6690.7
15.9
29
protein phosphatase 1, regulatory (inhibitor) subunit 16B
PPP1R16B


39729_at
1792.3
1477.1
23054
26.2
29
peroxiredoxin 2
PRDX2


201810_s_at
1070.1
610.6
10902
33.6
29
SH3-domain binding protein 5 (BTK-associated)
SH3BP5


202716_at
2019.7
1174.5
1578.2
117.1
29
protein tyrosine phosphatase, non-receptor type 1
PTPN1


202781_s_at
1392.7
858.7
1351.8
120.4
29
skeletal muscle and kidney enriched inositol phosphatase
SKIP


204817_at
1160.2
785.1
1589.1
61.1
29
extra spindle poles like 1 (S. cerevisiae)
ESPL1


214508_x_at
418.7
356.9
732.4
21.5
29
cAMP responsive element modulator
CREM


215151_at
278.2
98.2
400.7
6.6
29
dedicator of cytokinesis 10
DOCK10


221521_s_at
1660.7
1195.7
2488.9
12.3
29
DNA replication complex GINS protein PSF2
Pfs2


203068_at
278.5
56.5
1212.6
10.2
29
kelch-like 21 (Drosophila)
KLHL21


205590_at
1491.4
641.4
3396.4
11.1
29
RAS guanyl releasing protein 1 (calcium and DAG-
RASGRP1








regulated)



216449_x_at
1656.1
608.9
3772
27.5
29
tumor rejection antigen (gp96) 1
TRA1


208068_x_at
663.4
497.8
1784.6
30.3
29
chorionic somatomammotropin hormone 1 (placental
CSH1 ///








lactogen) /// chorionic somatomammotropin hormone 2 ///
CSH2 ///








chorionic somatomammotropin hormone-like 1 /// growth
CSHL1 ///








hormone 1 /// growth hormone 2
GH1 /// GH2


218888_s_at
386.1
148.1
1168.2
5.5
29
neuropilin (NRP) and tolloid (TLL)-like 2
NETO2


221261_x_at
492.8
164.3
1704.3
9.4
29
melanoma antigen family D, 4 /// melanoma antigen
MAGED4








family D, 4



207772_s_at
153.2
86.3
593.2
3.7
29
HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)
HRMT1L4


215931_s_at
180.6
43.6
533.8
5.3
29
ADP-ribosylation factor guanine nucleotide-exchange
ARFGEF2








factor 2 (brefeldin A-inhibited)



216184_s_at
163.6
106.5
770.8
5.9
29
regulating synaptic membrane exocytosis 1
RIMS1


201718_s_at
523.7
433.5
1918.3
9.7
29
erythrocyte membrane protein band 4.1-like 2
EPB41L2


220359_s_at
546.9
178.5
15891.5
3.9
29
cyclic AMP-regulated phosphoprotein, 21 kD
ARPP-21


201868_s_at
147.6
120.5
611.9
3.7
29
transducin (beta)-like 1X-linked
TBL1X


202289_s_at
157
84
1169.5
5.2
29
transforming, acidic coiled-coil containing protein 2
TACC2


220059_at
777.8
473.2
9891.4
15.3
29
BCR downstream signaling 1
BRDG1


200704_at
2127.5
1314.5
3636.2
50.4
29
lipopolysaccharide-induced TNF factor
LITAF


201396_s_at
517.4
358.8
590.4
20.8
29
small glutamine-rich tetratricopeptide repeat (TPR)-
SGTA








containing, alpha



201625_s_at
730.7
607.5
1053.5
75.3
29
insulin induced gene 1
INSIG1


201730_s_at
3624.8
1911
4999.2
138.9
29
translocated promoter region (to activated MET
TPR








oncogene)



207124_s_at
422.6
208.9
510
13.9
29
guanine nucleotide binding protein (G protein), beta 5
GNB5


209052_s_at
1267.4
568.8
2199.3
13.7
29
Wolf-Hirschhorn syndrome candidate 1
WHSC1


212035_s_at
759.8
598.6
1203.5
58.5
29
exocyst complex component 7
EXOC7


215174_at
249
135.5
491.3
8.6
29
flavin containing monooxygenase 6
FMO6


217370_x_at
1147.3
737
1707.2
38.8
29
fusion (involved in t(12; 16) in malignant liposarcoma)
FUS


218812_s_at
880.9
570.1
1354.3
76.4
29
chromosome 7 open reading frame 19
C7orf19


219094_at
316.3
236.8
547.6
6.6
29
armadillo repeat containing 8
ARMC8


219174_at
142.9
17.2
203.5
2.2
29
coiled-coil domain containing 2
CCDC2


221745_at
849
567.4
1216.1
16.3
29
WD repeat domain 68
WDR68


215234_at
198.1
112.5
396.3
7.1
29
MRNA, trapped exon e1b7, DCR1-16.0,
—


216573_at
204.4
57.2
559.1
4.7
29
Clone ds1-1 immunoglobulin lambda chain VJ region,
—








(IGL)



40837_at
435.6
331
1225.2
34.9
29
transducin-like enhancer of split 2 (E(sp1) homolog,
TLE2








Drosophila)



203857_s_at
1302.4
844.3
3509
46.3
29
protein disulfide isomerase family A, member 5
PDIA5


211088_s_at
230
164.8
555.7
7.6
29
polo-like kinase 4 (Drosophila) /// polo-like kinase 4
PLK4








(Drosophila)



211475_s_at
2071.5
1680.1
8077
413
29
BCL2-associated athanogene
BAG1


217127_at
112.2
61.5
291.3
2
29
cystathionase (cystathionine gamma-lyase)
CTH


202286_s_at
153.5
76.9
659.7
7.4
29
tumor-associated calcium signal transducer 2
TACSTD2


207517_at
131.2
61
680.2
4.1
29
laminin, gamma 2
LAMC2


220784_s_at
110.7
31.1
319.1
1.8
29
urotensin 2
UTS2


221152_at
131.1
81.2
448
2.8
29
collagen, type VIII, alpha 1
COL8A1


207894_s_at
269.4
156.9
687.1
21.3
29
T-cell leukemia/lymphoma 6
TCL6


201942_s_at
133.4
82.9
588.8
4.7
29
carboxypeptidase D
CPD


206935_at
54.9
18.9
294.4
0.8
29
protocadherin 8
PCDH8


211341_at
1031
133.9
10201.6
2.1
29
POU domain, class 4, transcription factor 1
POU4F1


201598_s_at
1332.6
1111.7
2082.9
189.5
28
inositol polyphosphate phosphatase-like 1
INPPL1


202769_at
2932.9
1532.5
3398
190.4
28
Cyclin G2
CCNG2


202900_s_at
1820.3
1430.3
2398.2
109.6
28
nucleoporin 88 kDa
NUP88


203113_s_at
12072.1
8841.5
11404.7
1180.8
28
eukaryotic translation elongation factor 1 delta (guanine
EEF1D








nucleotide exchange protein)



207499_x_at
922.1
720.5
1197.2
51.5
28
smooth muscle cell associated protein-1
SMAP-1


209535_s_at
889.7
507.2
808.6
65.3
28
—
—


211352_s_at
940.2
324.4
918.2
9.3
28
nuclear receptor coactivator 3
NCOA3


213286_at
422.7
215.1
583.7
12.7
28
zinc finger RNA binding protein
ZFR


214052_x_at
476.4
225.6
618.2
6.3
28
BAT2 domain containing 1
BAT2D1


214336_s_at
1446.5
518.3
1121.1
62.6
28
coatomer protein complex, subunit alpha
COPA


215509_s_at
771.4
220.1
1118.4
11
28
BUB1 budding uninhibited by benzimidazoles 1 homolog
BUB1








(yeast)



217966_s_at
290.5
157.6
489.7
7.8
28
chromosome 1 open reading frame 24
C1orf24


219207_at
373.8
241.9
568.8
6.8
28
hypothetical protein FLJ21128
FLJ21128


221611_s_at
254.3
148.8
390.6
11.1
28
PHD finger protein 7
PHF7


211274_at
165.9
85.1
342.9
8.3
28
T-box 1
TBX1


208023_at
181.6
76.3
382.3
5.6
28
tumor necrosis factor receptor superfamily, member 4
TNFRSF4


216872_at
120
52.7
514.8
1.8
28
Hr44 antigen
HR44


203836_s_at
444.9
329.7
1706
6.6
28
mitogen-activated protein kinase kinase kinase 5
MAP3K5


214651_s_at
115.1
59.9
7233.4
3
28
homeo box A9
HOXA9


201843_s_at
109.6
78.2
7630.9
4.4
28
EGF-containing fibulin-like extracellular matrix protein 1
EFEMP1


203241_at
1066.4
834.5
1885.9
152.9
28
UV radiation resistance associated gene
UVRAG


204970_s_at
749.8
468.4
1127.1
41.9
28
v-maf musculoaponeurotic fibrosarcoma oncogene
MAFG








homolog G (avian)



214941_s_at
2325.5
1206.9
2919.2
73.8
28
formin binding protein 3
FNBP3


216279_at
188.3
103.8
303
5.3
28
zinc finger protein 272
ZNF272


218810_at
797.5
275.2
968.6
25.1
28
zinc finger CCCH-type containing 12A
ZC3H12A


219717_at
769.6
568.7
1382.9
72.7
28
hypothetical protein FLJ20280
FLJ20280


221664_s_at
763.3
449.2
1121.6
24.1
28
F11 receptor
F11R


221154_at
188.5
47.7
392.8
1.3
28
tripartite motif-containing 49
TRIM49


222320_at
188.7
62.2
779
0.4
28
Cell division cycle 73, Paf1/RNA polymerase II complex
CDC73








component, homolog (S. cerevisiae)



203876_s_at
221.3
182.3
484.9
18.2
28
matrix metallopeptidase 11 (stromelysin 3)
MMP11


214295_at
178.6
121.5
991
6.2
28
KIAA0485 protein
KIAA0485


202859_x_at
705.3
181.2
4322.1
10.9
28
interleukin 8
IL8


212336_at
118.4
40.8
347.3
3.1
28
erythrocyte membrane protein band 4.1-like 1
EPB41L1


218834_s_at
183.7
97.4
471.7
10.5
28
heat shock 70 kDa protein 5 (glucose-regulated protein,
HSPA5BP1








78 kDa) binding protein 1



205612_at
119.4
66.5
613.8
1.8
28
multimerin 1
MMRN1


213400_s_at
404
207.8
1760.6
11.7
28
transducin (beta)-like 1X-linked
TBL1X


208983_s_at
634.7
438
5148
13.9
28
platelet/endothelial cell adhesion molecule (CD31
PECAM1








antigen)



201309_x_at
2136.9
1690.7
3920.1
205.2
27
chromosome 5 open reading frame 13
C5orf13


202154_x_at
3521.2
1931.5
5268.2
196.6
27
tubulin, beta 3
TUBB3


203318_s_at
1287.8
861.9
2184.2
162.8
27
zinc finger protein 148 (pHZ-52)
ZNF148


207556_s_at
1040.9
730.5
1867.1
30.2
27
diacylglycerol kinase, zeta 104 kDa
DGKZ


209610_s_at
1038.3
584.6
1530.4
53.6
27
solute carrier family 1 (glutamate/neutral amino acid
SLC1A4








transporter), member 4



210605_s_at
357.4
171.9
630.5
12.2
27
milk fat globule-EGF factor 8 protein
MFGE8


213182_x_at
210.3
28.2
399
4.5
27
cyclin-dependent kinase inhibitor 1C (p57, Kip2)
CDKN1C


216983_s_at
314.4
198.1
530.3
12.5
27
zinc finger protein 224
ZNF224


217924_at
374.4
211
591.3
11.3
27
chromosome 6 open reading frame 106
C6orf106


218219_s_at
826.9
399
920.1
13.4
27
LanC lantibiotic synthetase component C-Like 2 (bacterial)
LANCL2


218981_at
146.5
90.6
269.5
1.2
27
ACN9 homolog (S. cerevisiae)
ACN9


219339_s_at
483.5
242.8
515.2
9.8
27
euchromatic histone-lysine N-methyltransferase 1
EHMT1


221262_s_at
209.5
80.6
360.8
5
27
solute carrier family 2 (facilitated glucose transporter),
SLC2A11








member 11 /// solute carrier family 2 (facilitated glucose









transporter), member 11



221546_at
307.2
156.8
524.4
10.8
27
PRP18 pre-mRNA processing factor 18 homolog (yeast)
PRPF18


35436_at
470.9
214.4
673.4
19.5
27
golgi autoantigen, golgin subfamily a, 2
GOLGA2


208851_s_at
350.1
209.5
747.3
15.8
27
Thy-1 cell surface antigen
THY1


209201_x_at
27920.9
22826.8
56196.9
1417.6
27
chemokine (C—X—C motif) receptor 4
CXCR4


221829_s_at
2947.8
1924.8
7554.1
350.5
27
transportin 1
TNPO1


222063_s_at
151
55.8
320.1
2.5
27
CDP-diacylglycerol synthase (phosphatidate
CDS1








cytidylyltransferase) 1



216108_at
117.4
38.8
248.7
4.4
27
Transcribed locus, weakly similar to NP_055301.1
—








neuronal thread protein AD7c-NTP [Homo sapiens]



217585_at
133.6
76.5
392.2
4.7
27
nebulette
NEBL


211771_s_at
231.6
49.6
938.8
6.4
27
POU domain, class 2, transcription factor 2 /// POU
POU2F2








domain, class 2, transcription factor 2



215609_at
160.3
126.1
450.3
6.3
27
START domain containing 7
STARD7


202953_at
104.2
88
968.1
9.6
27
complement component 1, q subcomponent, beta
C1QB








polypeptide



201710_at
2306.4
789.5
2974.5
27.5
27
v-myb myeloblastosis viral oncogene homolog (avian)-like 2
MYBL2


203377_s_at
1193.9
412.3
871.2
27.2
27
cell division cycle 40 homolog (yeast)
CDC40


212085_at
16661.8
13263.8
21255.3
1445.2
27
solute carrier family 25 (mitochondrial carrier, adenine
SLC25A6








nucleotide translocator), member 6



217094_s_at
478.9
218.5
431.3
12.8
27
itchy homolog E3 ubiquitin protein ligase (mouse)
ITCH


218418_s_at
3248.2
1177.9
4104.1
69.6
27
ankyrin repeat domain 25
ANKRD25


202545_at
554
284.5
2142.8
20.2
27
protein kinase C, delta
PRKCD


203263_s_at
351.6
271.3
737
8.3
27
Cdc42 guanine nucleotide exchange factor (GEF) 9
ARHGEF9


203653_s_at
408.8
335.3
883.7
8.1
27
coilin
COIL


206850_at
540.4
204.2
1160.3
16.3
27
RAS-related on chromosome 22
RRP22


207526_s_at
205
117.9
519.5
4.7
27
interleukin 1 receptor-like 1
IL1RL1


215203_at
847.9
423.2
2505.9
52
27
golgi autoantigen, golgin subfamily a, 4
GOLGA4


217607_x_at
225
134.6
475.7
2
27
eukaryotic translation initiation factor 4 gamma, 2
EIF4G2


220140_s_at
442.2
264.5
1143.6
19.5
27
sorting nexin 11
SNX11


220296_at
283.9
169.2
806
13.1
27
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-
GALNT10








acetylgalactosaminyltransferase 10 (GalNAc-T10)



205547_s_at
358.7
262.2
1771
11.8
27
transgelin
TAGLN


207479_at
130.3
26.9
503.6
1.7
27
—
—


211538_s_at
335.4
178.3
6151.6
10.9
27
heat shock 70 kDa protein 2
HSPA2


217302_at
201.1
124.7
577.8
8.8
27
olfactory receptor, family 2, subfamily F, member 2
OR2F2


220550_at
126.2
51.7
542.1
2.6
27
F-box protein 4
FBXO4


207357_s_at
235
109.4
1081.7
9.9
27
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-
GALNT10








acetylgalactosaminyltransferase 10 (GalNAc-T10)



212392_s_at
203.4
152.7
545
11.9
27
phosphodiesterase 4D interacting protein (myomegalin)
PDE4DIP


213606_s_at
198.8
76.2
989.3
1.2
27
Rho GDP dissociation inhibitor (GDI) alpha
ARHGDIA


202040_s_at
1505.6
1348.4
2800
323.2
27
Jumonji, AT rich interactive domain 1A (RBBP2-like)
JARID1A


202588_at
475.2
260
665.6
33.5
27
adenylate kinase 1
AK1


203272_s_at
767.6
394.4
820.6
38.4
27
tumor suppressor candidate 2
TUSC2


203869_at
227.4
154.5
412.2
7.5
27
ubiquitin specific peptidase 46
USP46


205315_s_at
583.5
457.3
879.7
21.4
27
syntrophin, beta 2 (dystrophin-associated protein A1,
SNTB2








59 kDa, basic component 2)



208503_s_at
955.4
562.3
1110.6
62.7
27
GATA zinc finger domain containing 1
GATAD1


