# Patent

## Title
Classification, diagnosis and prognosis of acute myeloid leukemia by gene expression profiling

## Abstract

The present invention relates to methods of genetic analysis for the classification, diagnosis and prognosis of acute myeloid leukemia (AML). The invention provides a method for producing a classification scheme for AML comprising the steps of a) providing a plurality of reference samples, the reference samples comprising cell samples from a plurality of reference subjects affected by AML; b) providing reference profiles by establishing a gene expression profile for each of the reference samples individually; c) clustering the individual reference profiles according to similarity; and d) assigning an AML class to each cluster. The invention further relates to a method for classifying the AML of an AML-affected subject, to a method for diagnosing AML in a subject, and to a method of determining the prognosis for an AML-affected subject.

## Background
TECHNICAL FIELD
The present invention is in the field of medicine. The invention relates in particular to methods of genetic analysis for the classification, diagnosis and prognosis of acute myeloid leukemia. Also, the invention relates to nucleic acid expression profiles as obtained from cells of AML patients, which profiles by similarity group into a plurality of distinct and defined clusters that characterize different classes of AML. The invention relates to the use of such expression profiles and compositions in diagnosis and therapy of AML and specifically in the prediction of prognostically important AML classes.
The invention further relates to methods for the diagnosis of AML and for the determination of the prognosis of a subject affected by AML and to kits of parts comprising sets of nucleic acid probes suitable for performing methods of the invention either by means of genomics or proteomics.
BACKGROUND OF THE INVENTION
Acute myeloid leukemia (AML) is a collection of neoplasms with heterogeneous pathophysiology, genetics and prognosis. Based on cytogenetics and molecular analysis, AML patients are presently classified into groups or subsets of AML with markedly contrasting prognosis. For instance, the genetic translocations inv(16), t(8;21) and t(15;17) characterize AML with a relatively favorable prognosis, whereas the cytogenetically bad-risk leukemia's include patients with abnormalities involving 11q23, loss of 5(q) or 7(q), t(6;9) and t(9;22) (Löwenberg et al., 1999).
The most common molecular abnormality in AML is the internal tandem duplication (ITD) in the fms-like tyrosine kinase-3 gene (FLT3), a hematopoietic growth factor receptor (Levis & Small, 2003). FLT3 ITD mutations confer a bad prognosis to AML patients (Levis & Small, 2003). AML patients with mutations in the transcription factor cEBPa have been associated with good outcome (Preudhomme et al., 2002; van Waalwijk van Doorn-Khosrovani et al., 2003), while elevated expression of the transcription factor EVI1 predicts for notoriously poor survival (van Waalwijk van Doorn-Khosrovani et al., 2003). These examples of novel molecular prognostic markers underscore the importance of an extension of molecular analyses in AML.
Approximately thirty percent of all patients with acute myeloid leukemia (AML) are currently classified based on specific abnormal karyotypes in groups with either good or bad prognosis. The remaining seventy percent of patients, however, are not classifiable because of the lack of cytogenetic markers.
One of the aims of the present invention is to provide more accurate risk assessment tools for the diagnosis of AML. It is another aim to classify AML patients in which specific abnormal karyotypes have not been found and to distinguish these groups not only from the molecularly well-defined AML classes, but also to define prognostic subgroups within these unclassified AML types. The presence of additional prognostic classes in AML, not recognizable with currently available methods, may provide important insights into their pathophysiology. Therefore, it is an aim of the present invention to provide a more complete way of prognostication to patients with AML.
SUMMARY OF THE INVENTION
The present invention is based on the discovery that unique correlations within gene expression profiles and also with cytogenetic aberrations can be recognized with high accuracy within a representative cohort of AML patients. It has, for instance, been found that gene expression profiles obtained from a large number of AML patients can be clustered according to similarity. This enables the recognition of distinct classes of AML with similar expression profiles characterizing such a class. It was thus found that AML could be classified into distinct subclasses, each subclass being characterized by a specific clustering of gene expression profiles. Further, it was found that truly discriminative genes for most of these classes or clusters could be identified, a cluster, for instance, being characterized therein that the expression of multiple genes is up-regulated or down-regulated in that cluster whereas their expression in another cluster is unaffected.
Based on these findings, the present invention now provides in a first aspect a method for producing a classification scheme for AML comprising the steps of:

    
    
        a) providing a plurality of reference samples, the reference samples comprising cell samples from a plurality of reference subjects affected by AML;
        b) providing reference profiles by establishing a gene expression profile for each of the reference samples individually;
        c) clustering the individual reference profiles according to similarity, and
        d) assigning an AML class to each cluster.
    
    


In a preferred embodiment of such a method, the clustering of reference profiles is performed based on the information of genes that are differentially expressed between profiles, and in an even more preferred embodiment of such a method, the clustering of the reference profiles is performed on the basis of the information of the genes of Table 1, still more preferably of the genes of Table 2, which tables are provided hereinbelow.
In a further aspect, the present invention provides a method for classifying the AML of an AML-affected subject, comprising the steps of:

    
    
        a) providing a classification scheme for AML by producing such a scheme according to the method of any one of claims 1-3;
        b) providing a subject profile by establishing a gene expression profile for the subject;
        c) clustering the subject profile together with the reference profiles;
        d) determining in the scheme the clustered position of the subject profile among the reference profiles, and
        e) assigning to the AML of the subject the AML class that corresponds to the clustered position in case the subject profile is within any cluster of reference profiles, or assigning to the AML of the subject a new AML class.
    
    


In yet a further aspect, the present invention provides a method for diagnosing AML in an AML-affected subject comprising:

    
    
        a) producing a classification scheme for AML according to a method of the invention;
        b) defining cluster-specific genes for each cluster by selecting those genes of which the expression level characterizes the clustered position of the corresponding AML class among the various AML classes within the scheme;
        c) determining the level of expression of a sufficient number of the cluster-specific genes in an AML-affected subject;
        d) establishing whether the level of expression of the cluster-specific genes in the subject shares sufficient similarity to the level of expression that characterizes an individual AML class to thereby determine the presence of AML corresponding to the class in the subject.
    
    


In one embodiment of such a method for diagnosing AML, the cluster-specific genes may comprise all genes comprised in the gene expression profile. In a preferred embodiment of such a method, the cluster-specific genes comprise a set of 1 to 3000 genes of the genes of Table 1, more preferably 1 to 600 genes of the genes of Table 1, still more preferably 1 to 50 genes of the genes of Table 1. In an even more preferred embodiment the cluster-specific genes comprise a set of 1 to 600 genes of the genes of Table 2, still more preferably 1 to 50 genes of the genes of Table 2, and even more preferably 1 to 25 genes of the genes of Table 2. Most preferred in such a method is the use of the differentially expressed genes as shown in Table 3 for the diagnosis of a specific AML class in a subject.
In yet another aspect, the present invention provides a method of determining the prognosis for an AML-affected subject, the method comprising the steps of:

    
    
        a) providing a classification scheme for AML by producing such a scheme according to a method of the invention;
        b) determining the prognosis for each AML class in the scheme based on clinical records for the AML subjects comprised in the class;
        c) establishing the AML class of an AML-affected subject by diagnosing and/or classifying AML in the subject according to a method of the invention, and
        d) assigning to the subject the prognosis corresponding to the established AML class of the AML-affected subject.
    
    


The present invention further provides a classification scheme for AML, the scheme comprising a plurality of distinct AML classes that are differentiated on the basis of similarity clustering of gene expression profiles obtained from a plurality of reference subjects affected by AML.
The classification scheme is, for instance, obtainable by a method of the invention for producing such a scheme. Preferably, the classification scheme is obtained by a method involving K-means clustering of gene expression profiles based on, for instance, gene chip array-acquired values for hybridization intensities for each gene, such as, for instance, those obtainable by using an Affymetrix gene chip.
Analysis of gene expression profiles obtained by using such gene chips preferably involves log 2 transformation of all intensity values in order to detect subtle modulations between the various genes. For each gene the geometric mean (i.e., the mean expression value determined for all individual genes in all profiles to be analyzed) is calculated. Deviation from this geometric mean is termed differential expression. Genes that are expressed at values allowing assignment of being differentially expressed are used for hierarchical clustering. Subsequently the gene signatures (characteristic expression profiles) of all samples/patients are compared with each other by means of a Pearson correlation coefficient analysis showing the (pathway) resemblance within clinical distinct groups of the total patient population.
The present invention further provides genes that are modulated (up- and down-regulated) in AML compared to the geometric mean calculated from all patients. Such genes and the proteins they encode are useful for diagnostic and prognostic purposes, and may also be used as targets for screening therapeutic compounds that modulate AML, such as antibodies. The methods of detecting nucleic acids of the invention or their encoded proteins can be used for a number of purposes. Examples include early detection of AML, monitoring and early detection of relapse following treatment of AML, monitoring response to therapy of AML, determining prognosis of AML, directing therapy of AML, selecting patients for postoperative chemotherapy or radiation therapy, selecting therapy, determining tumor prognosis, treatment, or response to treatment, and early detection of precancerous condition. Other aspects of the invention will become apparent to the skilled artisan by the following description of the invention.
In one aspect, the present invention provides a method of detecting an AML-associated transcript in one or more cells from a patient, the method comprising contacting a biological sample from the patient with a polynucleotide, such as an oligonucleotide, that selectively hybridizes to a sequence at least 80% identical to a sequence of a gene as shown in Tables 1 or 2. In one embodiment, the polynucleotide selectively hybridizes to a sequence at least 95% identical to a sequence of a gene as shown in Tables 1 or 2. In another embodiment, the polynucleotide comprises a sequence of a gene as shown in Tables 1 or 2.
In one embodiment, the biological sample used in such methods of detection is a tissue sample. In another embodiment, the biological sample comprises isolated nucleic acids, e.g., mRNA. In one embodiment, the polynucleotide is labeled, e.g., with a fluorescent label. In one embodiment, the polynucleotide is immobilized on a solid surface.



DESCRIPTION OF THE DRAWINGS
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
FIG. 1 shows, in panel (A), a Correlation View of 286 AML patients. The Correlation Visualization tool displays pair-wise correlations between the samples. The patient samples in the visualization are colored by Pearson's correlation coefficient values with deeper colors indicating higher positive (red) or negative (blue) correlations, indicating similarity in the underlying pathway indicative for the subgroups reflecting the heterogeneity within the patient population. The scale bar indicates 100% correlation (red) towards 100% anti correlation (blue). In order to reveal correlation patterns, a matrix ordering method is applied to rearrange the samples. The ordering algorithm starts with the most correlated sample pair and, through an iterative process, sorts all the samples into correlated blocks. Each sample is joined to a block in an ordered manner so that a correlation trend is formed within a block with the most correlated samples at the center. The blocks are then positioned along the diagonal of the plot in a similar ordered manner.
Panel (B) of FIG. 1 shows an adapted Correlation View of 286 AML patients (right panel) and top40 genes defining the 16 individual clusters of patients (left panel). All 16 clusters identified on the basis of the Correlation View are indicated (1 to 16). FAB classification and karyotype based on cytogenetics are depicted in the columns along the original diagonal of the Correlation View (FAB M1-green, M2-purple, M3-orange, M4-yellow, M5-blue, M6-grey; karyotype: normal-green, inv(16)-yellow, t(8;21)-purple, t(15;17)-orange, 11q23 abnormalities-blue, other-grey). FLT3 ITD, FLT3 TKD, N-RAS, K-RAS and cEBRα mutations and EVI1 overexpression are depicted in the same set of columns (red bar: positive and green bar: negative). The expression levels of the top40 genes identified by Significance Analysis of Microarrays (SAM) analyses of each of the 16 clusters are visualized in the left panel. The scale bar indicates four-fold up-regulation-(red) towards four-fold down-regulation (green) relative to the geometric mean of all samples.
FIG. 2 shows the overall survival (panel A), event free survival (panel B) and relapse rate after CR (panel C) of AML patients in cluster #5 (M4/M5), cluster #9 (inv(16)), cluster #10 (EVI1/monosomy 7), cluster #12 (t(15;17)) and cluster #13 (t(8;21)), indicating that expression profiles in acute myeloid leukemia associate with diverse genetic aberrations and have prognostic impact.
FIG. 3 provides a guideline on how to read the Omniviz Correlation View. The figure shows the Correlation View and FAB classification (right-hand edge of figure) of the cohort of 286 AML patients (2856 probe sets). A total of 16 distinct cluster can be identified on the right edge of the figure. X-axis and Y-axis show the regions of the various clusters 1-16 from top to bottom and from left to right, respectively. An exemplary correlation between cluster #5 and #16 is indicated by rectangle. Both clusters predominantly consist of AML-M5 (not visible) and correlate. However, they do form separate clusters. Anti-correlation, for instance, between cluster 5 and cluster #13, which merely contains AML-M2, is indicated by the dashed rectangle. Correlation and anti-correlation between every individual (sub)cluster can be extracted from the Correlation View and (sub)clusters can subsequently be assigned, e.g., cluster #6, #7 and #8 (dotted lines). FAB: M0-bright green, M1-green, M2-pink, M3-orange, M4-purple, M5-turquoise, M6-yellow (with number).
FIGS. 4-10 provide supporting results of the Pearson's correlation coefficient analyses using Omniviz with different probe subsets. In the Correlation View all 286 patients are plotted against all 286 AML patients. FAB classification and karyotype based on cytogenetics are depicted in the columns along the original diagonal (left-hand edge) of the Correlation View (FAB M0-red, M1-green, M2-purple, M3-orange, M4-yellow, M5-blue, M6-grey; karyotype: normal-green, inv(16)-yellow, t(8;21)-purple, t(15;17)-orange, 11q23 abnormalities-blue, 7(q) abnormalities-red, +8-pink, complex-black, other-grey). FLT3 ITD, FLT3 TKD, N-RAS, K-RAS and cEBPα mutations and EVI1 overexpression are depicted in the same set of columns (red bar: positive and green bar: negative). FIG. 4: 147 probe; FIG. 5: 293 probe sets; FIG. 6: 569 probe sets; FIG. 7: 984 probe sets; FIG. 8: 1692 probe sets; FIG. 9: 2856 probe sets; FIG. 10: 5071 probe sets.
FIG. 11 shows the Southern blot analyses AML patients with cryptic inv(16). Southern blot analyses was carried out with a myosine heavy chain 11 specific probe (NT 010393, 136753-137404 nt) on material of AML (WT, no inv(16)), AML with known inv(16) breakpoint (type A and E) and three patients that clustered with all known AML and inv(16) patients in the Correlation View (FIG. 1).
FIG. 12 shows the Expression of MYH11 as determined by Affymetrix GeneChip analyses in 286 cases of AML and controls. Expression levels of MYH11 were high in AML patients and inv(16), whereas low levels were detected in the other AML patients, CD34-positive cells and normal bone marrow.
FIG. 13 shows a snapshot of Correlation View showing the AML-M3 t(15;17) patients. FAB M2-purple, M3-orange, M4-yellow. Karyotype: normal-green, t(15;17)-orange, other-grey. The AML-M3 t(15;17) patients are divided into two groups, i.e., low white blood cell count (WBC) and FLT3 ITD negative (green bar) versus high WBC/FLT3 ITD positive (red bar). Karyotype is based on cytogenetics and WBC is depicted as 10 (cells/1).
FIG. 14 shows the Expression of ETO as determined by Affymetrix GeneChip analyses in 286 cases of AML and controls. Expression levels of ETO were high in AML patients and t(8;21), whereas low levels were detected in the other AML patients, CD34-positive cells and normal bone marrow.



DETAILED DESCRIPTION OF THE INVENTION
The term “classifying” is used in its art-recognized meaning and thus refers to arranging or ordering items, i.e., gene expression profiles, by classes or categories or dividing them into logically hierarchical classes, subclasses, and sub-subclasses based on the characteristics they have in common and/or that distinguish them. In particular “classifying” refers to assigning, to a class or kind, an unclassified item. A “class” then being a grouping of items, based on one or more characteristics, attributes, properties, qualities, effects, parameters, etc., which they have in common, for the purpose of classifying them according to an established system or scheme.
The term “classification scheme” is used in its art-recognized meaning and thus refers to a list of classes arranged according to a set of pre-established principles, for the purpose of organizing items in a collection or into groups based on their similarities and differences.
The term “clustering” refers to the activity of collecting, assembling and/or uniting into a cluster or clusters items with the same or similar elements, a “cluster” referring to a group or number of the same or similar items, i.e., gene expression profiles; gathered or occurring closely together based on similarity of characteristics. “Clustered” indicates an item has been subjected to clustering.
The term “clustered position” refers to the location of an individual item, i.e., a gene expression profile, in amongst a number of clusters, the location being determined by clustering the item with at least a number of items from known clusters.
The process of clustering used in a method of to the present invention may be any mathematical process known to compare items for similarity in characteristics, attributes, properties, qualities, effects, parameters, etc. Statistical analysis, such as, for instance, multivariance analysis, or other methods of analysis may be used. Preferably, methods of analysis such as self-organizing maps, hierarchical clustering, multidimensional scaling, principle component analysis, supervised learning, k-nearest neighbors, support vector machines, discriminant analyze, partial least square methods and/or Pearson's correlation coefficient analysis are used. In another preferred embodiment of a method of the present invention Pearson's correlation coefficient analysis, significance analysis of microarrays (SAM) and/or prediction analysis of microarrays (PAM) are used to cluster gene expression profiles according to similarity. A highly preferred method of clustering comprises similarity clustering of gene expression profiles, wherein the expression level of differentially expressed genes, having markedly lower or higher expression than the geometric mean expression level determined for all genes in all profiles to be clustered, is log(2) transformed, and wherein the transformed expression levels of all differentially expressed genes in all profiles to be clustered is clustered by using K-means. A numerical query may then be used to select a subset of genes used in the process of hierarchical clustering (Eisen et al., 1998), thus, numerical queries may be run to select differentially expressed genes relative to the calculated geometric mean to select a smaller group of genes for hierarchical clustering.
Unsupervised sample clustering using genes obtained by numerical or threshold filtering is used to identify discrete clusters of samples as well as the gene-signatures associated with these clusters. The term gene signatures is used herein to refer to the set of genes that define the discrete position of the cluster apart from all other clusters, and includes cluster-specific genes. A numerical or threshold filtering is used to select genes for the analysis that are most likely of diagnostic relevance. Hierarchical clustering allows for visualization of large variation in gene expression across samples or present in most samples, and these genes could be used for unsupervised clustering so that clustering results are not affected by the noise from absent or non-changed genes.
Thus, while, K-means clustering may be performed on all genes, the Pearson correlation is preferably calculated based on a subset of genes and patients. Generally speaking the larger the threshold for accepting a deviation or change from the geometric mean, the smaller the number of genes that is selected by this filtering procedure. Different cut-off or threshold values were used to prepare lists with different numbers of genes. The higher the number of genes selected and included on such lists, the more noise is generally encountered within the dataset, because there will be a relatively large contribution of non-leukemia pathway related genes in such lists. The filtering and selection procedure is preferably optimized such that the analysis is performed on as much genes as possible, while minimizing the noise.
All genes with changed expression values higher than or equal to 1.5 times the log(2) transformed expression values and genes with changed expression values lower than or equal to −1.5 times the log(2) transformed expression values are selected for hierarchical clustering.
The subset of genes showing a markedly higher or lower expression than the geometric mean may, for instance, be a value that is more than 1.5 times the geometric mean value, preferably more than 2 times the geometric mean value, even more preferably more than 3 times the geometric mean value. Likewise, a markedly lower expression than the geometric mean expression level may, for instance, be a value that is less than 0.8 times the geometric mean value, preferably less than 0.6 times the geometric mean value, more preferably less than 0.3 times the geometric mean value.
The same selection of genes that is used for the hierarchical clustering, is used for clustering of the patients by Pearson correlation coefficient analysis.
Gene expression profiling has previously been demonstrated to be useful in distinguishing myeloid from lymphoid malignancies as well as subclasses within these diseases (Alizadeh et al., 2000; Armstrong et al., 2002; Debernardi et al., 2003; Ross et al., 2003; Yeoh; Schoch et al., 2002; Golub et al., 1999), but it was hitherto unknown whether suitable distinctions on the basis of gene expression alone could be made between various types of AML, let alone whether such distinctions could bear any relevance to prognosis of the disease.
The present invention now provides several methods to accurately identify known as well as newly discovered diagnostically, prognostically and therapeutically relevant subgroups of acute myeloid leukemia (AML), herein below also addressed as AML classes, as well as methods that can predict which approaches in treatment are likely to be effective. The basis of these methods resides in the measurement of (AML-specific) gene expression in AML-affected subjects. The methods and compositions of the invention thus provide tools useful in choosing a therapy for AML patients, including methods for assigning an AML patient to an AML class or AML cluster, methods of choosing a therapy for an AML patient, methods of determining the efficacy of a therapy in an AML patient, and methods of determining the prognosis for an AML patient.
The methods of the invention comprise in various aspects the steps of establishing a gene expression profile of subject samples, for instance, of reference subjects affected by AML or of a subject diagnosed or classified for AML. The expression profiles of the present invention are generated from samples from subjects affected by AML, including subjects having AML, subjects suspected of having AML, subjects having a propensity to develop AML, or subjects who have previously had AML, or subjects undergoing therapy for AML. The samples from the subject used to generate the expression profiles of the present invention can be 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. The tissue or cell source may include a tissue biopsy sample, a cell sorted population, cell culture, or a single cell. Sources for the sample of the present invention include cells from peripheral blood or bone marrow, such as blast cells from peripheral blood or bone marrow.
In selecting a sample, the percentage of the sample that constitutes cells having differential gene expression in AML classes should be considered. Samples may comprise at least 20%, at least 30%, at least 40%, at least 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% cells having differential expression in AML classes, with a preference for samples having a high percentage of such cells. In some embodiments, these cells are blast cells, such as leukemic cells. The percentage of a sample that constitutes blast cells may be determined by methods well known in the art; see, for example, the methods described in WO 03/083140.
“Gene expression profiling” or “expression profiling” is used herein in its art-recognized meaning and refers to a method for measuring the transcriptional state (mRNA) or the translational state (protein) of a plurality of genes in a cell. Depending on the method used, such measurements may involve the genome-wide assessment of gene expression, but also the measurement of the expression level of selected genes, resulting in the establishment of a “gene expression profile” or “expression profile,” which terms are used in that meaning hereinbelow. As used herein, an “expression profile” comprises one or more values corresponding to a measurement of the relative abundance of a gene expression product. Such values may include measurements of RNA levels or protein abundance. Thus, the expression profile can comprise values representing the measurement of the transcriptional state or the translational state of the gene. In relation thereto, reference is made to U.S. Pat. Nos. 6,040,138, 5,800,992, 6,020135, 6,344,316, and 6,033,860.
The transcriptional state of a sample includes the identities and relative abundance of the RNA species, especially mRNAs present in the sample. Preferably, a substantial fraction of all constituent RNA species in the sample are measured, but at least a sufficient fraction to characterize the transcriptional state of the sample is measured. The transcriptional state can be conveniently determined by measuring transcript abundance by any of several existing gene expression technologies.
Translational state includes the identities and relative abundance of the constituent protein species in the sample. As is known to those of skill in the art, the transcriptional state and translational state are related.
Each value in the expression profiles as determined and embodied in the present invention is a measurement representing the absolute or the relative expression level of a differentially expressed gene. The expression levels of these genes may be determined by any method known in the art for assessing the expression level of an RNA or protein molecule in a sample. 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, to which explicit reference is made. The gene expression monitoring system may also comprise nucleic acid probes in solution.
In one embodiment of the invention, 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, the Experimental section. See also, U.S. Pat. Nos. 6,040,138, 5,800,992 and 6,020,135, 6,033,860, and 6,344,316, to which explicit reference is made. High-density oligonucleotide arrays are particularly useful for determining the gene expression profile for a large number of RNAs in a sample.
In one approach, total mRNA isolated from the sample is converted to labeled cRNA and then hybridized to an oligonucleotide array. Each sample is hybridized to a separate array. Relative transcript levels are calculated by reference to appropriate controls present on the array and in the sample. See, for example, the Experimental section.
In another embodiment, 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 antibody can be a polyclonal, monoclonal, recombinant, e.g., a chimeric or humanized, fully human, non-human, e.g., murine, or single chain antibody. In a preferred embodiment it has effector function and can fix complement. The antibody can be coupled to a toxin or imaging agent. A full-length protein product from a differentially expressed gene, or an antigenic peptide fragment of the protein product can be used as an immunogen. Preferred epitopes encompassed by the antigenic peptide are regions of the protein product of the differentially expressed gene that are located on the surface of the protein, e.g., hydrophilic regions, as well as regions with high antigenicity. The antibody can be used to detect the protein product of the 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 levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given therapy. Detection 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, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, (3-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; 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.
Once the values comprised in the subject expression profile and the reference expression profile or expression profiles are established, the subject profile is compared to the reference profile to determine whether the subject expression profile is sufficiently similar to the reference profile. Alternatively, the subject expression profile is compared to a plurality of reference expression profiles to select the reference expression profile that is most similar to the subject expression profile. Any method known in the art for comparing two or more data sets to detect similarity between them may be used to compare the subject expression profile to the reference expression profiles. In some embodiments, the subject expression profile and the reference profile are compared using a supervised learning algorithm such as the support vector machine (SVM) algorithm, prediction by collective likelihood of emerging patterns (PCL) algorithm, the k-nearest neighbor algorithm, or the Artificial Neural Network algorithm. To determine whether a subject expression profile shows “statistically significant similarity” or “sufficient similarity” to a reference profile, statistical tests may be performed to determine whether the similarity between the subject expression profile and the reference expression profile is likely to have been achieved by a random event. Any statistical test that can calculate the likelihood that the similarity between the subject expression profile and the reference profile results from a random event can be used. The accuracy of assigning a subject to an AML class based on similarity between differentially expressed genes is affected largely by the heterogeneity within the patient population, as is reflected by the deviation from the geometric mean. Therefore, when more accurate diagnoses are required, the stringency in evaluating the similarity between the subject and the reference profile should be increased by changing the numerical query.
The method used for comparing a subject expression profile to one or more reference profiles is preferably carried out by re-running the subsequent analyses in a (n+1) modus by performing clustering methods as described herein. Also, in order to identify the AML class reference profile that is most similar to the subject expression profile, as performed in the methods for establishing the AML class of an AML-affected subject, i.e., by diagnosing AML in a subject or by classifying the AML in a subject, profiles are clustered according to similarity and it is determined whether the subject profile corresponds to a known class of reference profiles. In assigning a subject AML to a specific AML class, for instance, this method is used wherein the clustered position of the subject profile, obtained after performing the clustering analysis of the present invention, is compared to any known AML class. If the clustered position of the subject profile is within a cluster of reference profiles, i.e., forms a cluster therewith after performing the similarity clustering method, it is said that the AML of the subject corresponds to the AML class of reference profiles. If a subject profile is not within a cluster of reference profiles, i.e., does not form a cluster therewith after performing the similarity clustering method, then a new AML class may be assigned to that subject profile, one of such classes being subjects not having AML.
In some embodiments of the present invention, the expression profiles comprise values representing the expression levels of genes that are differentially expressed in AML classes. The term “differentially expressed” as used herein means that the measured expression level of a particular gene in the expression profile of one subject differs at least n-fold from the geometric mean calculated from all patient profiles. The expression level may be also be up-regulated or down-regulated in a sample from a subject having a particular form of AML in comparison with a sample from a subject having a different form of AML. For example, in one embodiment, the differentially expressed genes of the present invention may be expressed at different levels in different AML classes. Examples of genes that are differentially expressed in the various AML classes are shown in Tables 1 and 2.
It should be noted that many genes will occur, of which the measured expression level differs at least n-fold from the geometric mean expression level for that gene of all reference profiles. This may, for instance, be due to the different physiological state of the measured cells, to biological variation or to the present of other diseased states. Therefore, the presence of a differentially expressed gene is not necessarily informative for determining the presence of different AML classes, nor is every differentially expressed gene suitable for performing diagnostic tests. Moreover, a cluster-specific differential gene expression, as defined herein, is most likely to be informative only in a test among subjects having AML. Therefore, a diagnostic test performed by using cluster-specific gene detection should preferably be performed on a subject in which the presence of AML is confirmed. This confirmation may, for instance, be obtained by performing the method for classifying an AML in an AML-affected subject according to the present invention, or by any other test.
The present invention provides groups of genes that are differentially expressed in diagnostic AML samples of patients in different AML classes. Some of these genes were identified based on gene expression levels for 13,000 probes in 286 AML samples. Values representing the expression levels of the nucleic acid molecules detected by the probes were analyzed as described in the Experimental section using Omniviz, SAM and PAM analysis tools. Omniviz software was used to perform all clustering steps such as K-means, Hierarchical and Pearson correlation tests. SAM was used specifically to identify the genes underlying the clinically relevant groups identified in the Pearson correlation analysis. PAM is used to decide the minimum number of genes necessary to diagnose all individual patients within the given groups of the Pearson correlation.
In short, expression profiling was carried out on AML blasts from 286 de novo AML patients. Unsupervised clustering was used to identify novel (sub)groups within the Pearson correlation following the hierarchical clustering. The Pearson correlation test resulted in the identification of 16 groups or classes of AML patients with distinct molecular signatures.
The hierarchical clustering and Pearson correlation allow the detection of the genetic heterogeneity (16 clusters). This may provide for a mechanistic signature of AML. After running the SAM and PAM analysis, the diagnostic gene-signatures (including cluster-specific genes) were obtained.
While several of the molecularly assigned classes correspond to the well-defined AML subgroups with favorable cytogenetics, such as the well-recognized genetic lesions AML1/ETO, PML/RARα and CBFβ/MYH11, we identified several additional distinct classes of patients that were not identified as distinct classes of AML before. For instance, new identified AML clusters comprised genetic lesions such as CEBPα mutations, or FLT3 ITD mutations, or 11q23 aberrations, indicating that these cytogenetic markers alone are not sufficient to determine the prognosis of an AML patient or the most optimal intervention strategy (drug treatment).
Whereas the well-defined AML subgroups AML1/ETO, PML/RARα and CBFβ/MYH11, could be identified based on measurement of the expression level of only one or two genes in a cell sample, many of the newly discovered AML classes were defined on the basis of differential expression of a plurality of genes. Genes that define an AML class are hereinafter also termed cluster-specific genes or signature genes. Prediction Analysis of Microarrays (PAM) was applied to determine the minimal gene sets that predict these prognostically important clusters with high accuracy. In one of the novel clusters half of the AML patients had unfavorable markers, such as elevated expression of EVI1 and/or loss of chromosome 7(q). Interestingly, more than 90 percent of patients in this cluster (cluster no. 10, see Example) responded poorly to therapy. The fact that a distinct gene expression signature defines this class of AML patients, suggests the existence of a currently unknown gene- or pathway defect that corresponds with poor treatment outcome.
The present invention thus provides a method of classifying AML. Using this method, a total of 286 AML samples analyzed on a DNA microarray consisting of 22283 probe sets, representing approximately 13,000 genes could be classified into at least 16 distinct clusters. These 16 distinct clusters of AML patients were assigned on the basis of strong correlation between their individual differential expression profiles for 2856 probe sets (Table 1; FIG. 1). The methods used to analyze the expression level values to identify differentially expressed genes were employed such that optimal results in clustering, i.e., unsupervised ordering, were obtained. This then resulting in the definition of the 16 clusters of reference profiles based on molecular signature. The genes that defined the position or clustering of these 16 individual clusters could be determined and the minimal sets of genes required to accurately predict the prognostically important AML classes corresponding to these clusters could be derived. It should be understood that the method for classifying AML according to the present invention may result in a distinct clustering pattern and therefore in a different classification scheme when other (numbers of) subjects are used as reference, or when other types of oligonucleotide microarrays for establishing gene expression profiles are used.
The present invention thus provides a comprehensive classification of AML covering various previously identified genetically defined classes. Further analysis of classes by prediction analysis of microarrays (PAM) to determine the minimum number of genes that defined or predicted these prognostically important classes resulted in the establishment of cluster-specific genes or signature genes. The presence of distinct gene expression profiles defining the novel classes suggests the presence of yet unknown common gene defects or pathway defects among AML cases in those classes. Several classes could be distinguished on the basis of the expression level of a single gene, whereas others could only be distinguished on the basis of 20 or more differentially expressed genes (Table 3).
The methods of the present invention comprise in some aspects the step of defining cluster-specific genes by selecting those genes of which the expression level characterizes the clustered position of the corresponding AML class among the various AML classes within a classification scheme of the present invention. Such cluster-specific genes are selected preferably on the basis of PAM analysis. This method of selection comprises the following.
PAM, or partition round medoids, is one of the k-medoids methods. Different from usual k-means approach, it also accepts a dissimilarity matrix, and it is more robust because it minimizes a sum of dissimilarities instead of a sum of squared Euclidean distances. The PAM-algorithm is based on the search for “k” representative objects or medoids among the observations of the dataset, which should represent the structure of the data. After finding a set of “k” medoids, “k” clusters are constructed by assigning each observation to the nearest medoid. The goal is to find “k” representative objects that minimize the sum of the dissimilarities of the observations to their closest representative object. The distance metric to be used for calculating dissimilarities between observations are “euclidean” and “manhattan.” Euclidean distances are root sum-of-squares of differences, and manhattan distances are the sum of absolute differences. PAM calculates how many genes are necessary to identify all members (patients) belonging to a certain cluster.
The methods of the present invention comprise in some aspects the step of establishing whether the level of expression of cluster-specific genes in a subject shares sufficient similarity to the level of expression that is characteristic for an individual AML class. This step is necessary in determining the presence of that particular AML class in a subject under investigation, in which case the expression of that gene is used as a disease marker. Whether the level of expression of cluster-specific genes in a subject shares sufficient similarity to the level of expression of that particular gene in an individual AML class may, for instance, be determined by setting a threshold value.
The present invention also reveals genes with a high differential level of expression in specific AML classes compared the geometric mean of all reference subjects. These highly differentially expressed genes are selected from the genes shown in Table 2. These genes and their expression products are useful as markers to detect the presence of AML in a patient. Antibodies or other reagents or tools may be used to detect the presence of these markers of AML.
The present invention also reveals gene expression profiles comprising values representing the expression levels of genes in the various identified AML classes. In a preferred embodiment, these expression profiles comprise the values representing the differential expression levels. Thus, in one embodiment the expression profiles of the invention comprise one or more values representing the expression level of a gene having differential expression in a defined AML class. Each expression profile contains a sufficient number of values such that the profile can be used to distinguish one AML class from another. In some embodiments, the expression profiles comprise only one value. For example, it can be determined whether a subject affected by AML is in the AML class defined by cluster #9 (inv(16)) based only on the expression level of MYH11 201497_x_at (see Tables 2 and 31). Similarly, it can be determined whether a subject affected by AML is in the AML class defined by cluster #12 (t(15,17)) based only on the expression level of the cDNA of 2 genes FGF 13 205110_s_at and HGF 210997_at and 210998_s_at (see Tables 2 and 34). In this case, the expression profile comprises two values corresponding to two differentially expressed genes. In other embodiments, the expression profile comprises more than one or two values corresponding to a differentially expressed gene, for example, at least 3 values, at least 4 values, at least 5 values, at least 6 values, at least 7 values, at least 8 values, at least 9 values, at least 10 values, at least 11 values, at least 12 values, at least 13 values, at least 14 values, at least 15 values, at least 16 values, at least 17 values, at least 18 values, at least 19 values, at least 20 values, at least 22 values, at least 25 values, at least 27 values, at least 30 values, at least 35 values, at least 40 values, at least 45 values, at least 50 values, at least 75 values, at least 100 values, at least 125 values, at least 150 values, at least 175 values, at least 200 values, at least 250 values, at least 300 values, at least 400 values, at least 500 values, at least 600 values, at least 700 values, at least 800 values, at least 900 values, at least 1000 values, at least 1200 values, at least 1500 values, or at least 2000 or more values.
It is recognized that the diagnostic accuracy of assigning a subject to an AML class will vary based on the number of values contained in the expression profile. Generally, the number of values contained in the expression profile is selected such that the diagnostic accuracy is at least 85%, at least 87%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%, as calculated using methods described elsewhere herein, with an obvious preference for higher percentages of diagnostic accuracy.
It is recognized that the diagnostic accuracy of assigning a subject to an AML class will vary based on the strength of the correlation between the expression levels of the differentially expressed genes within that specific AML class. When the values in the expression profiles represent the expression levels of genes whose expression is strongly correlated with that specific AML class, it may be possible to use fewer number of values (genes) in the expression profile and still obtain an acceptable level of diagnostic or prognostic accuracy.
The strength of the correlation between the expression level of a differentially expressed gene and a specific AML class may be determined by a statistical test of significance. For example, the chi square test used to select genes in some embodiments of the present invention assigns a chi square value to each differentially expressed gene, indicating the strength of the correlation of the expression of that gene to a specific AML class. Similarly, the T-statistics metric and the Wilkins' metric both provide a value or score indicative of the strength of the correlation between the expression of the gene and its specific AML class. These scores may be used to select the genes of which the expression levels have the greatest correlation with a particular AML class to increase the diagnostic or prognostic accuracy of the methods of the invention, or in order to reduce the number of values contained in the expression profile while maintaining the diagnostic or prognostic accuracy of the expression profile. Preferably, a database is kept wherein the expression profiles of reference subjects are collected and to which database new profiles can be added and clustered with the already existing profiles such as to provide the clustered position of the new profile among the already present reference profiles. Furthermore, the addition of new profiles to the database will improve the diagnostic and prognostic accuracy of the methods of the invention. Preferably, in a method of the present invention SAM or PAM analysis tools are used to determine the strength of such correlations.
The methods of the invention comprise the steps of providing an expression profile from a sample from a subject affected by AML and comparing this subject expression profile to one or more reference profiles that are associated with a particular AML class, a class with a known prognosis, or a class with a favorable response to therapy. By identifying the AML class reference profile that is most similar to the subject expression profile, e.g., when their clustered positions fall together, the subject can be assigned to an AML class. The AML class assigned is that with which the reference profile(s) are associated. Similarly, the prognosis of a subject affected by AML can be predicted by determining whether the expression profile from the subject is sufficiently similar to a reference profile associated with an established prognosis, such as a good prognosis or a bad prognosis. Whenever a subject's expression profile can be assigned to an established AML class, a preferred intervention strategy, or therapeutic treatment can then be proposed for the subject, and the subject can be treated according to the assigned strategy. As a result, treatment of a subject with AML can be optimized according to the specific class of AML with which the subject is affected. For instance, the AML class belonging to cluster #12, characterized by the presence of t(15,17), may be treated with retinoic acid. Within one class or cluster, further division may be made according to responders and non-responders to treatment or therapy. Such divisions may provide for further detailed characterization of AML subjects. In another embodiment, the subject expression profile is from a subject affected by AML who is undergoing a therapy to treat the AML. The subject expression profile is compared to one or more reference expression profiles to monitor the efficacy of the therapy.
In some embodiments, the assignment of a subject affected by AML to an AML class is used in a method of choosing a therapy for the subject affected by AML. A therapy, as used herein, refers to a course of treatment intended to reduce or eliminate the affects or symptoms of a disease, in this case AML. A therapy regime will typically comprise, but is not limited to, a prescribed dosage of one or more drugs or hematopoietic stem cell transplantation. Therapies, ideally, will be beneficial and reduce the disease state but in many instances, the effect of a therapy will have non-desirable effects as well.
In one aspect, the present invention provides a method of determining the prognosis for an AML-affected subject, the method comprising the steps of providing a classification scheme for AML by producing such a scheme according to a method of the invention and determining the prognosis for each AML class in the scheme based on clinical records for the AML subjects comprised in the class. In order to predict the progression of the disease in a subject, one has to rely on clinical records. The present invention provides for the assignment of the various clinical data recorded with reference subjects affected by AML to the various AML classes as defined herein. This assignment preferably occurs in a database. This has the advantage that once a new subject is identified as belonging to a particular AML class, either by performing a specific AML diagnostic method of the invention using the cluster-specific genes as disease markers or by performing a method of classifying an AML in an AML-affected subject according to the invention, then the prognosis that is assigned to that class may be assigned to that subject.
The present invention provides compositions that are useful in determining the gene expression profile for a subject affected by AML and selecting a reference profile that is similar to the subject expression profile. These compositions include arrays comprising a substrate having capture probes that can bind specifically to nucleic acid molecules that are differentially expressed in AML classes. Also provided is a computer-readable medium having digitally encoded reference profiles useful in the methods of the claimed invention.
The present invention provides arrays comprising capture probes for detection of polynucleotides (transcriptional state) or for detection of proteins (translational state) in order to detect differentially expressed genes of the invention. By “array” is intended a solid support or substrate with peptide or nucleic acid probes attached to the support or substrate. Arrays typically comprise a plurality of different nucleic acid or peptide capture probes that are coupled to a surface of a substrate in different, known locations. These arrays, also described as “microarrays” or colloquially “chips” have been generally described in the art, and reference is made U.S. Pat. Nos. 5,143,854, 5,445,934, 5,744,305, 5,677,195, 6,040,193, 5,424,186, 6,329,143, and 6,309,831 and Fodor et al. (1991) Science 251:767-77. These arrays may generally be produced using mechanical synthesis methods or light directed synthesis methods which incorporate a combination of photolithographic methods and solid phase synthesis methods. Typically, “oligonucleotide microarrays” will be used for determining the transcriptional state, whereas “peptide microarrays” will be used for determining the translational state of a cell.
“Nucleic acid” or “oligonucleotide” or “polynucleotide” or grammatical equivalents used herein means at least two nucleotides covalently linked together. Oligonucleotides are typically from about 5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in length, up to about 100 nucleotides in length. Nucleic acids and polynucleotides are a polymers of any length, including longer lengths, e.g., 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000, etc. A nucleic acid of the present invention will generally contain phosphodiester bonds, although in some cases, nucleic acid analogs are included that may have alternate backbones, comprising, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphosphoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press); and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, Carbohydrate Modifications in Antisense Research, Sanghui & Cook, eds. Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made.
Particularly preferred are peptide nucleic acids (PNA) that include peptide nucleic acid analogs. These backbones are substantially non-ionic under neutral conditions, in contrast to the highly charged phosphodiester backbone of naturally occurring nucleic acids. This results in two advantages. First, the PNA backbone exhibits improved hybridization kinetics. PNAs have larger changes in the melting temperature (Tm) for mismatched versus perfectly matched basepairs. DNA and RNA typically exhibit a 2-4° C. drop in Tm for an internal mismatch. With the non-ionic PNA backbone, the drop is closer to 7-9° C. Similarly, due to their non-ionic nature, hybridization of the bases attached to these backbones is relatively insensitive to salt concentration. In addition, PNAs are not degraded by cellular enzymes, and thus can be more stable.
The nucleic acids may be double-stranded or single-stranded, as specified, or contain portions of both double-stranded or single-stranded sequence. As will be appreciated by those in the art, the depiction of a single strand also defines the sequence of the complementary strand; thus the sequences described herein also provide the complement of the sequence. The nucleic acid may be DNA, both genomic and cDNA, RNA or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine, isoguanine, etc.
“Transcript” typically refers to a naturally occurring RNA, e.g., a pre-mRNA, hnRNA, or mRNA. As used herein, the term “nucleoside” includes nucleotides and nucleoside and nucleotide analogs, and modified nucleosides such as amino modified nucleosides. In addition, “nucleoside” includes non-naturally occurring analog structures. Thus, e.g., the individual units of a peptide nucleic acid, each containing a base, are referred to herein as a nucleoside.
As used herein, a “nucleic acid probe or oligonucleotide” is defined as a nucleic acid capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. As used herein, a probe may include natural (i.e., A, G, C, or T) or modified bases (7-deazaguanosine, inosine, etc.). In addition, the bases in a probe may be joined by a linkage other than a phosphodiester bond, so long as it does not functionally interfere with hybridization. Thus, e.g., probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages. It will be understood by one of skill in the art that probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency of the hybridization conditions. The probes are preferably directly labeled such as with isotopes, chromophores, lumiphores, chromogens, or indirectly labeled such as with biotin to which a streptavidin complex may later bind or with enzymatic labels. By assaying for the hybridization of the probe to its target nucleic acid sequence, one can detect the presence or absence of the select sequence or subsequence. Diagnosis or prognosis may be based at the genomic level, or at the level of RNA or protein expression.
The skilled person is capable of designing oligonucleotide probes that can be used in diagnostic methods of the present invention. Preferably, such probes are immobilized on a solid surface as to form an oligonucleotide microarray of the invention. The oligonucleotide probes useful in methods of the present invention are capable of hybridizing under stringent conditions to AML-associated nucleic acids, such as to one or more of the genes selected from Table 1, preferably to one or more of the genes selected from Table 2, more preferably to one or more of the genes selected from Table 3.
Techniques for the synthesis of arrays using mechanical synthesis methods are described in, e.g., U.S. Pat. No. 5,384,261, to which reference is made herein. 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, for the purpose of which reference is made to U.S. Pat. Nos. 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992. Arrays may be packaged in such a manner as to allow for diagnostics or other manipulation of an all-inclusive device. Reference is, for example, made to U.S. Pat. Nos. 5,856,174 and 5,922,591.
The arrays provided by the present invention comprise capture probes that can specifically bind a nucleic acid molecule that is differentially expressed in AML classes. These arrays can be used to measure the expression levels of nucleic acid molecules to thereby create an expression profile for use in methods of determining the diagnosis and prognosis for AML patients, and for monitoring the efficacy of a therapy in these patients as described elsewhere herein.
In some embodiments, each capture probe in the array detects a nucleic acid molecule selected from the nucleic acid molecules designated in Tables 1 and 2. The designated nucleic acid molecules include those differentially expressed in AML classes selected from cluster #1-cluster #16 as depicted in FIG. 1.
The arrays of the invention comprise a substrate having a plurality of addresses, where each address has a capture probe that can specifically bind a target nucleic acid molecule. The number of addresses on the substrate varies with the purpose for which the array is intended. The arrays may be low-density arrays or high-density arrays and may contain 4 or more, 8 or more, 12 or more, 16 or more, 20 or more, 24 or more, 32 or more, 48 or more, 64 or more, 72 or more 80 or more, 96, or more addresses, or 192 or more, 288 or more, 384 or more, 768 or more, 1536 or more, 3072 or more, 6144 or more, 9216 or more, 12288 or more, 15360 or more, or 18432 or more addresses. In some embodiments, the substrate has no more than 12, 24, 48, 96, or 192, or 384 addresses, no more than 500, 600, 700, 800, or 900 addresses, or no more than 1000, 1200, 1600, 2400, or 3600 addresses.