208506_at
187.1
113.7
296.6
3.6
27
histone 1, H3f
HIST1H3F


208859_s_at
717.8
264.6
975.1
8.1
27
alpha thalassemia/mental retardation syndrome X-linked
ATRX








(RAD54 homolog, S. cerevisiae)



208879_x_at
523
396.2
924.3
10.8
27
chromosome 20 open reading frame 14
C20orf14


212794_s_at
6236.8
2719.2
8965.8
303
27
KIAA1033
KIAA1033


213223_at
1355.5
995.3
1388.3
48.2
27
ribosomal protein L28
RPL28


213879_at
680.6
451.6
1000.1
31.2
27
SMT3 suppressor of mif two 3 homolog 2 (yeast)
SUMO2


215001_s_at
6297.3
4027
11499.9
107.4
27
glutamate-ammonia ligase (glutamine synthetase)
GLUL


217208_s_at
515.6
370
839.4
18.8
27
discs, large homolog 1 (Drosophila)
DLG1


217480_x_at
3170.5
1483.4
3437.3
282.6
27
similar to Ig kappa chain
LOC339562


217813_s_at
845.4
613.1
1204.4
48.6
27
spindlin
SPIN


219148_at
688.6
300.2
1139.4
16.5
27
PDZ binding kinase
PBK


220068_at
11799.9
7578.4
22254.1
78.9
27
pre-B lymphocyte gene 3
VPREB3


221051_s_at
249.1
122
462.4
4.6
27
integrin beta 1 binding protein 3
ITGB1BP3


222165_x_at
844.1
506
1300
14.9
27
chromosome 9 open reading frame 16
C9orf16


213751_at
255.7
70.7
596.5
5.5
27
hypothetical protein LOC284352
LOC284352


218012_at
2264.7
844.4
8541.7
53
27
TSPY-like 2
TSPYL2


219264_s_at
432
188.2
1178.5
5.9
27
protein phosphatase 2 (formerly 2A), regulatory subunit
PPP2R3B








B′′, beta



219994_at
886.4
477.3
2329.5
31
27
amyloid beta (A4) precursor protein-binding, family B,
APBB1IP








member 1 interacting protein



206142_at
224.2
87
536.9
2.2
27
zinc finger protein 135 (clone pHZ-17)
ZNF135


217332_at
166
71.5
865.4
3.5
27
Hypothetical LOC387937
LOC387937


211751_at
89.3
37.7
420.3
2.9
27
phosphodiesterase 4D interacting protein (myomegalin)
PDE4DIP








/// phosphodiesterase 4D interacting protein









(myomegalin)



201204_s_at
331.7
173.1
1773.8
14
27
CDNA FLJ41000 fis, clone UTERU2016761, highly
—








similar to Homo sapiens ES/130 mRNA



204792_s_at
112
62.2
323.3
4.1
27
WD and tetratricopeptide repeats 2
WDTC2


211463_at
123.6
54.9
349.5
4
27
Zic family member 4
ZIC4


208690_s_at
6571.5
4976.5
24492
198.6
27
PDZ and LIM domain 1 (elfin)
PDLIM1


221037_s_at
61.6
35.4
551.3
0.5
27
solute carrier family 25 (mitochondrial carrier; adenine
SLC25A31








nucleotide translocator), member 31 /// solute carrier









family 25 (mitochondrial carrier; adenine nucleotide









translocator), member 31



206686_at
178
98.2
624.3
13.7
27
pyruvate dehydrogenase kinase, isoenzyme 1
PDK1


201161_s_at
15493.5
6381.9
21619.5
36.5
26
cold shock domain protein A
CSDA


203832_at
3801
1803.9
4672
216.6
26
enolase 1, (alpha) /// small nuclear ribonucleoprotein
ENO1 ///








polypeptide F
SNRPF


208919_s_at
2456.4
1631.2
2454.9
404.3
26
NAD kinase
NADK


209308_s_at
1454.5
1070.9
1764.3
94.4
26
BCL2/adenovirus E1B 19 kDa interacting protein 2
BNIP2


209336_at
509.8
276
745.3
15.7
26
PWP2 periodic tryptophan protein homolog (yeast)
PWP2H


211085_s_at
605.3
105.9
474.3
3.6
26
serine/threonine kinase 4 /// serine/threonine kinase 4
STK4


212078_s_at
932.1
633.4
1296.9
54.9
26
myeloid/lymphoid or mixed-lineage leukemia (trithorax
MLL








homolog, Drosophila)



218906_x_at
513.8
291.8
771.3
24.2
26
kinesin light chain 2
KLC2


219833_s_at
519.5
357.9
862.3
8.4
26
EF-hand domain (C-terminal) containing 1
EFHC1


90610_at
3305.2
2444.1
2899
500.2
26
leucine-rich repeats and calponin homology (CH) domain
LRCH4








containing 4



204180_s_at
596.7
442.4
1360.7
53.5
26
zinc finger protein 297B
ZNF297B


219213_at
336.6
193.6
1089.7
15.2
26
junctional adhesion molecule 2
JAM2


205106_at
185
127.5
477.4
17.3
26
mature T-cell proliferation 1
MTCP1


215669_at
218.9
124.5
1632.2
7.2
26
major histocompatibility complex, class II, DR beta 4
HLA-DRB4


208511_at
264.1
220
656.1
11.5
26
pituitary tumor-transforming 3
PTTG3


213906_at
210.5
99.7
700.2
5.6
26
v-myb myeloblastosis viral oncogene homolog (avian)-like 1
MYBL1


216070_at
96
60.7
453
1.9
26
ATPase, Na+/K+ transporting, beta 1 polypeptide
ATP1B1


221674_s_at
165.4
84.5
539.1
11.1
26
chordin
CHRD


215901_at
117.6
99
461
3.6
26
zinc finger protein 81 (HFZ20)
ZNF81


217085_at
70.6
36.4
382.5
2.3
26
Solute carrier family 14 (urea transporter), member 2
SLC14A2


205376_at
93.9
65.4
516.9
2.1
26
inositol polyphosphate-4-phosphatase, type II, 105 kDa
INPP4B


208096_s_at
76.5
45.3
480.1
3.1
26
collagen, type XXI, alpha 1 /// collagen, type XXI, alpha 1
COL21A1


205933_at
434.8
329.6
2712.4
9.5
26
SET binding protein 1
SETBP1


204446_s_at
2632.3
1297.5
12918.8
3.8
26
arachidonate 5-lipoxygenase
ALOX5


201518_at
1663.8
1366.3
2814.1
80.4
26
chromobox homolog 1 (HP1 beta homolog Drosophila)
CBX1


202407_s_at
689.2
443.7
649.4
8.1
26
PRP31 pre-mRNA processing factor 31 homolog (yeast)
PRPF31


202937_x_at
632.3
314
1072.3
19.1
26
CGI-96 protein
CGI-96


203362_s_at
1114.5
849.3
2198.2
97
26
MAD2 mitotic arrest deficient-like 1 (yeast)
MAD2L1


208750_s_at
2763.3
1990.4
4772.1
326.7
26
ADP-ribosylation factor 1
ARF1


210458_s_at
140.3
64.3
256.2
1.9
26
TRAF family member-associated NFKB activator
TANK


210633_x_at
3072.4
2422
4202.8
624.1
26
keratin 10 (epidermolytic hyperkeratosis; keratosis
KRT10








palmaris et plantaris)



211804_s_at
761.5
573.6
1161.4
27.6
26
cyclin-dependent kinase 2
CDK2


213548_s_at
604.8
443
972.2
22.9
26
hypothetical protein H41
H41


217157_x_at
1340.3
507.1
1638.1
29.4
26
IGK mRNA for immunoglobulin kappa light chain VLJ
—








region, partial cds, clone: K142



219131_at
276.1
193.2
503.7
22.3
26
UbiA prenyltransferase domain containing 1
UBIAD1


219366_at
442.9
229.7
607.7
18.4
26
apoptosis, caspase activation inhibitor
AVEN


219807_x_at
1785.1
1074.6
1756
54.9
26
RAB4B, member RAS oncogene family
RAB4B


221734_at
583.9
329.7
1064.7
32.7
26
hypothetical protein MGC12103
LOC133619


222082_at
382.4
342.7
743.2
13
26
zinc finger and BTB domain containing 7A
ZBTB7A


41386j_at
2681.1
1537.2
3237.1
299.7
26
—
—


203753_at
5156.3
3589.5
11739.6
100.6
26
transcription factor 4
TCF4


206530_at
440.9
314.6
1126.1
26.8
26
RAB30, member RAS oncogene family
RAB30


211514_at
184.3
57.5
481.6
6.7
26
receptor interacting protein kinase 5
RIPK5


216894_x_at
256
28.2
537.5
3.6
26
cyclin-dependent kinase inhibitor 1C (p57, Kip2)
CDKN1C


220898_at
253.3
172.7
581.6
6.1
26
—
—


46142_at
786.4
434.8
1628.2
19.2
26
hypothetical protein FLJ12681
FLJ12681


214443_at
248.3
149.3
1045.7
9.7
26
poliovirus receptor
PVR


220702_at
484.2
331.2
1135.3
11.6
26
—
—


208180_s_at
481.3
295.3
1335.4
3.3
26
histone 1, H4h
HIST1H4H


207228_at
160.2
88
418.2
10.3
26
protein kinase, cAMP-dependent, catalytic, gamma
PRKACG


204257_at
1371.7
1160.5
6143
100.4
26
fatty acid desaturase 3
FADS3


205420_at
90.8
54.9
421.3
2.7
26
peroxisomal biogenesis factor 7
PEX7


213582_at
106.3
74.3
395.4
1.6
26
ATPase, Class VI, type 11A
ATP11A


213222_at
324.3
226.9
1351.7
3.6
26
phospholipase C, beta 1 (phosphoinositide-specific)
PLCB1


220893_at
128.5
44.9
548.2
4.2
26
uncharacterized gastric protein ZA52P
LOC57399


210848_at
153.2
122.9
459.4
5.4
26
—
—


214649_s_at
130.4
97.7
420
3.5
26
myotubularin related protein 2
MTMR2


209825_s_at
519.7
444.7
1963.8
8
26
uridine-cytidine kinase 2
UCK2


200914_x_at
913.4
714.2
983.4
106.9
26
kinectin 1 (kinesin receptor)
KTN1


203787_at
3369.3
2320.4
4268
120.7
26
single-stranded DNA binding protein 2
SSBP2


205932_s_at
529.7
159.8
978.8
11.1
26
msh homeo box homolog 1 (Drosophila)
MSX1


207700_s_at
2273.6
996.8
1781
167.3
26
nuclear receptor coactivator 3
NCOA3


210461_s_at
570.6
262.9
974.7
43.7
26
actin binding LIM protein 1
ABLIM1


213186_at
473.6
342.9
532
9.9
26
zinc finger DAZ interacting protein 3
DZIP3


214738_s_at
607.5
372.4
1062
13.5
26
NIMA (never in mitosis gene a)-related kinase 9
NEK9


218774_at
539.9
338.8
850.7
24.2
26
decapping enzyme, scavenger
DCPS


218908_at
525.1
270.4
786.4
17.6
26
alveolar soft part sarcoma chromosome region,
ASPSCR1








candidate 1



211386_at
286.8
178.2
604.1
5
26
hypothetical protein MGC12488
MGC12488


211177_s_at
344.7
152.3
781.9
16.1
26
thioredoxin reductase 2
TXNRD2


215117_at
661.4
193.7
1613.1
2.8
26
recombination activating gene 2
RAG2


206166_s_at
157.6
100.6
383.3
8.1
26
chloride channel, calcium activated, family member 2
CLCA2


211620_x_at
292.2
158.1
710.2
5.8
26
runt-related transcription factor 1 (acute myeloid leukemia
RUNX1








1; aml1 oncogene)



214828_s_at
268.6
174.9
680.9
10.9
26
similar to CGI-96
dJ222E13.2


209125_at
133.6
97.9
826.3
5.4
26
keratin 6A /// keratin 6C /// keratin 6E
KRT6A ///









KRT6C ///









KRT6E


219666_at
924.1
459.5
7946.9
14.9
26
membrane-spanning 4-domains, subfamily A, member
MS4A6A








6A



35974_at
3454.6
2149.4
18984.7
227.5
26
lymphoid-restricted membrane protein
LRMP


208015_at
324.6
243.5
3779.8
5
26
SMAD, mothers against DPP homolog 1 (Drosophila)
SMAD1


202718_at
113.1
58.5
4105.7
4.9
26
insulin-like growth factor binding protein 2, 36 kDa
IGFBP2


203401_at
837
652.7
1491.4
29.4
25
phosphoribosyl pyrophosphate synthetase 2
PRPS2


203907_s_at
2033.9
1446.6
3024.1
138
25
IQ motif and Sec7 domain 1
IQSEC1


205017_s_at
339.5
185.8
617.6
12.6
25
muscleblind-like 2 (Drosophila)
MBNL2


208248_x_at
3004.5
1846.7
5417.3
311.7
25
amyloid beta (A4) precursor-like protein 2
APLP2


213007_at
1438.7
874.5
1714.6
104.6
25
hypothetical protein FLJ10719
FLJ10719


216187_x_at
9608.3
6081
10136.8
1384.5
25
Kinesin 2
KNS2


218308_at
2167.3
1016.3
2296.8
32.3
25
transforming, acidic coiled-coil containing protein 3
TACC3


219203_at
407.8
60.7
564.5
13.9
25
chromosome 14 open reading frame 122
C14orf122


222027_at
535.7
147
680
13.7
25
Nuclear casein kinase and cyclin-dependent kinase
NUCKS1








substrate 1



206408_at
211
62.4
454.5
6.6
25
leucine rich repeat transmembrane neuronal 2
LRRTM2


213623_at
330.1
213.7
833
8.8
25
kinesin family member 3A
KIF3A


215459_at
317
169.2
668
7.5
25
Tax1 (human T-cell leukemia virus type I) binding
TAX1BP3








protein 3



206079_at
343.8
180.7
938.1
11.4
25
choroideremia-like (Rab escort protein 2)
CHML


208465_at
135.9
43.4
1907.9
7.2
25
glutamate receptor, metabotropic 2
GRM2


61732_r_at
83.1
23.6
198.2
0.3
25
coiled-coil domain containing 2
CCDC2


64900_at
95.8
29.2
263.9
3
25
carbohydrate (N-acetylglucosamine 6-O)
CHST5 ///








sulfotransferase 5 /// hypothetical protein MGC15429
MGC15429


215653_at
66.6
14.5
411.1
0.3
25
Glypican 5
GPC5


208054_at
83.6
43.8
792.6
2.8
25
hect domain and RLD 4
HERC4


219948_x_at
55.7
18.7
366
1
25
UDP glucuronosyltransferase 2 family, polypeptide A3
UGT2A3


208394_x_at
81.2
54.2
1063.4
2.3
25
endothelial cell-specific molecule 1
ESM1


207555_s_at
356.3
210.5
600.8
14.6
25
thromboxane A2 receptor
TBXA2R


208319_s_at
2462.3
1579.7
4284.6
231.2
25
RNA binding motif (RNP1, RRM) protein 3
RBM3


208415_x_at
2728.8
1776.8
2291.1
315.2
25
inhibitor of growth family, member 1
ING1


209878_s_at
832.2
497.4
1166.4
19.8
25
v-rel reticuloendotheliosis viral oncogene homolog A,
RELA








nuclear factor of kappa light polypeptide gene enhancer









in B-cells 3, p65 (avian)



212475_at
260.3
199.7
517.2
18.7
25
KIAA0241 protein
KIAA0241


212867_at
1495.5
1330.8
1768.6
356.9
25
Nuclear receptor coactivator 2 /// Nuclear receptor
NCOA2








coactivator 2



213351_s_at
489.6
270.8
934.5
9.5
25
transmembrane and coiled-coil domain family 1
TMCC1


214447_at
467.1
178.1
514.6
7.8
25
v-ets erythroblastosis virus E26 oncogene homolog 1
ETS1








(avian)



214861_at
273.2
180.4
482.4
8.3
25
jumonji domain containing 2C
JMJD2C


215415_s_at
378.9
114.3
474.7
7.7
25
lysosomal trafficking regulator
LYST


216172_at
429.1
230.1
708.1
23.5
25
Exosome component 2
EXOSC2


219971_at
237.9
51.2
428
6.2
25
interleukin 21 receptor
IL21R


210057_at
163.6
112.5
892.7
2.5
25
PI-3-kinase-related kinase SMG-1
SMG1


212949_at
375.3
184.4
766.8
20.7
25
barren homolog (Drosophila)
BRRN1


220674_at
323.7
255.8
689.3
6.1
25
hypothetical protein FLJ22814
FLJ22814


63825_at
491.4
340.1
1073.4
14.8
25
—
—


203334_at
444
238.8
946.9
17.3
25
DEAH (Asp-Glu-Ala-His) box polypeptide 8
DHX8


209145_s_at
251.4
105.7
544.1
9.8
25
core-binding factor, runt domain, alpha subunit 2;
CBFA2T2








translocated to, 2



216898_s_at
139.4
62.3
546.7
2.9
25
collagen, type IV, alpha 3 (Goodpasture antigen)
COL4A3