The invention also provides a computer-readable medium comprising one or more digitally encoded expression profiles, where each profile has one or more values representing the expression of a gene that is differentially expressed in an AML class. The preparation and use of such profiles is well within the reach of the skilled person (see, e.g., WO 03/083140). In some embodiments, the digitally encoded expression profiles are comprised in a database. See, for example, U.S. Pat. No. 6,308,170.
The present invention also provides kits useful for diagnosing, treating, and monitoring the disease state in subjects affected by AML. These kits comprise an array and a computer readable medium. The array comprises a substrate having addresses, where each address has a capture probe that can specifically bind a nucleic acid molecule (by using an oligonucleotide array) or a peptide (by using a peptide array) that is differentially expressed in at least one AML class. The results are converted into a computer-readable medium that has digitally encoded expression profiles containing values representing the expression level of a nucleic acid molecule detected by the array.
By using the array described above, the amounts of various kinds of nucleic acid molecules contained in a nucleic acid sample can be simultaneously determined. In addition, there is an advantage such that the determination can be carried out even with a small amount of the nucleic acid sample. For instance, mRNA in the sample is labeled, or labeled cDNA is prepared by using mRNA as a template, and the labeled mRNA or cDNA is subjected to hybridization with the array, so that mRNAs being expressed in the sample are simultaneously detected, whereby their expression levels can be determined.
Genes each of which expression is altered due to AML can be found by determining expression levels of various genes in the AML-affected cells and classified into certain types as described above and comparing the expression levels with the expression level in a control tissue.
The method for determining the expression levels of genes is not particularly limited, and any of techniques for confirming alterations of the gene expressions mentioned above can be suitably used. Among all, the method using the array is especially preferable because the expressions of a large number of genes can be simultaneously determined. Suitable arrays are commercially available, e.g., from Affymetrix.
For instance, mRNA is prepared from blast cells, and then reverse transcription is carried out with the resulting mRNA as a template. During this process, labeled cDNA can be obtained by using, for instance, any suitable labeled primers or labeled nucleotides.
As to the labeling substance used for labeling, there can be used substances such as radioisotopes, fluorescent substances, chemiluminescent substances and substances with fluophor, and the like. For instance, the fluorescent substance includes Cy2, Fluor X, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, fluorescein isothiocyanate (FITC), Texas Red, Rhodamine and the like. In addition, it is desired that samples to be tested (cancer samples to be tested in the present selection method) and a sample to be used as a control are each labeled with different fluorescent substances, using two or more fluorescent substances, from the viewpoint of enabling simultaneous detection. Here, labeling of the samples is carried out by labeling mRNA in the samples, cDNA derived from the mRNA, or nucleic acids produced by transcription or amplification from cDNA.
Next, the hybridization is carried out between the above-mentioned labeled cDNA and the array to which a nucleic acid corresponding to a suitable gene or its fragment is immobilized. The hybridization may be performed according to any known processes under conditions that are appropriate for the array and the labeled cDNA to be used. For instance, the hybridization can be performed under the conditions described in Molecular Cloning, A laboratory manual, 2nd ed., 9.52-9.55 (1989).
The hybridization between the nucleic acids derived from the samples and the array is carried out, under the above-mentioned hybridization conditions. When much time is needed for the time period required for procedures from the collection of samples to the determination of expression levels of genes, the degradation of mRNA may take place due to actions of ribonuclease. In order to determine the difference in the gene expressions in the samples to be tested (i.e., cell or tissue samples of AML patients) and the gene expressions in a control sample, it is preferable that the mRNA levels in both of these samples are adjusted using a standard gene with relatively little alterations in expressions.
Thereafter, by comparing the hybridization results of the samples to be tested with those of the control sample, genes exhibiting differential expression levels in both samples can be detected. Concretely, a signal that is appropriate depending upon the method of labeling used, is detected for the array, which is subjected to hybridization with the nucleic acid sample labeled by the method as described above, whereby the expression levels in the samples to be tested can be compared with the expression level in the control sample for each of the genes on the array.
The genes thus obtained which have a significant difference in signal intensities are genes each of which expression is altered specifically for certain AML classes.
The present invention also provides a computer-readable medium comprising a plurality of digitally encoded expression profiles wherein each profile of the plurality has a plurality of values, each value representing the expression of a gene that is differentially expressed in at least one AML class. The invention also provides for the storage and retrieval of a collection of data relating to AML-specific gene expression data of the present invention, including sequences and expression levels in a computer data storage apparatus, which can include magnetic disks, optical disks, magneto-optical disks, DRAM, SRAM, SGRAM, SDRAM, RDRAM, DDR RAM, magnetic bubble memory devices, and other data storage devices, including CPU registers and on-CPU data storage arrays. Typically, the data records are stored as a bit pattern in an array of magnetic domains on a magnetizable medium or as an array of charge states or transistor gate states, such as an array of cells in a DRAM device (e.g., each cell comprised of a transistor and a charge storage area, which may be on the transistor).
For use in diagnostic, research, and therapeutic applications suggested above, kits are also provided by the invention. In the diagnostic and research applications such kits may include any or all of the following: assay reagents, buffers, AML class-specific nucleic acids or antibodies, hybridization probes and/or primers, antisense polynucleotides, ribozymes, dominant negative AML polypeptides or polynucleotides, small molecules inhibitors of AML-associated sequences, arrays, antibodies, Fab fragments, capture peptides etc. In addition, the kits may include instructional materials containing directions (i.e., protocols) for the practice of the methods of this invention. While the instructional materials typically comprise written or printed materials, they are not limited to such. Any medium capable of storing such instructions and communicating them to an end user is contemplated by this invention. Such media include, but are not limited to electronic storage media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media may include addresses to internet sites that provide such instructional materials. One such internet site may provide a database of AML reference expression profiles useful for performing similarity clustering of a newly determine subject expression profiles with a large set of reference profiles of AML subjects comprised in the database. Preferably, the database includes clinically relevant data such as patient prognosis, successful methods of treatment and cytogenetic characteristics for the various AML classes in the database.
The invention encompasses, for instance, kits comprising an array of the invention and a computer-readable medium having digitally encoded reference profiles with values representing the expression of nucleic acid molecules detected by the arrays. These kits are useful for assigning a subject affected by AML to an AML class and for diagnosing AML in a subject.
The present invention also provides for kits for screening for modulators of AML-associated sequences. Such kits can be prepared from readily available materials and reagents. For example, such kits can comprise one or more of the following materials: an AML-associated polypeptide or polynucleotide, reaction tubes, and instructions for testing AML-associated activity. Optionally the kit may comprise an array for detecting AML-associated genes, specifically cluster-defining genes according to the invention. A wide variety of kits and components can be prepared according to the present invention, depending upon the intended user of the kit and the particular needs of the user.
Diagnosis would typically involve evaluation of a plurality of genes or products. The genes will be selected based on correlations with important parameters in disease that may be identified in historical or outcome data.
In a preferred embodiment, a kit-of-parts according to the invention comprises an oligonucleotide microarray according to the invention and means for comparing a gene expression profile determined by using the microarray with a database of AML reference expression profiles. The present invention also comprises kits of parts suitable for performing a method of the invention as well as the use of the various products of the invention, including databases, microarrays, oligonucleotide probes and classification schemes in diagnostic or prognostic methods of the invention.
The methods and compositions of the invention may be used to screen test compounds to identify therapeutic compounds useful for the treatment of AML. In one embodiment, the test compounds are screened in a sample comprising primary cells or a cell line representative of a particular AML class. After treatment with the test compound, the expression levels in the sample of one or more of the differentially expressed genes of the invention are measured using methods described elsewhere herein. Values representing the expression levels of the differentially expressed genes are used to generate a subject expression profile. This subject expression profile is then compared to a reference profile associated with the AML class represented by the sample to determine the similarity between the subject expression profile and the reference expression profile. Differences between the subject expression profile and the reference expression profile may be used to determine whether the test compound has anti-leukemogenic activity.
The test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the “one-bead one compound” library method; and synthetic library methods using . . . affinity chromatography selection. The biological library approach is limited to polypeptide libraries, while the other four approaches are applicable to polypeptide, non-peptide oligomer or small molecule libraries of compounds (Lam (1997) Anticancer Drug Res. 12:145).
Examples of methods for the synthesis of molecular libraries can be found in the art, for example, in DeWitt et al. (1993) Proc. Natl. Acad. Sci. USA 90:6909; Erb et al. (1994) Proc. Natl. Acad. Sci. USA 91:11422; Zuckermann et al. (1994) J. Med. Chem. 37:2678; Cho et al. (1993) Science 261:1303; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061; and in Gallop et al. (1994) J. Med. Chem. 37:1233. Libraries of compounds may be presented in solution (e.g., Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (U.S. Pat. No. 5,223,409), spores (U.S. Pat. No. 5,223,409), plasmids (Cull et al. (1992) Proc. Natl. Acad. Sci. USA 89:1865-1869) or on phage (Scott and Smith (1990) Science 249:386-390; Devlin (1990) Science 249:404-406; Cwirla et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 97:6378-6382; Felici (1991) J. Mol. Biol. 222:301-310).
Candidate compounds include, for example, 1) peptides such as soluble peptides, including Ig-tailed fusion peptides and members of random peptide libraries (see, e.g., Lam et al. (1991) Nature 354:82-84; Houghten et al. (1991) Nature 354:84-86) and combinatorial chemistry-derived molecular libraries made of D- and/or L-configuration amino acids; 2) phosphopeptides (e.g., members of random and partially degenerate, directed phosphopeptide libraries, see, e.g., Songyang et al. (1993) Cell 72:767-778); 3) antibodies (e.g., polyclonal, monoclonal, humanized, anti-idiotypic, chimeric, and single chain antibodies as well as Fab, F(ab′)Z, Fab expression library fragments, and epitope-binding fragments of antibodies); 4) small organic and inorganic molecules (e.g., molecules obtained from combinatorial and natural product libraries; 5) zinc analogs; 6) leukotriene A4 and derivatives; 7) classical aminopeptidase inhibitors and derivatives of such inhibitors, such as bestatin and arphamenine A and B and derivatives; 8) and artificial peptide substrates and other substrates, such as those disclosed herein above and derivatives thereof.
The present invention discloses a number of genes that are differentially expressed in AML classes. These differentially expressed genes are shown in Tables 1 and 2. Because the expression of these genes is associated with AML risk factors, these genes may play a role in leukemogenesis. Accordingly, these genes and their gene products are potential therapeutic targets that are useful in methods of screening test compounds to identify therapeutic compounds for the treatment of AML. Genes that are common between a number of AML classes are preferred as targets for therapeutic treatment, since a broader working over the patient population can be expected. It is very likely that genes that are present in more than one AML class, as defined in the present invention, are involved in general processes underlying AML. Thus, the expression of these genes is likely to be associated with AML risk factors and thus play a role in leukemogenesis. Genes that are present in several classes or clusters may thus define superclusters, which superclusters may define the processes that play an important role in leukemogenesis in general, and AML in particular.
The differentially expressed genes of the invention may be used in cell-based screening assays involving recombinant host cells expressing the differentially expressed gene product. The recombinant host cells are then screened to identify compounds that can activate the product of the differentially expressed gene (i.e., agonists) or inactivate the product of the differentially expressed gene (i.e., antagonists).
Any of the leukemogenic functions mediated by the product of the differentially expressed gene may be used as an endpoint in the screening assay for identifying therapeutic compounds for the treatment of AML. Such endpoint assays include assays for cell proliferation, assays for modulation of the cell cycle, assays for the expression of markers indicative of AML, and assays for the expression level of genes differentially expressed in AML classes as described above. Modulators of the activity of a product of a differentially expressed gene identified according to these drug-screening assays provided above can be used to treat a subject with AML. These methods of treatment include the steps of administering the modulators of the activity of a product of a differentially expressed gene in a pharmaceutical composition as described herein, to a subject in need of such treatment.
The following examples are offered by way of illustration and not by way of limitation.
EXAMPLE 1
Methods Used
Patients and Cell Samples
Patients with a confirmed diagnosis of de novo AML were included in this study (Table 4). All patients were treated according to the HOVON (Dutch-Belgian Hematology-Oncology Co-operative group) protocols (WorldWideWeb.hovon.nl). The treatment protocols have been described previously Rombouts et al., 2001). Bone marrow or peripheral blood aspirations of AML patients at diagnosis (n=286) and healthy volunteers (n=5) were taken after informed consent. Blasts and mononuclear cells were purified by Ficoll-Hypaque (Nygaard, Oslo, Norway) centrifugation and cryopreserved. CD34-positive cells of healthy volunteers (n=3) were sorted using the fluorescent activated cell sorter (FACS). According to cytological analysis, the AML samples contained 80-100% blast cells after thawing independent of the blast count at diagnosis.
RNA Isolation and Quality Control
After thawing, cells were washed once with Hanks balanced salt solution. High quality total RNA was extracted by lyses with guanidinium isothiocyanate followed by cesium chloride gradient purification (Chomczynski & Sacchi, 1987). RNA concentration, quality and purity were examined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent, Amstelveen, The Netherlands). None of the samples showed RNA degradation (28S/18S rRNA ratio≧2) or DNA contamination.
Gene Profiling and Quality Control
286 newly diagnosed cases of AML (Table 3) were analyzed by gene profiling using the Affymetrix U133A GeneChip. The U133A GeneChips contain 22283 probe sets representing approximately 13000 distinct genes. Ten micrograms of total RNA was used for the production of antisense biotinylated RNA. Single-stranded cDNA and double-stranded cDNA were synthesized according to the manufactures protocol (Invitrogen Life Technologies, Breda, The Netherlands) using the T7-(dT)24-primer (Genset Corp, Paris France). In vitro transcription was performed with biotin-11-CTP and biotin-16-UTP (Perkin Elmer, Hoofddorp, The Netherlands) and the MEGAScript T7 labeling kit (Ambion, Cambridgeshire, UK). Double-stranded cDNA and cRNA were purified and fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, Calif.). Biotinylated RNA was subsequently hybridized to the Affymetrix U133A GeneChip (45° C. for 16 hours). Staining, washing and scanning procedures were carried out as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, Calif.). All GeneChips were visually inspected for obvious irregularities. The global method of scaling/normalization was applied and the differences between the scaling/normalization factors of all GeneChips (n=294) were less than three-fold (0.70, SD 0.26). All additional quality metrics, i.e., percent genes present (50.6, SD 3.8), actin 3′ to 5′ ratio (1.24, SD 0.19) and GAPDH 3′ to 5′ ratio (1.05, SD 0.14) indicated high overall sample and assay quality.
Data Normalization, Analysis and Visualization
The mean intensity values of all probe sets were calculated by the global method of scaling/normalization using MAS5.0. As most genes with values below 30 are absent (83% of all absent calls), these values were classified as unreliable and set to 30. This process resulted also in the exclusion of possibly unreliable present calls (10% of all present calls). The ratios between measured intensity and geometric mean intensity were calculated for each probe set and log 2 transformed to be used for further data analyses with Omniviz©, SAM© and PAM©.
Omniviz© (Maynard, Mass. (version 3.6))—Different numbers of probe sets were selected by filtering for those genes that in one or more samples differed at least n-fold from the geometric mean expression level of all AML patients. By using various ratios different numbers of differentially expressed probe sets were selected for the correlation visualization tool (Table 2). For each number of selected probe sets the clustering of the AML patients in specific molecularly recognizable groups was investigated using the Correlation Visualization tool of Omniviz.
Table 5 (below) shows the evaluation of the Correlation View results on the basis of the clustering of AML patients with similar molecular abnormalities.). The few AML cases with abnormalities involving chromosome 5 were excluded. Ratio: ratio between measured intensity and geometric mean intensity by which probe sets were selected.
SAM© (version 1.21) Trustees of Leland Stanford Junior University—All supervised analyses were performed using Significance Analysis of Microarrays (SAM) (Tusher et al., 2001). The criterion to identify the top40 genes for the assigned clusters was: at least a two-fold difference between selected cluster and the remaining AML samples and a q-value of less than 5%.
PAM© (version 1.12) Trustees of Leland Stanford Junior University—All supervised class prediction analyses were performed by applying Prediction Analysis of Microarrays (PAM) software in R (version 1.7.1) (Tibshirani et al., 2002).
RT-PCR and Sequence Analyses
Reverse trancriptase-polymerase chain reactions (RT-PCR) and sequence analyses for mutations in FLT3-ITD, FLT3-TKD, N-RAS, K-RAS and cEBPα, as well as real-time PCR for EVI1 were performed as described previously (van Waalwijk van Doorn-Khosrovani et al., 2003a; van Waalwijk van Doorn-Khosrovani et al., 2003b; Valk et al., 2004; Care et al., 2003).
Statistical Analyses of Survival
Statistical analyses were performed with Stata Statistical Software, Release 7.0 (Stata, College Station, Tex.). Actuarial probabilities of overall survival (OS, with failure death due to any cause) and event-free survival (EFS, with failure in case of no complete remission at day 1, at relapse or death in first CR) were estimated by the method of Kaplan and Meier.
Results
Correlation Visualization of De Novo AML by Gene Expression
The best unsupervised ordering by applying the visualization tool of Omniviz of the AML cases in relation to different molecular markers was reached using 2856 probe sets (representing 2008 annotated genes and 146 ESTs) (FIG. 1A and Table 5). Sixteen distinct groups of AML patients were assigned on the basis of strong correlation between adjacent AML patients, i.e., within one red square along the diagonal, as well as the correlation and anti-correlation between the different groups, i.e., between the red squares along the diagonal (FIG. 1A). The final Omniviz Correlation View generated with 2856 probe sets was adapted such that cytological, cytogenetic and molecular parameters could be plotted directly adjacent to the original diagonal. This resulted in a unique way of visualization of the groups of patients with high correlation and related parameters (FIG. 1B).
Distinct clusters of AML t(8;21), AML inv(16) and AML t(15;17) were apparent (FIG. 1B). Although these distinct clusters were readily identified with less probe sets using the correlation tool, clusters of AML patients with mutations in FLT3 or cEBPα, or with overexpression of EVI1 were only apparent with 2856 probe sets (Table 5 and FIGS. 4 to 10). When more genes were used for the correlation visualization this compact clustering vanished (Table 5).
Unique genes characteristic for each of the 16 identified clusters were obtained by supervised analysis using SAM. The expression profiles of the top40 genes are plotted in FIG. 1B alongside the Correlation View. The SAM analyses resulted in only 599 discriminating genes (Tables 23-39) since a distinct gene profile for cluster #14 could not be identified, suggesting tight overlap with genes in clusters #7 and #8.
AML and Recurrent Translocations
CBFβ/MYH11—All inv(16) AML patients clustered within cluster #9 (FIG. 1B). Of note, four patients who were previously not known to harbor an inv(16) were included within this cluster. Molecular analysis and Southern blotting revealed the presence of CBFβ/MYH11 fusion gene in those cases (FIG. 11). SAM analysis revealed that MYH11 was the most prominent discriminating gene for this cluster. Interestingly, CBFβ anti-correlated with this cluster, suggesting that the CBFβ/MYH11 fusion protein down modulates the expression of the CBF/3 allele.
PML/RARα—Cluster #12 contains all cases of acute promyelocytic leukemia (APL) with t(15;17) (FIG. 1B), including two patients previously recognized as APL with PML/RARα by RT-PCR only. SAM analyses revealed that genes encoding growth factors such as hepatocyte growth factor (HGF), macrophage-stimulating 1 (hepatocyte growth factor-like (MST1)) and fibroblast growth factor 13 (FGF13) were specific for this cluster. In addition, cluster #12 could be separated into two subgroups with either high or low white blood cell count (WBC). This subdivision corresponds with FLT3 ITD mutation status (FIG. 1B).
AML1/ETO—All patients with a t(8;21) grouped within cluster #13 (FIG. 1B), including one patient without a t(8;21) (2496). SAM identified ETO as the most discriminative gene for this cluster.
AML with 11q23 Abnormalities
AML patients with 11q23 abnormalities were intermingled within the 286 AML patients, although two subgroups were apparent, i.e., cluster #1 and cluster #16 (FIG. 1B). Cluster #16 contains four cases of t(9;11) and one case of t(11;19) (5/11 cases (45%)). SAM analyses identified a strong signature with a group of genes specifically up-regulated in the majority of cases in this cluster (FIG. 1B). Although seven of 14 (50%) cases within cluster #1 have chromosome 11 abnormalities as well, this subgroup appears quite heterogeneous with a less uniform signature (FIG. 1B).
AML and cEBPα Mutations
Interestingly, two separate clusters (#4 and #15) comprise AML patients with predominantly normal karyotypes and a high frequency of mutations in cEBPα (FIG. 1B (Clusters #4 (8/15 cases (53%)) and #15 (5/8 cases (62%))). In cluster #4a set of up- and down-regulated genes could be defined, which appeared to discriminate the AML cases in cluster #4 from cluster #15. The up-regulated genes represent certain T-cell genes, such as the CD7 antigen (CD7) and the T-cell receptor delta locus (TRD@), which are known to be expressed on immature subsets of AML as well (Lo Coco et al., 1989; Boeckx et al., 2002). All but one of the top40 genes of cluster #15 are down-regulated. Interestingly, these genes are similarly down-regulated in cluster #4 (FIG. 1B). The genes encoding alpha1-catenin (CTNNA1), tubulin beta-5 (TUBBS) and Nedd4 family interacting protein 1 (NDFIP1) were the only genes down-modulated and among the top40 in both cluster #4 and #15.
AML and EVI1 Overexpression
A separate cluster (#10) of AML was identified in which 44% (10/22 cases) showed increased expression of EVI1. Aberrant expression of EVI1 in cluster #10 correlated with chromosome 7 abnormalities (6/10 EVI1-positive cases). This complete group of patients could be discriminated based on a selection of genes, suggesting that all patients, even the EVI1-negative cases, carry abnormalities in a common pathway. Cluster #8 also contains a relatively high number of chromosome 7 aberrations (5/13 cases), but it displays a different molecular signature compared to cluster #10 (FIG. 1B). This suggests that high expression of EVI1 and/or EVI1-related proteins determines the molecular profile of cluster #10. Four out of 14 cases within the heterogeneous cluster #1 also demonstrated increased EVI1 expression. These patients may cluster outside cluster #10 since their molecular signatures are most likely the result of EVI1 overexpression and an 11q23 abnormality.
AML with FLT3 Mutations
Groups of patients with mutations in the FLT3 receptor gene were recognized within the Correlation View (FIG. 1B). In fact, clusters #2 and #6 merely consist of patients with a FLT3 ITD. Interestingly, almost all of these patients have a normal karyotype. In addition, the FLT3 ITD mutation status seems to divide several clusters into two groups, e.g., clusters #3, #5 and AML with t(15;17) (#12). Other individual cases of AML with FLT3 ITD were more dispersed over the whole group of AML patients. AML patients with mutations in the tyrosine kinase domain (TKD) of FLT3 did not cluster. Likewise patients with mutations in codons 12, 13 or 61 of the small GTPase RAS (N-RAS and K-RAS) do not have apparent signatures and do not aggregate in the Correlation View (FIG. 1B).
Other Unique AML Clusters
AML patients with normal karyotypes clustered in several subgroups within the assigned clusters (FIG. 1B). In fact, the majority of patients in cluster #11 have normal karyotypes without any consistent additional abnormality. Other unique clusters, i.e., cluster #3, #5, #7, #8 and #14, were identified which could not be annotated with any known cytogenetic or molecular abnormality. Cluster #5 mainly contains AML patients that belong to the French-American-British (FAB) classification M4 or M5 subtypes (FIG. 1B), suggesting that the morphology was the main determinant for classifying these cases within this subgroup. Clusters #3, #7, #8, #11 and #14 contain AML cases, that do not belong to one FAB subtype, but can be discriminated based on distinct gene expression profiles.
Class Prediction of Distinct Clusters in AML
All 286 AML cases were randomized and divided into a training- (n=190) and a validation set (n=96). PAM was applied on the dataset to determine the minimal number of genes to predict distinct abnormalities with prognostic value in AML1, i.e., t(8;21), inv(16), t(15;17), 11q23 (cluster #16), EVI1/monosomy 7 (cluster #10), cEBPα (clusters #4 and #15) (Table 3). In addition, since FLT3 ITD mutations are frequent abnormalities in AML and associated with poor outcome2, the minimal set of genes to predict FLT3 ITD mutations in AML were identified.
All patients with favorable cytogenetics within the validation set were predicted with 100% accuracy and with only few genes (Table 3). As expected from the SAM analyses, ETO for t(8;21), MYH11 for inv(16) and HGF for t(15;17) were among the most predictive genes. Interestingly, cluster #10 (EVI1/monosomy 7) was predicted with high accuracy, although with a higher ten-fold cross-validation error. Cluster #16 (11q23) was predicted with fairly high accuracy. Since cluster #15 (cEBPα) consists of few patients only, we combined both cEBPα clusters. These two clusters could subsequently be predicted within the validation set with fairly high accuracy. A highly predictive signature for the FLT3 ITD cluster could not be defined by means of expression profiling within the AML patient cohort investigated.
Table 3 (below) shows the class prediction using PAM (ten-fold CV error: ten-fold cross-validation prediction error on training set (n=190), Error validation set: prediction error on validation set (n=96), #Probe sets: Number of probe sets used for prediction, #Genes: number of genes represented by probe sets used for prediction. *After randomization none of the AML patients from cEBPα cluster #15 were included in the validation set.
Survival Analyses
Overall survival (OS), event free survival (EFS) and relapse rate (RR) of AML patients from clusters containing >20 cases in the Correlation View, were determined, i.e., clusters #5 (M4/M5), #9 (inv(16)), #10 (EVI1/monosomy 7), #12 (t(15;17)) and #13 (t(8;21)). Patients with a complete clinical data set were included in the survival analyses (FIG. 2). The mean actuarial OS and DFS probabilities at 60 months of the patients with favorable cytogenetics were 62% (±8.7%) and 50% (±2.4%), respectively. AML patients included in cluster #5 had intermediate survival (OS 27% and EFS 32%), whereas patients from cluster #10 showed poor treatment response (OS 6% (P=0.001) and EFS 18% (P=0.004)) mainly as a result of increased relapse incidence (FIG. 2C).
Discussion
The results of the study presented here show profound diagnostic impact of expression profiling. Among AML with considerable genetic diversity, expression profiling provides an approach to distinguish these highly variable genetic subsets into clusters with distinct signatures. Patients with AML were classified in 16 groups based on their gene expression profiles by unsupervised Pearson's correlation coefficient analyses. The results show that each of the assigned clusters represents true AML subgroups with specific molecular signatures.
Firstly, all cases with t(8;21) (AML1/ETO), inv(16) (CBFβ/MYH11) or t(15;17) (PML/RARα), including patients that could not be recognized by karyotyping, could be clustered in three separate clusters with unique gene expression profiles. Unique correlations between gene expression profiles: and favorable cytogenetic aberrations have been shown in the prior (Debernardi et al., 2003; Schoch et al., 2002), however, here we demonstrate that these patients can even be recognized with high accuracy within a representative cohort of AML patients.
Secondly, Significance Analyses of Microarrays (SAM) and Prediction Analyses of Microarrays (PAM), showed a strong concordance between the specific genes identified for the different assigned clusters, demonstrating that we identified truly discriminative genes for all the clusters that we assigned. For instance, we identified two distinct clusters (#4 and #15) with overlapping signatures, which both included cases with normal karyotypes and mutations in cEBPα. Multiple genes appeared to be down-regulated in both subclasses but were unaffected in any other AML subgroup.
Thirdly, the discriminative genes identified by SAM and PAM may in addition reveal specific functional pathways critical for the pathophysiology of AML. This is suggested by the identification of several functionally important genes implicated in specific subtypes of AML, such as the IL5Rα in AML with t(8;21) (Touw et al., 1991) and the bona fide FLT3/STAT5 targets IL2Rα (Kim et al., 2001) and PIM1 (Lilly et al., 1992) in AML with FLT3 ITD mutations.
Five clusters (#5, #9, #10, #12 and #13) 20 or more cases were evaluated in relation to outcome of therapy. As expected, clusters #9 (CBFβ/MYH11), #12 (PML/RARα) and #13 (AML1/ETO), comprised cases with a favorable response to therapy. However, cases that belong to cluster #10 showed a distinct poor outcome. Patients in this cluster could be predicted with high accuracy in an independent validation set with a minimal set of genes. The high frequency of poor prognostic markers, e.g., −7(q), −5(q), t(9;22) or high EVI1 is in agreement with the observation that this cluster represents a bad-risk AML group. However, since the cluster contains AML cases with a variety of genetically defined poor risk markers and since a significant portion of the cases did not express any of these lesions, this suggests that a unique pathway represented by the molecular signature of this cluster of AML patients is associated with bad outcome.
This hypothesis is further strengthened by the fact that large numbers of cases with the same poor-risk markers were present in other clusters (#1, #2, #8 and #16). Analysis of the genes up- or down-regulated in AML cases from cluster #10 may predict the pathway(s) involved the pathophysiology of this subgroup of AML patients. This might also shed light on the findings that the other cases with distinct poor-prognostic markers are grouped in different clusters. Unfortunately, these latter groups were too small for an accurate analysis of treatment outcome.
The 44 AML patients in cluster #5 showed an intermediate survival estimate. Since these cases belong to AML FAB-M4 or -M5 subtype, it is possible that monocyte/macrophage related genes mainly drove clustering of these cases. Unsupervised clustering of larger numbers of only AML FAB-M4 or -M5 cases with a normal karyotype may result in the identification of specific subgroups with unique gene expression profiles and perhaps variable prognosis.
Three clusters mainly consisting of patients with normal karyotype were identified. The majority of patients in two of those clusters (#2 and #6) were also characterized by FLT3 ITD mutations, whereas patients in cluster #11, with a discriminative molecular signature, did not contain any consistent abnormality.
Two clusters (#1 and #16) were recognized, which harbored 11q23 abnormalities, representing defects involving the mixed-lineage leukemia gene. The reason for the separation of these two subgroups is most likely caused by different additional genetic defects in the cases of the distinct clusters, causing different gene expression profiles. In cluster #1 this abnormality may be the frequently observed high expression of EVI1, which is not apparent in AML cases from cluster #16. A similar explanation may hold for AML cases in clusters #4 and #15, both comprising cEBPα mutant cases, AML patients in clusters #1 and #10 (high EVI1 expression), or patients in clusters #8 and #10 with frequent monosomy 7. Given the fact that each of these clusters expressed such a distinct molecular signature most probably means that in the cases without the characteristic genetic lesion, other currently unidentified mutations affecting the same pathways are responsible for the genetic profiles.
Internal tandem duplications (ITD) in the FLT3 gene adversely affect clinical outcome (Levis & Small, 2003). The molecular signature induced by the constitutively activated the FLT3 receptor appears not strong enough to distinguish FLT3 ITD carrying AML patients from the other cases. However, the clustering of FLT3 ITD-positive patients within assigned clusters, as is the case in the APL subgroup (cluster #12), demonstrates that the presence of FLT3 ITD results in different biological entities within one type of disease.
To this end, our study demonstrates that cytogenetically known as well as new clusters of AML with characteristic gene expression signatures can be identified with one single assay. The quality of genome-wide analysis will further advance with the availability of novel whole genome arrays, improved sequence annotation and the development of more sophisticated protocols and software, allowing analysis of subtle differences in gene expression and comprehensive pathway prediction. These studies, while augmenting our understanding of the pathways involved in pathophysiology of AML, will result in improved diagnostics and possibly lead the way to the development anti-cancer drugs that interfere with disease related pathways.
EXAMPLE 2
Analyses of Novel AML Patients
Patients and Cell Samples
Eligible patients have a diagnosis of primary AML, confirmed by cytological examination of blood and bone marrow. Blasts and mononuclear cells should be purified by Ficoll-Hypaque (Nygaard, Oslo, Norway) centrifugation. Add 1:1 diluted peripheral blood or bone marrow 1:4 diluted both in PBS up to 20-25 ml on to 15 ml Ficoll-Hypaque. Spin 15 minutes at 1880 rpm. Collect interphase with mononuclear cells and wash twice with PBS (total volume 50 ml, 8 minutes 2000 rpm). The pellet contains the mononuclear cells, including the blast cells. As a result, the AML samples should contain 80-100 percent blast cells, regardless of the blast count at diagnosis. 30×106 cells/ml should be frozen in 1 vol PBS/1 vol heat inactivated FCS/0.5 vol DMSO stored in liquid nitrogen.
RNA Isolation and Quality Control
After thawing, cells were washed once with Hanks balanced salt solution. High quality total RNA should extracted by lysis with guanidinium isothiocyanate followed by cesium chloride gradient purification. RNA concentration, quality and purity should be examined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent, Amstelveen, The Netherlands). None of the samples should show RNA degradation (28S/18S rRNA ratio≧2) or contamination by DNA.
Gene Profiling and Quality Control
Ten μg of total RNA should be used to prepare antisense biotinylated RNA. Single-stranded cDNA and double-stranded cDNA should be synthesized according to the manufacturer's protocol (Invitrogen Life Technologies, Breda, The Netherlands) using the T7-(dT)24-primer (Genset Corp, Paris, France). In vitro transcription should be performed with biotin-11-CTP and biotin-16-UTP (Perkin Elmer, Hoofddorp, The Netherlands) and the MEGAScript T7 labeling kit (Ambion, Cambridgeshire, UK). Double-stranded cDNA and cRNA should be purified and fragmented with the GeneChip® Sample Cleanup Module (Affymetrix, Santa Clara, Calif.). Biotinylated RNA should be hybridized to the Affymetrix U133A GeneChip® (45° C. for 16 hours). Samples should be analyzed using Affymetrix U133A or U133 Plus2.0 GeneChips®. The U133A GeneChip® contains 22283 probe sets, representing approximately 13000 genes. These probe sets can also be selected from the U133 Plus2.0 GeneChip®. Staining, washing and scanning procedures should be carried out as described in the GeneChip® Expression Analysis Technical Manual (Affymetrix, Santa Clara, Calif.). All GeneChips® should be visually inspected for irregularities. The global method of scaling/normalization should be applied and the differences between the scaling/normalization factors of all GeneChips® up to the Target Gene Intensity of 100 (reference value n=285: scaling factor=0.70, SD 0.26). All additional measures of quality—percent genes present (reference value n=285: 50.6±3.8), actin 3′ to 5′ ratio (reference value n=285: 1.24±0.19) and GAPDH 3′ to 5′ ratio (reference value n=285: 1.05±0.14)—should indicate high overall sample and assay quality.
Reference Data Set
A reference data set (gene expression data and detailed clinical and molecular data) of 285 AML patients should be downloaded from the Gene Expression Omnibus (WorldWideWeb.ncbi.nlm.nih.gov/geo, accession number GSE1159).
Data Normalization, Analysis and Visualization
All intensity values (reference set (n=285) and new AML patients to be included) should be scaled to an average value of 100 per GeneChip® according to the method of global scaling/normalization, available in the Affymetrix Microarray Suite (MAS5.0). All other setting should be default according to the manufacturer.
As our methods reliably identify samples with an average intensity value >30 but do not reliably discriminate values from 0-<30, these values should be set to 30.
For each probe set, the geometric mean of the hybridization intensities of all patient samples should calculated. The level of expression of each probe set in every sample was determined relative to this geometric mean and transformed to log2 to ascribe equal weight to gene-expression levels with similar relative distances to the geometric mean. The transformed expression data should be subsequently imported into Omniviz.
Pearson's Correlation Visualization tool of Omniviz (Maynard, Mass. (version 3.6))—The Omniviz package should be used to perform and visualize unsupervised cluster analysis. The clustering of molecularly recognizable specific groups of patients should be investigated with the 2856 probe sets (Table 1) taking the reference set (n=285) and new patients to be analyzed into account.
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    Kim H. P., J. Kelly, and W. J. Leonard. The basis for IL-2-induced IL-2 receptor alpha chain gene regulation: importance of two widely separated IL-2 response elements. Immunity 2001; 15:159-72.
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TABLE 1







About 2856 genes used for classifying AML of 286 patients into


defined clusters as identified in Correlation View









Affymetrix probe set id
gene symbol
unigene ID





117_at
HSPA6
Hs.3268


1405_i_at
CCL5
Hs.241392


1598_g_at
GAS6
Hs.437710


200067_x_at
SNX3
Hs.12102


200075_s_at
GUK1
Hs.376933


200099_s_at
—
— // —


200602_at
APP
Hs.177486


200606_at
DSP
Hs.349499


200612_s_at
AP2B1
Hs.370123


200616_s_at
KIAA0152
Hs.181418


200628_s_at
WARS
Hs.82030


200629_at
WARS
Hs.82030


200632_s_at
NDRG1
Hs.318567


200644_at
MLP
Hs.75061


200648_s_at
GLUL
Hs.442669


200660_at
S100A11
Hs.417004


200661_at
PPGB
Hs.118126


200665_s_at
SPARC
Hs.111779


200671_s_at
SPTBN1
Hs.205401


200672_x_at
SPTBN1
Hs.205401


200675_at
CD81
Hs.54457


200678_x_at
GRN
Hs.180577


200696_s_at
GSN
Hs.446537


200697_at
HK1
Hs.118625


200703_at
DNCL1
Hs.5120


200704_at
LITAF
Hs.76507


200706_s_at
LITAF
Hs.76507


200736_s_at
GPX1
Hs.76686


200762_at
DPYSL2
Hs.173381


200765_x_at
CTNNA1
Hs.254321


200766_at
CTSD
Hs.343475


200771_at
LAMC1
Hs.432855


200780_x_at
GNAS
Hs.157307


200782_at
ANXA5
Hs.145741


200784_s_at
LRP1
Hs.162757


200785_s_at
LRP1
Hs.162757


200791_s_at
IQGAP1
Hs.1742


200795_at
SPARCL1
Hs.75445


200796_s_at
MCL1
Hs.86386


200799_at
HSPA1A
Hs.75452


200800_s_at
HSPA1A
Hs.75452


200808_s_at
ZYX
Hs.75873


200832_s_at
SCD
Hs.119597


200838_at
CTSB
Hs.135226


200839_s_at
CTSB
Hs.135226


200853_at
H2AFZ
Hs.119192


200871_s_at
PSAP
Hs.406455


200872_at
S100A10
Hs.143873


200878_at
EPAS1
Hs.8136


200895_s_at
FKBP4
Hs.848


200897_s_at
KIAA0992
Hs.194431


200907_s_at
KIAA0992
Hs.194431


200921_s_at
BTG1
Hs.255935


200923_at
LGALS3BP
Hs.79339


200931_s_at
VCL
Hs.75350


200952_s_at
CCND2
Hs.376071


200953_s_at
CCND2
Hs.376071


200962_at
RPL31
Hs.375921


200965_s_at
ABLIM1
Hs.442540


200981_x_at
GNAS
Hs.157307


200982_s_at
ANXA6
Hs.412117


200983_x_at
CD59
Hs.278573


200985_s_at
CD59
Hs.278573


200986_at
SERPING1
Hs.384598


200989_at
HIF1A
Hs.412416


200991_s_at
SNX17
Hs.278569


200998_s_at
CKAP4
Hs.74368


200999_s_at
CKAP4
Hs.74368


201005_at
CD9
Ns.387579


201008_s_at
TXNIP
Ns.179526


201012_at
ANXA1
Hs.287558


201013_s_at
PAICS
Hs.444439


201015_s_at
JUP
Hs.2340


201024_x_at
IF2
Hs.158688


201034_at
ADD3
Hs.324470


201037_at
PFKP
Hs.26010


201041_s_at
DUSP1
Hs.171695


201043_s_at
ANP32A
Hs.124977


201044_x_at
DUSP1
Hs.171695


201047_x_at
RAB6A
Hs.5636


201050_at
PLD3
Hs.74573


201052_s_at
PSMF1
Hs.437495


201058_s_at
MYL9
Hs.433814


201060_x_at
STOM
Hs.439776


201061_s_at
STOM
Hs.439776


201069_at
MMP2
Hs.367877


201105_at
LGALS1
Hs.407909


201107_s_at
THBS1
Hs.164226


201108_s_at
THBS1
Hs.164226


201109_s_at
THBS1
Hs.164226


201110_s_at
THBS1
Hs.164226


201123_s_at
EIF5A
Hs.310621


201125_s_at
ITGB5
Hs.149846


201131_s_at
CDH1
Hs.194657


201136_at
PLP2
Hs.77422


201137_s_at
HLA-DPB1
Hs.368409


201141_at
GPNMB
Hs.389964


201160_s_at
CSDA
Hs.221889


201161_s_at
CSDA
Hs.221889


201162_at
IGFBP7
Hs.435795


201163_s_at
IGFBP7
Hs.435795


201169_s_at
BHLHB2
Hs.171825


201170_s_at
BHLHB2
Hs.171825


201174_s_at
TERF2IP
Hs.274428


201178_at
FBXO7
Hs.5912


201189_s_at
ITPR3
Hs.77515


201193_at
IDH1
Hs.11223


201195_s_at
SLC7A5
Hs.184601


201201_at
CSTB
Hs.695


201218_at
CTBP2
Hs.171391


201220_x_at
CTBP2
Hs.171391


201222_s_at
RAD23B
Hs.159087


201223_s_at
RAD23B
Hs.159087


201234_at
ILK
Hs.6196


201242_s_at
ATP1B1
Hs.78629


201249_at
SLC2A1
Hs.169902


201250_s_at
SLC2A1
Hs.169902


201251_at
PKM2
Hs.198281


201272_at
AKR1B1
Hs.75313


201285_at
MKRN1
Hs.7838


201291_s_at
TOP2A
Hs.156346


201294_s_at
WSB1
Hs.315379


201295_s_at
WSB1
Hs.315379


201300_s_at
PRNP
Hs.438582


201301_s_at
ANXA4
Hs.422986


201302_at
ANXA4
Hs.422986


201307_at
FLJ10849
Hs.386784


201309_x_at
C5orf13
Hs.508742


201313_at
ENO2
Hs.146580


201324_at
EMP1
Hs.306692


201325_s_at
EMP1
Hs.306692


201328_at
ETS2
Hs.292477


201329_s_at
ETS2
Hs.292477


201333_s_at
ARHGEF12
Hs.413112


201334_s_at
ARHGEF12
Hs.413112


201348_at
GPX3
Hs.386793


201360_at
CST3
Hs.304682


201373_at
PLEC1
Hs.79706


201389_at
ITGA5
Hs.149609


201392_s_at
IGF2R
Hs.76473


201393_s_at
IGF2R
Hs.76473


201412_at
LRP10
Hs.28368


201416_at
SOX4
Hs.357901


201417_at
SOX4
Hs.357901


201418_s_at
SOX4
Hs.357901


201422_at
IFI30
Hs.14623


201425_at
ALDH2
Hs.436437


201426_s_at
VIM
Hs.435800


201427_s_at
SEPP1
Hs.275775


201431_s_at
DPYSL3
Hs.150358


201445_at
CNN3
Hs.194662


201459_at
RUVBL2
Hs.6455


201462_at
KIAA0193
Hs.75137


201464_x_at
JUN
Hs.78465


201465_s_at
JUN
Hs.78465


201466_s_at
JUN
Hs.78465


201473_at
JUNB
Hs.400124


201487_at
CTSC
Hs.128065


201497_x_at
MYH11
Hs.78344


201506_at
TGFBI
Hs.421496


201508_at
IGFBP4
Hs.1516


201518_at
CBX1
Hs.77254


201522_x_at
SNRPN
Hs.48375


201531_at
ZFP36
Hs.343586


201536_at
na
Hs.181046


201539_s_at
FHL1
Hs.421383


201540_at
FHL1
Hs.421383


201548_s_at
PLU-1
Hs.143323


201549_x_at
PLU-1
Hs.143323


201550_x_at
ACTG1
Hs.14376


201563_at
SORD
Hs.878


201564_s_at
FSCN1
Hs.118400


201565_s_at
ID2
Hs.180919


201566_x_at
ID2
Hs.180919


201579_at
FAT
Hs.166994


201590_x_at
ANXA2
Hs.437110


201596_x_at
KRT18
Hs.406013


201599_at
OAT
Hs.75485


201601_x_at
IFITM1
Hs.458414


201631_s_at
IER3
Hs.76095


201644_at
TSTA3
Hs.404119


201655_s_at
HSPG2
Hs.211573


201656_at
ITGA6
Hs.212296


201666_at
TIMP1
Hs.446641


201667_at
GJA1
Hs.74471


201668_x_at
MARCKS
Hs.318603


201669_s_at
MARCKS
Hs.318603


201670_s_at
MARCKS
Hs.318603


201688_s_at
TPD52
Hs.162089


201689_s_at
TPD52
Hs.162089


201690_s_at
TPD52
Hs.162089


201693_s_at
EGR1
Hs.326035


201694_s_at
EGR1
Hs.326035


201695_s_at
NP
Hs.75514


201700_at
CCND3
Hs.83173


201711_x_at
RANBP2
Hs.199179


201714_at
TUBG1
Hs.21635


201720_s_at
LAPTM5
Hs.436200


201734_at
CLCN3
Hs.372528


201735_s_at
CLCN3
Hs.372528


201739_at
SGK
Hs.296323


201743_at
CD14
Hs.75627


201746_at
TP53
Hs.426890


201752_s_at
ADD3
Hs.324470


201753_s_at
ADD3
Hs.324470


201790_s_at
DHCR7
Hs.11806


201791_s_at
DHCR7
Hs.11806


201792_at
AEBP1
Hs.439463


201795_at
LBR
Hs.435166


201798_s_at
FER1L3
Hs.362731


201809_s_at
ENG
Hs.76753


201810_s_at
SH3BP5
Hs.109150


201811_x_at
SH3BP5
Hs.109150


201824_at
RNF14
Hs.170926


201831_s_at
VDP
Hs.325948


201839_s_at
TACSTD1
Hs.692


201841_s_at
HSPB1
Hs.76067


201842_s_at
EFEMP1
Hs.76224


201850_at
CAPG
Hs.82422


201852_x_at
COL3A1
Hs.443625


201858_s_at
PRG1
Hs.1908


201859_at
PRG1
Hs.1908


201860_s_at
PLAT
Hs.274404


201883_s_at
B4GALT1
Hs.396798


201887_at
IL13RA1
Hs.285115


201888_s_at
IL13RA1
Hs.285115


201890_at
RRM2
Hs.226390


201893_x_at
DCN
Hs.156316


201909_at
RPS4Y
Hs.180911


201912_s_at
GSPT1
Hs.2707


201923_at
PRDX4
Hs.83383


201938_at
CDK2AP1
Hs.433201


201944_at
HEXB
Hs.69293


201952_at
ALCAM
Hs.10247


201963_at
FACL2
Hs.406678


201968_s_at
PGM1
Hs.1869


201995_at
EXT1
Hs.184161


202007_at
NID
Hs.356624


202014_at
PPP1R15A
Hs.76556


202016_at
MEST
Hs.416498


202017_at
EPHX1
Hs.89649


202018_s_at
LTF
Hs.437457


202059_s_at
KPNA1
Hs.161008


202068_s_at
LDLR
Hs.213289


202071_at
SDC4
Hs.252189


202073_at
OPTN
Hs.390162


202074_s_at
OPTN
Hs.390162


202083_s_at
SEC14L1
Hs.75232


202085_at
TJP2
Hs.75608


202086_at
MX1
Hs.436836


202087_s_at
CTSL
Hs.418123


202088_at
LIV-1
Hs.79136


202096_s_at
BZRP
Hs.202


202107_s_at
MCM2
Hs.57101


202112_at
VWF
Hs.440848


202119_s_at
CPNE3
Hs.14158


202124_s_at
ALS2CR3
Hs.154248


202125_s_at
ALS2CR3
Hs.154248


202129_s_at
RIOK3
Hs.209061


202130_at
RIOK3
Hs.209061


202131_s_at
RIOK3
Hs.209061


202145_at
LY6E
Hs.77667


202153_s_at
NUP62
Hs.437023


202177_at
GAS6
Hs.437710


202191_s_at
GAS7
Hs.226133


202192_s_at
GAS7
Hs.226133


202193_at
LIMK2
Hs.278027


202201_at
BLVRB
Hs.76289


202203_s_at
AMFR
Hs.295137


202204_s_at
AMFR
Hs.295137


202206_at
ARL7
Hs.111554


202207_at
ARL7
Hs.111554


202208_s_at
ARL7
Hs.111554


202219_at
SLC6A8
Hs.388375


202234_s_at
SLC16A1
Hs.75231


202236_s_at
SLC16A1
Hs.75231


202237_at
NNMT
Hs.364345


202238_s_at
NNMT
Hs.364345


202241_at
C8FW
Hs.444947


202242_at
TM4SF2
Hs.439586


202252_at
RAB13
Hs.151536


202265_at
BMI1
Hs.380403


202269_x_at
GBP1
Hs.62661


202270_at
GBP1
Hs.62661


202283_at
SERPINF1
Hs.173594


202284_s_at
CDKN1A
Hs.370771


202286_s_at
TACSTD2
Hs.23582


202291_s_at
MGP
Hs.365706


202295_s_at
CTSH
Hs.114931


202310_s_at
COL1A1
Hs.172928


202336_s_at
PAM
Hs.352733


202340_x_at
NR4A1
Hs.1119


202345_s_at
FABP5
Hs.408061


202364_at
MXI1
Hs.118630


202379_s_at
NKTR
Hs.369815


202388_at
RGS2
Hs.78944


202391_at
BASP1
Hs.79516


202395_at
NSF
Hs.431279


202403_s_at
COL1A2
Hs.232115


202409_at
na
Hs.251664


202411_at
IFI27
Hs.278613


202425_x_at
PPP3CA
Hs.272458


202426_s_at
RXRA
Hs.20084


202429_s_at
PPP3CA
Hs.272458


202431_s_at
MYC
Hs.202453


202435_s_at
CYP1B1
Hs.154654


202436_s_at
CYP1B1
Hs.154654


202437_s_at
CYP1B1
Hs.154654


202443_x_at
NOTCH2
Hs.8121


202452_at
ZYG
Hs.29285


202456_s_at
ZYG
Hs.29285


202457_s_at
PPP3CA
Hs.272458


202459_s_at
LPIN2
Hs.437425


202460_s_at
LPIN2
Hs.437425


202464_s_at
PFKFB3
Hs.195471


202478_at
TRB2
Hs.155418


202479_s_at
TRB2
Hs.155418


202481_at
SDR1
Hs.17144


202492_at
FLJ22169
Hs.323363


202497_x_at
SLC2A3
Hs.419240


202498_s_at
SLC2A3
Hs.419240


202499_s_at
SLC2A3
Hs.419240


202500_at
DNAJB2
Hs.77768


202503_s_at
KIAA0101
Hs.81892


202510_s_at
TNFAIP2
Hs.101382


202523_s_at
SPOCK2
Hs.436193


202524_s_at
SPOCK2
Hs.436193


202545_at
PRKCD
Hs.155342


202546_at
VAMP8
Hs.172684


202548_s_at
ARHGEF7
Hs.172813


202551_s_at
CRIM1
Hs.170752


202554_s_at
GSTM3
Hs.2006


202555_s_at
MYLK
Hs.386078


202565_s_at
SVIL
Hs.163111


202566_s_at
SVIL
Hs.163111


202581_at
HSPA1A
Hs.274402


202587_s_at
AK1
Hs.76240


202589_at
TYMS
Hs.87491


202599_s_at
NRIP1
Hs.155017


202600_s_at
NRIP1
Hs.155017


202609_at
EPS8
Hs.2132


202614_at
C4orf1
Hs.364615


202624_s_at
CABIN1
Hs.435798


202626_s_at
LYN
Hs.80887


202627_s_at
SERPINE1
Hs.414795


202628_s_at
SERPINE1
Hs.414795


202637_s_at
ICAM1
Hs.168383


202638_s_at
ICAM1
Hs.168383


202643_s_at
TNFAIP3
Hs.211600


202644_s_at
TNFAIP3
Hs.211600


202660_at
—
Hs.406751


202671_s_at
MGC15873
Hs.284491


202672_s_at
ATF3
Hs.460


202686_s_at
AXL
Hs.83341


202687_s_at
TNFSF10
Hs.387871


202688_at
TNFSF10
Hs.387871


202704_at
TOB1
Hs.178137


202708_s_at
HIST2H2BE
Hs.2178


202718_at
IGFBP2
Hs.433326


202720_at
TES
Ha.129129


202724_s_at
FOXO1A
Hs.170133


202728_s_at
LTBP1
Hs.241257


202729_s_at
LTBP1
Hs.241257


202741_at
PRKACB
Hs.156324


202742_s_at
PRKACB
Hs.156324


202746_at
ITM2A
Hs.17109


202747_s_at
ITM2A
Hs.17109


202748_at
GBP2
Hs.386567


202759_s_at
AKAP2
Hs.42322


202760_s_at
AKAP2
Hs.42322


202761_s_at
SYNE2
Hs.444069


202763_at
CASP3
Hs.141125


202768_at
FOSB
Hs.75678


202800_at
SLC1A3
Hs.371369


202803_s_at
ITGB2
Hs.375957


202804_at
ABCC1
Hs.391464


202813_at
TARBP1
Hs.151518


202820_at
AHR
Hs.170087


202833_s_at
SERPINA1
Hs.297681


202838_at
FUCA1
Hs.576


202845_s_at
RALBP1
Hs.75447


202850_at
ABCD3
Hs.76781


202855_s_at
SLC16A3
Hs.386678


202859_x_at
IL8
Hs.624


202861_at
PER1
Hs.445534


202869_at
OAS1
Hs.442936


202871_at
TRAF4
Hs.8375


202877_s_at
C1QR1
Hs.97199


202878_s_at
C1QR1
Hs.97199


202887_s_at
RTP801
Hs.111244


202888_s_at
ANPEP
Hs.1239


202901_x_at
CTSS
Hs.181301


202902_s_at
CTSS
Hs.181301


202906_s_at
NBS1
Hs.25812


202908_at
WFS1
Hs.26077


202912_at
ADM
Hs.441047


202917_s_at
S100A8
Hs.416073


202923_s_at
GCLC
Hs.414985


202926_at
NAG
Hs.413771


202944_at
NAGA
Hs.75372


202947_s_at
GYPC
Hs.81994


202948_at
IL1R1
Hs.82112


202949_s_at
FHL2
Hs.8302


202953_at
C1QB
Hs.8986


202974_at
MPP1
Hs.422215


202988_s_at
RGS1
Hs.75256


202990_at
PYGL
Hs.771


203021_at
SLPI
Hs.251754


203037_s_at
MTSS1
Hs.77694


203038_at
PTPRK
Hs.354262


203040_s_at
HMBS
Hs.82609


203045_at
NINJ1
Hs.11342


203052_at
C2
Hs.2253


203056_s_at
PRDM2
Hs.413375


203057_s_at
PRDM2
Hs.413375


203060_s_at
PAPSS2
Hs.274230


203063_at
PPM1F
Hs.278441


203065_s_at
CAV1
Hs.74034


203066_at
GALNAC4S-6ST
Hs.6079


203069_at
SV2A
Hs.7979


203074_at
ANXA8
Hs.87268


203088_at
FBLN5
Hs.11494


203097_s_at
PDZGEF1
Hs.373588


203104_at
CSF1R
Hs.174142


203115_at
FECH
Hs.443610


203116_s_at
FECH
Hs.443610


203126_at
IMPA2
Hs.5753


203130_s_at
KIF5C
Hs.6641


203139_at
DAPK1
Hs.244318


203140_at
BCL6
Hs.155024


203146_s_at
GABBR1
Hs.167017


203151_at
MAP1A
Hs.194301


203153_at
IFIT1
Hs.20315


203180_at
ALDH1A3
Hs.75746


203184_at
FBN2
Hs.79432


203186_s_at
S100A4
Hs.81256


203192_at
ABCB6
Hs.107911


203196_at
ABCC4
Hs.307915


203213_at
CDC2
Hs.334562


203215_s_at
MYO6
Hs.118483


203216_s_at
MYO6
Hs.118483


203221_at
TLE1
Hs.406491


203234_at
UP
Hs.314828


203236_s_at
LGALS9
Hs.81337


203276_at
LMNB1
Hs.89497


203289_s_at
C16orf35
Hs.19699


203290_at
HLA-DQA1
Hs.387679


203299_s_at
AP1S2
Hs.40368


203300_x_at
AP1S2
Hs.40368


203304_at
NMA
Hs.348802


203305_at
F13A1
Hs.80424


203308_x_at
HPS1
Hs.404568


203309_s_at
HPS1
Hs.404568


203323_at
CAV2
Hs.139851


203324_s_at
CAV2
Hs.139851


203325_s_at
COL5A1
Hs.433695


203333_at
KIFAP3
Hs.433442


203349_s_at
ETV5
Hs.43697


203372_s_at
SOCS2
Hs.405946


203373_at
SOCS2
Hs.405946


203381_s_at
APOE
Hs.169401


203382_s_at
APOE
Hs.169401


203387_s_at
TBC1D4
Hs.173802


203388_at
ARRB2
Hs.435811


203397_s_at
GALNT3
Hs.278611


203402_at
KCNAB2
Hs.440497


203407_at
PPL
Hs.192233


203408_s_at
SATB1
Hs.416026


203411_s_at
LMNA
Hs.436441


203413_at
NELL2
Hs.79389


203430_at
HEBP2
Hs.439081


203434_s_at
MME
Hs.307734


203435_s_at
MME
Hs.307734


203440_at
CDH2
Hs.334131


203456_at
JM4
Hs.29595


203470_s_at
PLEK
Hs.77436


203471_s_at
PLEK
Hs.77436


203476_at
TPBG
Hs.82128


203485_at
RTN1
Hs.99947


203502_at
BPGM
Hs.198365


203504_s_at
ABCA1
Hs.147259


203505_at
ABCA1
Hs.147259


203508_at
TNFRSF1B
Hs.256278


203509_at
SORL1
Hs.438159


203513_at
FLJ21439
Hs.431338


203518_at
CHS1
Hs.130188


203523_at
LSP1
Hs.56729


203524_s_at
MPST
Hs.248267


203535_at
S100A9
Hs.112405


203542_s_at
BTEB1
Hs.150557


203543_s_at
BTEB1
Hs.150557


203544_s_at
STAM
Hs.441498


203547_at
CD4
Hs.17483


203548_s_at
LPL
Hs.180878


203549_s_at
LPL
Hs.180878


203555_at
PTPN18
Hs.210913


203556_at
ZHX2
Hs.30209


203559_s_at
ABP1
Hs.437420


203561_at
FCGR2A
Hs.352642


203562_at
FEZ1
Hs.79226


203570_at
LOXL1
Hs.65436


203574_at
NFIL3
Hs.79334


203585_at
ZNF185
Hs.16622


203591_s_at
CSF3R
Hs.381027


203627_at
IGF1R
Hs.239176


203628_at
IGF1R
Hs.239176


203638_s_at
FGFR2
Hs.404081


203641_s_at
KIAA0977
Hs.300855


203642_s_at
KIAA0977
Hs.300855


203645_s_at
CD163
Hs.74076


203661_s_at
TMOD1
Hs.374849


203662_s_at
TMOD1
Hs.374849


203665_at
HMOX1
Hs.202833


203666_at
CXCL12
Hs.436042


203675_at
NUCB2
Hs.423095


203676_at
GNS
Hs.334534


203680_at
PRKAR2B
Hs.77439


203690_at
TUBGCP3
Hs.9884


203691_at
PI3
Hs.112341


203695_s_at
DFNA5
Hs.304365


203708_at
PDE4B
Hs.188


203710_at
ITPR1
Hs.149900


203716_s_at
DPP4
Hs.44926


203717_at
DPP4
Hs.44926


203725_at
GADD45A
Hs.80409


203726_s_at
LAMA3
Hs.83450


203753_at
TCF4
Hs.359289


203757_s_at
CEACAM6
Hs.436718


203758_at
CTSO
Hs.75262


203760_s_at
SLA
Hs.75367


203761_at
SLA
Hs.75367


203764_at
DLG7
Hs.77695


203767_s_at
STS
Hs.79876


203768_s_at
STS
Hs.79876


203795_s_at
BCL7A
Hs.371758


203796_s_at
BCL7A
Hs.371758


203799_at
DCL-1
Hs.2441


203802_x_at
WBSCR20A
Hs.272820


203819_s_at
IMP-3
Hs.79440


203820_s_at
IMP-3
Hs.79440


203821_at
DTR
Hs.799


203828_s_at
NK4
Hs.943


203836_s_at
MAP3K5
Hs.151988


203845_at
PCAF
Hs.203475


203853_s_at
GAB2
Hs.30687


203859_s_at
PALM
Hs.78482


203860_at
PCCA
Hs.80741


203868_s_at
VCAM1
Hs.109225


203878_s_at
MMP11
Hs.143751


203887_s_at
THBD
Hs.2030


203888_at
THBD
Hs.2030


203895_at
PLCB4
Hs.151408


203911_at
RAP1GA1
Hs.433797


203913_s_at
HPGD
Hs.77348


203914_x_at
HPGD
Hs.77348


203915_at
CXCL9
Hs.77367


203921_at
CHST2
Hs.8786


203922_s_at
CYBB
Hs.88974


203923_s_at
CYBB
Hs.88974


203925_at
GCLM
Hs.315562


203932_at
HLA-DMB
Hs.1162


203933_at
Rab11-FIP3
Hs.119004


203936_s_at
MMP9
Hs.151738


203939_at
NT5E
Hs.153952


203946_s_at
ARG2
Hs.172851


203948_s_at
MPO
Hs.458272


203949_at
MPO
Hs.458272


203966_s_at
PPM1A
Hs.130036


203973_s_at
KIAA0146
Hs.381058


203979_at
CYP27A1
Hs.82568


203980_at
FABP4
Hs.391561


203987_at
FZD6
Hs.114218


203989_x_at
F2R
Hs.128087


204004_at
—
Hs.503576 // est


204006_s_at
FCGR3A
Hs.372679


204007_at
FCGR3A
Hs.372679


204011_at
SPRY2
Hs.18676


204018_x_at
HBA1
Hs.449630


204030_s_at
SCHIP1
Hs.61490


204035_at
SCG2
Hs.436577


204039_at
CEBPA
Hs.76171


204044_at
QPRT
Hs.8935


204051_s_at
SFRP4
Hs.105700


204057_at
ICSBP1
Hs.14453


204059_s_at
ME1
Hs.14732


204069_at
MEIS1
Hs.170177


204070_at
RARRES3
Hs.17466


204073_s_at
C11orf9
Hs.184640


204081_at
NRGN
Hs.232004


204082_at
PBX3
Hs.294101


204083_s_at
TPM2
Hs.300772


204086_at
PRAME
Hs.30743


204099_at
SMARCD3
Hs.444445


204103_at
CCL4
Hs.75703


204112_s_at
HNMT
Hs.42151


204116_at
IL2RG
Hs.84


204118_at
CD48
Hs.901


204122_at
TYROBP
Hs.9963


204131_s_at
FOXO3A
Hs.423523


204132_s_at
FOXO3A
Hs.423523


204134_at
PDE2A
Hs.154437


204141_at
TUBB
Hs.300701


204147_s_at
TFDP1
Hs.79353


204150_at
STAB1
Hs.301989


204151_x_at
AKR1C1
Hs.295131


204153_s_at
MFNG
Hs.371768


204158_s_at
TCIRG1
Hs.46465


204159_at
CDKN2C
Hs.4854


204160_s_at
ENPP4
Hs.54037


204165_at
WASF1
Hs.75850


204170_s_at
CKS2
Hs.83758


204172_at
CPO
Hs.89866


204174_at
ALOX5AP
Hs.100194


204182_s_at
ZNF297B
Hs.355581


204187_at
GMPR
Hs.1435


204192_at
CD37
Hs.153053


204197_s_at
RUNX3
Hs.170019


204198_s_at
RUNX3
Hs.170019


204203_at
CEBPG
Hs.2227


204214_s_at
RAB32
Hs.32217


204222_s_at
GLIPR1
Hs.401813


204224_s_at
GCH1
Hs.86724


204232_at
FCER1G
Hs.433300


204235_s_at
CED-6
Hs.107056


204237_at
CED-6
Hs.107056


204254_s_at
VDR
Hs.2062


204257_at
FADS3
Hs.21765


204259_at
MMP7
Hs.2256


204270_at
SKI
Hs.2969


204285_s_at
PMAIP1
Hs.96


204286_s_at
PMAIP1
Hs.96


204298_s_at
LOX
Hs.102267


204301_at
KIAA0711
Hs.5333


204304_s_at
PROM1
Hs.370052


204319_s_at
RGS10
Hs.82280


204321_at
NEO1
Hs.388613


204326_x_at
MT1X
Hs.374950


204341_at
TRIM16
Hs.241305


204351_at
S100P
Hs.2962


204362_at
SCAP2
Hs.410745


204363_at
F3
Hs.62192


204379_s_at
FGFR3
Hs.1420


204381_at
LRP3
Hs.143641


204385_at
KYNU
Hs.444471


204388_s_at
MAOA
Hs.183109


204392_at
CAMK1
Hs.434875


204396_s_at
GPRK5
Hs.211569


204403_x_at
KIAA0738
Hs.406492


204409_s_at
EIF1AY
Hs.205080


204410_at
EIF1AY
Hs.205080


204415_at
G1P3
Hs.287721


204416_x_at
APOC1
Hs.268571


204419_x_at
HBG2
Hs.302145


204420_at
FOSL1
Hs.283565


204429_s_at
SLC2A5
Hs.33084


204430_s_at
SLC2A5
Hs.33084


204438_at
MRC1
Hs.75182


204439_at
C1orf29
Hs.389724


204440_at
CD83
Hs.79197


204445_s_at
ALOX5
Hs.89499


204446_s_at
ALOX5
Hs.89499


204447_at
ProSAPiP1
Hs.90232


204451_at
FZD1
Hs.94234


204457_s_at
GAS1
Hs.65029


204466_s_at
SNCA
Hs.76930


204467_s_at
SNCA
Hs.76930


204468_s_at
TIE
Hs.78824


204470_at
CXCL1
Hs.789


204490_s_at
CD44
Hs.306278


204494_s_at
LOC56905
Hs.306331


204497_at
ADCY9
Hs.20196


204498_s_at
ADCY9
Hs.20196


204501_at
NOV
Hs.235935


204502_at
SAMHD1
Hs.371264


204505_s_at
EPB49
Hs.274122


204517_at
PPIC
Hs.110364


204526_s_at
TBC1D8
Hs.442657


204529_s_at
TOX
Hs.439767


204533_at
CXCL10
Hs.413924


204537_s_at
GABRE
Hs.22785


204540_at
EEF1A2
Hs.433839


204547_at
RAB40B
Hs.302498


204548_at
STAR
Hs.440760


204560_at
FKBP5
Hs.7557


204561_x_at
APOC2
Hs.75615


204562_at
IRF4
Hs.127686


204563_at
SELL
Hs.82848


204581_at
CD22
Hs.262150


204588_s_at
SLC7A7
Hs.194693


204604_at
PFTK1
Hs.57856


204611_s_at
PPP2R5B
Hs.75199


204614_at
SERPINB2
Hs.75716


204619_s_at
CSPG2
Hs.434488


204620_s_at
CSPG2
Hs.434488


204621_s_at
NR4A2
Hs.82120


204622_x_at
NR4A2
Hs.82120


204623_at
TFF3
Hs.82961


204625_s_at
ITGB3
Hs.87149


204626_s_at
ITGB3
Hs.87149


204627_s_at
ITGB3
Hs.87149


204628_s_at
ITGB3
Hs.87149


204638_at
ACP5
Hs.1211


204639_at
ADA
Hs.407135


204647_at
HOMER3
Hs.410683


204655_at
CCL5
Hs.241392


204661_at
CDW52
Hs.276770


204670_x_at
HLA-DRB4
Hs.449633


204671_s_at
ANKRD6
Hs.30991


204677_at
CDH5
Hs.76206


204679_at
KCNK1
Hs.376874


204682_at
LTBP2
Hs.83337


204684_at
NPTX1
Hs.84154


204698_at
ISG20
Hs.105434


204713_s_at
F5
Hs.30054


204714_s_at
F5
Hs.30054


204720_s_at
DNAJC6
Hs.44896


204729_s_at
STX1A
Hs.75671


204736_s_at
CSPG4
Hs.436301


204745_x_at
MT1G
Hs.433391


204747_at
IFIT4
Hs.181874


204748_at
PTGS2
Hs.196384


204749_at
NAP1L3
Hs.21365


204750_s_at
DSC2
Hs.95612


204751_x_at
DSC2
Hs.95612


204753_s_at
HLF
Hs.250692


204755_x_at
HLF
Hs.250692


204774_at
EVI2A
Hs.70499


204777_s_at
MAL
Hs.80395


204787_at
Z39IG
Hs.8904


204788_s_at
PPOX
Hs.376314


204789_at
FMNL
Hs.100217


204790_at
MADH7
Hs.370849


204793_at
GASP
Hs.113082


204794_at
DUSP2
Hs.1183


204798_at
MYB
Hs.407830


204806_x_at
HLA-F
Hs.411958


204808_s_at
TMEM5
Hs.112986


204811_s_at
CACNA2D2
Hs.389415


204820_s_at
BTN3A3
Hs.167741


204823_at
NAV3
Hs.306322


204829_s_at
FOLR2
Hs.433159


204834_at
FGL2
Hs.351808


204848_x_at
HBG1
Hs.449631


204858_s_at
ECGF1
Hs.435067


204872_at
BCE-1
Hs.99824


204881_s_at
UGCG
Hs.432605


204885_s_at
MSLN
Hs.408488


204890_s_at
LCK
Hs.1765


204891_s_at
LCK
Hs.1765


204896_s_at
PTGER4
Hs.199248


204897_at
PTGER4
Hs.199248


204899_s_at
SAP30
Hs.413835


204900_x_at
SAP30
Hs.413835


204908_s_at
BCL3
Hs.31210


204912_at
IL10RA
Hs.327


204914_s_at
SOX11
Hs.432638


204916_at
RAMP1
Hs.32989


204917_s_at
MLLT3
Hs.404


204923_at
CXorf9
Hs.61469


204924_at
TLR2
Hs.439608


204949_at
ICAM3
Hs.353214


204951_at
ARHH
Hs.109918


204959_at
MNDA
Hs.153837


204961_s_at
NCF1
Hs.1583


204971_at
CSTA
Hs.412999


204972_at
OAS2
Hs.414332


204976_s_at
LOC286505
Hs.433256 // —


204984_at
GPC4
Hs.58367


204990_s_at
ITGB4
Hs.85266


204992_s_at
PFN2
Hs.91747


204998_s_at
ATF5
Hs.9754


205000_at
DDX3Y
Hs.99120


205001_s_at
DDX3Y
Hs.99120


205012_s_at
HAGH
Hs.155482


205019_s_at
VIPR1
Hs.348500


205020_s_at
ARL4
Hs.245540


205027_s_at
MAP3K8
Hs.432453


205033_s_at
DEFA1
Hs.274463


205035_at
CTDP1
Hs.4076


205041_s_at
ORM1
Hs.572


205047_s_at
ASNS
Hs.446546


205049_s_at
CD79A
Hs.79630


205051_s_at
KIT
Hs.81665


205055_at
ITGAE
Hs.389133


205067_at
IL1B
Hs.126256


205076_s_at
CRA
Hs.425144


205081_at
CRIP1
Hs.423190


205098_at
CCR1
Hs.301921


205099_s_at
CCR1
Hs.301921


205110_s_at
FGF13
Hs.6540


205114_s_at
CCL3
Hs.73817


205118_at
FPR1
Hs.753


205119_s_at
FPR1
Hs.753


205130_at
RAGE
Hs.104119


205131_x_at
SCGF
Hs.105927


205157_s_at
KRT17
Hs.2785


205159_at
CSF2RB
Hs.285401


205174_s_at
QPCT
Hs.79033


205179_s_at
ADAM8
Hs.86947


205193_at
MAFF
Hs.51305


205200_at
TNA
Hs.65424


205205_at
RELB
Hs.307905


205207_at
IL6
Hs.130210


205213_at
CENTB1
Hs.337242


205214_at
STK17B
Hs.88297


205220_at
HM74
Hs.458425


205227_at
IL1RAP
Hs.143527


205229_s_at
COCH
Hs.21016


205230_at
RPH3A
Hs.21239


205237_at
FCN1
Hs.440898


205239_at
AREG
Hs.270833


205240_at
LGN
Hs.278338


205241_at
SCO2
Hs.410944


205249_at
EGR2
Hs.1395


205254_x_at
TCF7
Hs.169294


205255_x_at
TCF7
Hs.169294


205262_at
KCNH2
Hs.188021


205266_at
LIF
Hs.2250


205267_at
POU2AF1
Hs.2407


205268_s_at
ADD2
Hs.113614


205270_s_at
LCP2
Hs.2488


205278_at
GAD1
Hs.420036


205281_s_at
PIGA
Hs.51


205289_at
BMP2
Hs.73853


205297_s_at
CD79B
Hs.89575


205312_at
SPI1
Hs.157441


205321_at
EIF2S3
Hs.433518


205328_at
CLDN10
Hs.26126


205330_at
MN1
Hs.268515


205348_s_at
DNCI1
Hs.65248


205349_at
GNA15
Hs.73797


205353_s_at
PBP
Hs.433863


205361_s_at
PFDN4
Hs.91161


205366_s_at
HOXB6
Hs.98428


205382_s_at
DF
Hs.155597


205389_s_at
ANK1
Hs.443711


205390_s_at
ANK1
Hs.443711


205391_x_at
ANK1
Hs.443711


205392_s_at
CCL15
Hs.272493


205400_at
WAS
Hs.2157


205402_x_at
PRSS2
Hs.367767


205403_at
IL1R2
Hs.25333


205409_at
FOSL2
Hs.301612


205414_s_at
KIAA0672
Hs.6336


205419_at
EBI2
Hs.784


205445_at
PRL
Hs.1905


205453_at
HOXB2
Hs.290432


205456_at
CD3E
Hs.3003


205463_s_at
PDGFA
Hs.376032


205466_s_at
HS3ST1
Hs.40968


205469_s_at
IRF5
Hs.334450


205471_s_at
DACH
Hs.63931


205472_s_at
DACH
Hs.63931


205476_at
CCL20
Hs.75498


205479_s_at
PLAU
Hs.77274


205483_s_at
G1P2
Hs.458485


205484_at
SIT
Hs.88012


205488_at
GZMA
Hs.90708


205495_s_at
GNLY
Hs.105806


205513_at
TCN1
Hs.2012


205528_s_at
CBFA2T1
Hs.90858


205529_s_at
CBFA2T1
Hs.90858


205544_s_at
CR2
Hs.73792


205547_s_at
TAGLN
Hs.433401


205550_s_at
BRE
Hs.80426


205552_s_at
OAS1
Hs.442936


205557_at
BPI
Hs.303523


205568_at
AQP9
Hs.104624


205570_at
PIP5K2A
Hs.108966


205572_at
ANGPT2
Hs.115181


205582_s_at
GGTLA1
Hs.437156


205590_at
RASGRP1
Hs.189527


205592_at
SLC4A1
Hs.443948


205593_s_at
PDE9A
Hs.389777


205599_at
TRAF1
Hs.438253


205608_s_at
ANGPT1
Hs.2463


205609_at
ANGPT1
Hs.2463


205612_at
MMRN
Hs.268107


205614_x_at
MST1
Hs.349110


205624_at
CPA3
Hs.646


205627_at
CDA
Hs.72924


205632_s_at
PIP5K1B
Hs.297604


205633_s_at
ALAS1
Hs.78712


205653_at
CTSG
Hs.421724


205660_at
OASL
Hs.118633


205668_at
LY75
Hs.153563


205681_at
BCL2A1
Hs.227817


205683_x_at
TPSB2
Hs.405479


205707_at
IL17R
Hs.129751


205712_at
PTPRD
Hs.323079


205715_at
BST1
Hs.169998


205717_x_at
PCDHGC3
Hs.283794


205718_at
ITGB7
Hs.1741


205721_at
—
Hs.441202 // est


205739_x_at
ZFD25
Hs.50216


205743_at
STAC
Hs.56045


205758_at
CD8A
Hs.85258


205767_at
EREG
Hs.115263


205769_at
SLC27A2
Hs.11729


205780_at
BIK
Hs.155419


205786_s_at
ITGAM
Hs.172631


205789_at
CD1D
Hs.1799


205790_at
SCAP1
Hs.411942


205798_at
IL7R
Hs.362807


205801_s_at
RASGRP3
Hs.24024


205819_at
MARCO
Hs.67726


205821_at
D12S2489E
Hs.387787


205826_at
MYOM2
Hs.443683


205831_at
CD2
Hs.89476


205837_s_at
GYPA
Hs.34287


205838_at
GYPA
Hs.34287


205839_s_at
BZRAP1
Hs.112499


205844_at
VNN1
Hs.12114


205848_at
GAS2
Hs.135665


205856_at
SLC14A1
Hs.101307


205857_at
SLC18A2
Hs.50458


205859_at
LY86
Hs.184018


205861_at
SPIB
Hs.437905


205863_at
S100A12
Hs.19413


205879_x_at
RET
Hs.350321


205882_x_at
ADD3
Hs.324470


205884_at
ITGA4
Hs.145140


205891_at
ADORA2B
Hs.45743


205896_at
SLC22A4
Hs.441130


205898_at
CX3CR1
Hs.78913


205899_at
CCNA1
Hs.417050


205900_at
KRT1
Hs.80828


205901_at
PNOC
Hs.371809


205919_at
HBE1
Hs.117848


205922_at
VNN2
Hs.293130


205927_s_at
CTSE
Hs.1355


205929_at
GPA33
Hs.437229


205933_at
SETBP1
Hs.201369


205935_at
FOXF1
Hs.155591


205936_s_at
HK3
Hs.411695


205942_s_at
SAH
Hs.409501


205944_s_at
CLTCL1
Hs.184916


205950_s_at
CA1
Hs.23118


205960_at
PDK4
Hs.8364


205983_at
DPEP1
Hs.109


205984_at
CRHBP
Hs.115617


205987_at
CD1C
Hs.1311


206001_at
NPY
Hs.1832


206011_at
CASP1
Hs.2490


206025_s_at
TNFAIP6
Hs.407546


206026_s_at
TNFAIP6
Hs.407546


206034_at
SERPINB8
Hs.368077


206039_at
RAB33A
Hs.56294


206042_x_at
SNRPN
Hs.48375


206046_at
ADAM23
Hs.432317


206049_at
SELP
Hs.73800


206059_at
ZNF91
Hs.8597


206067_s_at
WT1
Hs.1145


206070_s_at
EPHA3
Hs.123642


206074_s_at
HMGA1
Hs.57301


206077_at
KEL
Hs.420322


206093_x_at
TNXB
Hs.411644


206106_at
MAPK12
Hs.432642


206108_s_at
SFRS6
Hs.6891


206110_at
HIST1H3H
Hs.70937


206111_at
RNASE2
Hs.728


206115_at
EGR3
Hs.74088


206118_at
STAT4
Hs.80642


206130_s_at
ASGR2
Hs.1259


206134_at
ADAMDEC1
Hs.145296