219181_at
218.6
128.5
1224.7
4.1
25
lipase, endothelial
LIPG


221606_s_at
156.6
78.7
352
3.4
25
nucleosomal binding protein 1
NSBP1


205577_at
361.7
123.3
1258.9
10.9
25
phosphorylase, glycogen; muscle (McArdle syndrome,
PYGM








glycogen storage disease type V)



217505_at
84
10.4
833.9
0.6
25
kelch-like 23 (Drosophila)
KLHL23


208961_s_at
5616
1346.2
20947.3
27.6
25
Kruppel-like factor 6
KLF6


217787_s_at
322.8
234.4
1316.5
6.6
25
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-
GALNT2








acetylgalactosaminyltransferase 2 (GalNAc-T2)



207575_at
148
70.7
549.6
7
25
golgi autoantigen, golgin subfamily a, 6
GOLGA6/


206556_at
102.7
72.1
364.7
7.4
25
clusterin-like 1 (retinal)
CLUL1


211646_at
69.8
34.3
452.3
2.7
25
Similar to KIAA1501 protein /// Similar to KIAA1501
LOC388248








protein



213836_s_at
140
94.2
467.8
8.7
25
WD40 repeat protein Interacting with phosphoInositides
WIPI49








of 49 kDa



216498_at
96.5
66.5
393.4
4.2
25
—
—


219157_at
991.2
639.9
6082.6
20.2
25
kelch-like 2, Mayven (Drosophila)
KLHL2


214282_at
60.3
31.1
462.2
0.3
25
Hermansky-Pudlak syndrome 3
HPS3









Normal” Controls
In one embodiment, a “normal control” used in the methods and kits of the invention are taken from a subject, or pool of subjects diagnosed and validated as “normal.” As discussed elsewhere herein, the corresponding predictive markers which are assayed in these samples can include, but are not limited to, CD19, CD10, CD34, CD45, CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 and CD300a or combinations thereof. In embodiments of the invention, specimens from normal controls correspond to blood or bone marrow specimens classified as nonmalignant, benign, and/or other conditions that are not considered to be indicative of clinical disease.
In specific embodiments, it may be necessary to phenotypically differentiate “hematogones” in normal controls from leukemic cells in ALL specimens. Hematogones are benign lymphoid precursors whose morphology and immunophenotype are similar to the blasts found in ALL, but are considered distinctive from cells indicative of MRD or ALL. Hematogone cells are more commonly found in pediatric bone marrow aspirates following therapy.
It is recognized that the accuracy of detecting and diagnosing minimal residual disease in ALL leukemia will vary based on the strength of the correlation between the expression levels of the differentially expressed genes when compared to normal controls. When the values in the expression profiles represent the expression levels of genes whose expression is strongly correlated with the physiologic condition, it may be possible to use a fewer number of values in the expression profile and still obtain an acceptable level of diagnostic or prognostic accuracy.
RNA Expression Profiling
The values in the expression profiles of the invention are measurements representing the absolute or the relative expression level of differentially expressed genes. The expression levels of marker genes may be determined by any method known in the art for assessing the expression level of an RNA molecule in a specimen. For example, expression levels of RNA may be monitored using a membrane blot (such as used in hybridization analysis such as Northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are expressly incorporated herein by reference. Gene expression detection may also comprise nucleic acid probes in solution. Expression levels of RNA may also be monitored using the reverse transcriptase polymerase chain reaction (e.g., TaqMan®).
In one embodiment, microarrays are used to measure the values to be included in the expression profiles. Microarrays are particularly well suited for this purpose because of the reproducibility between different experiments. DNA microarrays provide one method for the simultaneous measurement of the expression levels of large numbers of genes. Each array consists of a reproducible pattern of capture probes attached to a solid support. Labeled RNA or DNA is hybridized to complementary probes on the array and then detected by laser scanning. Hybridization intensities for each probe on the array are determined and converted to a quantitative value representing relative gene expression levels. See, TABLE 1 and TABLE 2. See also, U.S. Pat. Nos. 6,040,138, 5,800,992 and 6,020,135, 6,033,860, and 6,344,316, which are incorporated herein by reference. High-density oligonucleotide arrays are particularly useful for determining the gene expression profile for a large number of RNA's in a sample.
In one approach, total mRNA isolated from cells taken from the subject is converted to labeled cDNA and then hybridized to an oligonucleotide array. Each specimen is hybridized to a separate array. Relative transcript levels are calculated by reference to appropriate controls present on the array and in the sample.
Embodiments of the invention, can include, but are not limited to, the detection of mRNA expression with probes specific for genes shown in TABLE 1 comprising genes overexpressed in B-lineage ALL. Other embodiments of the invention, can include, but are not limited to, the detection of mRNA expression with probes specific for genes shown in TABLE 2 comprising genes underexpressed in B-lineage ALL.
In embodiments of the invention, an expression profile is generated by the detection of nucleic acid corresponding to the expression of mRNA from a specimen. As a first step, a specimen is contacted with a set of probes to CD19 and CD10, wherein a first probe specifically binds to CD19 and a second probe specifically binds to CD10. As a second step a CD19+/CD10+ cell is isolated from said specimen. As a third step, an expression level of at least two gene products encoding CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a is determined in said CD19+/CD10+ isolated cell population from step two. As a forth step, an expression profile is generated of the CD19+/CD10+ cells of step two. The expression profile of step four, displaying a modulated level of at least one gene product, is indicative of minimal residual disease in acute lymphoblastic leukemia. In embodiments of the invention, modulation of the gene product detected from gene products encoding CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 and CD300a, relative to a normal control, is indicative of minimal residual disease in acute lymphoblastic leukemia.
As is well understood in the art and in yet other embodiments of the invention, various subsets of cells can be isolated for analysis, for example, it may be advantageous to compare CD19+, CD10− cells. In yet other embodiments, other combinations of probes may be included in the first step, for example, CD19, CD10, CD45, and CD34. For example, the subpopulations of cells that can be isolated by contacting a specimen with probes to markers CD19, CD10, CD45, and CD34 can include, but are not limited to: CD19+, CD10+, CD45+, and CD34+ cells; CD19+, CD10−, CD45+, and CD34+ cells; CD19+, CD10−, CD45−, and CD34+ cells; CD19+, CD10−, CD45+, and CD34−; CD19+, CD10+, CD45−, and CD34+ cells; CD19+, CD10+, CD45+, and CD34−; and CD19+, CD10+, CD45−, and CD34− cells. All of the preceeding subpopulations of cell can be isolated by contacting the specimen with said plurality of probes, but in addition, modulated activity of any one probe of that combination could also be selected thereby increasing the number of subpoplations analysed. The design of assays to optimize detection conditions and determining cell sorting conditions is standard and well within the routine capabilities of those of ordinary skill in the art.
In embodiments of the invention, determining the expression profile of the specimen that is CD10+/CD19+ further comprises probe combinations comprising (a) CD38, CD24, and CD44; (b) CD38, CD58, and CD44; (c) CD38, CD73, and CD15; (d) CD38, CD200, and CD44; (e) CD66c, CD123, and CD86; (f) CD72, CD13, and CD33; or (g) CD79b, HSPB1, and Bcl-2. In embodiments of the invention said modulated level comprises overexpression of CD44, CD58, CD73, CD200, CD86, HSPB1, BCL2, CD164, CD97, CD99, or CD300a and/or the underexpression of CD38, CD72, or CD79b, relative to a normal control.
In embodiments of the invention, determining the expression level of a gene product in cells expressing each of CD19, CD10, CD34, and CD45, can further comprise probes to detect at least four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, twenty-one, or twenty-two markers comprising: CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a.
Protein Expression Profile and Antibody Detection
In other embodiments, the values in the expression profile are obtained by measuring the abundance of the protein products of the differentially-expressed genes. The abundance of these protein products can be determined, for example, using antibodies specific for the protein products of the differentially-expressed genes. The term “antibody” as used herein refers to an immunoglobulin molecule or immunologically active portion thereof, i.e., an antigen-binding portion. Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab′)2 fragments, which can be generated by treating the antibody with an enzyme such as pepsin.
The terms “antibody” and “antibodies” broadly encompass naturally occurring forms of antibodies and recombinant antibodies such as single-chain antibodies, chimeric and humanized antibodies and multi-specific antibodies as well as fragments and derivatives of all of the foregoing, which fragments and derivatives have at least an antigenic binding site (e.g., Fab′, F(ab)2, Fv, single chain antibodies, diabodies). Antibody derivatives may comprise a protein or chemical moiety conjugated to the antibody.
In embodiments of the invention, the antibody can be a polyclonal, monoclonal, or recombinant, e.g., a chimeric or humanized, fully human, non-human (e.g., murine, or single chain antibody). The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts.
The term “polyclonal antibody” as used herein refers to an antibody obtained from a population of heterogeneous antibodies derived from a multiple B cell response to an antigen which will recognize a variety of epitopes on the antigen. Polyclonal antibodies can be prepared by immunizing a suitable subject (e.g., rabbit, goat, mouse, or other mammal) with a marker protein immunogen. The antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized biomarker protein. At an appropriate time after immunization, e.g., when the antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein, C. (1975) Nature 256:495-497, the human B cell hybridoma technique (Kozbor, et al. (1983) Immunol. Today 4:72), the EBV-hybridoma technique (Cole, et al. (1985) in Monoclonal Antibodies and Cancer Therapy, ed. Reisfeld and Sell (Alan R. Liss, Inc., New York, N.Y.), pp. 77-96) or trioma techniques. The technology for producing hybridomas is well known (see generally Coligan, et al. eds. (1994) Current Protocols in Immunology (John Wiley & Sons, Inc., New York, N.Y.); Galfre et al. (1977) Nature 266:550-52; Kenneth (1980) in Monoclonal Antibodies: A New Dimension In Biological Analyses (Plenum Publishing Corp., NY); and Lerner (1981) Yale J. Biol. Med., 54:387 402).
As an alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with a marker protein to thereby isolate immunoglobulin library members that bind the marker protein. Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAPTM Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, U.S. Pat. No. 5,223,409; PCT Publication Nos. WO 92/18619; WO 91/17271; WO 92/20791; WO 92/15679; 93/01288; WO 92/01047; 92/09690; and 90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBO J. 12:725-734.
Antigen-binding fragments and variants of the monoclonal antibodies disclosed herein are contemplated and within the scope of the present invention. Such variants, for example, will retain the desired binding properties of the parent antibody. Methods for making antibody fragments and variants are generally available in the art. For example, amino acid sequence variants of a monoclonal antibody described herein can be prepared by mutations in the cloned DNA sequence encoding the antibody of interest. Methods for mutagenesis and nucleotide sequence alterations are well known in the art. See, for example, Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York); Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods Enzymol. 154:367-382; Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, N.Y.); U.S. Pat. No. 4,873,192; and the references cited therein; herein incorporated by reference. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the polypeptide of interest may be found in the model of Dayhoff et al. (1978) in Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C.), herein incorporated by reference. Conservative substitutions, such as exchanging one amino acid with another having similar properties, may be preferred.
Preferably, variants of an antibody to a reference marker will have amino acid sequences that have at least 70% or 75% sequence identity, preferably at least 80% or 85% sequence identity, more preferably at least 90%, 91%, 92%, 93%, 94% or 95% sequence identity to the amino acid sequence for the reference antibody molecule, or to a shorter portion of the reference antibody molecule. More preferably, the molecules share at least 96%, 97%, 98% or 99% sequence identity. For purposes of the present invention, percent sequence identity is determined using the Smith-Waterman homology search algorithm using an affine gap search with a gap open penalty of 12 and a gap extension penalty of 2, BLOSUM matrix of 62. The Smith-Waterman homology search algorithm is taught in Smith and Waterman (1981) Adv. Appl. Math. 2:482-489. A variant may, for example, differ from the reference antibody by as few as 1 to 15 amino acid residues, as few as 1 to 10 amino acid residues, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
In embodiments of the invention, an antibody can be used to detect the marker or protein product of a differentially expressed gene in order to evaluate the abundance and pattern of expression of the protein. These antibodies can also be used diagnostically to monitor protein expression levels over time as part of a clinical monitoring procedure, e.g., determine the efficacy of a given therapy and reoccurrence of disease.
In embodiments of the invention, antibodies specifically bind to and detect markers comprising CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
In embodiments of the invention antibodies specifically bind to and detect markers comprising CD19, CD10, CD34, CD45, CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a.
Embodiments of the invention include antibodies described in TABLE 3, TABLE 4, and TABLE 5.
Optical Detection Methods:
Detection of antibodies can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance (i.e., antibody labeling). Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials (fluorophores, flurochromes), luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of fluorophores/flurochromes, include phycoerythrin (PE), fluorescein isothiocyanate (FITC), peridinin-chlorophyll (PerCP), allophycocyanin (APC), R-phycoerythrin conjugated with cyanine dye (PE-Cy7), allophycocyanin-cyanine tandem (APC-H7), coumarin dye (Horizon v450), sulphonyl chloride (Texas Red), cyanine (CY3, CY5, Cy7), FAM, JOE, TAMRA, TET, VIC, rhodamine; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 125I, 131I, 35S or 3H. The skilled artisan will understand that additional moieties may be suitable for the method of the invention.
A detectable moiety generally refers in one embodiment to a composition or moiety that is detectable by spectroscopic, photochemical, biochemical, immunochemical, electromagnetic, radiochemical or chemical means such as fluorescence, chemifluorescence, or chemiluminescence, or any other appropriate means. The terms “fluorophore” and “fluorochrome” are defined as a chemical group, or component of a molecule that causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. A fluorophore/fluorchrome can refer to various fluorescent substances, including dyes, used in fluorescence microscopy or flow cytometry to stain specimens. The terms fluorophore” and “fluorochrome” are herein used interchangeably.
Fluorochromes may be conjugated to antibodies, proteins, polypeptides, peptides, or nucleotide probes which specifically bind to antigens, proteins, polypeptides, peptides, polysaccharides, DNA, or RNA sequences. Thus, binding of an antibody, protein, polypeptide, peptide, or nucleotide probe to an antigen, protein, polypeptide, peptide, polysaccharide, DNA, or RNA may be detected by measuring a signal generated from a fluorochrome by flow cytometry, or any suitable optical imaging technique. Detection of a signal may indicate binding, whereas lack of detection of a signal may indicate lack of binding.
Methods and compositions for detectably labeling nucleic acid probes, such as oligonucleotides, DNA-RNA hybrids, etc. are well known in the art. See, e.g., U.S. Pat. Nos. 6,316,230; 6,297,016; 6,316,610; 6,060,240; 6,150,107; and 6,028,290, each of which is hereby incorporated by reference in their entirety.
The compositions of the invention further comprise monoclonal antibodies and variants and fragments thereof that specifically bind to marker proteins of interest, thereby forming a detectable complex. The monoclonal antibodies may be labeled with a detectable substance to facilitate marker protein detection in the sample. Such antibodies find use in practicing the methods of the invention. Monoclonal antibodies having the binding characteristics of the antibodies disclosed herein are also encompassed by the present invention. Compositions further comprise antigen-binding variants and fragments of the monoclonal antibodies.
In embodiments of the invention, a probe is an antibody, including but not limited to a whole antibody molecule, a F(ab′)2, Fab′, Fv, Fd′, or Fd fragment. In yet other embodiments, an antibody can be conjugated with a detectable moiety, wherein the detectable moiety can be, for example, a fluorophore, a chromophore, a radionuclide, or an enzyme. In embodiments of the invention a fluorophore can for example, can be, but is not limited to, phycoerythrin (PE), fluorescein isothiocyanate (FITC), peridinin-chlorophyll (PerCP), allophycocyanin (APC), R-phycoerythrin conjugated with cyanine dye (PE-Cy7), allophycocyanin-cyanine tandem (APC-H7), and coumarin dye (Horizon v450). Detection of complexes formed between an antibody probe and marker can be achieved by an optical detection technique, including, but not limited to flow cytometry and microscopy.
“Cell staining” when used in reference to an antibody means that the antibody recognizes an marker and binds to marker in the specimen forming a complex, thereby “labeling” or otherwise “staining” the cell expressing the marker to make it visible and/or detectable by microscopy or flow cytometry. Combinations of antibodies can be collectively added a specimen and thereby “stain the cell” for later analysis by visualization with a flow cytometer or microscope, for example. One of skill in the art could determine whether a cell expressed a specific protein based on the level of antibody that bound to the cell using standard methods.
The methods of the invention can also be used in immunofluorescence histochemistry. This technique involves the use of antibodies labeled with various fluorophores to detect substances within a specimen. In exemplary embodiments a pathologist can derive a great deal of morphological information of diagnostic value by examining a specimen from a subject by microscope. Immunohistochemistry is particularly relevant to, for example, the early diagnosis of cancer or pre-acute states such as minimal residual disease in ALL. Combinations of fluorophores or other detectable labels can be used by the methods on this invention, thereby greatly increasing the number of distinguishable signals in multicolor protocols.
In another embodiment, the method employs flow cytometry. In another embodiment, in a peripheral blood sample or blood sample, lymphocyte, monocyte and granulocyte populations can be defined on the basis of forward and side scatter. Forward and side scatter are used in one embodiment to exclude debris and dead cells.
Flow cytometry is an optical technique that analyzes particles or cells in a fluid mixture based on their optical characteristics, via the use of a flow cytometer (See, for example, Shapiro, “Practical Flow Cytometry,” Third Ed. (Alan R. Liss, Inc., 1995); and Melamed et al. “Flow Cytometry and Sorting,” Second Ed. (Wiley-Liss 1990)). Flow cytometers hydrodynamically focus a fluid suspension of particles/cells into a thin stream so that they flow down the stream in substantially single file and pass through an examination zone. A focused light beam, such as a laser beam illuminates the particles as they flow through the examination zone. Optical detectors within the flow cytometer measure certain characteristics of the light as it interacts with the particles/cells. Commonly used flow cytometers such as the Becton-Dickinson Immunocytometry Systems “FACSCAN” (San Jose, Calif.) can measure forward light scatter (generally correlated with the refractive index and size of the particle/cell being illuminated), side light scatter (generally correlated with the cell granularity), and particle fluorescence at one or more wavelengths. Data acquisition and analysis can be done using FASCALIBER® LSRII flow cytometers (Becton Dickinson), and CELLQUEST ProTM, BD FACSDIVATM software (both from Becton Dickinson), FLOWJO software (Tree Star, Ashland, Oreg.) and/or KALUZATM software (Beckman Coulter, Miami, Fla.) (Campana, D. (2009) Hematol Oncol Clin North Am. 23; 1083-98, vii).
In embodiments of the invention, determining an expression profile of a specimen is generated using combinations of probes that bind specifically to CD10, CD19, CD34, and CD45, wherein combinations comprise (a) CD10, CD19, CD34, CD45, CD38, CD24, and CD44; (b) CD10, CD19, CD34, CD45, CD38, CD58, and CD44; (c) CD10, CD19, CD34, CD45, CD38, CD73, and CD15; (d) CD10, CD19, CD34, CD45, CD38, CD200, and CD44; (e) CD10, CD19, CD34, CD45, CD66c, CD123, and CD86; (f) CD10, CD19, CD34, CD45, CD72, CD13, and CD33; or (g) CD10, CD19, CD34, CD45, CD79b, HSPB1, and Bcl-2.
In other embodiments of the invention, antibodies can be directly conjugated for simultaneous detection. For example, a method of the invention can comprise antibodies directly conjugated to a detectable fluorochrome for simultaneous detection of a plurality of markers wherein: CD34 is conjugated to PerCP, CD19 is conjugated to APC, CD10 is conjugated to PE-Cy5, CD45 is coupled to APC-H7, CD38 is conjugated to FITC, CD24 is conjugated to PE, CD44 is conjugated to Horizon v450, CD58 is conjugated to PE, CD73 is conjugated to PE, CD15 is conjugated to Horizon v450, CD200 is conjugated to PE, CD66c is conjugated to FITC, CD123 is conjugated to PE, CD86 is conjugated to Horizon v450, CD72 is conjugated to FITC, CD13 is conjugated to PE, CD33 is conjugated to v450, CD79b is conjugated to FITC, HSPB1 is conjugated to PE, and Bcl2 is conjugated to Horizon V450. The skilled artisan will understand that any one antibody marker can be coupled to any fluorochrome for use in combination with any other antibody, and that preferred combinations can be used simultaneously with other antibody markers by the selection of different combinations of antibodies labeled with different flurochromes.
TABLE 3 shows exemplary marker combinations for detection of MRD in B-lineage ALL incorporating the top 10 differentially expressed markers including CD24, CD44, CD73, CD200, CD123, CD86, CD72, CD79b, HSPB1, and Bcl2.