206135_at
ST18
Hs.151449


206145_at
RHAG
Hs.368178


206146_s_at
RHAG
Hs.368178


206148_at
IL3RA
Hs.389251


206150_at
TNFRSF7
Hs.355307


206157_at
PTX3
Hs.2050


206159_at
GDF10
Hs.2171


206167_s_at
ARHGAP6
Hs.250830


206169_x_at
RoXaN
Hs.25347


206177_s_at
ARG1
Hs.440934


206187_at
PTGIR
Hs.393


206196_s_at
RPIP8
Hs.6755


206206_at
LY64
Hs.87205


206207_at
CLC
Hs.889


206222_at
TNFRSF10C
Hs.119684


206232_s_at
B4GALT6
Hs.369994


206233_at
B4GALT6
Hs.369994


206235_at
LIG4
Hs.166091


206244_at
CR1
Hs.334019


206245_s_at
IVNS1ABP
Hs.197298


206255_at
BLK
Hs.389900


206277_at
P2RY2
Hs.339


206279_at
PRKY
Hs.183165


206281_at
ADCYAP1
Hs.68137


206283_s_at
TAL1
Hs.498079


206298_at
RhoGAP2
Hs.87241


206302_s_at
NUDT4
Hs.355399


206303_s_at
NUDT4
Hs.355399


206304_at
MYBPH
Hs.927


206310_at
SPINK2
Hs.98243


206331_at
CALCRL
Hs.152175


206332_s_at
IFI16
Hs.370873


206337_at
CCR7
Hs.1652


206341_at
IL2RA
Hs.130058


206342_x_at
IDS
Hs.352304


206343_s_at
NRG1
Hs.172816


206359_at
SOCS3
Hs.436943


206360_s_at
SOCS3
Hs.436943


206361_at
GPR44
Hs.299567


206363_at
MAF
Hs.134859


206366_x_at
XCL1
Hs.174228


206367_at
REN
Hs.3210


206371_at
FOLR3
Hs.352


206372_at
MYF6
Hs.35937


206374_at
DUSP8
Hs.41688


206377_at
FOXF2
Hs.44481


206380_s_at
PFC
Hs.53155


206381_at
SCN2A2
Hs.435796


206390_x_at
PF4
Hs.81564


206398_s_at
CD19
Hs.96023


206404_at
FGF9
Hs.111


206420_at
IGSF6
Hs.135194


206433_s_at
SPOCK3
Hs.159425


206453_s_at
NDRG2
Hs.243960


206461_x_at
MT1H
Hs.438462


206464_at
BMX
Hs.27372


206471_s_at
PLXNC1
Hs.286229


206472_s_at
TLE3
Hs.287362


206478_at
KIAA0125
Hs.38365


206485_at
CD5
Hs.58685


206488_s_at
CD36
Hs.443120


206491_s_at
NAPA
Hs.75932


206493_at
ITGA2B
Hs.411312


206494_s_at
ITGA2B
Hs.411312


206508_at
TNFSF7
Hs.99899


206513_at
AIM2
Hs.105115


206515_at
CYP4F3
Hs.106242


206519_x_at
SIGLEC6
Hs.397255


206520_x_at
SIGLEC6
Hs.397255


206522_at
MGAM
Hs.122785


206545_at
CD28
Hs.1987


206546_at
SYCP2
Hs.202676


206574_s_at
PTP4A3
Hs.43666


206580_s_at
EFEMP2
Hs.381870


206582_s_at
GPR56
Hs.6527


206584_at
LY96
Hs.69328


206589_at
GFI1
Hs.73172


206591_at
RAG1
Hs.73958


206618_at
IL18R1
Hs.159301


206622_at
TRH
Hs.182231


206624_at
USP9Y
Hs.371255


206631_at
PTGER2
Hs.2090


206632_s_at
APOBEC3B
Hs.226307


206634_at
SIX3
Hs.227277


206637_at
GPR105
Hs.2465


206643_at
HAL
Hs.190783


206647_at
HBZ
Hs.272003


206655_s_at
PNUTL1
Hs.283743


206660_at
IGLL1
Hs.348935


206662_at
GLRX
Hs.28988


206665_s_at
BCL2L1
Hs.305890


206666_at
GZMK
Hs.277937


206674_at
FLT3
Hs.385


206676_at
CEACAM8
Hs.41


206682_at
CLECSF13
Hs.54403


206697_s_at
HP
Hs.403931


206698_at
XK
Hs.78919


206700_s_at
SMCY
Hs.80358


206707_x_at
C6orf32
Hs.389488


206710_s_at
EPB41L3
Hs.103839


206724_at
CBX4
Hs.5637


206726_at
PGDS
Hs.128433


206752_s_at
DFFB
Hs.133089


206759_at
FCER2
Hs.1416


206760_s_at
FCER2
Hs.1416


206761_at
TACTILE
Hs.142023


206762_at
KCNA5
Hs.150208


206765_at
KCNJ2
Hs.1547


206788_s_at
CBFB
Hs.179881


206793_at
PNMT
Hs.1892


206804_at
CD3G
Hs.2259


206834_at
HBD
Hs.36977


206851_at
RNASE3
Hs.73839


206857_s_at
FKBP1B
Hs.306834


206858_s_at
HOXC6
Hs.820


206871_at
ELA2
Hs.99863


206877_at
MAD
Hs.379930


206881_s_at
LILRA3
Hs.113277


206918_s_at
RBM12
Hs.166887


206924_at
IL11
Hs.1721


206932_at
CH25H
Hs.47357


206934_at
SIRPB1
Hs.194784


206937_at
SPTA1
Hs.418378


206940_s_at
POU4F1
Hs.458303


206950_at
SCN9A
Hs.2319


206951_at
HIST1H4E
Hs.240135


206953_s_at
LPHN2
Hs.24212


206978_at
CCR2
Hs.395


206991_s_at
CCR5
Hs.54443


206999_at
IL12RB2
Hs.413608


207001_x_at
DSIPI
Hs.420569


207008_at
IL8RB
Hs.846


207030_s_at
CSRP2
Hs.10526


207031_at
BAPX1
Hs.105941


207034_s_at
GLI2
Hs.111867


207038_at
SLC16A6
Hs.42645


207043_s_at
SLC6A9
Hs.442590


207067_s_at
HDC
Hs.1481


207072_at
IL18RAP
Hs.158315


207075_at
CIAS1
Hs.159483


207076_s_at
ASS
Hs.160786


207085_x_at
CSF2RA
Hs.227835


207087_x_at
ANK1
Hs.443711


207090_x_at
ZFP30
Hs.276763


207094_at
IL8RA
Hs.194778


207104_x_at
LILRB1
Hs.149924


207111_at
EMR1
Hs.2375


207113_s_at
TNF
Hs.241570


207117_at
H-plk
Hs.250693


207134_x_at
TPSB2
Hs.405479


207161_at
KIAA0087
Hs.69749


207172_s_at
CDH11
Hs.443435


207173_x_at
CDH11
Hs.443435


207206_s_at
ALOX12
Hs.1200


207216_at
TNFSF8
Hs.177136


207224_s_at
SIGLEC7
Hs.274470


207237_at
KCNA3
Hs.169948


207269_at
DEFA4
Hs.2582


207275_s_at
FACL2
Hs.406678


207292_s_at
MAPK7
Hs.150136


207316_at
HAS1
Hs.57697


207329_at
MMP8
Hs.390002


207332_s_at
TFRC
Hs.185726


207339_s_at
LTB
Hs.376208


207341_at
PRTN3
Hs.928


207357_s_at
GALNT10
Hs.13785


207358_x_at
MACF1
Hs.372463


207376_at
VENTX2
Hs.125231


207384_at
PGLYRP
Hs.137583


207387_s_at
GK
Hs.1466


207389_at
GP1BA
Hs.1472


207419_s_at
RAC2
Hs.301175


207425_s_at
MSF
Hs.288094


207433_at
IL10
Hs.193717


207435_s_at
SRRM2
Hs.433343


207459_x_at
GYPB
Hs.438658


207467_x_at
CAST
Hs.440961


207496_at
MS4A2
Hs.386748


207509_s_at
LAIR2
Hs.43803


207511_s_at
CGI-57
Hs.4973


207522_s_at
ATP2A3
Hs.5541


207526_s_at
IL1RL1
Hs.66


207533_at
CCL1
Hs.72918


207535_s_at
NFKB2
Hs.73090


207540_s_at
SYK
Hs.192182


207542_s_at
AQP1
Hs.76152


207550_at
MPL
Hs.84171


207571_x_at
C1orf38
Hs.10649


207574_s_at
GADD45B
Hs.110571


207605_x_at
H-plk
Hs.250693


207610_s_at
EMR2
Hs.137354


207651_at
H963
Hs.159545


207655_s_at
BLNK
Hs.167746


207667_s_at
MAP2K3
Hs.180533


207674_at
FCAR
Hs.193122


207675_x_at
ARTN
Hs.194689


207677_s_at
NCF4
Hs.196352


207691_x_at
ENTPD1
Hs.205353


207695_s_at
IGSF1
Hs.22111


207697_x_at
LILRB3
Hs.306230


207705_s_at
KIAA0980
Hs.227743


207741_x_at
TPSB2
Hs.405479


207793_s_at
EPB41
Hs.37427


207794_at
CCR2
Hs.395


207795_s_at
KLRD1
Hs.41682


207801_s_at
RNF10
Hs.387944


207802_at
SGP28
Hs.404466


207826_s_at
ID3
Hs.76884


207827_x_at
SNCA
Hs.76930


207836_s_at
RBPMS
Hs.195825


207838_x_at
PBXIP1
Hs.8068


207850_at
CXCL3
Hs.89690


207854_at
GYPE
Hs.395535


207857_at
LILRB1
Hs.149924


207872_s_at
LILRB1
Hs.149924


207890_s_at
MMP25
Hs.290222


207911_s_at
TGM5
Hs.129719


207938_at
PI15
Hs.129732


207978_s_at
NR4A3
Hs.279522


207979_s_at
CD8B1
Hs.405667


207983_s_at
STAG2
Hs.8217


208018_s_at
HCK
Hs.89555


208029_s_at
LAPTM4B
Hs.296398


208034_s_at
PROZ
Hs.1011


208056_s_at
CBFA2T3
Hs.110099


208067_x_at
UTY
Hs.115277


208071_s_at
LAIR1
Hs.407964


208078_s_at
TCF8
Hs.232068


208091_s_at
DKFZP564K0822
Hs.4750


208112_x_at
EHD1
Hs.155119


208116_s_at
MAN1A1
Hs.255149


208120_x_at
—
— // —


208130_s_at
TBXAS1
Hs.444510


208131_s_at
PTGIS
Hs.302085


208132_x_at
BAT2
Hs.436093


208146_s_at
CPVL
Hs.95594


208151_x_at
DDX17
Hs.349121


208161_s_at
ABCC3
Hs.90786


208187_s_at
—
— // —


208248_x_at
APLP2
Hs.279518


208255_s_at
FKBP8
Hs.173464


208296_x_at
GG2-1
Hs.17839


208304_at
CCR3
Hs.506190


208306_x_at
HLA-DRB4
Hs.449633


208335_s_at
FY
Hs.183


208352_x_at
ANK1
Hs.443711


208353_x_at
ANK1
Hs.443711


208370_s_at
DSCR1
Hs.282326


208416_s_at
SPTB
Hs.438514


208436_s_at
IRF7
Hs.166120


208438_s_at
FGR
Hs.1422


208443_x_at
SHOX2
Hs.55967


208450_at
LGALS2
Hs.113987


208451_s_at
C4A
Hs.150833


208459_s_at
XPO7
Hs.172685


208470_s_at
HP
Hs.403931


208476_s_at
FLJ10210
Hs.171532


208488_s_at
CR1
Hs.334019


208490_x_at
HIST1H2BF
Hs.182137


208498_s_at
AMY1A
Hs.274376


208501_at
GFI1B
Hs.118539


208502_s_at
PITX1
Hs.84136


208523_x_at
HIST1H2BI
Hs.182140


208527_x_at
HIST1H2BE
Hs.182138


208534_s_at
POLR2J2
Hs.433879


208540_x_at
—
— // —


208546_x_at
HIST1H4G
Hs.247815


208553_at
HIST1H1E
Hs.248133


208579_x_at
H2BFS
Hs.473961


208581_x_at
MT1X
Hs.374950


208592_s_at
CD1E
Hs.249217


208594_x_at
LILRB3
Hs.306230


208601_s_at
TUBB1
Hs.303023


208602_x_at
CD6
Hs.436949


208605_s_at
NTRK1
Hs.406293


208609_s_at
TNXB
Hs.411644


208613_s_at
FLNB
Hs.81008


208614_s_at
FLNB
Hs.81008


208621_s_at
VIL2
Hs.403997


208622_s_at
VIL2
Hs.403997


208623_s_at
VIL2
Hs.403997


208631_s_at
HADHA
Hs.75860


208632_at
RNF10
Hs.387944


208633_s_at
MACF1
Hs.372463


208634_s_at
MACF1
Hs.372463


208636_at
na
Hs.447510 // —


208646_at
RPS14
Hs.381126


208650_s_at
CD24
Hs.375108


208651_x_at
CD24
Hs.375108


208653_s_at
CD164
Hs.43910


208657_s_at
MSF
Hs.288094


208677_s_at
BSG
Hs.371654


208683_at
CAPN2
Hs.350899


208690_s_at
PDLIM1
Hs.75807


208691_at
TFRC
Hs.185726


208702_x_at
APLP2
Hs.279518


208703_s_at
APLP2
Hs.279518


208704_x_at
APLP2
Hs.279518


208711_s_at
CCND1
Hs.371468


208712_at
CCND1
Hs.371468


208719_s_at
DDX17
Hs.349121


208729_x_at
HLA-B
Hs.77961


208744_x_at
HSPH1
Hs.36927


208747_s_at
C1S
Hs.458355


208751_at
NAPA
Hs.75932


208767_s_at
LAPTM4B
Hs.296398


208771_s_at
LTA4H
Hs.81118


208782_at
FSTL1
Hs.433622


208789_at
PTRF
Hs.437191


208791_at
CLU
Hs.436657


208792_s_at
CLU
Hs.436657


208797_s_at
GOLGIN-67
Hs.182982


208798_x_at
GOLGIN-67
Hs.182982


208812_x_at
HLA-C
Hs.274485


208820_at
PTK2
Hs.434281


208827_at
PSMB6
Hs.77060


208854_s_at
STK24
Hs.168913


208855_s_at
STK24
Hs.168913


208869_s_at
GABARAPL1
Hs.336429


208886_at
H1F0
Hs.226117


208890_s_at
PLXNB2
Hs.3989


208891_at
DUSP6
Hs.298654


208892_s_at
DUSP6
Hs.298654


208893_s_at
DUSP6
Hs.298654


208894_at
HLA-DRA
Hs.409805


208906_at
BSCL2
Hs.438912


208914_at
GGA2
Hs.133340


208924_at
RNF11
Hs.96334


208928_at
POR
Hs.354056


208937_s_at
ID1
Hs.410900


208949_s_at
LGALS3
Hs.411701


208953_at
KIAA0217
Hs.192881


208960_s_at
COPEB
Hs.285313


208961_s_at
COPEB
Hs.285313


208962_s_at
FADS1
Hs.132898


208965_s_at
IFI16
Hs.370873


208966_x_at
IFI16
Hs.370873


208970_s_at
UROD
Hs.78601


208971_at
UROD
Hs.78601


208978_at
CRIP2
Hs.70327


208981_at
PECAM1
Hs.78146


208982_at
PECAM1
Hs.78146


208983_s_at
PECAM1
Hs.78146


208997_s_at
UCP2
Hs.80658


209007_s_at
DJ465N24.2.1
Hs.259412


209018_s_at
PINK1
Hs.439600


209022_at
STAG2
Hs.8217


209023_s_at
STAG2
Hs.8217


209030_s_at
IGSF4
Hs.156682


209031_at
IGSF4
Hs.156682


209032_s_at
IGSF4
Hs.156682


209035_at
MDK
Hs.82045


209037_s_at
EHD1
Hs.155119


209039_x_at
EHD1
Hs.155119


209040_s_at
PSMB8
Hs.180062


209046_s_at
GABARAPL2
Hs.6518


209047_at
AQP1
Hs.76152


209079_x_at
PCDHGC3
Hs.283794


209081_s_at
COL18A1
Hs.413175


209083_at
CORO1A
Hs.415067


209086_x_at
MCAM
Hs.211579


209087_x_at
MCAM
Hs.211579


209094_at
DDAH1
Hs.380870


209098_s_at
JAG1
Hs.409202


209099_x_at
JAG1
Hs.409202


209101_at
CTGF
Hs.410037


209116_x_at
HBB
Hs.155376


209117_at
WBP2
Hs.231840


209118_s_at
TUBA3
Hs.433394


209122_at
ADFP
Hs.3416


209129_at
TRIP6
Hs.380230


209138_x_at
—
Hs.505407


209140_x_at
HLA-B
Hs.77961


209152_s_at
TCF3
Hs.371282


209153_s_at
TCF3
Hs.371282


209156_s_at
COL6A2
Hs.420269


209160_at
AKR1C3
Hs.78183


209167_at
GPM6B
Hs.5422


209168_at
GPM6B
Hs.5422


209170_s_at
GPM6B
Hs.5422


209173_at
AGR2
Hs.226391


209182_s_at
DEPP
Hs.93675


209183_s_at
DEPP
Hs.93675


209184_s_at
IRS2
Hs.143648


209185_s_at
IRS2
Hs.143648


209189_at
FOS
Hs.25647


209191_at
TUBB-5
Hs.274398


209193_at
PIM1
Hs.81170


209199_s_at
MEF2C
Hs.368950


209200_at
MEF2C
Hs.368950


209201_x_at
CXCR4
Hs.421986


209205_s_at
LMO4
Hs.3844


209208_at
MPDU1
Hs.6710


209216_at
JM5
Hs.21753


209217_s_at
JM5
Hs.21753


209239_at
NFKB1
Hs.160557


209250_at
DEGS
Hs.299878


209264_s_at
TM4SF7
Hs.26518


209267_s_at
BIGM103
Hs.284205


209273_s_at
MGC4276
Hs.270013


209274_s_at
MGC4276
Hs.270013


209276_s_at
GLRX
Hs.28988


209281_s_at
ATP2B1
Hs.20952


209282_at
PRKD2
Hs.205431


209285_s_at
RAP140
Hs.23440


209286_at
CDC42EP3
Hs.352554


209287_s_at
CDC42EP3
Hs.352554


209288_s_at
CDC42EP3
Hs.352554


209297_at
ITSN1
Hs.66392


209301_at
CA2
Hs.155097


209304_x_at
GADD45B
Hs.110571


209305_s_at
GADD45B
Hs.110571


209312_x_at
HLA-DRB3
Hs.308026


209318_x_at
PLAGL1
Hs.132911


209325_s_at
RGS16
Hs.413297


209339_at
SIAH2
Hs.20191


209340_at
UAP1
Hs.21293


209344_at
TPM4
Hs.250641


209348_s_at
MAF
Hs.134859


209357_at
CITED2
Hs.82071


209360_s_at
RUNX1
Hs.410774


209367_at
STXBP2
Hs.379204


209369_at
ANXA3
Hs.442733


209374_s_at
IGHM
Hs.153261


209377_s_at
HMGN3
Hs.77558


209383_at
DDIT3
Hs.392171


209386_at
TM4SF1
Hs.351316


209387_s_at
TM4SF1
Hs.351316


209392_at
ENPP2
Hs.23719


209394_at
ASMTL
Hs.458420


209395_at
CHI3L1
Hs.382202


209396_s_at
CHI3L1
Hs.382202


209398_at
HIST1H1C
Hs.7644


209436_at
SPON1
Hs.5378


209437_s_at
SPON1
Hs.5378


209452_s_at
VTI1B
Hs.419995


209457_at
DUSP5
Hs.2128


209458_x_at
HBA1
Hs.449630


209473_at
ENTPD1
Hs.205353


209474_s_at
ENTPD1
Hs.205353


209480_at
HLA-DQB1
Hs.409934


209487_at
RBPMS
Hs.195825


209488_s_at
RBPMS
Hs.195825


209498_at
CEACAM1
Hs.434918


209499_x_at
TNFSF13
Hs.54673


209500_x_at
TNFSF13
Hs.54673


209514_s_at
RAB27A
Hs.298530


209515_s_at
RAB27A
Hs.298530


209524_at
HDGFRP3
Hs.127842


209526_s_at
HDGFRP3
Hs.127842


209536_s_at
EHD4
Hs.55058


209540_at
IGF1
Hs.308053


209541_at
IGF1
Hs.308053


209542_x_at
IGF1
Hs.308053


209543_s_at
CD34
Hs.374990


209545_s_at
RIPK2
Hs.103755


209555_s_at
CD36
Hs.443120


209560_s_at
DLK1
Hs.169228


209561_at
THBS3
Hs.169875


209568_s_at
RGL
Hs.79219


209576_at
GNAI1
Hs.203862


209581_at
HRASLS3
Hs.417630


209582_s_at
MOX2
Hs.79015


209583_s_at
MOX2
Hs.79015


209585_s_at
MINPP1
Hs.95907


209587_at
PITX1
Hs.84136


209598_at
PNMA2
Hs.7782


209604_s_at
GATA3
Hs.169946


209606_at
PSCDBP
Hs.270


209615_s_at
PAK1
Hs.64056


209616_s_at
CES1
Hs.278997


209619_at
CD74
Hs.446471


209627_s_at
OSBPL3
Hs.197955


209628_at
NXT2
Hs.25010


209629_s_at
NXT2
Hs.25010


209636_at
NFKB2
Hs.73090


209651_at
TGFB1I1
Hs.25511


209652_s_at
PGF
Hs.252820


209670_at
TRA@
Hs.74647


209671_x_at
TRA@
Hs.74647


209676_at
TFPI
Hs.102301


209679_s_at
LOC57228
Hs.206501


209686_at
S100B
Hs.422181


209687_at
CXCL12
Hs.436042


209695_at
PTP4A3
Hs.43666


209696_at
FBP1
Hs.360509


209699_x_at
AKR1C2
Hs.201967


209702_at
FTO
Hs.284741


209706_at
NKX3-1
Hs.55999


209710_at
GATA2
Hs.367725


209716_at
CSF1
Hs.173894


209717_at
—
Hs.387251


209727_at
GM2A
Hs.387156


209728_at
HLA-DRB4
Hs.449633


209732_at
CLECSF2
Hs.85201


209735_at
ABCG2
Hs.194720


209757_s_at
MYCN
Hs.25960


209763_at
NRLN1
Hs.440324


209771_x_at
—
Hs.376280 // —


209772_s_at
CD24
Hs.375108


209773_s_at
RRM2
Hs.226390


209774_x_at
CXCL2
Hs.75765


209790_s_at
CASP6
Hs.3280


209791_at
PADI2
Hs.33455


209795_at
CD69
Hs.82401


209803_s_at
TSSC3
Hs.154036


209806_at
HIST1H2BK
Hs.247817


209813_x_at
—
Hs.407442


209815_at
na
Hs.454253 // —


209822_s_at
VLDLR
Hs.370422


209823_x_at
HLA-DQB1
Hs.409934


209829_at
C6orf32
Hs.389488


209835_x_at
CD44
Hs.306278


209845_at
MKRN1
Hs.7838


209863_s_at
TP73L
Hs.137569


209870_s_at
APBA2
Hs.26468


209875_s_at
SPP1
Hs.313


209879_at
SELPLG
Hs.423077


209881_s_at
LAT
Hs.437775


209884_s_at
SLC4A7
Hs.250072


209890_at
TM4SF9
Hs.8037


209892_at
FUT4
Hs.390420


209893_s_at
FUT4
Hs.390420


209894_at
LEPR
Hs.23581


209900_s_at
SLC16A1
Hs.75231


209901_x_at
AIF1
Hs.76364


209905_at
HOXA9
Hs.127428


209906_at
C3AR1
Hs.155935


209911_x_at
HTST1H2BD
Hs.180779


209921_at
SLC7A11
Hs.6682


209930_s_at
NFE2
Hs.75643


209949_at
NCF2
Hs.949


209950_s_at
VILL
Hs.103665


209959_at
NR4A3
Hs.279522


209960_at
HGF
Hs.396530


209961_s_at
HGF
Hs.396530


209962_at
EPOR
Hs.127826


209963_s_at
EPOR
Hs.127826


209967_s_at
CREM
Hs.231975


209968_s_at
NCAM1
Hs.78792


209969_s_at
STAT1
Hs.21486


209982_s_at
NRXN2
Hs.124085


209993_at
ABCB1
Hs.21330


209994_s_at
ABCB1
Hs.21330


209995_s_at
TCL1A
Hs.2484


210001_s_at
SOCS1
Hs.50640


210004_at
OLR1
Hs.445299


210016_at
MYT1L
Hs.434418


210024_s_at
UBE2E3
Hs.4890


210031_at
CD3Z
Hs.97087


210032_s_at
SPAG6
Hs.158213


210033_s_at
SPAG6
Hs.158213


210036_s_at
KCNH2
Hs.188021


210038_at
PRKCQ
Hs.408049


210042_s_at
CTSZ
Hs.252549


210074_at
CTSL2
Hs.87417


210075_at
LOC51257
Hs.331308


210084_x_at
TPSB2
Hs.405479


210088_x_at
MYL4
Hs.356717


210095_s_at
IGFBP3
Hs.440409


210102_at
LOH11CR2A
Hs.152944


210105_s_at
FYN
Hs.390567


210107_at
CLCA1
Hs.194659


210113_s_at
DEFCAP
Hs.104305


210116_at
SH2D1A
Hs.151544


210118_s_at
IL1A
Hs.1722


210123_s_at
CHRNA7
Hs.2540


210134_x_at
SHOX2
Hs.55967


210135_s_at
SHOX2
Hs.55967


210139_s_at
PMP22
Hs.372031


210140_at
CST7
Hs.143212


210142_x_at
FLOT1
Hs.179986


210146_x_at
LILRB3
Hs.306230


210151_s_at
DYRK3
Hs.164267


210152_at
LILRB4
Hs.67846


210164_at
GZMB
Hs.1051


210166_at
TLR5
Hs.114408


210172_at
SF1
Hs.440835


210190_at
STX11
Hs.118958


210215_at
TFR2
Hs.63758


210222_s_at
RTN1
Hs.99947


210225_x_at
LILRB3
Hs.306230


210230_at
—
— // —


210237_at
ARTN
Hs.194689


210239_at
IRX5
Hs.25351


210244_at
CAMP
Hs.51120


210247_at
SYN2
Hs.445503


210254_at
MS4A3
Hs.99960


210260_s_at
GG2-1
Hs.17839


210262_at
TPX1
Hs.2042


210264_at
GPR35
Hs.239891


210269_s_at
DXYS155E
Hs.21595


210279_at
GPR18
Hs.88269


210298_x_at
FHL1
Hs.421383


210299_s_at
FHL1
Hs.421383


210313_at
LIR9
Hs.406708


210314_x_at
TNFSF13
Hs.54673


210321_at
GZMH
Hs.348264


210340_s_at
CSF2RA
Hs.227835


210356_x_at
MS4A1
Hs.438040


210357_s_at
C20orf16
Hs.433337


210368_at
PCDHGC3
Hs.283794


210387_at
HIST1H2BG
Hs.352109


210395_x_at
MYL4
Hs.356717


210397_at
DEFB1
Hs.32949


210422_x_at
SLC11A1
Hs.135163


210423_s_at
SLC11A1
Hs.135163


210425_x_at
GOLGIN-67
Hs.356225


210426_x_at
RORA
Hs.388617


210427_x_at
ANXA2
Hs.437110


210429_at
RHD
Hs.458333


210430_x_at
RHD
Hs.283822


210432_s_at
SCN3A
Hs.300717


210446_at
GATA1
Hs.765


210448_s_at
P2RX5
Hs.408615


210461_s_at
ABLIM1
Hs.442540


210473_s_at
GPR125
Hs.356876


210479_s_at
RORA
Hs.388617


210487_at
DNTT
Hs.397294


210495_x_at
FN1
Hs.418138


210504_at
KLF1
Hs.37860


210508_s_at
KCNQ2
Hs.4975


210512_s_at
VEGF
Hs.73793


210514_x_at
HLA-A
Hs.181244


210517_s_at
AKAP12
Hs.197081


210524_x_at
MT1F
Hs.438737


210538_s_at
BIRC3
Hs.127799


210546_x_at
CTAG1
Hs.167379


210548_at
CCL23
Hs.169191


210549_s_at
CCL23
Hs.169191


210554_s_at
CTBP2
Hs.171391


210561_s_at
WSB1
Hs.315379


210582_s_at
LIMK2
Hs.278027


210586_x_at
RHD
Hs.458333


210605_s_at
MFGE8
Hs.3745


210606_x_at
KLRD1
Hs.41682


210612_s_at
SYNJ2
Hs.434494


210638_s_at
FBXO9
Hs.388387


210640_s_at
GPR30
Hs.113207


210649_s_at
SMARCF1
Hs.170333


210655_s_at
FOXO3A
Hs.14845


210660_at
LILRB1
Hs.149924


210663_s_at
KYNU
Hs.444471


210664_s_at
TFPI
Hs.102301


210665_at
TFPI
Hs.102301


210666_at
IDS
Hs.352304


210681_s_at
USP15
Hs.339425


210693_at
SPPL2B
Hs.284161


210724_at
EMR3
Hs.438468


210744_s_at
IL5RA
Hs.68876


210746_s_at
EPB42
Hs.368642


210755_at
HGF
Hs.396530


210756_s_at
NOTCH2
Hs.8121


210762_s_at
DLC1
Hs.8700


210772_at
FPRL1
Hs.99855


210773_s_at
FPRL1
Hs.99855


210783_x_at
SCGF
Hs.105927


210784_x_at
LILRB3
Hs.306230


210785_s_at
C1orf38
Hs.10649


210786_s_at
FLI1
Hs.257049


210794_s_at
MEG3
Hs.418271


210796_x_at
SIGLEC6
Hs.397255


210815_s_at
CALCRL
Hs.152175


210825_s_at
STOM
Hs.439776


210835_s_at
CTBP2
Hs.171391


210839_s_at
ENPP2
Hs.23719


210840_s_at
IQGAP1
Hs.1742


210844_x_at
CTNNA1
Hs.254321


210845_s_at
PLAUR
Hs.179657


210854_x_at
SLC6A8
Hs.388375


210869_s_at
MCAM
Hs.211579


210873_x_at
APOBEC3A
Hs.348983


210889_s_at
FCGR2B
Hs.126384


210895_s_at
CD86
Hs.27954


210904_s_at
IL13RA1
Hs.285115


210915_x_at
TRB@
Hs.419777


210916_s_at
CD44
Hs.306278


210948_s_at
LEF1
Hs.44865


210951_x_at
RAB27A
Hs.298530


210972_x_at
TRA@
Hs.74647


210973_s_at
FGFR1
Hs.748


210976_s_at
PFKM
Hs.75160


210982_s_at
HLA-DRA
Hs.409805


210986_s_at
TPM1
Hs.133892


210987_x_at
—
— // —


210992_x_at
FCGR2B
Hs.126384


210993_s_at
MADH1
Hs.388294


210997_at
HGF
Hs.396530


210998_s_at
HGF
Hs.396530


210999_s_at
GRB10
Hs.81875


211005_at
LAT
Hs.437775


211024_s_at
TITF1
Hs.197764


211025_x_at
COX5B
Hs.1342


211031_s_at
CYLN2
Hs.104717


211052_s_at
TBCD
Hs.12570


211066_x_at
PCDHGC3
Hs.283794


211071_s_at
AF1Q
Hs.75823


211100_x_at
LILRB1
Hs.149924


211101_x_at
LILRB1
Hs.149924


211102_s_at
LILRB1
Hs.149924


211126_s_at
CSRP2
Hs.10526


211133_x_at
LILRB3
Hs.306230


211135_x_at
LILRB3
Hs.306230


211143_x_at
NR4A1
Hs.1119


211144_x_at
TRGC2
Hs.385086


211148_s_at
ANGPT2
Hs.115181


211163_s_at
TNFRSF10C
Hs.119684


211202_s_at
PLU-1
Hs.143323


211207_s_at
FACL6
Hs.14945


211210_x_at
SH2D1A
Hs.151544


211254_x_at
RHAG
Hs.368178


211269_s_at
IL2RA
Hs.130058


211284_s_at
GRN
Hs.180577


211286_x_at
CSF2RA
Hs.227835


211302_s_at
PDE4B
Hs.188


211307_s_at
FCAR
Hs.193122


211336_x_at
LILRB1
Hs.149924


211339_s_at
ITK
Hs.211576


211340_s_at
MCAM
Hs.211579


211341_at
POU4F1
Hs.458303


211354_s_at
LEPR
Hs.23581


211355_x_at
LEPR
Hs.23581


211356_x_at
LEPR
Hs.23581


211367_s_at
CASP1
Hs.2490


211368_s_at
CASP1
Hs.2490


211372_s_at
IL1R2
Hs.25333


211395_x_at
FCGR2B
Hs.126384


211404_s_at
APLP2
Hs.279518


211413_s_at
PADI4
Hs.397050


211421_s_at
RET
Hs.350321


211423_s_at
SC5DL
Hs.434074


211429_s_at
SERPINA1
Hs.297681


211430_s_at
IGHG3
Hs.413826


211434_s_at
CCRL2
Hs.302043


211450_s_at
MSH6
Hs.445052


211456_x_at
na
Hs.456549


211458_s_at
GABARAPL3
Hs.334497


211464_x_at
CASP6
Hs.3280


211478_s_at
SERPINB6
Hs.41072


211474_s_at
DPP4
Hs.44926


211495_x_at
TNFSF13
Hs.54673


211506_s_at
—
— // —


211517_s_at
IL5RA
Hs.68876


211521_s_at
PSCD4
Hs.7189


211527_x_at
VEGF
Hs.73793


211529_x_at
HLA-A
Hs.181244


211535_s_at
FGFR1
Hs.748


211546_x_at
SNCA
Hs.76930


211548_s_at
HPGD
Hs.77348


211560_s_at
ALAS2
Hs.440455


211566_x_at
BRE
Hs.80426


211571_s_at
CSPG2
Hs.434488


211597_s_at
HOP
Hs.13775


211633_x_at
—
Hs.406615


211634_x_at
—
Hs.449011


211635_x_at
—
Hs.449011


211637_x_at
—
Hs.383169


211639_x_at
—
Hs.383438


211641_x_at
—
Hs.64568 // —


211643_x_at
na
Hs.377975


211644_x_at
na
Hs.377975


211645_x_at
na
Hs.377975


211649_x_at
—
Hs.449057


211650_x_at
—
Hs.448957


211653_x_at
AKR1C2
Hs.201967


211654_x_at
HLA-DQB1
Hs.409934


211656_x_at
HLA-DQB1
Hs.409934


211657_at
CEACAM6
Hs.436718


211658_at
PRDX2
Hs.432121


211661_x_at
—
— // —


211663_x_at
PTGDS
Hs.446429


211668_s_at
PLAU
Hs.77274


211674_x_at
CTAG1
Hs.167379


211675_s_at
HIC
Hs.132739


211682_x_at
UGT2B28
Hs.137585


211696_x_at
HBB
Hs.155376


211699_x_at
HBA1
Hs.449630


211709_s_at
SCGF
Hs.105927


211719_x_at
FN1
Hs.418138


211726_s_at
FMO2
Hs.361155


211732_x_at
HNMT
Hs.42151


211734_s_at
FCER1A
Hs.897


211742_s_at
EVI2B
Hs.5509


211743_s_at
PRG2
Hs.99962


211745_x_at
HBA1
Hs.449630


211748_x_at
PTGDS
Hs.446429


211764_s_at
UBE2D1
Hs.129683


211776_s_at
EPB41L3
Hs.103839


211781_x_at
—
— // —


211796_s_at
—
— // —


211798_x_at
IGLJ3
Hs.102950


211799_x_at
HLA-C
Hs.274485


211813_x_at
DCN
Hs.156316


211816_x_at
FCAR
Hs.193122


211820_x_at
GYPA
Hs.34287


211821_x_at
GYPA
Hs.34287


211858_x_at
GNAS
Hs.157307


211864_s_at
FER1L3
Hs.362731


211868_x_at
—
— // —


211876_x_at
PCDHGC3
Hs.283794


211881_x_at
IGLJ3
Hs.102950


211883_x_at
CEACAM1
Hs.434918


211893_x_at
CD6
Hs.436949


211896_s_at
DCN
Hs.156316


211900_x_at
CD6
Hs.436949


211902_x_at
TRA@
Hs.74647


211911_x_at
HLA-B
Hs.77961


211919_s_at
CXCR4
Hs.421986


211922_s_at
CAT
Hs.395771


211924_s_at
PLAUR
Hs.179657


211941_s_at
PBP
Hs.433863


211959_at
IGFBP5
Hs.380833


211962_s_at
ZFP36L1
Hs.85155


211964_at
COL4A2
Hs.407912


211965_at
ZFP36L1
Hs.85155


211966_at
COL4A2
Hs.407912


211970_x_at
ACTG1
Hs.14376


211983_x_at
ACTG1
Hs.14376


211986_at
MGC5395
Hs.378738


211990_at
HLA-DPA1
Hs.914


211991_s_at
HLA-DPA1
Hs.914


211992_at
PRKWNK1
Hs.43129


211993_at
PRKWNK1
Hs.43129


211994_at
PRKWNK1
Hs.43129


211995_x_at
ACTG1
Hs.14376


211996_s_at
na
Hs.406494 // —


212012_at
D2S448
Hs.118893 // —


212013_at
D2S448
Hs.118893 // —


212014_x_at
CD44
Hs.306278


212046_x_at
MAPK3
Hs.861


212055_at
DKFZP586M1523
Hs.22981


212056_at
KIAA0182
Hs.222171


212057_at
KIAA0182
Hs.222171


212062_at
ATP9A
Hs.406434 // —


212067_s_at
C1R
Hs.376414 // —


212069_s_at
MGC10526
Hs.389588


212070_at
GPR56
Hs.6527


212077_at
CALD1
Hs.443811


212086_x_at
LMNA
Hs.436441


212089_at
LMNA
Hs.436441


212090_at
GRINA
Hs.339697


212091_s_at
COL6A1
Hs.415997


212097_at
CAV1
Hs.74034


212099_at
ARHB
Hs.406064


212143_s_at
—
Hs.450230 // —


212148_at
PBX1
Hs.408222


212151_at
PBX1
Hs.408222


212154_at
SDC2
Hs.1501


212157_at
SDC2
Hs.1501


212158_at
SDC2
Hs.1501


212166_at
XPO7
Hs.172685


212172_at
AK2
Hs.294008


212173_at
AK2
Hs.294008


212181_s_at
NUDT4
Hs.355399


212183_at
NUDT4
Hs.355399


212185_x_at
MT2A
Hs.118786


212187_x_at
PTGDS
Hs.446429


212188_at
LOC115207
Hs.109438


212190_at
SERPINE2
Hs.21858


212192_at
LOC115207
Hs.109438


212203_x_at
IFITM3
Hs.374650


212221_x_at
na
Hs.303154 // —


212223_at
na
Hs.303154 // —


212224_at
ALDH1A1
Hs.76392


212225_at
SUI1
Hs.150580


212236_x_at
KRT17
Hs.2785


212242_at
TUBA1
Hs.75318


212254_s_at
BPAG1
Hs.443518


212263_at
QKI
Hs.22248


212265_at
QKI
Hs.22248


212273_x_at
GNAS
Hs.157307


212285_s_at
AGRN
Hs.273330 // —


212311_at
KIAA0746
Hs.49500 // —


212312_at
BCL2L1
Hs.305890


212314_at
KIAA0746
Hs.49500 // —


212330_at
TFDP1
Hs.79353


212334_at
GNS
Hs.334534


212340_at
MGC21416
Hs.82719


212341_at
MGC21416
Hs.82719


212355_at
KIAA0323
Hs.7911


212358_at
CLIPR-59
Hs.7357


212363_x_at
ACTG1
Hs.14376


212372_at
MYH10
Hs.280311 // —


212377_s_at
NOTCH2
Hs.8121


212382_at
TCF4
Hs.359289


212385_at
TCF4
Hs.359289


212386_at
TCF4
Hs.359289


212387_at
TCF4
Hs.359289


212390_at
PDE4DIP
Hs.265848


212414_s_at
38961
Hs.90998


212428_at
KIAA0368
Hs.445255


212430_at
RNPC1
Hs.236361


212464_s_at
FN1
Hs.418138


212467_at
KIAA0678
Hs.12707 // —


212472_at
MICAL2
Hs.309674


212473_s_at
MICAL2
Hs.309674


212479_s_at
FLJ13910
Hs.75277


212488_at
COL5A1
Hs.433695


212489_at
COL5A1
Hs.433695


212492_s_at
KIAA0876
Hs.301011 // —


212501_at
CEBPB
Hs.99029


212509_s_at
—
Hs.356623 // est


212512_s_at
CARM1
Hs.371416 // —


212526_at
SPG20
Hs.205088


212531_at
LCN2
Hs.204238


212535_at
MEF2A
Hs.415033


212540_at
CDC34
Hs.423615


212543_at
AIM1
Hs.422550 // —


212558_at
GDAP1L1
Hs.20977


212560_at
SORL1
Hs.438159


212570_at
KIAA0830
Hs.167115


212586_at
CAST
Hs.440961


212589_at
RRAS2
Hs.206097


212592_at
IGJ
Hs.381568


212599_at
AUTS2
Hs.296720


212602_at
WDFY3
Hs.105340


212611_at
MPEG1
Hs.62264 // —


212614_at
MRF2
Hs.12702 // —


212624_s_at
CHN1
Hs.380138


212636_at
QKI
Hs.22248


212645_x_at
BRE
Hs.80426


212646_at
RAFTLIN
Hs.436432 // —


212647_at
RRAS
Hs.9651


212657_s_at
IL1RN
Hs.81134


212659_s_at
IL1RN
Hs.81134


212670_at
ELN
Hs.252418


212671_s_at
HLA-DQA1
Hs.387679


212680_x_at
PPP1R14B
Hs.120197


212681_at
EPB41L3
Hs.103839


212686_at
KIAA1157
Hs.21894 // —


212692_s_at
LRBA
Hs.209846


212699_at
SCAMP5
Hs.7934


212713_at
MFAP4
Hs.296049


212719_at
PLEKHE1
Hs.38176 // —


212724_at
ARHE
Hs.6838


212732_at
MEG3
Hs.418271


212741_at
MAOA
Hs.183109


212750_at
PPP1R16B
Hs.45719


212758_s_at
TCF8
Hs.232068


212761_at
TCF7L2
Hs.214039


212762_s_at
TCF7L2
Hs.214039


212764_at
TCF8
Hs.232068


212768_s_at
GW112
Hs.273321


212769_at
TLE3
Hs.287362


212771_at
LOC221061
Hs.66762 // —


212776_s_at
KIAA0657
Hs.6654 // —


212812_at
na
Hs.288232 // —


212820_at
RC3
Hs.200828


212827_at
IGHM
Hs.153261


212828_at
SYNJ2
Hs.434494


212829_at
—
Hs.57079 // —


212830_at
EGFL5
Hs.5599 // —


212831_at
EGFL5
Hs.5599 // —


212842_x_at
—
Hs.452310 // est


212843_at
NCAM1
Hs.78792


212859_x_at
MT1E
Hs.418241


212865_s_at
COL14A1
Hs.403836


212873_at
na
Hs.165728 // —


212884_x_at
APOC4
Hs.110675


212895_s_at
ABR
Hs.434004


212906_at
na
Hs.347534 // —


212907_at
SLC30A1
Hs.55610


212912_at
RPS6KA2
Hs.301664


212915_at
SEMACAP3
Hs.177635


212930_at
ATP2B1
Hs.20952


212937_s_at
COL6A1
Hs.415997


212942_s_at
KIAA1199
Hs.212584


212956_at
KIAA0882
Hs.411317 // —


212958_x_at
PAM
Hs.352733


212973_at
RPIA
Hs.79886


212977_at
RDC1
Hs.231853


212987_at
FBXO9
Hs.388387


212988_x_at
ACTG1
Hs.14376


212989_at
MOB
Hs.153716


212993_at
na
Hs.349356 // —


212998_x_at
HLA-DQB2
Hs.375115


212999_x_at
HLA-DQB1
Hs.409934


213002_at
MARCKS
Hs.318603


213005_s_at
KANK
Hs.77546


213006_at
KIAA0146
Hs.381058


213015_at
na
Hs.171553 // —


213035_at
KIAA0379
Hs.273104 // —


213036_x_at
ATP2A3
Hs.5541


213038_at
FLJ90005
Hs.128366


213060_s_at
CHI3L2
Hs.154138


213061_s_at
LOC123803
Hs.351573


213075_at
LOC169611
Hs.357004


213089_at
na
Hs.166361 // —


213094_at
GPR126
Hs.419170


213095_x_at
AIF1
Hs.76364


213096_at
HUCEP11
Hs.6360


213110_s_at
COL4A5
Hs.169825


213122_at
KIAA1750
Hs.173094


213125_at
DKFZP586L151
Hs.43658


213135_at
TIAM1
Hs.115176


213146_at
KIAA0346
Hs.103915 // —


213147_at
HOXA10
Hs.110637


213150_at
HOXA10
Hs.110637


213182_x_at
CDKN1C
Hs.106070


213193_x_at
TRB@
Hs.419777


213194_at
ROBO1
Hs.301198


213201_s_at
TNNT1
Hs.73980


213212_x_at
—
Hs.459128 // est


213214_x_at
ACTG1
Hs.14376


213217_at
ADCY2
Hs.414591


213236_at
SASH1
Hs.166311


213241_at
PLXNC1
Hs.286229


213258_at
TFPI
Hs.102301


213260_at
FOXC1
Hs.348883


213274_s_at
CTSB
Hs.135226


213275_x_at
CTSB
Hs.135226


213288_at
LOC129642
Hs.90797


213309_at
PLCL2
Hs.54886


213317_at
na
Hs.21103


213338_at
RIS1
Hs.35861


213348_at
CDKN1C
Hs.106070


213350_at
RPS11
Hs.433529


213361_at
PCTAIRE2BP
Hs.416543


213362_at
PTPRD
Hs.323079


213375_s_at
CG018
Hs.277888


213394_at
MAPKBP1
Hs.376657 // —


213395_at
MLC1
Hs.74518


213413_at
SBLF
Hs.54961


213415_at
CLIC2
Hs.54570


213418_at
HSPA6
Hs.3268


213428_s_at
COL6A1
Hs.415997


213435_at
SATB2
Hs.412327 // —


213437_at
RIPX
Hs.7972


213439_x_at
—
Hs.500197 // est


213446_s_at
IQGAP1
Hs.1742


213451_x_at
TNXB
Hs.411644


213478_at
KIAA1026
Hs.368823


213479_at
NPTX2
Hs.3281


213482_at
DOCK3
Hs.7022


213484_at
na
Hs.66187 // —


213488_at
FLJ00133
Hs.7949


213492_at
COL2A1
Hs.408182


213502_x_at
LOC91316
Hs.435211 // —


213503_x_at
ANXA2
Hs.437110


213506_at
F2RL1
Hs.154299


213515_x_at
HBG2
Hs.302145


213521_at
PTPN18
Hs.210913


213524_s_at
G0S2
Hs.432132


213537_at
HLA-DPA1
Hs.914


213539_at
CD3D
Hs.95327


213541_s_at
ERG
Hs.45514


213545_x_at
SNX3
Hs.12102


213549_at
SLC18A2
Hs.50458


213553_x_at
APOC1
Hs.268571


213566_at
RNASE6
Hs.23262


213572_s_at
SERPINB1
Hs.381167


213605_s_at
na
Hs.166361 // —


213608_s_at
TFIP11
Hs.20225


213618_at
CENTD1
Hs.427719


213624_at
ASM3A
Hs.277962


213629_x_at
MT1F
Hs.438737


213666_at
38961
Hs.90998


213668_s_at
SOX4
Hs.357901


213674_x_at
—
Hs.439852


213716_s_at
SECTM1
Hs.95655


213737_x_at
—
Hs.50787 // est


213757_at
EIF5A
Hs.310621


213791_at
PENK
Hs.339831


213797_at
cig5
Hs.17518


213808_at
na
Hs.12514 // —


213817_at
na
Hs.170056 // —


213823_at
HOXA11
Hs.249171


213825_at
OLIG2
Hs.176977


213830_at
TRD@
Hs.2014


213831_at
HLA-DQA1
Hs.387679


213841_at
na
Hs.301281 // —


213842_x_at
WBSCR20C
Hs.436034


213843_x_at
SLC6A8
Hs.388375


213844_at
HOXA5
Hs.37034


213848_at
DUSP7
Hs.3843


213857_s_at
CD47
Hs.446414


213888_s_at
DJ434O14.3
Hs.147434


213891_s_at
TCF4
Hs.359289


213894_at
LOC221981
Hs.23799 // —


213906_at
MYBL1
Hs.300592 // —


213908_at
LOC339005
Hs.212670 // —


213915_at
NKG7
Hs.10306


213931_at
—
Hs.502810 // est


213943_at
TWIST1
Hs.66744


213958_at
CD6
Hs.436949


213960_at
na
Hs.185701 // —


213975_s_at
LYZ
Hs.234734


213988_s_at
SAT
Hs.28491


213994_s_at
SPON1
Hs.5378


214016_s_at
SFPQ
Hs.180610


214020_x_at
ITGB5
Hs.149846


214022_s_at
IFITM1
Hs.458414


214032_at
ZAP70
Hs.234569


214039_s_at
LAPTM4B
Hs.296398


214040_s_at
GSN
Hs.446537


214041_x_at
RPL37A
Hs.433701


214043_at
PTPRD
Hs.323079


214049_x_at
CD7
Hs.36972


214054_at
DOK2
Hs.71215


214058_at
MYCL1
Hs.437922


214059_at
IFI44
Hs.82316


214061_at
MGC21654
Hs.95631


214063_s_at
TF
Hs.433923


214084_x_at
na
Hs.448231 // —


214085_x_at
HRB2
Hs.269857


214093_s_at
FUBP1
Hs.118962


214100_x_at
WBSCR20C
Hs.436034


214121_x_at
ENIGMA
Hs.436339


214131_at
CYorf15B
Hs.145010


214146_s_at
PPBP
Hs.2164


214153_at
ELOVL5
Hs.343667


214183_s_at
TKTL1
Hs.102866


214203_s_at
PRODH
Hs.343874


214211_at
FTH1
Hs.418650


214218_s_at
LOC139202
Hs.83623 // —


214228_x_at
TNFRSF4
Hs.129780


214230_at
CDC42
Hs.355832


214235_at
CYP3A5
Hs.150276


214255_at
ATP10A
Hs.125595


214273_x_at
C16orf35
Hs.19699


214290_s_at
HIST2H2AA
Hs.417332


214295_at
KIAA0485
Hs.89121 // —


214297_at
CSPG4
Hs.436301


214321_at
NOV
Hs.285935


214329_x_at
TNFSF10
Hs.387871


214349_at
—
Hs.464403 // est


214366_s_at
ALOX5
Hs.89499


214370_at
S100A8
Hs.416073


214407_x_at
GYPB
Hs.438658


214414_x_at
HBA1
Hs.449630


214421_x_at
CYP2C9
Hs.418127


214428_x_at
C4A
Hs.150833


214433_s_at
SELENBP1
Hs.334841


214446_at
ELL2
Hs.192221


214450_at
CTSW
Hs.416848


214453_s_at
IFI44
Hs.82316


214455_at
HIST1H2BC
Hs.356901


214459_x_at
HLA-C
Hs.274485


214464_at
CDC42BPA
Hs.18586


214467_at
GPR65
Hs.131924


214469_at
HIST1H2AE
Hs.121017


214470_at
KLRB1
Hs.169824


214472_at
HIST1H3D
Hs.239458


214481_at
HIST1H2AM
Hs.134999


214500_at
H2AFY
Hs.75258


214505_s_at
FHL1
Hs.421383


214511_x_at
FCGR1A
Hs.77424


214522_x_at
HIST1H3D
Hs.239458


214523_at
CEBPE
Hs.426867


214530_x_at
EPB41
Hs.37427


214535_s_at
ADAMTS2
Hs.120330


214539_at
SERPINB10
Hs.158339


214548_x_at
GNAS
Hs.157307


214551_s_at
CD7
Hs.36972


214564_s_at
PCDHGC3
Hs.283794


214574_x_at
LST1
Hs.410065


214575_s_at
AZU1
Hs.72885


214581_x_at
TNFRSF21
Hs.159651


214590_s_at
UBE2D1
Hs.129683


214614_at
HLXB9
Hs.37035


214617_at
PRF1
Hs.2200


214620_x_at
PAM
Hs.352733


214627_at
EPX
Hs.46295


214637_at
OSM
Hs.248156


214651_s_at
HOXA9
Hs.127428


214657_s_at
TncRNA
Hs.433324 // —


214667_s_at
TP53I11
Hs.433813 // —


214669_x_at
na
Hs.377975


214677_x_at
IGLJ3
Hs.449601


214682_at
PKD1
Hs.75813


214696_at
MGC14376
Hs.417157


214721_x_at
CDC42EP4
Hs.3903


214722_at
FLJ21272
Hs.218329


214743_at
CUTL1
Hs.438974


214761_at
OAZ
Hs.158593


214768_x_at
na
Hs.377975


214770_at
MSR1
Hs.436887


214777_at
na
Hs.377975


214789_x_at
SRP46
Hs.155160


214790_at
SUSP1
Hs.435628


214805_at
EIF4A1
Hs.129673


214836_x_at
na
Hs.377975


214867_at
NDST2
Hs.225129


214870_x_at
—
— // —


214875_x_at
APLP2
Hs.279518


214903_at
na
Hs.25422 // —


214909_s_at
DDAH2
Hs.247362


214916_x_at
—
Hs.448957


214920_at
LOC221981
Hs.23799 // —


214950_at
—
Hs.459588 // est


214953_s_at
APP
Hs.177486


214973_x_at
—
Hs.448982 // —


214983_at
na
Hs.433656 // —


214989_x_at
PEPP2
Hs.242537


215012_at
ZNF451
Hs.188662


215016_x_at
BPAG1
Hs.443518


215032_at
—
Hs.300934 // —


215034_s_at
TM4SF1
Hs.351316


215037_s_at
BCL2L1
Hs.305890


215047_at
BIA2
Hs.323858


215049_x_at
CD163
Hs.74076


215051_x_at
AIF1
Hs.76364


215054_at
EPOR
Hs.127826


215071_s_at
—
Hs.28777 // —


215076_s_at
COL3A1
Hs.443625


215078_at
SOD2
Hs.384944


215089_s_at
RBM10
Hs.348276


215111_s_at
TSC22
Hs.114360


215116_s_at
DNM1
Hs.436132


215118_s_at
MGC27165
Hs.366


215121_x_at
—
Hs.356861


215123_at
—
Hs.375005 // —


215137_at
—
Hs.467531 // est


215143_at
FLJ36166
Hs.351178 // —


215146_s_at
KIAA1043
Hs.387856


215150_at
DKFZp451J1719
Hs.391944 // —


215163_at
—
Hs.203349 // —


215176_x_at
—
Hs.503443 // —


215177_s_at
ITGA6
Hs.212296


215193_x_at
HLA-DRB1
Hs.411726


215200_x_at
na
Hs.456817 // —


215204_at
—
Hs.288575 // —


215214_at
—
Hs.449579 // —


215222_x_at
MACF1
Hs.372463


215223_s_at
SOD2
Hs.384944


215224_at
RPL23
Hs.406300


215242_at
PIGC
Hs.386487


215248_at
GRB10
Hs.81875


215284_at
—
Hs.12432 // —


215288_at
TRPC2
Hs.131910 // —


215306_at
—
Hs.161283 // —


215311_at
na
Hs.185701 // —


215320_at
DKFZP434M131
Hs.189296 // —


215338_s_at
NKTR
Hs.369815


215342_s_at
KIAA0471
Hs.242271


215375_x_at
—
Hs.438377 // —


215379_x_at
IGLJ3
Hs.449601


215382_x_at
TPSB2
Hs.405479


215388_s_at
HFL1
Hs.296941


215401_at
—
Hs.507633 // —


215411_s_at
C6orf4
Hs.437508


215415_s_at
CHS1
Hs.130188


215438_x_at
GSPT1
Hs.2707


215446_s_at
—
— // —


215447_at
TFPI
Hs.102301


215449_at
na
Hs.357392 // —


215485_s_at
ICAM1
Hs.168383


215489_x_at
HOMER3
Hs.410683


215498_s_at
MAP2K3
Hs.180533


215499_at
MAP2K3
Hs.180533


215501_s_at
DUSP10
Hs.177534


215504_x_at
—
Hs.337534 // —


215537_x_at
DDAH2
Hs.247362


215571_at
—
Hs.287415 // —


215592_at
—
Hs.464205 // —


215594_at
na
Hs.296832 // —


215599_at
SMA3
Hs.440958


215602_at
FGD2
Hs.376059


215621_s_at
—
Hs.448957


215623_x_at
SMC4L1
Hs.50758


215630_at
—
Hs.475611 // —


215640_at
KIAA1055
Hs.438702


215646_s_at
CSPG2
Hs.434488


215663_at
MBNL1
Hs.28578


215666_at
HLA-DRB4
Hs.449633


215684_s_at
FLJ21588
Hs.436407


215692_s_at
C11orf8
Hs.432000


215716_s_at
ATP2B1
Hs.20952


215733_x_at
CTAG2
Hs.87225


215761_at
RC3
Hs.200828


215771_x_at
RET
Hs.350321


215775_at
THBS1
Hs.164226


215777_at
IGLV@
Hs.381262


215779_s_at
HIST1H2BG
Hs.352109


215783_s_at
ALPL
Hs.250769


215784_at
CD1E
Hs.249217


215806_x_at
TRGC2
Hs.385086


215807_s_at
PLXNB1
Hs.278311


215811_at
—
Hs.275706 // —


215812_s_at
—
Hs.499113 // est


215819_s_at
RHCE
Hs.278994


215836_s_at
PCDHGC3
Hs.283794


215838_at
LIR9
Hs.406708


215851_at
EVI1
Hs.436019


215853_at
—
Hs.287427 // —


215874_at
—
Hs.287730 // —


215891_s_at
GM2A
Hs.387156


215913_s_at
CED-6
Hs.107056


215925_s_at
CD72
Hs.116481


215933_s_at
HHEX
Hs.118651


215946_x_at
LOC91316
Hs.435211 // —


215949_x_at
—
— // —


215967_s_at
LY9
Hs.403857


215990_s_at
BCL6
Hs.155024


216012_at
—
Hs.159901 // —


216015_s_at
CIAS1
Hs.159483


216016_at
CIAS1
Hs.159483


216022_at
—
Hs.16074 // —


216025_x_at
CYP2C9
Hs.418127


216033_s_at
FYN
Hs.390567


216036_x_at
KIAA1037
Hs.172825


216041_x_at
GRN
Hs.180577


216052_x_at
ARTN
Hs.194689


216054_x_at
MYL4
Hs.356717


216056_at
CD44
Hs.306278


216063_at
—
Hs.470084 // est


216080_s_at
FADS3
Hs.21765


216109_at
KIAA1025
Hs.435249 // —


216129_at
ATP9A
Hs.406434 // —


216147_at
—
Hs.306504 // —


216180_s_at
SYNJ2
Hs.434494


216191_s_at
TRD@
Hs.2014


216197_at
—
Hs.434491 // —


216207_x_at
IGKV1D-13
Hs.390427


216218_s_at
PLCL2
Hs.54886


216236_s_at
SLC2A14
Hs.401274


216243_s_at
IL1RN
Hs.81134


216248_s_at
NR4A2
Hs.82120


216268_s_at
JAG1
Hs.409202


216286_at
—
Hs.306324 // —


216317_x_at
RHCE
Hs.278994


216320_x_at
MST1
Hs.349110


216331_at
ITGA7
Hs.74369


216333_x_at
TNXB
Hs.411644


216336_x_at
—
— // —


216356_x_at
BAIAP3
Hs.458427


216370_s_at
TKTL1
Hs.102866


216379_x_at
—
— // —


216380_x_at
—
— // —


216401_x_at
—
— // —


216417_x_at
HOXB9
Hs.321142


216442_x_at
na
Hs.287820 // —


216449_x_at
TRA1
Hs.192374


216474_x_at
TPSB2
Hs.405479


216491_x_at
—
— // —


216510_x_at
—
— // —


216511_s_at
—
— // —


216522_at
—
— // —


216526_x_at
HLA-C
Hs.274485


216541_x_at
—
— // —


216557_x_at
—
— // —


216560_x_at
—
— // —


216565_x_at
—
— // —


216576_x_at
na
Hs.377975


216598_s_at
CCL2
Hs.303649


216602_s_at
FARSL
Hs.23111


216614_at
—
— // —


216620_s_at
ARHGEF10
Hs.436196


216667_at
—
— // —


216693_x_at
HDGFRP3
Hs.127842


216705_s_at
ADA
Hs.407135


216733_s_at
GATM
Hs.75335


216766_at
—
— // —


216813_at
—
— // —


216832_at
CBFA2T1
Hs.90858


216833_x_at
GYPE
Hs.395535


216834_at
RGS1
Hs.75256


216841_s_at
SOD2
Hs.384944


216858_x_at
—
— // —


216860_s_at
GDF11
Hs.432439


216894_x_at
CDKN1C
Hs.106070


216913_s_at
KIAA0690
Hs.434251


216920_s_at
TRGC2
Hs.385086


216925_s_at
TAL1
Hs.73828


216950_s_at
FCGR1A
Hs.77424


216956_s_at
ITGA2B
Hs.411312


216984_x_at
—
Hs.449592 // —


217022_s_at
MGC27165
Hs.366


217023_x_at
—
— // —


217025_s_at
DBN1
Hs.89434


217028_at
CXCR4
Hs.421986


217118_s_at
KIAA0930
Hs.13255


217143_s_at
TRD@
Hs.2014


217147_s_at
TRIM
Hs.138701


217148_x_at
—
Hs.449592 // —


217157_x_at
—
Hs.449620 // —


217165_x_at
MT1F
Hs.438737


217179_x_at
—
Hs.440830


217192_s_at
PRDM1
Hs.381140


217227_x_at
—
Hs.449598 // —


217232_x_at
—
— // —


217234_s_at
VIL2
Hs.403997


217235_x_at
—
Hs.449593 // —


217258_x_at
—
Hs.449599 // —


217274_x_at
—
— // —


217276_x_at
dJ222E13.1
Hs.301947


217281_x_at
—
Hs.448987 // —


217284_x_at
dJ222E13.1
Hs.301947


217286_s_at
NDRG3
Hs.437338


217354_s_at
—
— // —


217378_x_at
—
— // —


217388_s_at
KYNU
Hs.444471


217404_s_at
COL2A1
Hs.408182


217414_x_at
—
— // —


217418_x_at
MS4A1
Hs.438040


217419_x_at
AGRN
Hs.273330 // —


217422_s_at
CD22
Hs.262150


217478_s_at
HLA-DMA
Hs.351279


217480_x_at
—
— // —


217502_at
IFIT2
Hs.169274


217507_at
SLC11A1
Hs.135163


217520_x_at
na
Hs.374397 // —


217521_at
HAL
Hs.190783


217523_at
CD44
Hs.306278


217526_at
—
Hs.502482 // est


217552_x_at
CR1
Hs.334019


217572_at
—
— // —


217591_at
SKIL
Hs.272108


217593_at
SNX11
Hs.15827


217610_at
—
Hs.506223 // est


217649_at
ZNF216
Hs.406096


217653_x_at
—
Hs.499531 // est


217655_at
—
Hs.407053 // —


217671_at
—
Hs.279706 // est


217673_x_at
GNAS
Hs.157307


217678_at
—
Hs.499751 // est


217712_at
—
Hs.369545 // est


217715_x_at
—
Hs.417310 // est


217728_at
S100A6
Hs.275243


217729_s_at
AES
Hs.446610


217735_s_at
HRI
Hs.434986


217736_s_at
HRI
Hs.434986


217738_at
PBEF
Hs.293464


217739_s_at
PBEF
Hs.293464


217748_at
ADIPOR1
Hs.5298


217752_s_at
CN2
Hs.149185


217757_at
A2M
Hs.74561


217762_s_at
RAB31
Hs.223025


217763_s_at
RAB31
Hs.223025


217764_s_at
RAB31
Hs.223025


217771_at
GOLPH2
Hs.352662


217799_x_at
UBE2H
Hs.372758


217800_s_at
NDFIP1
Hs.9788


217817_at
ARPC4
Hs.323342


217818_s_at
ARPC4
Hs.323342


217838_s_at
EVL
Hs.241471


217848_s_at
PP
Hs.380830


217867_x_at
BACE2
Hs.436490


217868_s_at
DREV1
Hs.279583


217901_at
DSG2
Hs.412597


217911_s_at
BAG3
Hs.15259


217941_s_at
ERBB2IP
Hs.8117


217963_s_at
NGFRAP1
Hs.448588


217966_s_at
C1orf24
Hs.48778


217967_s_at
C1orf24
Hs.48778


217977_at
SEPX1
Hs.279623


217979_at
TM4SF13
Hs.364544


217983_s_at
RNASE6PL
Hs.388130


217985_s_at
BAZ1A
Hs.436488


217986_s_at
BAZ1A
Hs.436488


217988_at
HEI10
Hs.107003


217995_at
SQRDL
Hs.435468


217996_at
PHLDA1
Hs.82101


217997_at
PHLDA1
Hs.82101


217999_s_at
PHLDA1
Hs.82101


218000_s_at
PHLDA1
Hs.82101


218012_at
SE20-4
Hs.136164


218034_at
TTC11
Hs.423968


218035_s_at
FLJ20273
Hs.95549


218039_at
ANKT
Hs.279905


218051_s_at
FLJ12442
Hs.84753


218066_at
SLC12A7
Hs.172613


218084_x_at
FXYD5
Hs.333418


218086_at
NPDC1
Hs.105547


218091_at
HRB
Hs.371589


218094_s_at
C20orf35
Hs.256086


218113_at
TMEM2
Hs.160417


218116_at
LOC51759
Hs.278429


218136_s_at
MSCP
Hs.283716


218141_at
E2-230K
Hs.16130


218145_at
C20orf97
Hs.344378


218205_s_at
MKNK2
Hs.75056


218211_s_at
MLPH
Hs.297405


218217_at
RISC
Hs.431107


218224_at
PNMA1
Hs.194709


218231_at
NAGK
Hs.7036


218232_at
C1QA
Hs.9641


218237_s_at
SLC38A1
Hs.132246


218243_at
RUFY1
Hs.306769


218273_s_at
PPM2C
Hs.22265


218280_x_at
HIST2H2AA
Hs.417332


218284_at
DKFZP586N0721
Hs.99843


218298_s_at
FLJ20950
Hs.285673


218319_at
PELI1
Hs.7886


218332_at
BEX1
Hs.334370


218345_at
HCA112
Hs.12126


218346_s_at
PA26
Hs.14125


218352_at
RCBTB1
Hs.58452


218376_s_at
NICAL
Hs.33476


218394_at
FLJ22386
Hs.22795


218400_at
OAS3
Hs.56009


218404_at
SNX10
Hs.418132


218417_s_at
FLJ20489
Hs.438867


218418_s_at
KIAA1518
Hs.284208


218454_at
FLJ22662
Hs.178470


218456_at
C1QDC1
Hs.234355


218468_s_at
CKTSF1B1
Hs.40098


218469_at
CKTSF1B1
Hs.40098


218487_at
ALAD
Hs.1227


218523_at
LHPP
Hs.20950


218532_s_at
FLJ20152
Hs.82273


218559_s_at
MAFB
Hs.169487


218589_at
P2RY5
Hs.123464


218596_at
FLJ10743
Hs.3376


218608_at
HSA9947
Hs.128866


218614_at
FLJ20696
Hs.236844


218618_s_at
FAD104
Hs.299883


218625_at
NRN1
Hs.103291


218644_at
PLEK2
Hs.170473


218660_at
DYSF
Hs.408679


218676_s_at
PCTP
Hs.285218


218686_s_at
RHBDF1
Hs.57988


218710_at
FLJ20272
Hs.26090


218711_s_at
SDPR
Hs.26530


218718_at
PDGFC
Hs.43080


218723_s_at
RGC32
Hs.76640


218729_at
LXN
Hs.124491


218742_at
HPRN
Hs.22158


218781_at
SMC6L1
Hs.424559


218786_at
—
Hs.374350


218788_s_at
SMYD3
Hs.8109


218793_s_at
SCML1
Hs.109655


218803_at
CHFR
Hs.23794


218805_at
IAN4L1
Hs.412331


218810_at
FLJ23231
Hs.288300


218824_at
FLJ10781
Hs.8395


218825_at
EGFL7
Hs.91481


218828_at
PLSCR3
Hs.433154


218831_s_at
FCGRT
Hs.111903


218847_at
IMP-2
Hs.30299


218853_s_at
DJ473B4
Hs.57549


218854_at
SART2
Hs.388014


218856_at
TNFRSF21
Hs.159651


218858_at
FLJ12428
Hs.87729


218864_at
TNS
Hs.439442


218865_at
FLJ22390
Hs.195345


218872_at
TSC
Hs.345908


218876_at
CGI-38
Hs.412685


218880_at
FOSL2
Hs.301612


218881_s_at
FLJ23306
Hs.5890


218899_s_at
BAALC
Hs.169395


218902_at
NOTCH1
Hs.311559


218927_s_at
CHST12
Hs.25204


218935_at
EHD3
Hs.368808


218952_at
PCSK1N
Hs.429437


218963_s_at
KRT23
Hs.9029


218964_at
DRIL2
Hs.10431


218974_at
FLJ10159
Hs.346203


218978_s_at
MSCP
Hs.283716


218986_s_at
FLJ20035
Hs.109309


218988_at
SLC35E3
Hs.445043


219019_at
LRDD
Hs.438986


219032_x_at
OPN3
Hs.170129


219033_at
FLJ21308
Hs.310185


219036_at
BITE
Hs.127217


219049_at
ChGn
Hs.341073


219054_at
FLJ14054
Hs.13528


219059_s_at
XLKD1
Hs.17917


219090_at
SLC24A3
Hs.439909


219093_at
FLJ20701
Hs.424598


219123_at
ZNF232
Hs.279914


219183_s_at
PSCD4
Hs.7189


219191_s_at
BIN2
Hs.14770


219218_at
FLJ23058
Hs.415799


219228_at
ZNF463
Hs.147644


219243_at
HIMAP4
Hs.30822


219247_s_at
ZDHHC14
Hs.292541


219255_x_at
IL17RB
Hs.5470


219256_s_at
FLJ20356
Hs.61053


219259_at
FLJ12287
Hs.408846


219277_s_at
FLJ10851
Hs.17860


219288_at
HT021
Hs.47166


219295_s_at
PCOLCE2
Hs.8944


219304_s_at
SCDGF-B
Hs.112885


219308_s_at
AK5
Hs.18268


219316_s_at
C14orf58
Hs.267566


219332_at
FLJ23471
Hs.376617


219339_s_at
Eu-HMTase1
Hs.416692


219358_s_at
CENTA2
Hs.415471


219359_at
FLJ22635
Hs.353181


219360_s_at
TRPM4
Hs.31608


219371_s_at
KLF2
Hs.107740


219373_at
DPM3
Hs.110477


219383_at
FLJ14213
Hs.183506


219396_s_at
NEIL1
Hs.197423


219403_s_at
HPSE
Hs.44227


219414_at
CLSTN2
Hs.12079


219434_at
TREM1
Hs.283022


219443_at
C20orf13
Hs.88367


219457_s_at
RIN3
Hs.413374


219463_at
C20orf103
Hs.22920


219471_at
C13orf18
Hs.413071


219478_at
WFDC1
Hs.36688


219480_at
SNAI1
Hs.48029


219489_s_at
RHBDL2
Hs.133999


219497_s_at
BCL11A
Hs.314623


219505_at
CECR1
Hs.170310


219506_at
FLJ23221
Hs.91283


219511_s_at
SNCAIP
Hs.24948


219519_s_at
SN
Hs.31869


219520_s_at
KIAA1280
Hs.12913


219528_s_at
BCL11B
Hs.57987


219534_x_at
CDKN1C
Hs.106070


219541_at
FLJ20406
Hs.149227


219546_at
BMP2K
Hs.20137


219559_at
C20orf59
Hs.353013


219563_at
C14orf139
Hs.41502


219569_s_at
MGC3295
Hs.101257


219593_at
PHT2
Hs.237856


219602_s_at
FLJ23403
Hs.293907


219607_s_at
MS4A4A
Hs.325960


219622_at
RAB20
Hs.179791


219628_at
WIG1
Hs.252406


219629_at
FLJ20635
Hs.265018


219630_at
MAP17
Hs.431099


219654_at
PTPLA
Hs.114062


219666_at
MS4A6A
Hs.371612


219667_s_at
BANK
Hs.193736


219669_at
PRV1
Hs.232165


219672_at
ERAF
Hs.274309


219681_s_at
RCP
Hs.96125


219686_at
HSA250839
Hs.58241


219695_at
FLJ10640
Hs.91753


219714_s_at
CACNA2D3
Hs.435112


219737_s_at
—
Hs.458282 // est


219738_s_at
PCDH9
Hs.404723


219740_at
FLJ12505
Hs.96885


219747_at
FLJ23191
Hs.16026


219753_at
STAG3
Hs.323634


219759_at
LRAP
Hs.374490


219777_at
hIAN2
Hs.105468


219788_at
PILRA
Hs.122591


219789_at
NPR3
Hs.237028


219790_s_at
NPR3
Hs.237028


219799_s_at
RDHL
Hs.179608


219806_s_at
FN5
Hs.416456


219812_at
STAG3
Hs.323634


219814_at
MBNL3
Hs.105134


219837_s_at
C17
Hs.13872


219859_at
CLECSF9
Hs.236516


219870_at
ATF7IP2
Hs.189813


219871_at
FLJ13197
Hs.29725


219872_at
DKFZp434L142
Hs.323583


219884_at
LHX6
Hs.103137


219890_at
CLECSF5
Hs.126355


219892_at
TM6SF1
Hs.151155


219895_at
FLJ20716
Hs.437563


219905_at
ERMAP
Hs.427672


219918_s_at
ASPM
Hs.121028


219919_s_at
SSH-3
Hs.29173


219922_s_at
LTBP3
Hs.289019


219932_at
VLCS-H1
Hs.49765


219947_at
CLECSF6
Hs.115515


219952_s_at
MCOLN1
Hs.372029


219978_s_at
ANKT
Hs.279905


219992_at
TAC3
Hs.9730


220001_at
PADI4
Hs.397050


220005_at
GPR86
Hs.13040


220006_at
FLJ12057
Hs.134807


220010_at
KCNE1L
Hs.146372


220014_at
LOC51334
Hs.157461


220017_x_at
CYP2C9
Hs.418127


220037_s_at
XLKD1
Hs.17917


220051_at
PRSS21
Hs.72026


220057_at
GAGED2
Hs.112208


220059_at
BRDG1
Hs.121128


220066_at
CARD15
Hs.135201


220068_at
VPREB3
Hs.136713


220088_at
C5R1
Hs.2161


220091_at
SLC2A6
Hs.244378


220110_s_at
NXF3
Hs.60386


220122_at
FLJ22344
Hs.107716


220173_at
C14orf45
Hs.260555


220179_at
LOC64180
Hs.302028


220220_at
FLJ10120
Hs.378860


220266_s_at
KLF4
Hs.376206


220306_at
FLJ20202
Hs.356216


220319_s_at
MIR
Hs.443793


220330_s_at
SAMSN1
Hs.221851


220335_x_at
FLJ21736
Hs.268700


220359_s_at
ARPP-21
Hs.412268


220370_s_at
KIAA1453
Hs.11387


220377_at
C14orf110
Hs.395486


220404_at
GPR97
Hs.383403


220416_at
ATP8B4
Hs.313841


220448_at
KCNK12
Hs.252617


220485_s_at
SIRPB2
Hs.50716


220496_at
CLEC2
Hs.409794


220507_s_at
UPB1
Hs.285512


220532_s_at
LR8
Hs.190161


220560_at
C11orf21
Hs.272100


220570_at
RETN
Hs.283091


220591_s_at
FLJ22843
Hs.301143


220595_at
DKFZp434B0417
Hs.380044


220617_s_at
FLJ10697
Hs.368756


220646_s_at
KLRF1
Hs.183125


220668_s_at
DNMT3B
Hs.251673


220684_at
TBX21
Hs.272409


220704_at
ZNFN1A1
Hs.435949


220720_x_at
FLJ14346
Hs.287640


220727_at
KCNK10
Hs.365690


220751_s_at
C5orf4
Hs.10235


220757_s_at
UBXD1
Hs.435255


220793_at
SAGE
Hs.195292


220807_at
HBQ1
Hs.247921


220811_at
PRG3
Hs.251386


220832_at
TLR8
Hs.272410


220864_s_at
GRIM19
Hs.279574


220898_at
—
— // —


220911_s_at
KIAA1305
Hs.496280


220918_at
RUNX1
Hs.410774


220937_s_at
SIAT7D
Hs.3972


220940_at
KIAA1641
Hs.503503


220941_s_at
C21orf91
Hs.293811


220945_x_at
FLJ10298
Hs.5999


220954_s_at
PILRB
Hs.349256


221004_s_at
ITM2C
Hs.111577


221011_s_at
LBH
Hs.57209


221012_s_at
TRIM8
Hs.54580


221019_s_at
COLEC12
Hs.29423


221059_s_at
CHST6
Hs.157439


221060_s_at
TLR4
Hs.174312


221063_x_at
RNF123
Hs.406364


221075_s_at
NCR2
Hs.194721


221140_s_at
G2A
Hs.441131


221205_at
—
— // —


221210_s_at
C1orf13
Hs.64896


221223_x_at
CISH
Hs.8257


221234_s_at
BACH2
Hs.88414


221237_s_at
OSBP2
Hs.7740


221245_s_at
DKFZP434E2135
Hs.17631


221246_x_at
TNS
Hs.439442


221261_x_at
MAGED4
Hs.376347


221269_s_at
SH3BGRL3
Hs.109051


221286_s_at
PACAP
Hs.409563


221345_at
GPR43
Hs.248056


221349_at
VPREB1
Hs.247979


221363_x_at
GPR25
Hs.248123


221425_s_at
MGC4276
Hs.270013


221477_s_at
SOD2
Hs.384944


221478_at
BNIP3L
Hs.132955


221479_s_at
BNIP3L
Hs.132955


221484_at
B4GALT5
Hs.107526


221491_x_at
HLA-DRB3
Hs.308026


221520_s_at
CDCA8
Hs.48855


221529_s_at
PLVAP
Hs.107125


221530_s_at
BHLHB3
Hs.437282


221541_at
DKFZP434B044
Hs.262958


221551_x_at
SIAT7D
Hs.3972


221558_s_at
LEF1
Hs.44865


221563_at
DUSP10
Hs.177534


221577_x_at
PLAB
Hs.296638


221578_at
RASSF4
Hs.319124


221581_s_at
WBSCR5
Hs.56607


221584_s_at
KCNMA1
Hs.354740


221601_s_at
TOSO
Hs.58831


221602_s_at
TOSO
Hs.58831


221607_x_at
ACTG1
Hs.14376


221627_at
TRIM10
Hs.274295


221646_s_at
ZDHHC11
Hs.50754


221651_x_at
na
Hs.377975


221658_s_at
IL21R
Hs.210546


221666_s_at
ASC
Hs.197875


221671_x_at
na
Hs.377975


221675_s_at
CHPT1
Hs.225567


221690_s_at
NALP2
Hs.369279


221698_s_at
CLECSF12
Hs.161786


221704_s_at
FLJ12750
Hs.77870


221724_s_at
CLECSF6
Hs.115515


221728_x_at
LOC139202
Hs.83623 // —


221731_x_at
CSPG2
Hs.434488


221747_at
TNS
Hs.439442


221748_s_at
TNS
Hs.439442


221756_at
MGC17330
Hs.26670


221757_at
MGC17330
Hs.26670


221760_at
MAN1A1
Hs.255149


221764_at
MGC16353
Hs.388956


221765_at
UGCG
Hs.432605


221766_s_at
C6orf37
Hs.10784


221768_at
SFPQ
Hs.180610


221779_at
MIRAB13
Hs.8535


221802_s_at
KIAA1598
Hs.98002


221807_s_at
PP2447
Hs.33026


221809_at
KIAA1464
Hs.441888 // —


221814_at
GPR124
Hs.17270


221824_s_at
c-MIR
Hs.288156


221840_at
PTPRE
Hs.437980


221841_s_at
KLF4
Hs.376206


221861_at
—
Hs.12853 // —


221870_at
EHD2
Hs.325650


221875_x_at
HLA-F
Hs.411958


221884_at
EVI1
Hs.436019


221902_at
na
Hs.7967 // —


221920_s_at
MSCP
Hs.283716


221932_s_at
C14orf87
Hs.294083


221942_s_at
GUCY1A3
Hs.433488


221950_at
EMX2
Hs.202095


221962_s_at
UBE2H
Hs.372758


221969_at
—
Hs.22030 // est


221978_at
HLA-F
Hs.411958


221983_at
MGC3035
Hs.22412


222001_x_at
—
Hs.503585 // est


222040_at
HNRPA1
Hs.356721


222067_x_at
HIST1H2BD
Hs.180779


222068_s_at
LOC123872
Hs.310164


222074_at
UROD
Hs.78601


222087_at
—
Hs.32458 // est


222088_s_at
SLC2A14
Hs.401274


222108_at
AMIGO2
Hs.121520


222125_s_at
PH-4
Hs.271224


222142_at
CYLD
Hs.386952


222144_at
KIF17
Hs.130411 // —


222145_at
na
Hs.406494 // —


222146_s_at
TCF4
Hs.359289


222154_s_at
DKFZP564A2416
Hs.230767


222162_s_at
ADAMTS1
Hs.8230


222186_at
—
Hs.306329 // —


222218_s_at
PILRA
Hs.122591


222221_x_at
EHD1
Hs.155119


222222_s_at
—
— // —


222258_s_at
SH3BP4
Hs.17667


222281_s_at
—
Hs.370494 // est


222284_at
—
Hs.373565 // est


222288_at
—
Hs.130526 // est


222294_s_at
RAB27A
Hs.298530


222303_at
ETS2
Hs.292477


222313_at
—
Hs.293334 // est


222315_at
—
Hs.292853 // est


222316_at
—
Hs.292689 // est


222326_at
—
Hs.432534 // est


222330_at
—
Hs.445711 // est


222363_at
—
Hs.132670 // est


222375_at
—
Hs.372146 // est


266_s_at
CD24
Hs.375108


31874_at
GAS2L1
Hs.322852


33304_at
ISG20
Hs.105434


336_at
—
— // —


33646_g_at
GM2A
Hs.387156


34210_at
CDW52
Hs.276770


35626_at
SGSH
Hs.31074


35666_at
SEMA3F
Hs.32981


35820_at
GM2A
Hs.387156


36553_at
—
Hs.461056 // est


36554_at
ASMTL
Hs.458420


36564_at
FLJ90005
Hs.128366


36711_at
MAFF
Hs.51305


37028_at
PPP1R15A
Hs.76556


37145_at
GNLY
Hs.105806


37986_at
EPOR
Hs.127826


38037_at
DTR
Hs.799


38487_at
STAB1
Hs.301989


38521_at
CD22
Hs.262150


39248_at
AQP3
Hs.234642


39318_at
TCL1A
Hs.2484


39402_at
IL1B
Hs.126256


396_f_at
EPOR
Hs.127826


39729_at
PRDX2
Hs.432121


40020_at
CELSR3
Hs.55173


40093_at
LU
Hs.155048


40850_at
FKBP8
Hs.173464


41386_i_at
KIAA0346
Hs.103915 // —


41469_at
PI3
Hs.112341


41577_at
PPP1R16B
Hs.45719


41644_at
SASH1
Hs.166311


44673_at
SN
Hs.31869


45297_at
EHD2
Hs.325650


46665_at
SEMA4C
Hs.7188


48031_r_at
C5orf4
Hs.10235


48106_at
FLJ20489
Hs.438867


48808_at
DHFR
Hs.83765


49306_at
RASSF4
Hs.319124


51158_at
—
Hs.27373 // —


53987_at
na
Hs.6343 // —


54037_at
HPS4
Hs.441481


55081_at
MIRAB13
Hs.8535


55705_at
—
Hs.498224 // est


57540_at
RBSK
Hs.11916


57588_at
SLC24A3
Hs.439909


64064_at
IAN4L1
Hs.412331


64942_at
na
Hs.7967 // —


AFFX-HUMISGF3A/
—
— // —


M97935_5_at


AFFX-HUMRGE/
—
— // —


M10098_3_at


AFFX-HUMRGE/
—
— // —


M10098_5_at


AFFX-HUMRGE/
—
— // —


M10098_M_at


AFFX-M27830_5_at
—
— // —


AFFX-M27830_M_at
—
— // —


AFFX-r2-Hs18SrRNA-3_s_at
—
— // —


AFFX-r2-Hs18SrRNA-5_at
—
— // —


AFFX-r2-Hs18SrRNA-M_x_at
—
— // —


AFFX-r2-Hs28SrRNA-3_at
—
— // —


AFFX-r2-Hs28SrRNA-M_at
—
— // —
















TABLE 2







About 599 genes defining assigned clusters of AML as


identified by SAM.