TABLE 3







Marker combinations used for MRD studies in B-lineage ALL


incorporating the top 10 differentially expressed markers


discovered in this study (in italics)



















Horizon


FITC
PE
PerCP
APC
PE-Cy7
APC-H7
v450





CD38
CD24
CD34
CD19
CD10
CD45
CD44


CD38
CD58
CD34
CD19
CD10
CD45
CD44


CD38
CD73
CD34
CD19
CD10
CD45
CD15


CD38
CD200
CD34
CD19
CD10
CD45
CD44


CD66c
CD123
CD34
CD19
CD10
CD45
CD86


CD72
CD13
CD34
CD19
CD10
CD45
CD33


CD79b
HSPB1
CD34
CD19
CD10
CD45
Bcl2









Cell Sorting and Selection of Subpopulations of Cells in a Specimen
Multiparameter flow cytometric cell analysis can be used as part of the methods of this invention. The simultaneous analysis of multiple predictive parameters using flow cytometry is known to those of skill in the art. In one embodiment, the population of cells to be analyzed is contacted with a panel of antibodies directed against distinct cell surface markers, under conditions effective to allow antibody probe binding. The antibodies employed can be monoclonal antibodies, and can, in another embodiment, be labeled in a manner to allow their subsequent detection.
In embodiments of the invention, fluorochromes can be excited by at least two different lasers to give off light of at least four different wavelengths, with the potential, for simultaneous analysis of at least four different markers. An additional two parameters include two light scattering parameters; direct and orthogonal, or side-scattering capability which can be analyzed concurrently with antibody detection, thereby allowing for cell analysis on the basis of at least 6 parameters. In embodiments of the invention at least five, six, seven, eight, nine, ten, eleven, or twelve different antibody probes, can be used simultaneously, thereby allowing for cell analysis on the basis of at least seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen different parameters.
Multiparameter cell sorting can be used in an embodiment of the invention to isolate cells based on a specific expression profile. For example, in one embodiment cell sorting analysis can be achieved using fluorescence-activated flow cytometry, by methods well described in the art. In one embodiment cells can be sorted based on the co-expression of markers CD19 and CD10, wherein in combination with the expression of CD19 and CD10 the expression of other markers can be interrogated. In another embodiment of the invention, mRNA expression profiles can be generated from a purified population of CD19+ and CD10+ cells isolated from a subject specimen for the purpose of diagnosing minimal residual disease.
As is well understood in the art and in yet other embodiments of the invention, various subsets of cells can be isolated for analysis, for example, it may be advantageous to compare CD19+, CD10+ cells and CD19+, CD10− cells. Both subpopulations can be isolated by contacting the specimen with probes to CD19 and CD10, whereas in one condition cells are positively selected (CD19+, CD10+), and in the later, are negatively selected (CD19+, CD10−). Likewise, in yet other embodiments, other combinations of probes may be included in a first step, for example, CD19, CD10, CD45, and CD34, wherein modulated levels of CD45 and CD34 may be reflected in the subsets that are isolated. For example, the subpopulations of cells that could be isolated by contacting a specimen with probes to markers CD19, CD10, CD45, and CD34 could include, but are not limited to: CD19+, CD10+, CD45+, and CD34+ cells; CD19+, CD10−, CD45+, and CD34+ cells; CD19+, CD10−, CD45−, and CD34+ cells; CD19+, CD10−, CD45+, and CD34−; CD19+, CD10+, CD45−, and CD34+ cells; CD19+, CD10+, CD45+, and CD34−; and CD19+, CD10+, CD45−, and CD34− cells. All the preceeding subpopulations of cell could be isolated from by contacting the specimen with said probes, but in addition, using flow cytometry for example, modulated activity could representative of a spectrum of expression to negative to positive, and also be selected. The number of potential subpopulations analyzed could thereby increase the number of subpoplations analysed. The design of assays to optimize detection conditions and determining cell sorting conditions to isolate specific subpopulations of cells is standard and well within the routine capabilities of those of ordinary skill in the art.
In yet other embodiments of the invention, enrichment of specific subpopulations of cells can be achieved by other methods as well. For example a wide variety of magnetic bead separation and isolation procedures can be used to selectively negatively and positively enrich samples for specific subpopulations of cells. For example, in some embodiments a mixture of magnetic beads coupled to lineage specific antibodies can be used to deplete, T cells, NK cells, monocytes, platelets, dendritic cells, granulocytes and erythrocytes, thereby negatively isolating B cells. The skilled artisan will understand that combinations of different antibodies can be used alone or in combination, and in multiple successive rounds of isolation, to positively and/or negatively select for subpopulations of cells.
One of skill in the art will recognize that optimization of reagents and conditions, for example, antibody titer and parameters for detection of antigen-antibody binding, is needed to maximize the signal to noise ratio for a particular antibody. Antibody concentrations that maximize specific binding to the markers of the invention and minimize non-specific binding (or “background”) will be determined. In particular embodiments, appropriate antibody titers are determined by initially testing various antibody dilutions on patient serum samples. The design of assays to optimize antibody titer and detection conditions is standard and well within the routine capabilities of those of ordinary skill in the art. Some antibodies require additional optimization to reduce background and/or to increase specificity and sensitivity.
The skilled artisan will recognize that optimization of multiparameter assays designed to detect a plurality of antibody probes simultaneously will be necessary. In embodiments of the invention, maximization of signal to noise ratio, as well an optimization of fluorochrome combinations will be necessary for each of the antibody probes combinations. Conjugated-antibody concentrations that maximize specific binding to the markers of the invention and minimize non-specific binding (or “background”) will be determined with other such conjugated antibody probes as is known in the art. The design of assays to optimize and compensate the signals detected for the various conjugated antibodies is standard and well within the routine capabilities of those of ordinary skill in the art. Some antibodies require additional optimization to reduce background and/or to increase specificity and sensitivity.
Antibody and Nucleic Acid Probes to Target Genes
The antibodies used to practice the invention are selected to have high specificity for the marker proteins of interest. Methods for making antibodies and for selecting appropriate antibodies are known in the art. In some embodiments, commercial antibodies directed to specific marker proteins may be used to practice the invention (see TABLE 4). The antibodies of the invention may be selected on the basis of desirable staining of cytological, rather than histological, samples. That is, in particular embodiments the antibodies are selected with the desired combination in mind and for binding specificity.
The markers and combinations of markers of the invention include genes or proteins that are selectively expressed, overexpressed or underexpressed in leukemia, and specifically in ALL, as defined herein above, and may be combined with known markers as well as those presently unknown in the art. In particular embodiments, markers are intracellular proteins, secreted proteins or proteins that are predicted to encode membranous proteins with transmembrane segments and extracellular domains. In some embodiments of the invention, probes can detect markers that are polypeptides expressed at the surface of the cell. In other embodiments, probes can detect markers that are polypeptides expressed intracellularly. In still other embodiments, probes detect markers that are polynucleotides. In still other embodiments, kits and methods of invention can comprise probes that can detect markers that include polypeptides and polynucleotides.
The methods of the invention can comprise MRD detection by gene array with preferred combinations of markers. MRD detection can be combined, for example, with at least 3 different marker combinations. Embodiments of the invention, can include, but are not limited to, the detection of mRNA expression with probes specific for genes shown in TABLE 1 comprising genes overexpressed in B-lineage ALL. Other embodiments of the invention, can include, but are not limited to, the detection of mRNA expression with probes specific for genes shown in TABLE 2 comprising genes underexpressed in B-lineage ALL.
Embodiments of the invention can include, but are not limited to, compositions and methods related to the detection of new markers for minimal residual disease (MRD) comprising: CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
In yet other embodiments, diagnosing minimal residual disease in a sample taken from a subject can comprise the detection of combinations of markers including, but not limited to markers CD19, CD10, CD34, and CD45, in combination with markers comprising CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
In yet other embodiments, diagnosing minimal residual disease in a sample taken from a subject can comprise the detection of combinations of markers including, but not limited to: CD19, CD10, CD34, and CD45, in combination with markers comprising CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a.
“CD” or “cluster designation” refers to a system to classify cell markers defining cells based on what molecules are present on their surface. These “cell markers” or “markers” are often used to associate cells with certain immune functions. While using one CD molecule to define populations is uncommon (though a few examples exist), combining markers is often used to identify cell types with very specific characteristics within the immune system. The system was originally intended for the classification of the monoclonal antibodies (mAbs) generated by different laboratories around the world against epitopes on the surface molecules of leukocytes (white blood cells). Since then, the use of the CD nomenclature has expanded to include many other cell types, and more than 320 CD unique clusters and subclusters have been identified. In some instances CD antigens are expressed only at certain stages of development or under certain conditions, for example after cell activation or in certain disease conditions. Unlike the morphological criteria used in classical hematology for the description of specific developmental stages of lymphocytes, the use of monoclonal antibodies, and the “CD”marker annotation, allows the objective and precise analysis and standardized typing of mature and immature normal and malignant cells of all hematopoietic cell lineages. Antibodies that recognize cell surface markers can also be referred to by the CD designation. The CD designation can help to delineate the biologic traits that distinguish normal immune and hematopoietic cells from their malignant counterparts, which is of fundamental importance in understanding hematological malignancies.
The CD designation of molecules is often used to identify cells and expression patterns detected by various applications including flow cytometry. Very generally, cell populations can be defined using a ‘+’ or ‘−’ a symbol to indicate whether a certain cell fraction expresses or lacks a CD molecule. For example, a “CD34+, CD31−” cell is one that expresses CD34, but not CD31. This exemplary CD combination typically corresponds to a stem cell, opposed to a fully-differentiated endothelial cell. Therefore, generally speaking, use of CD with a number X, as in “CDX,” can refer to a protein that in humans is encoded by the CDX gene, for example. Markers can be referred to by their CD designation, but can also be referred to by the gene or encoded protein name. Antibodies recognizing specific proteins can also be referred to by the CD number of the marker that is recognized.
CD34 (cluster designation 34) encompasses the human gene at locus 1q32 corresponding to sequences having GENBANK® Accession Nos: NM_001773, NP_001764.1. The protein is a monomeric cell surface antigen with a molecular mass of approximately 110 kDa that is selectively expressed on human hematopoietic progenitor cells.
CD19 (cluster designation 19) encompasses the human gene at locus 16p11.2 corresponding to sequences having GENBANK® Accession Nos: NM_01178098 and NP_001171569.1. CD19 is a cell surface molecule expressed only by B lymphocytes and follicular dendritic cells of the hematopoietic system. It is the earliest of the B-lineage-restricted antigens to be expressed and is present on most pre-B cells and most non-T-cell acute lymphocytic leukemia cells and B-cell type chronic lymphocytic leukemia cells (Tedder and Isaacs, 1989. J. Immun. 143: 712-717).
CD10 (cluster designation 10) encompasses the human gene at locus 3q21-q27 corresponding to sequences GENBANK® Accession Nos: NM_000902 and NP_000893.2. The protein is also known as “membrane metallo-endopeptidase (MME)” or “common acute lymphocytic leukemia antigen (CALLA).” The common acute lymphocytic leukemia antigen (CALLA) is an important cell surface marker in the diagnosis of human acute lymphocytic leukemia (ALL). It is present on leukemic cells of pre-B phenotype, which represents 85% of cases of ALL. The CALLA gene encodes a 100 kDa type II transmembrane glycoprotein Barker et al. (1989) J. Immun. 142: 283-287.
CD45 (cluster designation 45), encompasses the human gene at locus 1q31-q32 corresponding to sequences having GENBANK® Accession Nos: NM_002838, NP_002829.2. CD45 is also called B220; CD45R; GP180; LCA; LY5; and T200. It is a membrane-bound protein tyrosine phosphatase expressed in various isoforms, of between 180 and 220 kDa in size. CD45 is expressed on virtually all leukocytes, including myeloid and lymphoid precursors in bone marrow and mature lymphocytes in lymph nodes. CD45 (T200) is expressed on all hematopoietic cells except mature red cells and their immediate progenitors. It is not found, however, on other differentiated tissues; thus, it can be used as an antigenic marker with which to identify undifferentiated hematopoietic tumors.
CD38 (cluster designation 38) encompasses the human gene at locus 4p15.32 corresponding to sequences having GENBANK® Accession Nos: NM_001775.2, NP_001766.2, as set forth in SEQ ID NO: 1 and SEQ ID NO:2, respectively. CD38 is commonly used as a human leukocyte differentiation marker and is a novel multifunctional ectoenzyme widely expressed in cells and tissues especially in leukocytes. CD38 also functions in cell adhesion, signal transduction and calcium signaling. It has been demonstrated to be involved in the synthesis and hydrolysis of Cyclic ADP-ribose (cADPR) (Takasawa et al. (1993). J. Biol. Chem. 268: 26052-26054, 1993). Cyclic ADP-ribose is generated in pancreatic islets by glucose stimulation, serving as a second messenger for Ca(2+) mobilization in the endoplasmic reticulum for secretion of insulin (Takasawa et al. (1993) Science 259: 370-373).
CD24 (cluster designation 24) encompasses the human gene at locus 6q21 corresponding to sequences having GENBANK® Accession Nos: NM_013230, NP_037362.1, as set forth in SEQ ID NO: 3 and SEQ ID NO:4, respectively. CD24 is also known as “small cell lung carcinoma cluster 4 antigen” Studies with monoclonal antibodies indicate that most other hematopoietic cells, including T cells, monocytes, red blood cells, and platelets, seem not to express the CD24 antigen. CD24 has been implicated in both activation and differentiation of B lymphocytes because its expression pattern changes at critical times during B-cell development. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone ML5 which reacts with a 35-45 kDa two-chain glycoprotein (see TABLE 4, BD PharmingenTM Cat. NO. 555428) (Schlossman et al. ed. (1995) Leukocyte Typing V: White Cell Differentiation Antigens. New York: Oxford University Press).
CD44 (cluster designation 44) encompasses the human gene at locus 11p13 corresponding to sequences having GENBANK® Accession Nos: NM_000610, NP_000601.3, as set forth in SEQ ID NO:5 and SEQ ID NO:6, respectively. It is also known as “Indian blood group” antigen. It is a receptor for hyaluronic acid and can also interact with other ligands, such as osteopontin, collagens, and matrix metalloproteinases (MMPs). This integral cell membrane glycoprotein participates in a wide variety of cellular functions including lymphocyte activation, recirculation and homing, hematopoiesis, and tumor metastasis (Aruffo et al. (1990) Cell 61: 1303-1313). In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone 515 which reacts with a 85 kDa glycoprotein expressed on leukocytes, erythrocytes, epithelial cells and weakly on platelets (see TABLE 4, BD PharmingenTM, Cat. NO. 5500989) (Patel et al. “CD44 Workshop Panel Report” In: Kishimoto et al, ed. (1997) Leukocyte Typing Vi: White Cell Differentiation Antigens. New York: Garland Publishing Inc: 373-375).
CD58 (cluster designation 58) encompasses the human gene at locus 1p13 corresponding to sequences having GENBANK® Accession Nos: NM_001779, NP_001770.1, as set forth in SEQ ID NO:7 and SEQ ID NO:8, respectively. CD58 is also known as “lymphocyte function-associated antigen (LFA3)”. The CD58 gene encodes a CD2 receptor. The presence of these both CD2 and CD58 antigens on opposing cells optimizes immune recognition, facilitating contacts between helper T lymphocytes and antigen-presenting cells as well as between cytolytic effectors and target cells (Wang et al. (1999) Cell 97: 791-803).