Affymetrix
Gene
Cluster



probe set id
symbol
defined
Unigene ID





202672_s_at
ATF3
cluster1
Hs.460


201464_x_at
JUN
cluster1
Hs.78465


202497_x_at
SLC2A3
cluster1
Hs.419240


204622_x_at
NR4A2
cluster1
Hs.82120


216236_s_at
SLC2A14
cluster1
Hs.401274


216248_s_at
NR4A2
cluster1
Hs.82120


204621_s_at
NR4A2
cluster1
Hs.82120


222088_s_at
SLC2A14
cluster1
Hs.401274


220014_at
LOC51334
cluster1
Hs.157461


206762_at
KCNA5
cluster1
Hs.150208


213094_at
GPR126
cluster1
Hs.419170


218502_s_at
TRPS1
cluster1
Hs.26102


221530_s_at
BHLHB3
cluster1
Hs.437282


221884_at
EVI1
cluster1
Hs.436019


203642_s_at
KIAA0977
cluster1
Hs.300855


212827_at
IGHM
cluster1
Hs.153261


205612_at
MMRN
cluster1
Hs.268107


209200_at
MEF2C
cluster1
Hs.368950


214255_at
ATP10A
cluster1
Hs.125595


201539_s_at
FHL1
cluster1
Hs.421383


205717_x_at
PCDHGC3
cluster1
Hs.283794


222144_at
KIF17
cluster1
Hs.130411 // —


219922_s_at
LTBP3
cluster1
Hs.289019


215836_s_at
PCDHGC3
cluster1
Hs.283794


205861_at
SPIB
cluster1
Hs.437905


203372_s_at
SOCS2
cluster1
Hs.405946


209079_x_at
PCDHGC3
cluster1
Hs.283794


215811_at
—
cluster1
Hs.275706 // —


209199_s_at
MEF2C
cluster1
Hs.368950


207655_s_at
BLNK
cluster1
Hs.167746


203716_s_at
DPP4
cluster1
Hs.44926


219737_s_at
—
cluster1
Hs.458282 // est


204304_s_at
PROM1
cluster1
Hs.370052


203373_at
SOCS2
cluster1
Hs.405946


218237_s_at
SLC38A1
cluster1
Hs.132246


202265_at
BMI1
cluster1
Hs.380403


210298_x_at
FHL1
cluster1
Hs.421383


208436_s_at
IRF7
cluster1
Hs.166120


210032_s_at
SPAG6
cluster1
Hs.158213


206571_s_at
MAP4K4
cluster2
Hs.3628


213152_s_at
—
cluster2
Hs.476680 // est


214582_at
PDE3B
cluster2
Hs.337616


209458_x_at
HBA1
cluster2
Hs.449630


208623_s_at
VIL2
cluster2
Hs.403997


204018_x_at
HBA1
cluster2
Hs.449630


211745_x_at
HBA1
cluster2
Hs.449630


211696_x_at
HBB
cluster2
Hs.155376


214414_x_at
HBA1
cluster2
Hs.449630


209116_x_at
HBB
cluster2
Hs.155376


217232_x_at
—
cluster2
— // —


211699_x_at
HBA1
cluster2
Hs.449630


217414_x_at
—
cluster2
— // —


208792_s_at
CLU
cluster2
Hs.436657


216268_s_at
JAG1
cluster2
Hs.409202


208798_x_at
GOLGIN-67
cluster2
Hs.182982


213844_at
HOXA5
cluster2
Hs.37034


204030_s_at
SCHIP1
cluster2
Hs.61490


209193_at
PIM1
cluster2
Hs.81170


221942_s_at
GUCY1A3
cluster2
Hs.433488


208767_s_at
LAPTM4B
cluster2
Hs.296398


210425_x_at
GOLGIN-67
cluster2
Hs.356225


209409_at
GRB10
cluster2
Hs.81875


212070_at
GPR56
cluster2
Hs.6527


205453_at
HOXB2
cluster2
Hs.290432


208797_s_at
GOLGIN-67
cluster2
Hs.182982


206582_s_at
GPR56
cluster2
Hs.6527


207533_at
CCL1
cluster2
Hs.72918


206298_at
RhoGAP2
cluster2
Hs.87241


212276_at
LPIN1
cluster2
Hs.81412


219615_s_at
KCNK5
cluster2
Hs.444448


203187_at
DOCK1
cluster2
Hs.437620


206574_s_at
PTP4A3
cluster2
Hs.43666


204341_at
TRIM16
cluster2
Hs.241305


210145_at
PLA2G4A
cluster2
Hs.211587


205190_at
PLS1
cluster2
Hs.203637


215288_at
TRPC2
cluster2
Hs.131910 // —


211269_s_at
IL2RA
cluster2
Hs.130058


206341_at
IL2RA
cluster2
Hs.130058


207034_s_at
GLI2
cluster2
Hs.111867


212543_at
AIM1
cluster3
Hs.422550 // —


204500_s_at
AGTPBP1
cluster3
Hs.21542


211729_x_at
BLVRA
cluster3
Hs.435726


218831_s_at
FCGRT
cluster3
Hs.111903


221830_at
RAP2A
cluster3
Hs.48554


203773_x_at
BLVRA
cluster3
Hs.435726


206034_at
SERPINB8
cluster3
Hs.368077


212195_at
IL6ST
cluster3
Hs.71968


205707_at
IL17R
cluster3
Hs.129751


203973_s_at
KIAA0146
cluster3
Hs.381058


220377_at
C14orf110
cluster3
Hs.395486


201829_at
NET1
cluster3
Hs.25155


207838_x_at
PBXIP1
cluster3
Hs.8068


201427_s_at
SEPP1
cluster3
Hs.275775


214228_x_at
TNFRSF4
cluster3
Hs.129780


201663_s_at
SMC4L1
cluster3
Hs.50758


215388_s_at
HFL1
cluster3
Hs.296941


203187_at
DOCK1
cluster3
Hs.437620


219304_s_at
SCDGF-B
cluster3
Hs.112885


219602_s_at
FLJ23403
cluster3
Hs.293907


215471_s_at
MAP7
cluster3
Hs.254605


202890_at
MAP7
cluster3
Hs.254605


206582_s_at
GPR56
cluster3
Hs.6527


214039_s_at
LAPTM4B
cluster3
Hs.296398


204341_at
TRIM16
cluster3
Hs.241305


204160_s_at
ENPP4
cluster3
Hs.54037


213217_at
ADCY2
cluster3
Hs.414591


210116_at
SH2D1A
cluster3
Hs.151544


201664_at
SMC4L1
cluster3
Hs.50758


217975_at
LOC51186
cluster3
Hs.15984


202889_x_at
ANPEP
cluster3
Hs.254605


204044_at
QPRT
cluster3
Hs.8935


208029_s_at
LAPTM4B
cluster3
Hs.296398


206298_at
RhoGAP2
cluster3
Hs.87241


208767_s_at
LAPTM4B
cluster3
Hs.296398


213110_s_at
COL4A5
cluster3
Hs.169825


205190_at
PLS1
cluster3
Hs.203637


207533_at
CCL1
cluster3
Hs.72918


205848_at
GAS2
cluster3
Hs.135665


206950_at
SCN9A
cluster3
Hs.2319


210844_x_at
CTNNA1
cluster4
Hs.254321


200764_s_at
CTNNA1
cluster4
Hs.254321


200765_x_at
CTNNA1
cluster4
Hs.254321


209191_at
TUBB-5
cluster4
Hs.274398


202241_at
C8FW
cluster4
Hs.444947


217800_s_at
NDFIP1
cluster4
Hs.9788


202252_at
RAB13
cluster4
Hs.151536


201412_at
LRP10
cluster4
Hs.28368


201160_s_at
CSDA
cluster4
Hs.221889


208683_at
CAPN2
cluster4
Hs.350899


205382_s_at
DF
cluster4
Hs.155597


203233_at
IL4R
cluster4
Hs.75545


219371_s_at
KLF2
cluster4
Hs.107740


208923_at
CYFIP1
cluster4
Hs.26704


218627_at
FLJ11259
cluster4
Hs.416393


213416_at
ITGA4
cluster4
Hs.145140


205884_at
ITGA4
cluster4
Hs.145140


214757_at
—
cluster4
Hs.488749 // est


203987_at
FZD6
cluster4
Hs.114218


202242_at
TM4SF2
cluster4
Hs.439586


206726_at
PGDS
cluster4
Hs.128433


54037_at
HPS4
cluster4
Hs.441481


216525_x_at
PMS2L9
cluster4
Hs.278467


210448_s_at
P2RX5
cluster4
Hs.408615


209993_at
ABCB1
cluster4
Hs.21330


217147_s_at
TRIM
cluster4
Hs.138701


206233_at
B4GALT6
cluster4
Hs.369994


209994_s_at
ABCB1
cluster4
Hs.21330


220567_at
ZNFN1A2
cluster4
Hs.278963


207996_s_at
C18orf1
cluster4
Hs.285091


213910_at
IGFBP7
cluster4
Hs.435795


214049_x_at
CD7
cluster4
Hs.36972


214551_s_at
CD7
cluster4
Hs.36972


217143_s_at
TRD@
cluster4
Hs.2014


219383_at
FLJ14213
cluster4
Hs.183506


211682_x_at
UGT2B28
cluster4
Hs.137585


213830_at
TRD@
cluster4
Hs.2014


206232_s_at
B4GALT6
cluster4
Hs.369994


216191_s_at
TRD@
cluster4
Hs.2014


216286_at
—
cluster4
Hs.306324 // —


50221_at
TFEB
cluster5
Hs.23391


202895_s_at
EPHB4
cluster5
Hs.156114


205099_s_at
CCR1
cluster5
Hs.301921


200866_s_at
PSAP
cluster5
Hs.406455


208594_x_at
LILRB3
cluster5
Hs.306230


211135_x_at
LILRB3
cluster5
Hs.306230


213624_at
ASM3A
cluster5
Hs.277962


218559_s_at
MAFB
cluster5
Hs.169487


221578_at
RASSF4
cluster5
Hs.319124


212334_at
GNS
cluster5
Hs.334534


203769_s_at
STS
cluster5
Hs.79876


205686_s_at
CD86
cluster5
Hs.27954


205685_at
CD86
cluster5
Hs.27954


207104_x_at
LILRB1
cluster5
Hs.149924


220066_at
CARD15
cluster5
Hs.135201


201642_at
IFNGR2
cluster5
Hs.409200


204487_s_at
KCNQ1
cluster5
Hs.367809


217992_s_at
MGC4342
cluster5
Hs.301342


211732_x_at
HNMT
cluster5
Hs.42151


210660_at
LILRB1
cluster5
Hs.149924


204858_s_at
ECGF1
cluster5
Hs.435067


203768_s_at
STS
cluster5
Hs.79876


222218_s_at
PILRA
cluster5
Hs.122591


210146_x_at
LILRB3
cluster5
Hs.306230


220832_at
TLR8
cluster5
Hs.272410


219593_at
PHT2
cluster5
Hs.237856


204619_s_at
CSPG2
cluster5
Hs.434488


206278_at
PTAFR
cluster5
Hs.46


207224_s_at
SIGLEC7
cluster5
Hs.274470


203767_s_at
STS
cluster5
Hs.79876


204254_s_at
VDR
cluster5
Hs.2062


214590_s_at
UBE2D1
cluster5
Hs.129683


212681_at
EPB41L3
cluster5
Hs.103839


219872_at
DKFZp434L142
cluster5
Hs.323583


204392_at
CAMK1
cluster5
Hs.434875


219788_at
PILRA
cluster5
Hs.122591


206934_at
SIRPB1
cluster5
Hs.194784


211776_s_at
EPB41L3
cluster5
Hs.103839


207872_s_at
LILRB1
cluster5
Hs.149924


206710_s_at
EPB41L3
cluster5
Hs.103839


209083_at
CORO1A
cluster6
Hs.415067


204319_s_at
RGS10
cluster6
Hs.82280


217845_x_at
HIG1
cluster6
Hs.7917


205672_at
XPA
cluster6
Hs.288867


217118_s_at
KIAA0930
cluster6
Hs.13255


211990_at
HLA-DPA1
cluster6
Hs.914


210982_s_at
HLA-DRA
cluster6
Hs.409805


208982_at
PECAM1
cluster6
Hs.78146


209619_at
CD74
cluster6
Hs.446471


215193_x_at
HLA-DRB1
cluster6
Hs.411726


201641_at
BST2
cluster6
Hs.118110


213266_at
—
cluster6
Hs.497941 // est


202729_s_at
LTBP1
cluster6
Hs.241257


204751_x_at
DSC2
cluster6
Hs.95612


215573_at
CAT
cluster6
Hs.395771


220898_at
—
cluster6
— // —


215388_s_at
HFL1
cluster6
Hs.296941


219036_at
BITE
cluster6
Hs.127217


204750_s_at
DSC2
cluster6
Hs.95612


218786_at
—
cluster6
Hs.374350


208414_s_at
HOXB4
cluster6
Hs.147465


201431_s_at
DPYSL3
cluster6
Hs.150358


215623_x_at
SMC4L1
cluster6
Hs.50758


213260_at
FOXC1
cluster6
Hs.348883


219932_at
VLCS-H1
cluster6
Hs.49765


206377_at
FOXF2
cluster6
Hs.44481


202728_s_at
LTBP1
cluster6
Hs.241257


219651_at
FLJ10713
cluster6
Hs.317659


213217_at
ADCY2
cluster6
Hs.414591


218710_at
FLJ20272
cluster6
Hs.26090


219602_s_at
FLJ23403
cluster6
Hs.293907


215807_s_at
PLXNB1
cluster6
Hs.278311


212019_at
DKFZP564M182
cluster6
Hs.158995


204983_s_at
GPC4
cluster6
Hs.58367


204984_at
GPC4
cluster6
Hs.58367


221959_at
MGC39325
cluster6
Hs.34054


209702_at
FTO
cluster6
Hs.284741


219511_s_at
SNCAIP
cluster6
Hs.24948


51158_at
—
cluster6
Hs.27373 // —


221880_s_at
—
cluster6
Hs.27373 // —


201733_at
CLCN3
cluster7
Hs.372528


218978_s_at
MSCP
cluster7
Hs.283716


214433_s_at
SELENBP1
cluster7
Hs.334841


201249_at
SLC2A1
cluster7
Hs.169902


205389_s_at
ANK1
cluster7
Hs.443711


207793_s_at
EPB41
cluster7
Hs.37427


212804_s_at
DKFZP434C212
cluster7
Hs.287266


221237_s_at
OSBP2
cluster7
Hs.7740


216925_s_at
TAL1
cluster7
Hs.73828


206077_at
KEL
cluster7
Hs.420322


213843_x_at
SLC6A8
cluster7
Hs.388375


206145_at
RHAG
cluster7
Hs.368178


217274_x_at
—
cluster7
— // —


216063_at
—
cluster7
Hs.470084 // est


220751_s_at
C5orf4
cluster7
Hs.10235


210854_x_at
SLC6A8
cluster7
Hs.388375


210586_x_at
RHD
cluster7
Hs.458333


210395_x_at
MYL4
cluster7
Hs.356717


205262_at
KCNH2
cluster7
Hs.188021


208353_x_at
ANK1
cluster7
Hs.443711


208416_s_at
SPTB
cluster7
Hs.438514


219630_at
MAP17
cluster7
Hs.431099


208352_x_at
ANK1
cluster7
Hs.443711


207087_x_at
ANK1
cluster7
Hs.443711


211254_x_at
RHAG
cluster7
Hs.368178


206647_at
HBZ
cluster7
Hs.272003


214530_x_at
EPB41
cluster7
Hs.37427


203911_at
RAP1GA1
cluster7
Hs.433797


218864_at
TNS
cluster7
Hs.439442


207043_s_at
SLC6A9
cluster7
Hs.442590


205391_x_at
ANK1
cluster7
Hs.443711


210088_x_at
MYL4
cluster7
Hs.356717


216054_x_at
MYL4
cluster7
Hs.356717


206146_s_at
RHAG
cluster7
Hs.368178


204720_s_at
DNAJC6
cluster7
Hs.44896


205390_s_at
ANK1
cluster7
Hs.443711


56748_at
TRIM10
cluster7
Hs.274295


221577_x_at
PLAB
cluster7
Hs.296638


207854_at
GYPE
cluster7
Hs.395535


206116_s_at
TPM1
cluster7
Hs.133892


203115_at
FECH
cluster8
Hs.443610


208352_x_at
ANK1
cluster8
Hs.443711


48031_r_at
C5orf4
cluster8
Hs.10235


214433_s_at
SELENBP1
cluster8
Hs.334841


218853_s_at
DJ473B4
cluster8
Hs.57549


209890_at
TM4SF9
cluster8
Hs.8037


210586_x_at
RHD
cluster8
Hs.458333


213843_x_at
SLC6A8
cluster8
Hs.388375


207087_x_at
ANK1
cluster8
Hs.443711


204467_s_at
SNCA
cluster8
Hs.76930


216317_x_at
RHCE
cluster8
Hs.278994


202124_s_at
ALS2CR3
cluster8
Hs.154248


216833_x_at
GYPE
cluster8
Hs.395535


201886_at
WDR23
cluster8
Hs.283976


202074_s_at
OPTN
cluster8
Hs.390162


215812_s_at
—
cluster8
Hs.499113 // est


218864_at
TNS
cluster8
Hs.439442


211820_x_at
GYPA
cluster8
Hs.34287


203794_at
CDC42BPA
cluster8
Hs.18586


216925_s_at
TAL1
cluster8
Hs.73828


202219_at
SLC6A8
cluster8
Hs.388375


205838_at
GYPA
cluster8
Hs.34287


211649_x_at
—
cluster8
Hs.449057


217572_at
—
cluster8
— // —


202125_s_at
ALS2CR3
cluster8
Hs.154248


208353_x_at
ANK1
cluster8
Hs.443711


205837_s_at
GYPA
cluster8
Hs.34287


202364_at
MXI1
cluster8
Hs.118630


220751_s_at
C5orf4
cluster8
Hs.10235


214464_at
CDC42BPA
cluster8
Hs.18586


221237_s_at
OSBP2
cluster8
Hs.7740


205391_x_at
ANK1
cluster8
Hs.443711


210430_x_at
RHD
cluster8
Hs.283822


201333_s_at
ARHGEF12
cluster8
Hs.413112


212151_at
PBX1
cluster8
Hs.408222


40093_at
LU
cluster8
Hs.155048


202073_at
OPTN
cluster8
Hs.390162


209735_at
ABCG2
cluster8
Hs.194720


201131_s_at
CDH1
cluster8
Hs.194657


213338_at
RIS1
cluster8
Hs.35861


200675_at
CD81
cluster9
Hs.54457


202370_s_at
CBFB
cluster9
Hs.179881


211031_s_at
CYLN2
cluster9
Hs.104717


218927_s_at
CHST12
cluster9
Hs.25204


206788_s_at
CBFB
cluster9
Hs.179881


219218_at
FLJ23058
cluster9
Hs.415799


211026_s_at
MGLL
cluster9
Hs.409826


204198_s_at
RUNX3
cluster9
Hs.170019


213779_at
EMU1
cluster9
Hs.289106


218414_s_at
NDE1
cluster9
Hs.263925


200984_s_at
CD59
cluster9
Hs.278573


204197_s_at
RUNX3
cluster9
Hs.170019


203329_at
PTPRM
cluster9
Hs.154151


218876_at
CGI-38
cluster9
Hs.412685


210889_s_at
FCGR2B
cluster9
Hs.126384


212771_at
LOC221061
cluster9
Hs.66762 // —


202481_at
SDR1
cluster9
Hs.17144


205330_at
MN1
cluster9
Hs.268515


203939_at
NT5E
cluster9
Hs.153952


212912_at
RPS6KA2
cluster9
Hs.301664


201506_at
TGFBI
cluster9
Hs.421496


200665_s_at
SPARC
cluster9
Hs.111779


204787_at
Z39IG
cluster9
Hs.8904


207194_s_at
ICAM4
cluster9
Hs.435625


219308_s_at
AK5
cluster9
Hs.18268


209395_at
CHI3L1
cluster9
Hs.382202


205076_s_at
CRA
cluster9
Hs.425144


219694_at
FLJ11127
cluster9
Hs.91165


209396_s_at
CHI3L1
cluster9
Hs.382202


204885_s_at
MSLN
cluster9
Hs.408488


221019_s_at
COLEC12
cluster9
Hs.29423


205987_at
CD1C
cluster9
Hs.1311


203058_s_at
PAPSS2
cluster9
Hs.274230


203060_s_at
PAPSS2
cluster9
Hs.274230


206682_at
CLECSF13
cluster9
Hs.54403


212298_at
NRP1
cluster9
Hs.173548


206135_at
ST18
cluster9
Hs.151449


212358_at
CLIPR-59
cluster9
Hs.7357


207961_x_at
MYH11
cluster9
Hs.78344


201497_x_at
MYH11
cluster9
Hs.78344


214575_s_at
AZU1
cluster10
Hs.72885


205382_s_at
DF
cluster10
Hs.155597


209906_at
C3AR1
cluster10
Hs.155935


206111_at
RNASE2
cluster10
Hs.728


212071_s_at
SPTBN1
cluster10
Hs.205401


203796_s_at
BCL7A
cluster10
Hs.371758


218899_s_at
BAALC
cluster10
Hs.169395


209488_s_at
RBPMS
cluster10
Hs.195825


218086_at
NPDC1
cluster10
Hs.105547


204581_at
CD22
cluster10
Hs.262150


208614_s_at
FLNB
cluster10
Hs.81008


204540_at
EEF1A2
cluster10
Hs.433839


204917_s_at
MLLT3
cluster10
Hs.404


209437_s_at
SPON1
cluster10
Hs.5378


212827_at
IGHM
cluster10
Hs.153261


200672_x_at
SPTBN1
cluster10
Hs.205401


203756_at
P164RHOGEF
cluster10
Hs.45180


220377_at
C14orf110
cluster10
Hs.395486


209576_at
GNAI1
cluster10
Hs.203862


205330_at
MN1
cluster10
Hs.268515


212750_at
PPP1R16B
cluster10
Hs.45719


204484_at
PIK3C2B
cluster10
Hs.343329


209436_at
SPON1
cluster10
Hs.5378


209282_at
PRKD2
cluster10
Hs.205431


207836_s_at
RBPMS
cluster10
Hs.195825


209487_at
RBPMS
cluster10
Hs.195825


204083_s_at
TPM2
cluster10
Hs.300772


207788_s_at
SCAM-1
cluster10
Hs.301302


212558_at
GDAP1L1
cluster10
Hs.20977


209679_s_at
LOC57228
cluster10
Hs.206501


41577_at
PPP1R16B
cluster10
Hs.45719


213506_at
F2RL1
cluster10
Hs.154299


205933_at
SETBP1
cluster10
Hs.201369


204004_at
—
cluster10
Hs.503576 // est


213488_at
FLJ00133
cluster10
Hs.7949


200671_s_at
SPTBN1
cluster10
Hs.205401


209763_at
NRLN1
cluster10
Hs.440324


47560_at
FLJ11939
cluster10
Hs.94229


202551_s_at
CRIM1
cluster10
Hs.170752


219145_at
FLJ11939
cluster10
Hs.94229


201560_at
CLIC4
cluster11
Hs.25035


204401_at
KCNN4
cluster11
Hs.10082


212658_at
LHFPL2
cluster11
Hs.79299


221223_x_at
CISH
cluster11
Hs.8257


201559_s_at
CLIC4
cluster11
Hs.25035


201425_at
ALDH2
cluster11
Hs.436437


209543_s_at
CD34
cluster11
Hs.374990


203217_s_at
SIAT9
cluster11
Hs.415117


215116_s_at
DNM1
cluster11
Hs.436132


213848_at
DUSP7
cluster11
Hs.3843


200665_s_at
SPARC
cluster11
Hs.111779


211675_s_at
HIC
cluster11
Hs.132739


208873_s_at
DP1
cluster11
Hs.173119


205101_at
MHC2TA
cluster11
Hs.126714


209723_at
SERPINB9
cluster11
Hs.104879


200762_at
DPYSL2
cluster11
Hs.173381


201279_s_at
DAB2
cluster11
Hs.81988


217838_s_at
EVL
cluster11
Hs.241471


218589_at
P2RY5
cluster11
Hs.123464


216033_s_at
FYN
cluster11
Hs.390567


218966_at
MYO5C
cluster11
Hs.111782


31874_at
GAS2L1
cluster11
Hs.322852


203139_at
DAPK1
cluster11
Hs.244318


208886_at
H1F0
cluster11
Hs.226117


201656_at
ITGA6
cluster11
Hs.212296


219777_at
hIAN2
cluster11
Hs.105468


218237_s_at
SLC38A1
cluster11
Hs.132246


212171_x_at
VEGF
cluster11
Hs.73793


203542_s_at
BTEB1
cluster11
Hs.150557


203859_s_at
PALM
cluster11
Hs.78482


214953_s_at
APP
cluster11
Hs.177486


218805_at
IAN4L1
cluster11
Hs.412331


204385_at
KYNU
cluster11
Hs.444471


209583_s_at
MOX2
cluster11
Hs.79015


206042_x_at
SNRPN
cluster11
Hs.48375


201601_x_at
IFITM1
cluster11
Hs.458414


201522_x_at
SNRPN
cluster11
Hs.48375


218825_at
EGFL7
cluster11
Hs.91481


207076_s_at
ASS
cluster11
Hs.160786


209079_x_at
PCDHGC3
cluster11
Hs.283794


204425_at
ARHGAP4
cluster12
Hs.3109


203236_s_at
LGALS9
cluster12
Hs.81337


204152_s_at
MFNG
cluster12
Hs.371768


202600_s_at
NRIP1
cluster12
Hs.155017


204362_at
SCAP2
cluster12
Hs.410745


200931_s_at
VCL
cluster12
Hs.75350


202599_s_at
NRIP1
cluster12
Hs.155017


204153_s_at
MFNG
cluster12
Hs.371768


200935_at
CALR
cluster12
Hs.353170


210140_at
CST7
cluster12
Hs.143212


200656_s_at
P4HB
cluster12
Hs.410578


200654_at
P4HB
cluster12
Hs.410578


214203_s_at
PRODH
cluster12
Hs.343874


206105_at
FMR2
cluster12
Hs.54472


211663_x_at
PTGDS
cluster12
Hs.446429


207031_at
BAPX1
cluster12
Hs.105941


212204_at
DKFZP564G2022
cluster12
Hs.200692


200770_s_at
LAMC1
cluster12
Hs.432855


209960_at
HGF
cluster12
Hs.396530


207650_x_at
PTGER1
cluster12
Hs.159360


212509_s_at
—
cluster12
Hs.356623 // est


201276_at
RAB5B
cluster12
Hs.77690


209815_at
na
cluster12
Hs.454253 // —


209961_s_at
HGF
cluster12
Hs.396530


218043_s_at
AZ2
cluster12
Hs.437336


207895_at
NAALADASEL
cluster12
Hs.13967


212732_at
MEG3
cluster12
Hs.418271


203397_s_at
GALNT3
cluster12
Hs.278611


210755_at
HGF
cluster12
Hs.396530


206634_at
SIX3
cluster12
Hs.227277


203074_at
ANXA8
cluster12
Hs.87268


216320_x_at
MST1
cluster12
Hs.349110


202260_s_at
STXBP1
cluster12
Hs.325862


205663_at
PCBP3
cluster12
Hs.121241


205614_x_at
MST1
cluster12
Hs.349110


204537_s_at
GABRE
cluster12
Hs.22785


210794_s_at
MEG3
cluster12
Hs.418271


205110_s_at
FGF13
cluster12
Hs.6540


210998_s_at
HGF
cluster12
Hs.396530


210997_at
HGF
cluster12
Hs.396530


221581_s_at
WBSCR5
cluster13
Hs.56607


220560_at
C11orf21
cluster13
Hs.272100


208091_s_at
DKFZP564K0822
cluster13
Hs.4750


204494_s_at
LOC56905
cluster13
Hs.306331


208885_at
LCP1
cluster13
Hs.381099


203741_s_at
ADCY7
cluster13
Hs.172199


210010_s_at
SLC25A1
cluster13
Hs.111024


214946_x_at
FLJ10824
cluster13
Hs.375174 // —


211685_s_at
NCALD
cluster13
Hs.90063


206793_at
PNMT
cluster13
Hs.1892


209822_s_at
VLDLR
cluster13
Hs.370422


204073_s_at
C11orf9
cluster13
Hs.184640


219686_at
HSA250839
cluster13
Hs.58241


214920_at
LOC221981
cluster13
Hs.23799 // —


218742_at
HPRN
cluster13
Hs.22158


201655_s_at
HSPG2
cluster13
Hs.211573


204396_s_at
GPRK5
cluster13
Hs.211569


203088_at
FBLN5
cluster13
Hs.11494


213894_at
LOC221981
cluster13
Hs.23799 // —


201621_at
NBL1
cluster13
Hs.439671


216356_x_at
BAIAP3
cluster13
Hs.458427


206622_at
TRH
cluster13
Hs.182231


218613_at
DKFZp761K1423
cluster13
Hs.236438


212492_s_at
KIAA0876
cluster13
Hs.301011 // —


212496_s_at
KIAA0876
cluster13
Hs.301011 // —


203065_s_at
CAV1
cluster13
Hs.74034


204874_x_at
BAIAP3
cluster13
Hs.458427


206128_at
ADRA2C
cluster13
Hs.123022


216832_at
CBFA2T1
cluster13
Hs.90858


212097_at
CAV1
cluster13
Hs.74034


204990_s_at
ITGB4
cluster13
Hs.85266


211341_at
POU4F1
cluster13
Hs.458303


211517_s_at
IL5RA
cluster13
Hs.68876


210744_s_at
IL5RA
cluster13
Hs.68876


206940_s_at
POU4F1
cluster13
Hs.458303


204811_s_at
CACNA2D2
cluster13
Hs.389415


213194_at
ROBO1
cluster13
Hs.301198


216831_s_at
CBFA2T1
cluster13
Hs.90858


205528_s_at
CBFA2T1
cluster13
Hs.90858


205529_s_at
CBFA2T1
cluster13
Hs.90858


221737_at
GNA12
cluster15
Hs.182874


40489_at
DRPLA
cluster15
Hs.169488


218501_at
ARHGEF3
cluster15
Hs.25951


217853_at
TEM6
cluster15
Hs.12210


220974_x_at
BA108L7.2
cluster15
Hs.283844


209191_at
TUBB-5
cluster15
Hs.274398


212459_x_at
SUCLG2
cluster15
Hs.446476


212311_at
KIAA0746
cluster15
Hs.49500 // —


218847_at
IMP-2
cluster15
Hs.30299


215772_x_at
SUCLG2
cluster15
Hs.247309 // —


212314_at
KIAA0746
cluster15
Hs.49500 // —


202236_s_at
SLC16A1
cluster15
Hs.75231


201841_s_at
HSPB1
cluster15
Hs.76067


217800_s_at
NDFIP1
cluster15
Hs.9788


217226_s_at
PMX1
cluster15
Hs.443452


202391_at
BASP1
cluster15
Hs.79516


200765_x_at
CTNNA1
cluster15
Hs.254321


213400_s_at
TBL1X
cluster15
Hs.76536


213147_at
HOXA10
cluster15
Hs.110637


212906_at
na
cluster15
Hs.347534 // —


218552_at
FLJ10948
cluster15
Hs.170915


214651_s_at
HOXA9
cluster15
Hs.127428


210365_at
RUNX1
cluster15
Hs.410774


209374_s_at
IGHM
cluster15
Hs.153261


213150_at
HOXA10
cluster15
Hs.110637


201719_s_at
EPB41L2
cluster15
Hs.440387


218627_at
FLJ11259
cluster15
Hs.416393


219256_s_at
FLJ20356
cluster15
Hs.61053


205453_at
HOXB2
cluster15
Hs.290432


208962_s_at
FADS1
cluster15
Hs.132898


205600_x_at
HOXB5
cluster15
Hs.149548


204069_at
MEIS1
cluster15
Hs.170177


201867_s_at
TBL1X
cluster15
Hs.76536


209905_at
HOXA9
cluster15
Hs.127428


214835_s_at
SUCLG2
cluster15
Hs.446476


203542_s_at
BTEB1
cluster15
Hs.150557


212827_at
IGHM
cluster15
Hs.153261


211182_x_at
RUNX1
cluster15
Hs.410774


204661_at
CDW52
cluster15
Hs.276770


206676_at
CEACAM8
cluster15
Hs.41


220057_at
GAGED2
cluster16
Hs.112208


219360_s_at
TRPM4
cluster16
Hs.31608


219414_at
CLSTN2
cluster16
Hs.12079


220116_at
KCNN2
cluster16
Hs.98280


216370_s_at
TKTL1
cluster16
Hs.102866


205550_s_at
BRE
cluster16
Hs.80426


211566_x_at
BRE
cluster16
Hs.80426


214183_s_at
TKTL1
cluster16
Hs.102866


209031_at
IGSF4
cluster16
Hs.156682


212645_x_at
BRE
cluster16
Hs.80426


209030_s_at
IGSF4
cluster16
Hs.156682


213791_at
PENK
cluster16
Hs.339831


206508_at
TNFSF7
cluster16
Hs.99899


219506_at
FLJ23221
cluster16
Hs.91283


211421_s_at
RET
cluster16
Hs.350321


203241_at
UVRAG
cluster16
Hs.13137


213908_at
LOC339005
cluster16
Hs.212670 // —


207911_s_at
TGM5
cluster16
Hs.129719


214190_x_at
GGA2
cluster16
Hs.133340


204561_x_at
APOC2
cluster16
Hs.75615


209663_s_at
ITGA7
cluster16
Hs.74369


214259_s_at
AKR7A2
cluster16
Hs.6980


205472_s_at
DACH
cluster16
Hs.63931


216331_at
ITGA7
cluster16
Hs.74369


220010_at
KCNE1L
cluster16
Hs.146372


213484_at
na
cluster16
Hs.66187 // —


204497_at
ADCY9
cluster16
Hs.20196


215771_x_at
RET
cluster16
Hs.350321


209032_s_at
IGSF4
cluster16
Hs.156682


219714_s_at
CACNA2D3
cluster16
Hs.435112


219463_at
C20orf103
cluster16
Hs.22920


202139_at
AKR7A2
cluster16
Hs.6980


219143_s_at
FLJ20374
cluster16
Hs.8562


205996_s_at
AK2
cluster16
Hs.294008


219288_at
HT021
cluster16
Hs.47166


215663_at
MBNL1
cluster16
Hs.28578


213361_at
PCTAIRE2BP
cluster16
Hs.416543


210658_s_at
GGA2
cluster16
Hs.133340


213772_s_at
GGA2
cluster16
Hs.133340


212174_at
AK2
cluster16
Hs.294008




















TABLE 3







Error





10-fold
validation
#Probe


Abnormality
CV error
set
sets
#Genes



















t(8; 21) - AML1/ETO
0/190
0/96
3
2


t(15; 17) - PML/RARα
1/190
0/96
3
2


inv(16) - CBFβ/MYH11
0/190
0/96
1
1


11q23 (cluster #16)
3/190
3/96
31
25


EVI1 (cluster #10)
16/190 
0/96
28
25


cEBPα (cluster #4)
8/190
2/96
13
8


cEBPα (cluster #15)
17/190 
 6/96*
36
32


cEBPα (cluster #4 and #15)
5/190
2/96
9
5


FLT3 ITD
27/190 
21/96 
56
41
















TABLE 4







Clinical and molecular characteristics of the 286 patients


with de novo AML.