CD73 (cluster designation 73) encompasses the human gene at locus 6q14-q21 corresponding to sequences having GENBANK® Accession Nos: NM_002526 and NP_002517.1, as set forth in SEQ ID NO:9 and SEQ ID NO:10, respectively. CD73 is a membrane-bound enzyme also known as “ecto-5-prime-nucleotidase,” and is expressed on subsets of B-cells and T-cells as well as other cell types. The enzyme is used as a marker of lymphocyte differentiation. CD73 is thought to function as a cell adhesion molecule and to mediate lymphocyte binding to endothelial cells (Airas, L. et al. (1995) J. Exp. Med. 182(2): 1603-8) and adhesion between B-cells and follicular dendritic cells (Airas and Jalkanen (1996) Blood. 88(5):1755-64). In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone AD2 which reacts with a 70 kDa glycosyl phosphatidylinositol (GPI)-anchored glycoprotein expressed on subsets of T and B lymphocytes, follicular dendritic cells, epithelial cells, and endothelial cells (see TABLE 4, BD PharmingenTM, Cat. NO. 550257) (Schlossman et al. ed. (1995) Leukocyte Typing V: White Cell Differentiation Antigens. New York: Oxford University Press).
CD15 (cluster designation 15) encompasses the human gene at locus 11q12-qter corresponding to sequences having GENBANK® Accession Nos: NM_002033 and NP_002024.1, as set forth in SEQ ID NO:11 and SEQ ID NO:12, respectively. CD15 expresses a protein also known as “fucosyltransferase 4 (alpha (1,3),” “myeloid-specific fucosyltransferase,” “ELAM ligand fucosyltransferase,” and “galactoside 3-L-fucosyltransferase.” The product of this gene transfers fucose to N-acetyllactosamine polysaccharides to generate fucosylated carbohydrate structures. CD15 catalyzes the synthesis of the non-sialylated antigen, Lewis x (CD15).
CD200 (cluster designation 200) encompasses the human gene located at locus 3q12-q13 corresponding to sequences having GENBANK® Accession Nos: NM_001004196 and NP_001004196.2, as set forth in SEQ ID NO:13 and SEQ ID NO:14, respectively. CD200 was identified as a type II membrane glycoprotein expressed on a number of cell types relevant to the inflammatory and immune cascade, including dendritic cells, endothelial cells, and activated T cells. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone MRC OX-104 which recognizes a 40-45 kDa membrane glycoprotein expressed on resting and activated T cells and B cells, as well as a subset of CD34+ progenitor cells, but not on NK cells, monocytes, granulocytes, or platelets (see TABLE 4, BD PharmingenTM, Cat. NO. 552475) (Mason et al. ed. (2002) Leukocyte Typing VII. New York: Oxford University Press).
CD66c (cluster designation 66c) encompasses the human gene at locus 19q13.1-q13.2 corresponding to sequences having GENBANK® Accession Nos: NM_002483 and NP_002474.3, as set forth in SEQ ID NO:15 and SEQ ID NO:16, respectively. CD66c is also known as “carcinoembryonic antigen-related cell adhesion molecule.” CD66c is one of the most widely used tumor markers in serum immunoassay determinations of carcinoma.
CD123 (cluster designation 123) encompasses the human gene at loci Xp22.3 and Yp13.3 corresponding to sequences having GENBANK® Accession Nos: NM_002183 and NP_002174.1, as set forth in SEQ ID NO:17 and SEQ ID NO:18, respectively. CD123 is also known as the low affinity receptor for IL-3 encoding an interleukin 3 specific subunit of a heterodimeric cytokine receptor. The receptor is comprised of a ligand specific alpha subunit and a signal transducing beta subunit shared by the receptors for interleukin 3 (IL3), colony stimulating factor 2 (CSF2/GM-CSF), and interleukin 5 (IL5). CD123 is expressed on a subset of peripheral blood dendritic cells, progenitor cells, monocytes, eosinophils, basophils, and hematopoietic cells, such as erythroid cells and B cells. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone 9F5 which reacts to the α-chain of the interleukin-3 receptor (IL-3Rα) expressed on a subset of peripheral blood dendritic cells, on a subset of progenitor cells, monocytes, eosinophils, and basophils (see TABLE 4, BD PharmingenTM, Cat. NO. 303545) (Sun et al. (1996) Blood. 87: 88-92).
CD86 (cluster designation 86) encompasses the human gene at locus 3q21 corresponding to sequences having GENBANK® Accession Nos: NM_006889 and NP_008820.3, as set forth in SEQ ID NO:19 and SEQ ID NO:20, respectively. CD86 encodes a type I membrane protein that is a member of the immunoglobulin superfamily. This protein is expressed by antigen-presenting cells, and it is the ligand for two proteins at the cell surface of T cells: CD28 antigen and cytotoxic T-lymphocyte-associated protein 4. Binding of this protein with CD28 antigen is a co-stimulatory signal for activation of the T-cell. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone 2331 (FUN-1) which recognizes a 75 kDa cell surface protein expressed primarily on monocytes and activated B cells (see TABLE 4, BD PharmingenTM, Cat. NO. 555658) (Nozawa et al. (1993) J Path. 169(3):309-315).
CD72 (cluster designation 72) encompasses the human gene at locus 9p13.3 corresponding to sequences having GENBANK® Accession Nos: NM_001782 and NP_001773.1, as set forth in SEQ ID NO:21 and SEQ ID NO:22, respectively. CD72 is expressed on B cells and is the ligand for CD5. CD5 and/or CD72 engagement delivers critical co-stimulatory signals to B cells. It has been suggested that CD72 is a key molecule in regulating mature B cell differentiation, particularly in preventing the differentiation of naïve B cells into plasma cells (Yamazaki et al. (2005) Eur. J. Immunol.). In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone JA-117 which reacts with a 39-43 kDa type II integral membrane protein expressed on B cells from early precursor stages through mature B cells, although not on plasma cells (see TABLE 4, BD PharmingenTM, Cat. NO. 555918) (Schlossman et al. ed. (1995) Leukocyte Typing V. White Cell Differentiation Antigens. New York: Oxford University Press).
CD13 (cluster designation 13) encompasses the human gene at locus 15q25-q26 corresponding to sequences having GENBANK® Accession Nos: NM_001150 and NP_001141.2, as set forth in SEQ ID NO:23 and SEQ ID NO:24, respectively. CD13 encodes a surface antigen glycoprotein of about 150 kDa, also known as “aminopeptidase-N.” CD13 is an enzyme thought to be involved in the metabolism of regulatory peptides expressed by diverse cell types, including small intestinal and renal tubular epithelial cells, macrophages, granulocytes, and synaptic membranes from the CNS. Defects in this gene appear to be a cause of various types of leukemia or lymphoma.
CD79b (cluster designation 79b) encompasses the human gene at locus 17q23 corresponding to sequences having GENBANK® Accession Nos: NM_000626 and NP_000617.1, as set forth in SEQ ID NO:25 and SEQ ID NO:26, respectively. CD79b is a B lymphocyte antigen receptor that is a multimeric complex that includes the antigen specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. The CD79b gene encodes the Ig-beta protein of the B-cell antigen component. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone AT107-2 which recognizes an immunogen peptide containing 20 amino acid residues derived from murine CD79b (NP_032365.1, NM_008339.2). The antibody is cross reactive with human, rat, pig, and dog CD79b (see TABLE 4, AbDserotec, Cat. NO. MCA2209FT) (Dornan et al. (2009) Blood. 114:2721-9; Vendel et al. (2009) J. Immunol. 182: 1509-17).
CD33 (cluster designation 33) encompasses the human gene at locus 19q13.41 corresponding to sequences having GENBANK® Accession Nos: NM_001082618.1 and NP_001076087.1, as set forth in SEQ ID NO:27 and SEQ ID NO:28, respectively. CD33, or Siglec-3 is a transmembrane receptor expressed on cells of myeloid lineage. It is usually considered myeloid-specific, but it can also be found on some lymphoid cells. CD33 has been implicated in the negative regulation of cell proliferation of normal or leukemic myeloid cells. (Vitale et al. (1999) PNAS. 96, 15091-15096).
HSPB1 encompasses the human gene at locus 7q11.23 corresponding to sequences having GENBANK® Accession Nos: NM_001540 and NP_001531.1. HSPB1, as set forth in SEQ ID NO:29 and SEQ ID NO:30, respectively, is a gene that encodes the intercellular heat shock 27 kDa protein. Expression of this gene is induced by environmental stress and developmental changes. The encoded protein is involved in stress resistance and actin organization and translocates from the cytoplasm to the nucleus upon stress induction. Synthesis of the small (27-kDa) HSP has been shown to be correlated with the acquisition of thermotolerance. In some embodiments, the variants detected encompass an eptitope recognized by antibody HSP27, clone G3.1 conjugated to biotin that recognizes a 24-27 kDa hsp27 protein (early called 24K) expressed on approximately 50% of breast carcinomas and drug resistant cancer cells (See TABLE 4, Thermo Scientific, Cat. NO. MS-101-BO, -B1, or -B, for biotin labeled). In other embodiments, the variants encompass the eptitope recognized by the antibody HSPB1 derived from G3.1, conjugated to PE (see TABLE 4, Stressgen, Cat. NO. SPA-800PE) (Edward et al. (1980) Biochem Biophys Research Commun. 93:804-812; Ciocca et al. (1991) Breast Cancer Research and Treatment. 20:33-42).
Bcl-2 (B-cell lymphoma 2) encompasses the human gene at locus 18q21.3 corresponding to sequences having GENBANK® Accession Nos: NM_000633 and NM_000657, and NP_000624.2 and NP_000648.2, as set forth in SEQ ID NO:31 and SEQ ID NO:33, and SEQ ID NO:32 and SEQ ID NO:34, respectively. This gene encodes an integral outer mitochondrial membrane protein that blocks the apoptotic death of some cells such as lymphocytes. Bcl-2 derives its name from B-cell lymphoma 2, as it is the second member of a range of proteins initially described in chromosomal translocations involving chromosomes 14 and 18 in follicular lymphomas. Constitutive expression of BCL2, such as in the case of translocation of BCL2 to Ig heavy chain locus, is thought to be the cause of follicular lymphoma. The Bcl-2 gene has been implicated in a number of cancers, including melanoma, breast, prostate, and lung carcinomas. It is also thought to be involved in resistance to conventional cancer treatment. Two transcript variants, produced by alternate splicing, differ in their C-terminal ends. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone 100 which is expressed in lymphocytes and monocytes but not appreciably in granulocytes (see TABLE 4, Invitrogen, Cat. NO. MHBLC014) (Hill et al. (1996) Blood. 88:1046).
CD164 (cluster designation 164) encompasses the human gene at locus 6q21 corresponding to sequences having GENBANK® Accession Nos: NM_006016 and NP_006007.2, as set forth in SEQ ID NO:35 and SEQ ID NO:36, respectively. CD164 is a type-I integral transmembrane sialomucin that functions as an adhesion receptor. Sialomucins are a heterogeneous group of secreted or membrane-associated mucins that appear to play two key but opposing roles in vivo: first as cytoprotective or anti-adhesive agents, and second as adhesion receptors. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone N6B6 which recognizes a 80-90 kDa mucin-like molecule present on CD34+ progenitor cells during the early stages of B cell, erythroid cell and myelomonocytic cell development. It is also expressed on epithelial cells, peripheral blood monocytes and weakly on lymphocytes (see TABLE 4, BD PharmingenTM, Cat. NO. 551298) (Watt et al. (1998). Blood 92 (3):849-66; and Zannettino et al. (1998). Blood. 92 (8):2613-28).
CD304 (cluster designation 304) encompasses the human gene at locus 10p12 corresponding to sequences having GENBANK® Accession Nos: NM_001024628 and NP_001019799.1, as set forth in SEQ ID NO:37 and SEQ ID NO:38, respectively. CD304 is also known as “NRP1,” “Neuropilin-1 (NP-1),” and “BDCA-4,” and encodes a protein with numerous functions. On neurons, it is a receptor for axon growth guidance class-3 semaphorins SEMA3A and plexin-1. On endothelial and some tumor cells it is a VEGF165 receptor, and on plasmacytoid dendritic cells it has a similar role to CD303 but does not decrease interferon production upon activation. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone AD5-17F6 (see TABLE 4, Miltenyi Biotec Cat. NO. 130-090-533) (Dzionek, A., et al. (2000) J. Immunol. 165:6037-6046.)
CD97 (cluster designation 97) encompasses the human gene at locus 19p13 corresponding to sequences having GENBANK® Accession Nos: NM_078481 and NP_510966.1, as set forth in SEQ ID NO:39 and SEQ ID NO:40, respectively. The encoded product is a glycoprotein present on the surface of most activated leukocytes and spans the membrane seven times, which is a defining feature of G protein-coupled receptors. The protein has an extended extracellular region with several N-terminal epidermal growth factor (EGF)-like domains, which mediate binding to its cellular ligand, decay accelerating factor (DAF, CD55), a regulatory protein of the complement cascade. The presence of structural features characteristic of extracellular matrix proteins and transmembrane proteins suggests that this protein is a receptor involved in both cell adhesion and signaling processes early after leukocyte activation. Alternative splicing has been observed for this gene and three variants have been found. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone VIM3b which recognizes a triplet of membrane proteins of 74, 80 and 89 kDa strongly expressed on phytohemagglutinin (PHA)-activated T and B cells, virtually all monocytes and granulocytes, and several cell lines including HL-60, THP-1, and K562. It is weakly expressed on resting lymphocytes (see TABLE 4, BD PharmingenTM, Cat. NO. 555774) (Schlossman, et al. ed. (1995) Leukocyte Typing V. New York: Oxford University Press).
CD99 (cluster designation 99) encompasses the human gene at loci Xp22.32 and Yp11.3 corresponding to sequences having GENBANK® Accession Nos: NM_001122898 and NP_001116370.1, as set forth in SEQ ID NO:41 and SEQ ID NO:42, respectively. CD99 is a cell surface glycoprotein involved in leukocyte migration, T-cell adhesion, ganglioside GM1 and transmembrane protein transport, and T cell death by a caspase-independent pathway. Two transcript variants encoding different isoforms have been found for this gene. This variant 2 lacks an alternate in-frame exon compared to variant 1. The resulting isoform 2 has the same N- and C-termini but is shorter compared to isoform 1. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone TU 12 which recognizes a 32 kDa sialoglycoprotein expressed on all leukocyte lineages, although is differentially expressed during T and B-lymphoid and granulocytic development, with higher densities being expressed during early hematopoietic stages (see TABLE 4, BD PharmingenTM, Cat. NO. 555689) (Knapp et al, ed. (1989) Leucocyte Typing IV. New York: Oxford University Press; 1989).
CD102 (cluster designation 102) encompasses the human gene at locus 17q23-q25 corresponding to sequences having GENBANK® Accession Nos: NM_000873 and NP_000864.2, as set forth in SEQ ID NO:43 and SEQ ID NO:44, respectively. CD102 is also known as intercellular adhesion molecule 2 (ICAM-2). This variant (5) differs in the 5′ UTR compared to variant 1. All five variants encode the same protein. The protein encoded by this gene is a member of the intercellular adhesion molecule (ICAM) family. All ICAM proteins are type-I transmembrane glycoproteins, contain 2-9 immunoglobulin-like C2-type domains, and bind to the leukocyte adhesion LFA-1 protein. This protein may play a role in lymphocyte recirculation by blocking LFA-1-dependent cell adhesion. CD102 mediates adhesive interactions important for antigen-specific immune response, NK-cell mediated clearance, lymphocyte recirculation, and other cellular interactions important for immune response and surveillance. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone CBR-IC/2 which recognizes a type-I membrane glycoprotein with an approximate molecular weight of 55-65 kDa expressed on vascular endothelial cells, lymphocytes, monocytes, but not on granuloctyes. (see TABLE 4, BD PharmingenTM, Cat. NO. 558080) (Barclay et al. ed. (1997) The Leukocyte Antigen FactsBook. San Diego: Academic Press).
CD300a (cluster designation 300a) encompasses the human gene at locus 17q25.2 corresponding to sequences having GENBANK® Accession Nos: NM_007261 and NP_009192.2, as set forth in SEQ ID NO:45 and SEQ ID NO:46, respectively. CD300a also known as “inhibitory receptor protein (IRp60)” is a surface molecule of 60 kDa expressed by all human natural killer (NK) cells. The IRp60 gene, encodes a molecule that is highly O- and N-glycosylated, belonging to the immunoglobulin superfamily (Ig-SF). The ligand of the CD300a is still unknown but IRp60 does not appear to recognize HLA-class I molecules. In some embodiments, the variants detected encompass an eptitope recognized by the antibody derived from clone E59.126 expressed on T lymphocyte subsets, monocytes, and granulocytes (see TABLE 4, Beckman Coulter Cat. NO. A22328).
Intracellular Protein Targets
In some embodiments of the invention, the expression of intracellular proteins, for example, BCL2 and HSPB1, are detected using flow cytometry by first permeablizing the cell surface membrane to allow access of antibody through the membrane. In one embodiment a permeabilization reagent, such as those containing various surfactants (e.g., saponin, Triton X-100, Tween-20, N-acyl sarcosine, etc) or organic solvents (e.g., alcohols, acetone) or other similar solution, is used. A permeabilization reagent is optimally used in a sufficient amount enabling penetration of antibodies to the intercellular space, while substantially preserving the cellular membrane. Ideally, the permeabilizing agent creates apertures in the cell membrane without affecting the gross morphology of the cell such that flow cytometric light scattering characteristics of the cell are not affected. Such methods of permeabilizing cells are well known in the art.
In embodiments of the invention, the cell may be fixed prior to or during permeabilization to maintain the integrity of the cell. Methods of fixation are also well known in the art. In some embodiments, fixation and permeabilization can be combined. An example of a fixation/permeabilizing agent is INTRAPREPTM (Beckman Coulter, Inc.) which comprises 5.5% v/v formaldehyde as a fixation reagent and a phosphate buffered saline (PBS)-saponin-based permeabilization reagent.







TABLE 4







Antibodies against the new markers





















Negative


Marker
Antibody
Clone
Conjugate
Source
Catalogue #
Positive Control
Control*





CD44
CD44
515
PE
BD Biosciences
550989
Lymphocytes,
Jurkat cell line








monocytes



BCL2
Anti-Human
100
PE
Invitrogen
MHBCL04
Lymphocytes,
Ramos cell line



Bcl-2




monocytes



HSPB1
HSP27
G3.1
Biotin
Lab Vision
MS-101
Monocytes
Lymphocytes






Corporation





HSPB1
HSP27
G3.1
PE
Stressgen
SPA-800PE
Monocytes
Lymphocytes


CD73
CD73
AD2
PE
BD Biosciences
550257
Lymphocyte subset
Monocytes


CD24
CD24
ML5
PE
BD Biosciences
555428
B lymphocytes
T lymphocytes


CD123
CD123
9F5
PE
BD Biosciences
340545
Monocytes
T lymphocytes


CD72
CD72
J4-117
FITC
BD Biosciences
555918
B lymphocytes
T lymphocytes


CD86
CD86
2331
PE
BD Biosciences
555658
Monocytes
Lymphocytes


CD200
CD200
MRC OX-
PE
BD Biosciences
552475
B lymphocytes
Monocytes




104







CD79B
CD79b
AT107-2
FITC
Serotec
MCA2209F
B lymphocytes
T lymphocytes


CD164
CD164
N6B6
PE
BD Biosciences
551298
Monocytes
Granulocytes


CD304
CD304
AD5-17F6
PE
Miltenyi Biotec
130-090-533
Dendritic cells
Lymphocytes






inc

(doubled with









CD123)



CD97
CD97
VIM3b
PE
BD Biosciences
555774
Monocytes
Lymphocytes


ITG7
Anti-Human
FIB504
PE
BD Biosciences
555945
Lymphocyte subset
Lymphocyte



Integrin 7





subset


CD102
CD102
CBR-IC2/2
PE
BD Biosciences
558080
Monocytes,
Granulocytes








lymphocytes



CD99
CD99
TU12
PE
BD Biosciences
555689
T-ALL
Granulocytes


CD300a
Anti-IRp60
E59.126
PE
Beckman
A22328
Monocytes,
Lymphocyte






Coulter

lymphocyte subset
subset


CD130
CD130
AM64
PE
BD Biosciences
555757
Monocytes,
B lymphocytes








lymphocyte subset



PBX1
PBX1
4A2
None
Abnova
H00005087-
Cell line 697
Lymphocytes







M01




CTNNA1
Anti-
1G5
None
Abcam
Ab17259
Monocytes
Lymphocytes



Human








CD69
CD69
L78
PE
BD Biosciences
341652
Activated
Non-activated








lymphocytes
lymphocytes


CD49f
CD49f
GoH3
PE
BD Biosciences
555736
Monocytes
Subset of









lymphocytes


EPOR
Anti-Human
38409
PE
R&D Systems
FAB307P
Subset of
Lymphocytes



Epo-R




erythroblasts



CD1c
CD1c
AD5-8E7
PE
Miltenyi Biotec
130-090-508
B lymphocyte
Granulocytes








subset



BCL11B
Anti-Human
25B6
None
Abcam
Ab18465
Jurkat cell line
NALM6 cell line



BCL11B








CD120a
CD120a
H398
PE
Serotec
MCA1340PE
Monocytes
Lymphocyte









subsets


CD37
CD37
BL14
PE
Beckman
IM0458
B lymphocytes
T lymphocytes






Coulter





CD62L
CD62L
SK11
PE
BD Biosciences
341012
Monocytes,
Lymphoid subset








lymphoid subset



CD132
CD132
AG184
PE
BD Biosciences
555900
Monocytes,
Lymphocyte








lymphocyte subset
subset


CD83
CD83
HB15a
PE
Beckman
IM2218
Tonsillar
Resting






Coulter

lymphocyte subset
lymphocytes


IL13RA1
Anti-Human
GM-1C8
None
Abcam
Ab3772
Monocytes
Lymphocytes



IL-13









Receptor.1













Secondary antibodies/reagent










Goat F(Ab′)2 Anti-Mouse IgG2a
PE
Southern
1082-09




Biotechnology





Associates



Goat F(Ab′)2 Anti-Mouse IgG1
FITC
Southern
1072-02




Biotechnology





Associates



Goat F(Ab′)2 Anti-Mouse IgG1
FITC
Southern
1072-02




Biotechnology





Associates



Goat F(ab′)2 Anti-Rat IgG Fc
PE
Jackson
112-116-071




Immuno-





Research





Laboratories



Streptavidin
PE
Jackson
016-110-084




Immuno-





Research





Laboratories





*Dim or no expression













TABLE 5







Standard marker combinations used to monitor


MRD in childhood B-lineage ALL












FITC
PE
PerCP
APC







CD58
CD10
CD34
CD19



CD38
CD10
CD34
CD19



CD45
CD10
CD34
CD19



anti-TdT
CD10
CD34
CD19



CD13
CD10
CD34
CD19



anti-TdT*
anti-IgM
CD34
CD19



CD66c
CD10
CD34
CD19



CD33
CD10
CD34
CD19



CD15
CD10
CD34
CD19







*TdT, terminal deoxynucleotidyl transferase






RNA Expression Profiling:
In other embodiments, the expression of a marker of interest is detected at the nucleic acid level. Nucleic acid-based techniques for assessing expression are well known in the art and include, for example, determining the level of marker mRNA in a specimen taken from a patient. Many expression detection methods use isolated RNA. Generally, blood, serum, or tissue samples can readily be processed using techniques well known to those of skill in the art, such as, for example, the single-step RNA isolation process of Chomczynski (1989, U.S. Pat. No. 4,843,155).
Isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, polymerase chain reaction analyses and probe arrays. One method for the detection of mRNA levels involves contacting the isolated mRNA with a nucleic acid molecule (probe) that can hybridize to the mRNA encoded by the gene being detected. The nucleic acid probe can be, for example, a full-length cDNA, or a portion thereof, such as an oligonucleotide of at least 7, 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to an mRNA or genomic DNA encoding a marker of the present invention. Hybridization of an mRNA with the probe indicates that the marker in question is being expressed.
In one embodiment, the mRNA is immobilized on a solid surface and contacted with a probe, for example by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane, such as nitrocellulose. In an alternative embodiment, the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an Affymetrix gene chip array. A skilled artisan can readily adapt known mRNA detection methods for use in detecting the level of mRNA encoded by the markers of the present invention.
An alternative method for determining the level of marker mRNA in a sample involves the process of nucleic acid amplification, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88:189-193), self sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), rolling circle replication (Lizardi et al. U.S. Pat. No. 5,854,033) or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers. In particular aspects of the invention, marker expression is assessed by quantitative fluorogenic RT-PCR (i.e., the TaqMan® System). Such methods typically utilize pairs of oligonucleotide primers that are specific for the marker of interest. Methods for designing oligonucleotide primers specific for a known sequence are well known in the art.
Marker expression levels of RNA may be monitored using a membrane blot (such as used in hybridization analysis such as Northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are incorporated herein by reference. The detection of marker expression may also comprise using nucleic acid probes in solution.
In one embodiment of the invention, microarrays are used to detect marker expression. Microarrays are particularly well suited for this purpose because of the reproducibility between different experiments. DNA microarrays provide one method for the simultaneous measurement of the expression levels of large numbers of genes. Each array consists of a reproducible pattern of capture probes attached to a solid support. Labeled RNA or DNA is hybridized to complementary probes on the array and then detected by laser scanning. Hybridization intensities for each probe on the array are determined and converted to a quantitative value representing relative gene expression levels. See, U.S. Pat. Nos. 6,040,138, 5,800,992 and 6,020,135, 6,033,860, and 6,344,316, which are incorporated herein by reference. High-density oligonucleotide arrays are particularly useful for determining the gene expression profile for a large number of RNA's in a sample.
Techniques for the synthesis of these arrays using mechanical synthesis methods are described in, e.g., U.S. Pat. No. 5,384,261, incorporated herein by reference in its entirety for all purposes. Although a planar array surface is preferred, the array may be fabricated on a surface of virtually any shape or even a multiplicity of surfaces. Arrays may be peptides or nucleic acids on beads, gels, polymeric surfaces, fibers such as fiber optics, glass or any other appropriate substrate, see U.S. Pat. Nos. 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992, each of which is hereby incorporated in its entirety for all purposes. Arrays may be packaged in such a manner as to allow for diagnostics or other manipulation of an all-inclusive device. See, for example, U.S. Pat. Nos. 5,856,174 and 5,922,591 herein incorporated by reference.
In one approach, total mRNA isolated from a specimen is converted to labeled cRNA and then hybridized to an oligonucleotide array. Each specimen is hybridized to a separate array. Relative transcript levels may be calculated by reference to appropriate controls present on the array and in the sample. In one embodiment of the invention, RNA can be isolated from a subpopulation of cells with a characteristic expression profile, for example, cells co-expressing markers CD19 and CD10.
In embodiments of the invention, an expression profile can comprise values corresponding to gene expression detected by mRNA expression levels where the expression of many genes can be analyzed simultaneously and interpreted in one sample. In embodiments of the invention, an mRNA probe set can include probes corresponding to those in TABLE 1 and TABLE 2. Embodiments of the invention, include but are not limited to the detection of markers and combinations of markers in TABLE 1 comprising genes overexpressed in B-lineage ALL. Embodiments of the invention, include but are not limited to the detection of markers and combinations of markers in TABLE 2 comprising genes underexpressed in B-lineage ALL.
Embodiments of the invention can include, but are not limited to, compositions and methods related to the detection of new markers for the detection of minimal residual disease (MRD) comprising: CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
In embodiments of the invention, an expression profile is generated by the detection of nucleic acid corresponds to the expression of mRNA. Embodiments of the method comprise a method of diagnosing minimal residual disease in a subject by obtaining a specimen from the subject. The specimen is contacted with a plurality of probes, wherein each of the probes specifically binds to a distinct marker, wherein a first probe specifically binds to CD19 and a second probe specifically binds to CD10. A CD19+/CD10+ cell is isolated from the specimen. An expression level of at least one, two, three, four, five, six or more gene products expressed in said CD19+, CD10+ cell is determined, wherein the at least one, two, three, four, five, six or more gene products encode CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a. An expression profile is then generated by combining the expression values of the gene products. In such methods, the expression of CD19 and CD10 and a modulated level of at least one gene products encoding CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102, or CD300a relative to a normal control is indicative of minimal residual disease in acute lymphoblastic leukemia.
Other embodiments of the method comprise contacting a specimen with a plurality of probes to detect expression levels of markers comprising CD19 and CD10 and at least four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, twenty-one, or twenty-two markers comprising: CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a.
In embodiments of the invention, determining the expression profile of a specimen that is CD10+/CD19+ further comprises probe combinations comprising (a) CD38, CD24, and CD44; (b) CD38, CD58, and CD44; (c) CD38, CD73, and CD15; (d) CD38, CD200, and CD44; (e) CD66c, CD123, and CD86; (f) CD72, CD13, and CD33; or (g) CD79b, HSPB1, and Bcl-2.
In yet other embodiments of the invention, a kit for detecting minimal residual disease in a subject is disclosed. The kit can comprise a plurality of antibodies, antibody fragments, or molecular probes wherein each antibody, antibody fragment, or molecular probe is reactive to each of markers CD10, CD19, CD34, and CD45, and at least one additional of antibody, antibody fragment, or molecular probe that specifically binds to at least one additional marker comprising CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a. The kit can include at least one antibody, antibody fragment, or molecular probe that is detectably labeled. Embodiments of the invention include detectable labels, which can be, but are not limited to a radiolabel, a fluorophore, a peptide, an enzyme, a quantum dot, or a combination thereof.
In embodiments of the invention, a kit can comprise combinations of probes comprising (a) CD10, CD19, CD34, CD45, CD38, CD24, and CD44; (b) CD10, CD19, CD34, CD45, CD38, CD58, and CD44; (c) CD10, CD19, CD34, CD45, CD38, CD73, and CD15; (d) CD10, CD19, CD34, CD45, CD38, CD200, and CD44; (e) CD10, CD19, CD34, CD45, CD66c, CD123, and CD86; (f) CD10, CD19, CD34, CD45, CD72, CD13, and CD33; or (g) CD10, CD19, CD34, CD45, CD79b, HSPB1, and Bcl-2.
Data and Expression Profile Analysis
Any method known in the art for comparing two or more data sets to detect similarity and/or variance between them may be used to compare a subject expression profile to a normal expression profile. To determine whether two or more expression profiles show statistically significant similarity and/or variance, statistical tests may be performed to determine whether any differences between the expression profiles are likely to have been achieved by a random event. Methods for comparing gene expression profiles to determine whether they share statistically significant similarity or variance are known in the art and also reviewed in Holloway et al. (2002) Nature Genetics Suppl. 32:481-89, Churchill (2002) Nature Genetics Suppl. 32:490-95, Quackenbush (2002) Nature Genetics Suppl. 32: 496-501; Slonim (2002) Nature Genetics Suppl. 32:502-08; and Chuaqui et at (2002) Nature Genetics Suppl. 32:509-514; each of which is herein incorporated by reference in its entirety.
An expression profile is “distinguishable” or “statistically distinguishable” from a normal control expression profile according to the invention if the two expression profiles do not share statistically significant similarity.
Kits for Detection of Minimal Residual Disease
Kits for practicing the screening and diagnostic methods of the invention are further provided. The kits of the invention may also include methods for use in diagnosing minimal residual disease in ALL, detecting or diagnosing ALL, monitoring disease status in a patient for the recurrence of ALL, or monitoring the efficacy of a treatment for ALL. These methods are described elsewhere herein.
As used herein, “kit” refers to a set of reagents for the purpose of performing the method embodiments of the invention, more particularly, the detection of minimal residual disease in patient specimens. The term “kit” is intended to mean any manufacture (e.g., a package or a container) comprising at least one reagent, e.g., an antibody, a nucleic acid probe, etc. for specifically detecting the expression of a marker of the invention. The kit may be promoted, distributed, or sold as a unit for performing the methods of the present invention. Additionally, the kits may contain a package insert describing the kit and methods for its use.
In embodiments of the invention, expression of markers can be assessed at the protein level or nucleic acid level, or both in combination. In some embodiments, expression of protein expression is detected using specific antibody probes. Expression of identified markers can also be detected by nucleic acid based techniques, including, for example, hybridization and RT-PCR. Expression can be evaluated in a variety of specimens taken from the body including, but not limited to, blood cells or bone marrow cells, and cellular products extracted from blood and bone marrow cells, including, but not limited to protein and RNA extracted from blood and bone marrow cells.
The kit can comprise a plurality of antibodies, antibody fragments, or molecular probes wherein each antibody, antibody fragment, or molecular probe is specific for CD10, CD19, CD34, CD45, CD38, CD58, CD15, CD66c, CD13, CD33, CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
The kit can comprise a plurality of antibodies, antibody fragments, or molecular probes wherein each antibody, antibody fragment, or molecular probe is reactive to each of markers CD10, CD19, CD34, and CD45, and at least one additional antibody, antibody fragment, or molecular probe that specifically binds to at least one additional marker comprising CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, or CD49f.
The kit can comprise a plurality of antibodies, antibody fragments, or molecular probes wherein each antibody, antibody fragment, or molecular probe is reactive to each of markers CD10, CD19, CD34, and CD45, and at least one additional antibody, antibody fragment, or molecular probe that specifically binds to at least one additional marker comprising CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 or CD300a. The kit can include at least one antibody, antibody fragment, or molecular probe that is detectably labeled. Embodiments of the invention include detectable labels, which can be, but are not limited to a radiolabel, a fluorophore, a peptide, an enzyme, a quantum dot, or a combination thereof.
In embodiments of the invention, a kit can comprise combinations of probes comprising (a) CD10, CD19, CD34, CD45, CD38, CD24, and CD44; (b) CD10, CD19, CD34, CD45, CD38, CD58, and CD44; (c) CD10, CD19, CD34, CD45, CD38, CD73, and CD15; (d) CD10, CD19, CD34, CD45, CD38, CD200, and CD44; (e) CD10, CD19, CD34, CD45, CD66c, CD123, and CD86; (f) CD10, CD19, CD34, CD45, CD72, CD13, and CD33; or (g) CD10, CD19, CD34, CD45, CD79b, HSPB1, and Bcl-2.
In yet another embodiment, a kit can comprises an array having a substrate with a plurality of addresses, where each address has a capture probe that can specifically bind a nucleic acid molecule comprising CD38, CD58, CD66c, CD79b, CD164, CD44, BCL2, HSPB1, CD72, CD73, CD24, CD123, CD86, CD200, CD304, CD97, CD99, CD102 or CD300a.
The methods of the invention can comprise MRD detection by gene array with preferred combinations of probes to specific markers. MRD detection can be combined, for example, with at least 3 different probes. Embodiments of the invention, can include, but are not limited to, the detection of mRNA expression with probes specific for genes shown in TABLE 1 comprising genes overexpressed in B-lineage ALL. Other embodiments of the invention, can include, but are not limited to, the detection of mRNA expression with probes specific for genes shown in TABLE 2 comprising genes underexpressed in B-lineage ALL.
One of skill in the art will further appreciate that any or all steps in the screening and diagnostic methods of the invention could be implemented by personnel or, alternatively, performed in an automated fashion. For example, the methods can be performed in an automated, semi-automated, or manual fashion, and as one-step or multi-step processes. Furthermore, the methods disclosed herein can also be combined with other methods known or later developed to permit a more accurate identification of patients having an increased likelihood of having minimal residual disease or a more reliable diagnosis of ALL.
The article “a” and “an” are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one or more element.
Throughout the specification the word “comprising,” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.
Embodiments of the present invention are further defined in the following Examples. It should be understood that these Examples are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the embodiments of the invention to adapt it to various usages and conditions. Thus, various modifications of the embodiments of the invention, in addition to those shown and described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.
EXPERIMENTAL
Patients
Bone marrow samples were collected at presentation from 470 patients aged <1 to 18 years with newly diagnosed B-lineage ALL; 270 samples were included in genome-wide gene expression studies, and 200 were tested to validate the gene expression findings by flow cytometry. Bone marrow samples were obtained during therapy in 51 patients and samples obtained at relapse in 9. The diagnosis of B-lineage ALL was unequivocal and based on morphology, cytochemistry and cell marker expression. To determine gene expression and immunophenotype of normal lymphoid progenitors, bone marrow samples were collected from 22 healthy donors aged 2-25 yrs (median, 10 yrs) during the harvest of bone marrow for stem cell transplantation, and bone marrow samples obtained from 27 patients with B-lineage ALL, 7 with T-lineage ALL and 5 with acute myeloid leukemia (AML) during therapy.
Sample Preparation
Leukemic and normal mononuclear cells were collected after centrifugation on a density gradient (ACCUPREP, Nycomed, Oslo, Norway) and washed three times in phosphate-buffered saline (PBS). Leukemic cells used in gene expression studies were cryopreserved. Normal bone marrow CD19+ cells used for gene expression analysis were first enriched using a MACS separation system (Miltenyi Biotec, Auburn, Calif.) from fresh samples, yielding>98% CD19+ cell purity. Cells were then stained with anti-CD19 conjugated to phycoerythrin (PE) and anti-CD10 conjugated to fluorescein isothiocyanate (FITC; both from Becton Dickinson, San Jose, Calif.) and CD19+CD10+ cells were sorted using a Mono high-speed fluorescence-activated cell sorter (CYTOMATION®, Fort Collins, Colo.). All samples were processed or cryopreserved within 5 hours of collection.
Flow Cytometric Analysis and MRD Studies
Flow cytometry using the antibodies listed in TABLES 3-5 were used to verify the differential expression of gene products in ALL cells. In most tests, the antibodies were used in combination with anti-CD19 conjugated to allophycocyanin (APC), anti-CD10 conjugated to either FITC or PE, and anti-CD34 conjugated to peridinin chlorophyll protein (PerCP). Isotype-matched nonreactive antibodies were used as controls. For cell staining, monunucleated cells were washed in PBS containing 0.5% bovine serum albumin and 0.5% sodium azide (PBSA), mixed with rabbit serum to block surface Fc receptors, incubated with the antibodies for 10 minutes at 20° C. in the dark, washed twice in PBSA and fixed with 0.5% paraformaldehyde. For intracellular markers, cells were permeabilized and fixed before exposure to antibodies using a permeablization reagent 8E. Measurements of antibody labeling were performed by multiparameter flow cytometry, using a FACSCALIBER® flow cytometer (Becton Dickinson, San Jose, Calif.).
Studies of MRD by flow cytometry were performed using combinations of monoclonal antibodies that identified leukemia-associated immunophenotypes determined at diagnosis. Cell staining was essentially performed as described above, using a combination of 4 markers simultaneously (see TABLE 4) and, where indicated, with 6-marker combinations (SEE TABLE 3). Data acquisition and analysis was done as previously described, using BD FACSCALIBERTM LSRII flow cytometers (Becton Dickinson), BD CELLQUEST ProTM, BD FACSDIVATM software (both from Becton Dickinson), FLOWJO software (Tree Star, Ashland, Oreg.) and/or KALUZATM software (Beckman Coulter, Miami, Fla.). Determination of MRD by PCR amplification of immunoglobulin and T-cell receptor genes was done as previously described (Stow. P. (2010) Blood. 115:4657-4663). The results of MRD studies by the two methods were recorded independently.
Example 1. Identification of Genes Differentially Expressed in Leukemic and Normal Immature B Cells
Gene Expression Arrays Studies
A first-generation gene array study was previously performed (Chen et al. (2001) Blood. 97:2115-2120) and as previously described (Ross et al. (2003) Blood. 102:2951-2959). In Chen et al., diagnostic ALL samples from 4 patients were compared to CD19+ CD10+ bone marrow immature B cells taken from 2 healthy donors. The array contained probes for approximately 4000 genes.
In an embodiment of the invention, a gene expression array probing over 23,000 genes was used to screen a larger set of samples, including 270 cases of B-lineage ALL. The B-lineage ALLs encompassed the spectrum of genetic abnormalities occurring in ALL and were included to specifically identify other prognostic markers. Briefly, total RNA was isolated from freshly thawed B-lineage ALL cells and flow sorted normal CD19+CD10+ cells using the TRIZOL® reagent (Invitrogen, Carlsbad, Calif.). After generating cDNA, biotin-labeled cRNA was prepared according to the protocols of Affymetrix (Santa Clara, Calif.). The solutions were hybridized to HG-U133A oligonucleotide microarrays (Affymetrix). After staining with phycoerythrin-conjugated streptavidin, the arrays were read with a laser confocal scanner (Agilent, Palo Alto, Calif.). Signal values were computed from the image files using Affymetrix GENECHIP® Operating Software. Intensity values for a total of 22,283 probe sets on the U133A microarray were obtained (See Affymetrix Data Sheet (Part No. 701484 Rev. 4 (2003-2004), Santa Clara, Calif., USA, GENECHIP® Human Genome U133A 2.0 Array, Part Nos. #900471, 468, 469)
Expression data was generated using genome-wide expression data detected from 270 B-lineage ALL samples and CD19+CD10+ lymphoid progenitors obtained from the bone marrow of 4 healthy donors. Of the 23,000 genes compared, a total of 133 probe sets (corresponding to 112 genes, TABLE 1) had signals higher than 2-fold of the highest value obtained among normal CD19+CD10+ cells in 75% or more of ALL cases studied. Conversely, 192 probe sets (corresponding to 165, TABLE 2) had signals at least 50% lower than the lowest signal among the normal CD19+CD10+ cells in 75% or more of ALL cases. When the criteria for inclusion was extended to genes that were differentially expressed in at least 25% of ALL cases, 1405 probe sets were over-expressed and 1474 were under-expressed. The results are summarized in TABLES 1 and 2.
Among the genes that were differentially expressed, some had been previously identified as abnormally expressed in ALL cells. For example, CD58 was over-expressed in 81.9% of cases (See also Chen J. S., et al. (2001) Blood. 97:2115-2120), and WT1 in 32.6% of cases (See also Ogawa et al. (2002) Blood. 101:1698-1704) whereas PAX5 was under-expressed in 86.7% and CD38 in 73.7% of cases (See also Coustan-Smith et al. (2002) Blood. 100:52-58). Among the 23 ALL specimens with MLL gene rearrangements, 100% over-expressed galectin-1 and 91.3% under-expressed CD10, characteristic features of this subset of ALL (See also Juszczynski et al. (2010) Clin Cancer Res. 16:2122-2130; Pui et al. (1994) J. Clin. Oncol. 12:909-915); most of these cases also over-expressed a cohort of genes (e.g., FLT3, LMO2, ADAM10, MEIS1) previously reported to be associated with MLL-rearranged leukemia (see also Ferrando et al. (2003) Blood. 102:262-268).
All 26 cases with TCF3-PBX1 over-expressed PBX1 (See also Kamps et al. (1991). Genes Dev. 5:358-368), and, among the 62 cases with ETV6-RUNX1, 46.8% over-expressed CD13 and 29.0% CD33 (Baruchel et al. (1997) Br J HaematoL 99:101-106).
Example 2. Validation of Gene Expression Array Results by Flow Cytometry
Among the genes differentially expressed by gene array analysis, there were some already widely used for MRD studies by flow cytometry, i.e., CD58, CD38, CD13, and CD34, suggesting the possibility that other useful markers could be present among the remaining genes (Basso et al. (2009) J Clin Oncol. 27:5168-5174; Lucio et al. (2001) Leukemia. 15:1185-1192; Chen et al. (2001) Blood. 97:2115-2120; Coustan-Smith et al. (2002) Blood. 100:52-58).
To prioritize genes for validation by flow cytometry, an initial inclusion criteria was applied: a) differential expression in at least 25% of cases of ALL, or 40% of cases of a genetic subtype of ALL; b) over-expression in leukemic cells by at least 3-fold of the maximum value in normal cells, or under-expression by 3-fold of the minimum value in normal cells; and c) commercial availability of specific antibodies conjugated to fluorochromes suitable for flow cytometry. Guided by these criteria, 30 genes (25 overexpressed in ALL and 5 underexpressed) were selected (TABLE 6) and compared to determine whether the differential expression measured by microarray analysis at the mRNA level corresponded to differential expression of the encoded proteins.
After confirming the specificity of the antibodies with known positive and negative target cells (TABLE 6), the antibodies were tested for reactivity using ALL samples obtained at diagnosis (n=200) and leukemia-free bone marrow samples (n=61). Importantly, comparisons included not only bone marrow specimens from healthy donors (n=22) but also bone marrow from children with ALL (MRD-negative according to PCR amplification of antigen-receptor genes) and AML (MRD negative by flow cytometry) during chemotherapy (n=39), some with a high proportion of hematogones. When the overall expression in the ALL versus normal CD19+ CD10+ B-cell progenitor groups were compared the difference in overall expression was statistically significant (P<0.05) for 13 of the 30 markers tested. Additionally, 11 of the proteins encoded by the over-expressed genes were expressed at a significantly higher level in B-lineage ALL cells, while 2 of the 5 proteins encoded by under-expressed genes had a significantly lower expression (FIG. 1).







TABLE 6







Expression level in ALL cells and normal CD19+CD10+ cells of the genes


selected for study













Range






expression
Range





in normal
expression
% ALL cases



Gene
CD19+ CD10+
in ALL
with



symbol/CD
(n = 4)1
(n = 270)1
higher/lower













Probeset
number
Min
Max
Min
Max
expression










Overexpressed in ALL













203685_at
BCL2
149.1
229
150.1
5203.8
90%


201841_s_at
HSPB1
15.6
302
36.4
8938.9
87%


207643_s_at
TNFRSF1A/
94.4
234.7
28
3029.5
84%



CD120a







209933_s_at
CD300A
59.1
126.1
29.3
1481.7
81%


202910_s_at
CD97
149.2
303.4
31.5
6537
80%


212298_at
NRP1/CD304
5.6
10.6
3.3
2155.1
80%


204563_at
SELL/CD62L
288.1
415.7
205
16680.8
79%


210916_s_at
CD44
40.8
109.2
18.8
4864.2
78%


215177_s_at
ITGA6/CD49f
31.5
145.9
14.6
12400.9
75%


209583_s_at
CD200
313.2
423.9
42.3
3955.4
72%


203939_at
NT5E/CD73
54.3
121.1
5
5133.9
67%


213620_s_at
ICAM2/CD102
871.1
983
233.8
7321.1
65%


210895_s_at
CD86
31.9
106.9
13.6
1392.7
60%


204116_at
IL2RG/CD132
604
1213.2
574.9
8123.4
56%


201028_s_at
CD99
1148.8
2047.8
325.4
19384.2
50%


201887_at
IL13RA1
81.2
159.2
30.4
2829.5
41% (59% of








BCR-ABL1)


208654_s_at
CD164
754.9
1274.4
667.6
15234.8
39%








(71% of








hyperdiploid;








59% of BCR-








ABL1)


209963_s_at
EPOR
49.4
127.9
17.8
1950.4
36%


212151_at
PBX1
30.4
114.4
16.5
10825.3
36% (100% of








TCF3-PBX1)


205987_at
CD1C
16
249.7
9.7
7020.6
27% (71% of








hyperdiploid)


204863_s_at
IL6ST/CD130
119.4
160.9
8.5
837.1
27%


205718_at
ITGB7
12.1
208.5
10.9
3223.5
25% (50% of








BCR-ABL1)


206148_at
IL3RA/CD123
53.6
260.6
18.7
3497.2
22% (71% of








hyperdiploid)


208651_x_at
CD24
3125.7
4310.4
258.6
14231.4
17% (54% of








TCF3-PBX1)


209617_s_at
CTNNA1
23.3
68.7
6
424.5
9% (40.3% of








ETV6-RUNX1)







Underexpressed in ALL













205297_s_at
CD79B
11257.6
17637
19.1
8701
96%


204440_at
CD83
1759.5
4557.9
47.8
9729.2
91%


209795_at
CD69
6458.6
7502.8
31.6
16301.1
77%


204192_at
CD37
5624.7
13251.7
225.6
10302.9
67% (81% of








ETV6-RUNX1)


215925_s_at
CD72
1888.1
4238.1
9.1
4968.5
57%





1Data expressed as units calculated by MAS5.0 to a median target intensity of 500.






FIG. 1 shows the differential expression of markers in ALL cells compared to CD19+ CD10+ B cell progenitors. Shown are mean fluorescence intensity (MFI) values obtained in CD19+ leukemic lymphoblasts from bone marrow samples of patients with newly diagnosed ALL (“L”) and bone marrow CD19+CD10+ cells from healthy donors or from patients with leukemia in remission and no evidence of MRD (“N”). Each symbol indicates results of one sample; horizontal bars correspond to median values within each group
For the remaining 17 markers, the difference in overall expression between ALL cells and normal B-cell progenitors was not statistically significant (FIG. 2). FIG. 2 shows markers that were not expressed at levels significantly different (P>0.05) in ALL cells and CD19+CD10+ B-cell progenitors as determined by flow cytometry. Shown are mean fluorescence intensity (MFI) values obtained in CD19+ leukemic lymphoblasts from bone marrow samples of patients with newly diagnosed ALL (“L”) and bone marrow CD19+CD10+ cells from healthy donors or from patients with leukemia in remission and no evidence of MRD (“N”). Each symbol indicates results of one sample; horizontal bars correspond to median values within each group.
However, some these later markers were found to be overexpressed when the mean fluorescent intensity MFI values were compared to normal controls. For example, in some cases the MFI values of a marker in ALL specimens was higher than the highest mean fluorescence intensity (MFI) value recorded among normal B-cell progenitors. In other ALL specimens, markers were found to be underexpressed in ALL cells. For markers that were under-expressed in ALL cells, for example, specimens had at least 50% lower MFI values compared to the lowest MFI measured in normal B-cell progenitors. Using MFI levels as a criteria for differential expression, a substantial proportion of ALL cases expressed markers whose MFI values that were higher or lower than that of normal B cell progenitors. Overall, 22 of the 30 markers were found differentially expressed in 5%-81.4% (median, 35%) of cases These results are summarized in TABLE 6.
For example, CD44 was differentially expressed in 81.4% cases studied, BCL2 was over-expressed in 76.6%, HSPB1 (heat shock protein 27) in 63.4% and CD73 in 54.5%. Notably, CD44 and CD24 were over-expressed in some cases and under-expressed in others. Importantly, some of the markers, such as CD97, CD99 and CD102 appeared to be over-expressed in a much larger proportion of cases when the comparisons included only resting bone marrow samples. However, when regenerating specimens rich in hematogones were included, it became clear that expression in leukemic cells for many of these cases was not outside the range of normality. Of the 30 markers studied, only 8 (EPOR, CD1c, CD120a, CD37, CD62L, CD132, CD83 and IL13RA1) showed no clear differential expression by the above criteria and were excluded from further studies.
Example 3: Validation of the New Markers for MRD Detection
To determine the reliability of the new markers to identify leukemic cells in clinical samples, 128 bone marrow samples were collected during treatment (46 during or at the end of remission induction therapy and 82 during post-remission therapy) from 51 patients with B-lineage ALL in whom expression of the markers on the leukemic cells had been measured at diagnosis. The markers included in these studies were the top 16 differentially expressed markers listed in TABLE 7, for a total of 258 tests.
Newly identified markers (TABLE 3, 4) were compared to standard marker combinations presently used in for MRD detection (TABLE 5). Using a threshold of 0.01% ALL cells to define MRD positivity, no discordant results were observed except for one comparison in which MRD was negative with the standard markers and 0.012% with the new markers. Overall, there was an excellent correlation in MRD estimates between new and standard markers (r=0.9816, P<0.0001 by Spearman's regression analysis of the MRD-positive tests; FIG. 3).
FIG. 3 graphically illustrates the relationship between results of MRD monitoring using flow cytometry targeting the new markers and those of PCR amplification of antigen-receptor genes. Each symbol on the graph represents results obtained by 4-color flow cytometry including antibodies against CD19, CD10, CD34 and one of the new markers; r=0.8178, P<0.0001 by Spearman's regression analysis of the positive MRD results. The dashed line is the line of identity.
In a subset of 52 samples from 18 patients studied with some of the markers (CD44, BCL2, HSPB1, CD73, CD24, CD123, CD86, CD200, CD304, CD97, CD99,







TABLE 7







Expression of the new markers in ALL cells relative to


their expression in bone marrow CD19+ CD10+ cells


from healthy individuals as determined by flow cytometry











Number of
Number of
Number of



ALL cases
cases with
cases with


Marker
studied
overexpression (%)1
underexpression (%)2













CD44
86
46 (53.5%)
24 (27.9%)


BCL2
77
59 (76.6%)
—


HSPB1
93
59 (63.4%)
—


CD73
77
42 (54.5%)
—


CD24
139
16 (11.5%)
55 (39.6%)


CD123
142
72 (50.7%)
—


CD72
45
—
22 (48.9%)


CD86
135
63 (46.7%)
—


CD200
95
41 (43.2%)
—


CD79b
74
—
31 (41.9%)


CD164
75
31 (41.3%)
—


CD304
129
37 (28.7%)
—


CD97
81
22 (27.2%)
—


CD102
76
15 (19.7%)
2 (2.6%)


CD99
77
17 (22.1%)
—


CD300A
92
18 (19.6%)
—


CD130
71
12 (16.9%)
—


PBX1
64
 4 (11.8%)
—


CTNNA1
44
4 (9.1%)
—


ITGB7
90
7 (7.8%)
—


CD69
33
2 (6.1%)
—


CD49f
38
2 (5.3%)
—


EPOR
45
2 (4.4%)
—


CD1C
86
3 (3.5%)
—


CD120a
35
 1 (<2.9%)
—


CD37
46
 1 (<2.2%)
—


CD62L
34
0
—


CD132
33
0
—


CD83
33
0
—


IL13RA1
10
0
—





11 Number of ALL cases that expressed the indicated marker at levels higher than the highest mean fluorescence intensity (MFI) value recorded among normal B-cell progenitors, and had an MFI higher than 10.


2Number of ALL cases that expressed the indicated marker at levels lower than the lowest MFI measured in normal B-cell progenitors, excluded cases in which a marker had an MFI lower than 10 on normal B-cell progenitors.






CD102 and CD300a), MRD estimates by PCR amplification of clonally rearranged immunoglobulin and T-cell receptor genes were also available. Using the threshold of 0.01% ALL cells to define MRD positivity, MRD was negative (<0.01%) by flow cytometry and PCR analysis in 35 of the 52 samples studied. By contrast, MRD was ≧0.01% according to both methods in 15 samples. Two additional samples had MRD≧0.01% by flow cytometry while PCR showed detectable signals but below the 0.01% threshold: 0.007% and 0.003%. Among the 101 tests performed, MRD was <0.01% by flow cytometry in 63 and ≧0.01% in 38, with a good correlation in the MRD positive estimates by the two techniques (r=0.8178, P<0.0001). Two samples had MRD≧0.01% by flow cytometry (1 tested with two markers) and also had positive PCR but below the 0.01% threshold.

To determine stability of the new markers during the course of the disease, a prerequisite for reliable MRD tracking (Gaipa et al. (2005) Leukemia. 19:49-56) the level of expression was compared to that recorded during MRD monitoring in 10 patients who had persistent MRD during remission induction therapy (day 19 and 42 from diagnosis). FIG. 4 illustrates the results obtained in 4 representative cases showing the expression of the new markers before, during and at the end of remission induction therapy.
The long-term stability of the markers was assessed by comparing the immunophenotype of paired samples collected at diagnosis and relapse from nine patients whose leukemic cells at diagnosis expressed some of the newly identified markers identified. In FIG. 4 symbols indicate mean fluorescence intensity (MFI) of each marker as measured on ALL cells at diagnosis and on residual leukemic lymphoblasts detected on days 19 and 42 of remission induction therapy. At all time points, all markers were expressed at levels that exceeded those measured in normal CD19+CD10+ cells. Although levels of expression fluctuated during therapy, they consistently remained outside the range of normality in all cases studied.
As shown in TABLE 8, abnormal marker expression at diagnosis reverted to expression within the normal range at relapse in 7 of 55 (12.7%) of comparisons. In the remaining cases, marker expression remained abnormal. Importantly, in all 9 patients studied at least one marker remained abnormally expressed at relapse. In 58 additional comparisons where the markers at diagnosis were within the normal range, there were 10 instances (17.2%) in which expression became abnormal at relapse. These results suggest that false-negative results due to phenotypic shifts affecting these markers would be unlikely.







TABLE 8







Expression of new markers in paired samples of B-lineage ALL collected at diagnosis (D) and at relapse (R)1

















Patient 1
Patient 2
Patient 3
Patient 4
Patient 5
Patient 6
Patient 7
Patient 8
Patient 9

























Marker
D
R
D
R
D
R
D
R
D
R
D
R
D
R
D
R
D
R





CD44
—
—
233
235
372
—2
325
—2
—
—
—
—
 3
 4
208
 93
292
307


BCL2
254
249
240
262
—
—
286
326
144
137
332
562
150
151
 87
137
273
188


HSPB1
 18
 47
 44
 94
—
  743
169
143
141
165
 64
351
 23
267
 15
158
 80
 36


CD73
 30
 39
 37
 64
 56
149
 29
105
—
—
 95
 30
 33
—2
168
 33
103
 63


CD24
—
—
338
504
—
 3333
204
146
104
 2
—
 2773
—
—
—
—
—
  773


CD123
—
—
 62
 31
—
—
 45
133
—
—
—
—
—
—
—
—
—
  253


CD72
 6
 7
NT
NT
NT
NT
—
—
—
—
 5
 3
 8
 13
 6
 6
 4
 4


CD86
—
—
 26
 23
—
—
 33
—2
—
—
—
—
—
—
—
—
—
—


CD200
 86
 65
107
 88
—
—
 80
201
260
154
—
—
102
126
—
  723
 83
—2


CD164
—
—
 18
 49
—
—
—
—
—
—
—
—
—
  293
NT
NT
NT
NT


CD97
—
—
119
 53
—
—
 84
200
—
—
—
  543
—
—
—
—
—
—


CD102
—
—
—
—
—
—
 96
 92
—
—
—
—
—
 1003
—
—
—
 1363


CD99
—
—
—
—
—
—
—
 3293
184
—2
124
—2
—
—
—
—
122
488





NT, not tested


1Values indicate MFI as determined by flow cytometry. Dash indicates MFI within the normal range


2Significant change in expression: from abnormal expression at diagnosis to expression within the normal range at relapse


3Significant change in expression: from expression within the normal range at diagnosis to abnormal expression at relapse






Example 4. Association of the New Markers with Genetic Subtypes of ALL
The new markers used in embodiments of the invention were associated with known genetic subtypes of ALL, including hyperdiploidy (51-65 chromosomes), ETV6-RUNX1, TCF3-PBX1, BCR-ABL1, or MLL gene rearrangements. FIG. 5 shows the results of this analysis as a heat map including markers that were differentially expressed in at least 20% of cases. The heatmap graphically displays the percentage of cases among the main genetic subtypes of childhood ALL in which the markers studied were differentially expressed by flow cytometry. Percentages refer to cases in which each marker was over-expressed in ALL cases as compared to CD19+CD10+ cells from non-leukemic bone marrow samples; markers under-expressed in ALL cells are indicated by “u”.
Expression of some markers was clearly related to ALL genetic subtype. For example, among hyperdiploid (51-65 chromosomes) ALL cases, there was a significantly higher prevalence of CD123 (P<0.0001 by Fisher's exact test), CD86 (P<0.0001), CD200 (P=0.0003) and CD97 (P<0.0001) overexpression as compared to the other cases without this genetic abnormality. Among cases with ETV6-RUNX1, there was a higher prevalence of CD200 over-expression (P<0.0001), and of CD44 (P<0.0001), CD72 (P=0.0073) and CD79b (P=0.0109) under-expression. Finally, abnormal expression of CD164 was most prevalent among cases lacking all the genetic abnormalities analyzed (P=0.002).
Example 5: Comparisons Between New Markers and Established Leukemia-Associated Immunophenotypes
In a proportion of patients with ALL, MRD cannot currently be monitored because of the lack of suitable immunophenotypes differentiating ALL from normal controls. (Campana (2009) Hematol. Oncol Clin North Am. 23:1083-98, vii; Bruggemann et al. (2010) Leukemia. 24:521-535) In other patients, leukemic cells express only one set of markers, and have an increased risk of false-negative MRD results due to immunophenotypic shifts (Coustan-Smith et al. (1998) Lancet. 351:550-554). The availability of the additional markers of embodiments of the invention enables MRD studies in patients whose ALL cells currently lack suitable leukemia-associated immunophenotypes and minimize the risk of false-negative results.
Using a method of the invention, expression profiling was used to evaluate 171 ALL diagnostic samples including: 11 subjects lacking detectable leukemia-associated immunophenotypes with the standard panel of antibodies; and another 37 subjects having only one immunophenotypic abnormality detectable with the standard panel.
In contrast to the standard method, the method of the present invention detected a phenotypic abnormality indicative of MRD in all of the 11 cases previously lacking a leukemia-associated immunophenotype. Moreover, the method of the present invention identified additional abnormalities in 36 of the 37 cases with one standard abnormality. Thus, the new markers substantially improved the potential for flow cytometric monitoring of MRD in 47 of 48 cases that could not be adequately studied previously. The number of new markers differentially expressed ranged from two to twelve (median, six). In 45 of the 47 cases, one or more markers were expressed at levels that exceeded by at least two-fold the normal range, allowing a particularly clear identification of ALL cells.
The availability of additional markers of leukemia improved the resolution of leukemic and normal cells during flow cytometric analysis. This was clearly demonstrated in experiments in which mixtures of leukemia and normal cells were analyzed using either one standard phenotypic abnormality (e.g., under-expression of CD38), or additional abnormalities revealed by the new markers. An example of such an experiment is shown in FIG. 6.
FIG. 6 shows an example of the comparison of flow cytometric data from 5 non-leukemic bone marrow samples cells (gray dots) and one diagnostic ALL sample (black dots) that were merged and analyzed as radial plots using the KALUZATM software after selecting all CD19+ CD10+ CD34+ cells. Mixtures containing 0.01% ALL cells (top row) and 0.001% ALL cells (bottom row) are shown. Under-expression of CD38 alone, a standard MRD marker, could not discriminate well between ALL cells and normal CD19+ CD10+ CD34+ cells (left panels) in this case; the discrimination was improved by analyzing expression of CD97 (middle panels), and further improved by the inclusion of CD86 and the use of a 3-dimensional space (right panels). Using embodiments of the invention improve the discrimination between normal and leukemic CD19+, CD10+, CD34+ cells thereby allowing the unequivocal detection of ALL cells at a level of 0.001%.
All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.

## Claims

1. A method of diagnosing and treating minimal residual disease in a subject comprising:
(a) contacting a specimen comprising a plurality of markers obtained from a patient with a plurality of probes, wherein the specimen is selected from the group consisting of blood cells, bone marrow cells, and cellular products that are derived from blood and bone marrow cells: and wherein each of said plurality of probes specifically binds to a single marker, wherein a first probe specifically binds to the single marker CD19, a second probe specifically binds to the single marker CD10, a third probe specifically binds to the single marker CD34, a fourth probe specifically binds to the single marker CD45, and at least two additional probes that specifically bind to any two of the single markers selected from the group consisting of CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102, or CD300a, wherein each of said plurality of probes that specifically bind to a single marker comprises a detectable moiety;
(b) detecting a complex formed between each of said plurality of probes in step (a) with said plurality of markers, wherein a value is generated corresponding to an expression level of each of said single markers;
(c) generating an expression profile by combining the values generated in step (b); wherein the expression of CD19, and the differential expression of CD10, CD34 and CD45, and the differential expression of at least two additional markers selected from the group consisting of CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102, and CD300a relative to the expression profile for a plurality of the same markers in a normal control is indicative of minimal residual disease in acute lymphoblastic leukemia (ALL), and
(d) administering to the patient having at least one leukemic cell detected among 100,000 normal cells an effective amount of a therapy for treating minimal residual disease in ALL.

2. The method of claim 1, wherein said plurality of probes further comprises at least three additional probes, wherein each of the at least three additional probes specifically bind to a single marker selected from the group consisting of CD38, CD24, CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, CD97, CD99, CD102 and CD300a.

3. The method of claim 1, wherein said differential expression comprises an overexpression of at least one of the single markers selected from the group consisting of CD44, CD58, CD73, CD200, CD86, HSPB1, BCL2, CD164, CD97, CD99, and CD300a and/or an underexpression of at least one of the single markers selected from the group consisting of CD38, CD72, and CD79b, relative to expression level of the same single marker in a normal control.

4. The method of claim 1, wherein the at least two additional probes that selectively bind a single marker are CD38 and CD44.

5. The method of claim 1, wherein cells in the specimen are permeabilized prior to contacting the specimen with the plurality of probes which specifically bind to the single markers.

6. The method of claim 1, wherein at least one of the plurality of probes is an antibody.

7. The method of claim 1, wherein said detecting utilizes an optical detection technique.

8. The method of claim 7, wherein said optical detection technique is flow cytometry.

9. The method of claim 7, wherein said optical detection technique is microscopy.

10. The method of claim 1, wherein said detectable moiety is selected from the group consisting of a fluorophore, a chromophore, a radionuclide, and an enzyme.