#
%















Gender





Male
138
49



Female
148
51



Age groups



Younger than 35
77
27



35-60
177
62



60 and older
32
11











Age (median (range)
45.1 (15.2-77.6) 




White blood cell (WBC) count
75.5 (0.3-263) 



(109/l, median (range))



Blast count (%, median (range))
70 (0-98)   



Platelet count (109/l, median (range))
57 (3-931)  



FAB











M0
6
2



M1
64
22



M2
66
23



M3
19
7



M4
53
18



M5
65
23



M6
3
1



Mixed
8
3



Unclassified
2
1



Cytogenetic risk groups



Favourable
58
20



t(8; 21)
22
8



inv(16)
19
7



t(15; 17)
17
6



Unfavourable
39
14



11q23 abnormalities
17
6



−5/7(q) abnormalities
22
8



Normal Cytogenetics
118
41



Molecular abnormalities



Mutation



FLT3 ITD
78
27



FLT3 TKD
33
12



N-RAS
26
9



K-RAS
9
3



cEBPα
17
6



Overexpression



EVI1
24
8



















TABLE 5









#Probe sets:















147
293
569
984
1692
2856
5071









Ratio:















>32
>22.6
>16
>11.3
>8
>5.6
>4











chromosomal abnormalities














t(8; 21)
+/−
+
+
+
++
++
+


inv(16)
+/−
+/−
+/−
+
++
++
++


t(15; 17)
+/−
+
++
++
++
++
+


11q23
+/−
+/−
+/−
+/−
+
+
+/−


−7(q)
+/−
+/−
+/−
+/−
+/−
+
+/−







mutation














FLT3 ITD
+/−
+/−
+/−
+/−
+/−
+/−
+/−


FLT3 TKD
−
−
−
−
−
−
−


N-RAS
−
−
−
−
−
−
−


K-RAS
−
−
−
−
−
−
−


cEBPα
−
+/−
+/−
+
+
+
+







overexpression














EVI1
−
−
−
−
+/−
+
+/−





(++: 100% clustering, +: clustering in ≦2 recognizable clusters, +/−: clustering in ≧2 recognizable clusters, −: no clustering)













TABLE 6







Characteristics of cluster #1 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22),


3q abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





1595
#1
M1
NN
+
−
−
−
−
−


2187
#1
M1
NN
−
−
−
−
−
−


3488
#1
M1
Complex
−
−
−
−
−
−


1401
#1
M1
NN
−
−
−
−
−
−


2255
#1
M1
11q23 (t(4; 11))
−
−
−
+
−
−


2302
#1
M1
+11/11q23(sMLL)
−
−
−
−
−
−


2765
#1
M1
+11/+11/Other
−
−
−
−
−
−


2280
#1
M2
NN
−
−
−
−
−
−


3304
#1
M5
NN
+
−
−
−
−
−


3328
#1
M5
11q23 (t(11; 19))
−
−
−
−
+
−


2682
#1
M4
Other/11q23 (t(2; 9; 11))
−
−
−
−
+
−


2207
#1
M1
11q23 (t(6; 11))
−
−
−
−
+
−


2772
#1
M5
11q23 (t(6; 11))
−
−
−
−
+
−


2196
#1
M5
NN
−
−
−
−
+
−
















TABLE 7







Characteristics of cluster #2 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22),


3q abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





3330
#2
M4
+8
−
−
−
−
−
−


2681
#2
M1
NN
+
−
−
−
−
−


2688
#2
ND
NN
+
−
−
−
−
−


2685
#2
M4
−9q
−
+
−
−
−
−


2689
#2
M4
NN
−
−
−
−
−
−


2498
#2
M4
t(6; 9)
+
−
−
−
−
−


2183
#2
M4
NN
+
−
−
−
−
−


2214
#2
M5
NN
+
+
−
−
−
−


2201
#2
M5
NN
+
−
−
−
−
−


3100
#2
M1
NN
+
−
−
−
−
−


2672
#2
M5
NN
+
+
−
−
−
−


2195
#2
M4
NN
+
−
−
−
−
−


1747
#2
M2
NN
+
−
−
−
−
−


2774
#2
M4
NN
+
−
−
−
−
ND


1551
#2
M1
NN
+
−
−
−
−
−


2194
#2
M4
NN
+
−
−
−
−
+


2182
#2
M5
+8
+
−
−
−
−
−
















TABLE 8







Characteristics of cluster #3 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22),


3q abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2480
#3
M1
NN
+
−
−
−
−
−


3099
#3
M2
NN
+
−
−
−
−
−


2236
#3
M1
NN
+
−
−
−
−
−


3331
#3
M2
NN
+
−
−
−
−
−


2177
#3
M2
NN
+
−
−
−
−
−


2306
#3
M1
NN
−
−
−
−
−
−


2286
#3
M1
NN
+
−
−
−
−
−


2754
#3
M1
NN
+
−
−
−
−
−


3320
#3
M1
NN
+
−
−
−
−
−


2326
#3
M2
t(9; 22)
−
−
−
−
+
−


2270
#3
M1
+8/Other
−
+
−
−
−
−


2241
#3
M4
NN
−
ND
−
−
−
−


2288
#3
M4
−7/11q23
−
−
−
−
+
−


2205
#3
M2
t(6; 9)/Other
−
−
−
−
−
−


2665
#3
M5
t(6; 9)
+
−
−
−
−
−


2257
#3
M1
NN
−
−
−
−
−
−


2271
#3
M2
NN
−
+
−
−
−
−


2299
#3
M2
+21
−
+
−
−
−
−


2676
#3
M2
ND
+
−
−
−
−
−
















TABLE 9







Characteristics of cluster #4 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22), 3q


abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





3327
#4
M1
NN
−
−
−
−
−
−


2242
#4
M1
−9q
−
−
−
−
−
+


2668
#4
M0
Complex
−
−
−
−
−
−


2238
#4
M1
NN
−
−
−
−
−
−


3314
#4
ND
Complex(+8, +11)
−
−
−
−
−
−


2686
#4
M1
NN
−
−
−
−
−
+


3483
#4
M1
Other
−
−
−
−
−
−


3491
#4
M1
NN
−
−
−
−
−
−


2218
#4
M1
NN/11q23 (sMLL)
−
−
−
−
−
+


1316
#4
M1
NN
+
−
−
−
−
+


2273
#4
M1
NN
−
−
−
−
−
+


2545
#4
M1
NN
−
−
−
−
−
−


2169
#4
M1
NN
−
−
+
−
−
+


2753
#4
M1
−9q
−
−
−
−
−
+


2192
#4
M1
NN
−
−
−
−
−
+
















TABLE 10







Characteristics of cluster #5 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22), 3q


abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





3301
#5
M5
−5/7(q)
−
+
+
−
+
−


2228
#5
M4
NN
−
−
+
−
+
−


2272
#5
M5
+8/Other
+
−
−
−
−
−


2525
#5
M5
NN
−
−
ND
ND
−
−


2655
#5
M4
ND
−
−
−
+
−
−


2278
#5
M5
NN
−
−
−
−
−
−


2283
#5
M4
+8/Other
−
−
−
−
−
−


2279
#5
M4
NN
−
−
−
−
−
−


2259
#5
M4
Complex
−
−
−
−
−
−


2220
#5
M5
+11
−
−
−
−
−
−


3490
#5
M5
Other
−
−
−
−
−
−


2217
#5
M5
+8/Other
−
+
−
−
−
+


3486
#5
M4
NN
−
−
−
−
−
−


3097
#5
M4
+8/Other
−
−
−
−
−
−


2687
#5
M5
NN
−
−
−
−
−
−


3325
#5
M4
NN
−
−
−
−
−
−


2467
#5
M5
ND
−
−
−
−
−
−


2244
#5
M5
+8/3q/Other
−
−
−
+
−
−


2282
#5
M4
NN
−
−
−
−
−
−


2771
#5
M5
NN
−
+
−
−
−
−


2185
#5
M5
NN
+
−
−
−
−
−


3484
#5
M4
NN
−
−
−
−
−
−


2191
#5
ND
NN
−
−
−
+
−
−


3321
#5
M5
+8
+
−
−
−
−
−


3493
#5
M5
Other
−
−
−
−
−
−


2296
#5
M5
NN
+
−
−
−
−
−


2231
#5
M4
NN
+
−
−
−
−
−


2227
#5
M5
NN/11q23 (sMLL)
−
+
−
−
−
−


2275
#5
M5
NN
+
−
−
−
−
−


2692
#5
M5
NN
+
−
−
−
−
−


2174
#5
M5
NN
−
−
+
−
−
−


2669
#5
M5
NN
+
−
−
−
−
−


2175
#5
M5
NN
−
−
−
−
−
−


2291
#5
M5
+8
−
+
−
−
−
−


2670
#5
M5
t(6; 9)
+
−
−
−
−
−


2289
#5
M5
NN
+
+
−
−
−
−


2181
#5
M5
NN
+
−
−
−
−
−


2198
#5
M5
NN
−
−
−
−
−
−


3482
#5
M5
NN
+
−
−
−
−
−


1482
#5
M4
NN
−
−
+
+
−
−


2176
#5
M4
NN
+
−
−
−
−
−


2305
#5
M5
NN
+
−
−
−
−
−


2534
#5
M2
Complex
−
−
−
−
−
−


1197
#5
M0
Complex
−
−
−
−
−
−
















TABLE 11







Characteristics of cluster #6 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22),


3q abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2683
#6
M2
NN
+
−
−
−
−
−


1063
#6
M1
NN
+
−
−
+
−
−


3333
#6
M2
NN
+
−
−
+
−
−


2248
#6
M1
NN
+
−
−
−
−
−


2203
#6
M1
NN
+
−
−
−
−
−


2679
#6
M2
NN
+
−
−
−
−
−


2644
#6
M1
NN
+
−
−
−
−
−


2173
#6
M1
ND
+
+
−
−
−
−
















TABLE 12







Characteristics of cluster #7 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22), 3q


abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





3310
#7
M2
NN
−
−
−
−
−
−


3098
#7
M3
NN
−
−
−
−
−
−


2199
#7
M1
NN
+
−
−
−
−
−


2769
#7
M1
NN
−
−
−
−
−
−


2268
#7
M1
NN
+
−
−
−
−
−


2507
#7
M2
NN
+
−
−
−
−
−


3489
#7
M2
Other
−
−
−
−
−
−


2284
#7
M6
NN
−
−
−
−
−
−


2246
#7
M1
NN
−
−
−
−
−
−


2224
#7
M6
Other
−
−
−
−
−
−


2490
#7
M6
NN
+
−
−
−
−
−


3319
#7
M5
NN
−
−
−
−
−
−


3334
#7
ND
Other
−
−
−
−
−
−


2544
#7
M2
+8/Other
−
−
−
−
−
−


2251
#7
M2
Complex(3q/+8)
−
−
−
−
−
−


2222
#7
M1
NN
−
−
−
−
+
−


2252
#7
M2
NN
−
−
−
−
−
−


3293
#7
M3
ND
−
−
−
−
+
−
















TABLE 13







Characteristics of cluster #8 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22),


3q abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2223
#8
M2
+21
−
−
−
−
−
−


2514
#8
M5
Complex (−7(q)/+8)
−
−
−
−
−
−


3318
#8
M2
Complex
−
−
−
−
−
−





(11q23 (t(8; 11)), −5, 3q)


3481
#8
ND
+11/Other
−
−
−
−
−
−


3485
#8
M2
NN
−
−
−
−
−
−


3315
#8
ND
+8, −7(q)
−
−
+
−
−
−


2256
#8
M2
NN
−
−
−
−
−
−


3326
#8
M2
inv7(q)/other
−
−
−
−
−
−


2656
#8
M2
−7
−
−
−
−
−
−


2543
#8
M2
NN
−
−
−
−
−
−


2290
#8
M2
Other
−
−
−
−
−
−


2304
#8
M0
Other
−
−
−
−
−
−


2756
#8
M2
NN
−
−
−
−
−
−
















TABLE 14







Characteristics of cluster #9 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22), 3q


abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, BP: inv(16) breakpoint, RT: real-time PCR for CBF


β-MYH11 (Primer CBFβ 5′-AAGACTGGATGGTATGGGCTGT-3′


(sense), Primer 126REV 5′-CAGGGCCCGCTTGGA-3′ (antisense),


Probe CBFβ 6-FAM 5′-TGGAGTTTGATGAGGAGCGAGCCC-3′


TAMRA); FLT3 ITD: internal tandem duplication in FLT3; FLT3 TKD:


tyrosine kinase domain mutation in FLT3; N- or K-RAS: mutation in codon


12, 13 or 61 of N- or K-RAS; EVI1: EVI1 overexpression; CEPBA:


mutation in CEBPA, ND: not determined).


















Patient
Cluster
FAB
Karyotype
BP
RT
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





3277
#9
M1
idt(16)
A
+
−
−
−
−
−
−


3286
#9
M4
idt(16)
A
+
−
−
+
−
−
−


3309
#9
M4
idt(16)/−7(q)
A
+
−
+
+
−
−
−


3115
#9
M5
idt(16)
A
+
−
−
−
−
−
−


2235
#9
M4
idt(16)
A
+
−
−
−
−
−
−


2293
#9
M4
idt(16)
A
+
−
−
−
−
−
−


2696
#9
M4
NN
A
+
−
−
+
−
−
−


3324
#9
M5
idt(16)
A
+
−
−
−
−
−
−


2647
#9
M4
idt(16)
A
+
−
+
−
−
−
−


2172
#9
M4
NN
A
+
−
+
+
−
−
−


2254
#9
M4
idt(16)
A
+
−
−
−
−
−
−


2287
#9
M4
idt(16)
D
+
−
+
−
−
−
−


2189
#9
M4
idt(16)
A
+
−
−
+
−
−
−


2766
#9
M4
idt(16)
A
+
−
+
−
−
−
−


2249
#9
M5
−7(q)
A
+
−
+
−
−
−
−


2215
#9
M4
idt(16)/+8
A
+
−
−
+
−
−
−


2678
#9
M4
idt(16)
A
+
−
−
−
ND
−
−


2202
#9
M4
idt(16)
A
+
−
−
+
−
−
−


3487
#9
ND
idt(16)
A
+
−
−
−
+
−
−


3329
#9
M4
idt(16)
A
+
−
−
−
−
−
−


2274
#9
M4
NN
A
+
−
−
−
−
−
−


2750
#9
M2
idt(16)/+8
A
+
−
−
−
−
−
−


3285
#9
M4
idt(16)
A
+
−
−
+
−
−
−
















TABLE 15







Characteristics of cluster #10 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22),


3q abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2661
#10
M4
ND
−
−
−
−
+
−


3102
#10
M2
−7
−
−
−
−
+
−


2747
#10
M5
−7/3q
−
−
−
−
+
−


2327
#10
M2
−7(q)
+
−
−
−
+
−


2551
#10
M5
Other
−
−
−
−
+
−


2276
#10
M0
Other
−
−
−
−
+
−


2226
#10
M1
+11
−
−
+
−
−
−


3308
#10
M1
t(9; 22)
−
+
−
−
−
−


2546
#10
M1
+8
−
−
−
−
−
−


2757
#10
M5
−5
−
−
−
−
−
−


3313
#10
M0
Other
−
−
−
−
−
−


2664
#10
M0
−7/3q
−
−
+
−
+
−


2666
#10
M5
ND
−
−
−
−
+
−


1188
#10
M1
−7(q)
−
−
−
−
−
−


2550
#10
M1
Other
−
−
−
−
−
+


2539
#10
ND
ND
−
−
−
−
−
−


2250
#10
M1
−7
−
−
−
−
+
−


2773
#10
M2
NN
+
−
+
−
−
−


2186
#10
M5
−7
−
−
−
−
+
−


2301
#10
M1
NN
+
−
−
−
−
−


2497
#10
M1
Other
+
−
−
−
−
−


2247
#10
M1
Other
−
−
−
−
−
−
















TABLE 16







Characteristics of cluster #11 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22),


3q abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2209
#11
M4
Other
−
−
−
−
−
−


3096
#11
M4
NN
−
+
−
−
−
−


2239
#11
M5
Other
−
+
−
−
−
−


2261
#11
M5
NN
−
+
−
−
−
−


1299
#11
M2
NN
+
−
−
−
−
−


1432
#11
M1
NN
−
−
−
−
−
−


3311
#11
M5
NN
−
−
−
−
−
−


1766
#11
ND
NN
−
−
+
−
−
−


2206
#11
M5
NN
−
−
+
−
−
−
















TABLE 17







Characteristics of cluster #12 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22), 3q


abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR for PML-RARα (Primer PML3-for


5′-CCCCAGGAGCCCCGT-3′ (sense), Primer PML-kbr


5′-CCTGCAGGACCTCAGCTCTT-3′(sense), Primer RAR4-rev


5′-AAAGCAAGGCTTGTAGATGCG-3′(antisense), Probe


RARA 6-FAM 5′-AGTGCCCAGCCCTCCCTCGC-3′ TAMRA);


FLT3 ITD: internal tandem duplication in FLT3; FLT3 TKD: tyrosine kinase


domain mutation in FLT3; N- or K-RAS: mutation in codon 12, 13 or 61 of


N- or K-RAS; EVI1: EVI1 overexpression; CEPBA: mutation in CEBPA,


ND: not determined).

















Patient
Cluster
FAB
Karyotype
RT
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2466
#12
M3
t(15; 17)
+
−
−
−
−
−
−


2509
#12
M3
t(15; 17)
+
−
−
−
−
−
−


2219
#12
M3
t(15; 17)
+
−
+
−
−
−
−


2263
#12
M3
t(15; 17)
+
−
−
−
−
−
−


2307
#12
M3
t(15; 17)
+
−
−
−
−
−
−


2510
#12
M3
t(15; 17)
+
−
+
−
−
−
−


2297
#12
M3
t(15; 17)
+
−
+
−
−
−
−


2265
#12
M3
t(15; 17)/Other
+
−
−
−
−
−
−


2266
#12
M3
t(15; 17)/Other
+
−
−
−
−
−
−


3279
#12
M3
t(15; 17)
+
−
−
−
−
−
−


2170
#12
M3
t(15; 17)/Other
+
−
+
−
−
−
−


2680
#12
M2
t(15; 17)
+
+
−
−
−
−
−


2671
#12
M3
t(15; 17)
+
+
−
−
−
−
−


2516
#12
M3
t(15; 17)
+
−
+
−
−
−
−


2468
#12
M3
t(15; 17)
+
+
−
−
−
−
−


3278
#12
M3
t(15; 17)
+
−
−
−
−
−
−


322
#12
M3
Other*
+
+
−
−
−
−
−


2179
#12
M4
t(15; 17)/Other
+
+
−
−
−
−
−


1448
#12
M3
t(15; 17)/+8
+
+
−
−
−
−
−





*Full karyotype of patient 322: 46, XX, add(12)(p1?3).













TABLE 18







Characteristics of cluster #13 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22), 3q


abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR for AML1-ETO (Primer 821 For


5′-TCACTCTGACCATCACTGTCTTCA-3′ (sense), Primer 821 Rev


5′-ATTGTGGAGTGCTTCTCAGTACGAT-3′(antisense), Probe ETO


6-FAM 5′-ACCCACCGCAAGTCGCCACCT-3′ TAMRA); FLT3 ITD:


internal tandem duplication in FLT3; FLT3 TKD: tyrosine kinase domain


mutation in FLT3; N- or K-RAS: mutation in codon 12, 13 or 61 of N- or K-RAS;


EVI1: EVI1 overexpression; CEPBA: mutation in CEBPA, ND: not determined).

















Patient
Cluster
FAB
Karyotype
RT
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2243
#13
M2
t(+8; 21)/Other
+
−
−
−
−
−
+


2658
#13
M4
t(+8; 21)
+
−
−
−
−
−
−


2752
#13
M2
t(+8; 21)
+
−
−
−
−
−
−


2197
#13
M2
t(+8; 21)/Other
+
+
−
−
−
−
−


2245
#13
M2
t(+8; 21)/Other
+
−
+
−
−
−
−


3332
#13
M2
t(+8; 21)
+
−
−
−
−
−
−


2262
#13
M2
t(+8; 21)/Other
+
−
−
−
−
−
−


2178
#13
M2
t(+8; 21)/Other
+
−
−
−
−
−
−


2511
#13
M2
t(+8; 21)/+8/Other
+
−
−
−
−
−
−


2200
#13
M2
t(+8; 21)/Other
+
−
−
−
−
−
−


2208
#13
M2
t(+8; 21)
+
−
−
−
−
−
−


3295
#13
M2
t(+8; 21)
+
−
−
−
−
−
−


2204
#13
M2
t(+8; 21)/Other
+
−
−
+
−
−
−


3292
#13
M2
t(+8; 21)
+
−
−
−
−
−
−


2549
#13
M2
t(+8; 21)/Other
+
−
−
−
−
−
−


2267
#13
M2
t(+8; 21)/Other
+
−
−
−
−
−
−


2695
#13
M1
t(+8; 21)
+
−
−
−
−
−
−


2751
#13
M2
t(+8; 21)/Other
+
−
−
−
+
−
−


2211
#13
M2
t(+8; 21)/Other
+
−
−
−
−
−
−


2764
#13
M2
t(+8; 21)/Other
+
−
−
−
−
−
−


2210
#13
M2
t(+8; 21)/Other
+
−
−
+
−
−
−


2762
#13
M2
t(+8; 21)/Other
+
−
−
+
−
−
−
















TABLE 19







Characteristics of cluster #14 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22), 3q


abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2536
#14
ND
ND
−
−
−
−
−
−


2704
#14
M2
ND
+
−
−
−
−
−


2690
#14
M2
+8/Other
−
−
+
−
−
−


3289
#14
M2
11q23 (ND)
+
−
−
−
−
−


2212
#14
M2
−5(q)
−
−
−
−
−
−


2233
#14
M1
Complex(−5/−7/+8)
−
−
−
−
−
−


1201
#14
M4
Complex
−
+
−
−
−
−


2188
#14
M2
+8
−
−
−
−
−
−


3492
#14
M2
NN
+
+
−
−
−
−


2260
#14
M5
NN
−
−
−
−
−
−
















TABLE 20







Characteristics of cluster #15 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22),


3q abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2767
#15
M1
ND
−
+
−
−
−
−


2748
#15
M4
NN
−
−
−
−
−
+


2240
#15
M1
NN
−
−
−
−
−
+


3101
#15
M2
NN
+
−
+
−
−
+


2234
#15
M2
Other
−
−
−
−
−
+


2230
#15
M2
NN
+
−
−
−
−
−


2253
#15
M2
NN
−
−
−
−
−
+


2237
#15
M1
−7/Other
−
−
−
−
−
−
















TABLE 21







Characteristics of cluster #16 (Patient: patient number, Cluster: cluster


number (2856 probe sets); FAB: FAB subtype of AML; Karyotype: t(15; 17),


t(8; 21), inv(16)/t(16; 16), +8, +11, +21, −5(q), −7(q), t(9; 22), 3q


abnormalities, 11q23 abnormalities (translocation/self fusion (sMLL)),


complex(abnormalities involved) (>3 abnormalities) and normal karyotype


(NN) are indicated, RT: real-time PCR; FLT3 ITD: internal tandem duplication


in FLT3; FLT3 TKD: tyrosine kinase domain mutation in FLT3; N- or K-RAS:


mutation in codon 12, 13 or 61 of N- or KRAS; EVI1: EVI1 overexpression;


CEPBA: mutation in CEBPA, ND: not determined).
















Patient
Cluster
FAB
Karyotype
FLT3 ITD
FLT3 TKD
N-RAS
K-RAS
EVI1
CEBPA





2225
#16
M4
NN
−
−
−
−
−
−


2184
#16
M5
Other
−
−
−
−
−
−


2535
#16
M5
Other
−
−
−
−
−
−


3322
#16
M5
+8/11q23 (t(11; 19)
−
−
−
−
−
−


2285
#16
M5
11q23 (t(9; 11))
−
+
−
−
−
−


3316
#16
M5
Other/11q23 (t(9; 11))
−
−
−
−
−
−


2694
#16
M5
11q23 (t(9; 11))
−
−
−
−
−
−


3317
#16
M5
Other
−
−
−
−
−
−


2749
#16
M5
NN
−
−
−
−
−
−


2281
#16
M1
NN
−
−
−
−
−
−


2541
#16
M5
11q23 (t(9; 11))/−7
−
−
−
−
−
−
















TABLE 22





Frequency and percentage of cytogenetic and molecular abnormalities of all


AML patients within each of the assigned clusters. All patients with a specific


abnormality were considered, irrespective of the presence of additional


abnormalities (NC: patients not assigned to any of the 16 clusters).

















Cluster

















#1
#2
#3
#4
#5
#6
#7
#8
#9









Patients in cluster

















14
17
19
15
44
8
18
13
23





Cytogenetics


t(15; 17)


t(8; 21)


inv(16)/t(16; 16)








19 (83)


+8

 2 (12)
1 (5)
1 (7)
 7 (16)

 2 (11)
 2 (15)
2 (9)


+11
2 (14)


1 (7)
1 (2)


1 (8)


+21


1 (5)




1 (8)


−5







1 (8)


−5(q)


−7


1 (5)

1 (2)


1 (8)


−7(q)







 3 (23)
2 (9)


3q




1 (2)

1 (6)
1 (8)


t(6; 9)

1 (6)
 2 (11)

1 (2)


t(9; 22)


1 (5)


t(11q23)
6 (43)

1 (5)
 2 (13)
1 (2)


1 (8)


complex (>3 abn.)
1 (7) 


 2 (13)
3 (7)

1 (6)
 2 (15)


other non-complex
2 (14)
1 (6)
 2 (11)
 3 (20)
 7 (16)

 4 (22)
 4 (31)


normal
6 (43)
13 (76)
13 (68)
10 (67)
27 (61)
7 (88)
12 (67)
 4 (31)
 3 (13)


ND




2 (5)
1 (13)
1 (6)


Molecular markers


FLT3-ITD
2 (14)
14 (82)
10 (53)
1 (7)
14 (32)
 8 (100)
4 (22)


FLT3-TKD

 3 (18)
 3 (16)

 6 (14)
1 (13)


 6 (26)


N-RAS



1 (7)
4 (9)


1 (8)
 8 (35)


K-RAS
1 (7) 



4 (9)
2 (25)


1 (4)


EVI1
5 (36)

 2 (11)

2 (5)

 2 (11)


CEBPA

1 (6)

 8 (53)
1 (2)












Cluster

















#10
#11
#12
#13
#14
#15
#16
NC
total









Patients in cluster

















22
9
19
22
10
8
11
13
285





Cytogenetics


t(15; 17)


18 (95) 





18 (6) 


t(8; 21)



 22 (100)




22 (8) 


inv(16)/t(16; 16)








19 (7) 


+8
1 (5)

1 (5) 
1 (5)
3 (30)

1 (9)
2 (15)
26 (9) 


+11
1 (5)






1 (8) 
7 (2)


+21








2 (1)


−5
1 (5)



1 (10)



3 (1)


−5(q)




1 (10)



  1 (<1)


−7
 5 (23)



1 (10)
1 (13)
1 (9)
2 (15)
13 (5) 


−7(q)
2 (9)







7 (2)


3q







1 (8) 
4 (1)


t(6; 9)








4 (1)


t(9; 22)
1 (5)







2 (1)


t(11q23)




1 (10)

 5 (45)
2 (15)
19 (7) 


complex (>3 abn.)




2 (20)



11 (4) 


other non-complex
 6 (27)
2 (22)
4 (21)
15 (68)
1 (10)
2 (25)
 4 (36)
3 (23)
60 (21)


normal
2 (9)
7 (78)


2 (20)
5 (63)
 3 (27)
5 (38)
119 (42) 


ND
 3 (14)



2 (20)
1 (13)


10 (4) 


Molecular markers


FLT3-ITD
 4 (18)
1 (11)
6 (32)
1 (5)
3 (30)
2 (25)

8 (62)
78 (27)


FLT3-TKD
1 (5)
3 (33)
5 (26)
1 (5)
2 (20)
1 (13)
1 (9)

33 (12)


N-RAS
 3 (14)
2 (22)

 3 (14)
1 (10)
1 (13)

2 (15)
26 (9) 


K-RAS



1 (5)




9 (3)


EVI1
10 (45)






2 (15)
23 (8) 


CEBPA
1 (5)


1 (5)

5 (63)


17 (6) 
















TABLE 23







Top 40 genes of cluster #1














Locus


q-value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















220014_at
LOC51334
51334
NM_016644.1
7.09
1.96


206762_at
KCNA5
3741
NM_002234.1
6.68
1.96


213094_at
GPR126
57211
AL033377
6.18
1.96


218502_s_at
TRPS1
7227
NM_014112.1
5.95
1.96


221530_s_at
BHLHB3
79365
AB044088.1
5.63
1.96


221884_at
EVI1
2122
BE466525
5.40
1.96


203642_s_at
KIAA0977
22837
NM_014900.1
4.96
1.96


212827_at
IGHM
3507
X17115.1
4.85
1.96


205612_at
MMRN
22915
NM_007351.1
4.72
1.96


209200_at
MEF2C
4208
N22468
4.59
1.96


214255_at
ATP10A
57194
AB011138.1
4.41
1.96


201539_s_at
FHL1
2273
U29538.1
4.37
1.96


205717_x_at
PCDHGC3
5098
NM_002588.1
4.29
1.96


222144_at
KIF17
57576
AA909345
4.25
1.96


219922_s_at
LTBP3
4054
NM_021070.1
4.21
1.96


215836_s_at
PCDHGC3
5098
AK026188.1
4.20
1.96


205861_at
SPIB
6689
NM_003121.1
4.15
1.96


203372_s_at
SOCS2
8835
AB004903.1
4.12
1.96


209079_x_at
PCDHGC3
5098
AF152318.1
4.11
1.96


215811_at
—
—
AF238870.1
4.09
1.96


209199_s_at
MEF2C
4208
N22468
4.08
1.96


207655_s_at
BLNK
29760
NM_013314.1
4.05
1.96


203716_s_at
DPP4
1803
M80536.1
4.03
1.96


219737_s_at
—
—
AI524125
4.01
1.96


204304_s_at
PROM1
8842
NM_006017.1
3.97
1.96


203373_at
SOCS2
8835
NM_003877.1
3.95
1.96


218237_s_at
SLC38A1
81539
NM_030674.1
3.87
1.96


202265_at
BMI1
648
NM_005180.1
3.86
1.96


210298_x_at
FHL1
2273
AF098518.1
3.83
1.96


208436_s_at
IRF7
3665
NM_004030.1
3.77
1.96


210032_s_at
SPAG6
9576
AI651156
3.77
1.96


222088_s_at
SLC2A14
144195
AA778684
−3.76
1.96


204621_s_at
NR4A2
4929
AI935096
−3.80
1.96


216248_s_at
NR4A2
4929
S77154.1
−3.84
1.96


216236_s_at
SLC2A14
144195
AL110298.1
−3.85
1.96


204622_x_at
NR4A2
4929
NM_006186.1
−3.85
1.96


202497_x_at
SLC2A3
6515
NM_006931.1
−3.91
1.96


201464_x_at
JUN
3725
BG491844
−3.92
1.96


202672_s_at
ATF3
467
NM_001674.1
−4.11
1.96
















TABLE 24







Top 40 genes of cluster #2














Locus


q-value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















207034_s_at
GLI2
2736
NM_030379.1
10.30
1.04


206341_at
IL2RA
3559
NM_000417.1
9.15
1.04


211269_s_at
IL2RA
3559
K03122.1
8.24
1.04


215288_at
TRPC2
7221
AI769824
7.44
1.04


205190_at
PLS1
5357
NM_002670.1
7.34
1.04


210145_at
PLA2G4A
5321
M68874.1
7.31
1.04


204341_at
TRIM16
10626
NM_006470.1
7.23
1.04


206574_s_at
PTP4A3
11156
NM_007079.1
7.01
1.04


203187_at
DOCK1
1793
NM_001380.1
6.48
1.04


219615_s_at
KCNK5
8645
NM_003740.1
6.29
1.04


212276_at
LPIN1
23175
D80010.1
6.05
1.04


206298_at
RhoGAP2
58504
NM_021226.1
5.82
1.04


207533_at
CCL1
6346
NM_002981.1
5.69
1.04


206582_s_at
GPR56
9289
NM_005682.1
5.41
1.04


208797_s_at
GOLGIN-67
23015
AI829170
5.37
1.04


205453_at
HOXB2
3212
NM_002145.1
5.12
1.04


212070_at
GPR56
9289
AL554008
5.01
1.04


209409_at
GRB10
2887
D86962.1
4.99
1.04


210425_x_at
GOLGIN-67
23015
AF164622.1
4.97
1.04


208767_s_at
LAPTM4B
55353
AW149681
4.95
1.04


221942_s_at
GUCY1A3
2982
AI719730
4.95
1.04


209193_at
PIM1
5292
M24779.1
4.94
1.04


204030_s_at
SCHIP1
29970
NM_014575.1
4.89
1.04


213844_at
HOXA5
3202
NM_019102.1
4.74
1.04


208798_x_at
GOLGIN-67
23015
AF204231.1
4.70
1.04


216268_s_at
JAG1
182
U77914.1
4.68
1.04


208792_s_at
CLU
1191
M25915.1
4.60
1.04


217414_x_at
—
—
V00489
−4.62
1.04


211699_x_at
HBA1
3039
AF349571.1
−4.67
1.04


217232_x_at
—
—
AF059180
−4.71
1.04


209116_x_at
HBB
3043
M25079.1
−4.71
1.04


214414_x_at
HBA1
3039
T50399
−4.72
1.04


211696_x_at
HBB
3043
AF349114.1
−4.72
1.04


211745_x_at
HBA1
3039
BC005931.1
−4.75
1.04


204018_x_at
HBA1
3039
NM_000558.2
−4.83
1.04


208623_s_at
VIL2
7430
J05021.1
−4.91
1.04


209458_x_at
HBA1
3039
AF105974.1
−4.96
1.04


214582_at
PDE3B
5140
NM_000753.1
−5.29
1.04


213152_s_at
—
—
AI343248
−5.39
1.04


206571_s_at
MAP4K4
9448
NM_004834.1
−6.87
1.04
















TABLE 25







Top 40 genes of cluster #3














Locus


q-value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















206950_at
SCN9A
6335
NM_002977.1
10.09
0.21


205848_at
GAS2
2620
NM_005256.1
8.63
0.21


207533_at
CCL1
6346
NM_002981.1
8.56
0.21


205190_at
PLS1
5357
NM_002670.1
7.94
0.21


213110_s_at
COL4A5
1287
AW052179
7.51
0.21


208767_s_at
LAPTM4B
55353
AW149681
7.09
0.21


206298_at
RhoGAP2
58504
NM_021226.1
7.07
0.21


208029_s_at
LAPTM4B
55353
NM_018407.1
7.05
0.21


204044_at
QPRT
23475
NM_014298.2
7.04
0.21


202889_x_at
ANPEP
9053
T62571
6.84
0.21


217975_at
LOC51186
51186
NM_016303.1
6.81
0.21


201664_at
SMC4L1
10051
AL136877.1
6.81
0.21


210116_at
SH2D1A
4068
AF072930.1
6.74
0.21


213217_at
ADCY2
108
AU149572
6.53
0.21


204160_s_at
ENPP4
22875
AW194947
6.48
0.21


204341_at
TRIM16
10626
NM_006470.1
6.42
0.21


214039_s_at
LAPTM4B
55353
T15777
6.41
0.21


206582_s_at
GPR56
9289
NM_005682.1
6.28
0.21


202890_at
MAP7
9053
T62571
6.28
0.21


215471_s_at
MAP7
9053
AJ242502.1
6.23
0.21


219602_s_at
FLJ23403
63895
NM_022068.1
6.20
0.21


219304_s_at
SCDGF-B
80310
NM_025208.1
6.05
0.21


203187_at
DOCK1
1793
NM_001380.1
6.03
0.21


215388_s_at
HFL1
3078
X56210.1
6.00
0.21


201663_s_at
SMC4L1
10051
NM_005496.1
6.00
0.21


214228_x_at
TNFRSF4
7293
AJ277151
5.96
0.21


201427_s_at
SEPP1
6414
NM_005410.1
5.94
0.21


207838_x_at
PBXIP1
57326
NM_020524.1
5.92
0.21


201829_at
NET1
10276
AW263232
5.85
0.21


220377_at
C14orf110
29064
NM_014151.1
5.85
0.21


203973_s_at
KIAA0146
23514
NM_005195.1
−5.88
0.21


205707_at
IL17R
23765
NM_014339.1
−5.95
0.21


212195_at
IL6ST
3572
AL049265.1
−6.03
0.21


206034_at
SERPINB8
5271
NM_002640.1
−6.11
0.21


203773_x_at
BLVRA
644
NM_000712.1
−6.71
0.21


221830_at
RAP2A
5911
AI302106
−6.94
0.21


218831_s_at
FCGRT
2217
NM_004107.1
−7.10
0.21


211729_x_at
BLVRA
644
BC005902.1
−7.18
0.21


204500_s_at
AGTPBP1
23287
NM_015239.1
−8.15
0.21


212543_at
AIM1
202
U83115.1
−8.19
0.21
















TABLE 26







Top 40 genes of cluster #4














Locus


q-value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















216286_at
—
—
AV760769
13.34
0.11


216191_s_at
TRD@
6964
X72501.1
13.01
0.11


206232_s_at
B4GALT6
9331
NM_004775.1
12.59
0.11


213830_at
TRD@
6964
AW007751
11.85
0.11


211682_x_at
UGT2B28
54490
AF177272.1
11.60
0.11


219383_at
FLJ14213
79899
NM_024841.1
11.57
0.11


217143_s_at
TRD@
6964
X06557.1
11.55
0.11


214551_s_at
CD7
924
NM_006137.2
11.22
0.11


214049_x_at
CD7
924
AI829961
11.04
0.11


213910_at
IGFBP7
3490
AW770896
10.85
0.11


207996_s_at
C18orf1
753
NM_004338.1
10.65
0.11


220567_at
ZNFN1A2
22807
NM_016260.1
10.27
0.11


209994_s_at
ABCB1
5243
AF016535.1
9.90
0.11


206233_at
B4GALT6
9331
AF097159.1
9.66
0.11


217147_s_at
TRIM
50852
AJ240085.1
9.44
0.11


209993_at
ABCB1
5243
AF016535.1
9.40
0.11


210448_s_at
P2RX5
5026
U49396.1
9.36
0.11


216525_x_at
PMS2L9
5387
D38437.1
9.20
0.11


54037_at
HPS4
89781
AL041451
9.16
0.11


206726_at
PGDS
27306
NM_014485.1
8.79
0.11


202242_at
TM4SF2
7102
NM_004615.1
8.79
0.11


203987_at
FZD6
8323
NM_003506.1
8.63
0.11


214757_at
—
—
BG178274
8.50
0.11


205884_at
ITGA4
3676
NM_000885.2
8.49
0.11


213416_at
ITGA4
3676
BG532690
8.37
0.11


218627_at
FLJ11259
55332
NM_018370.1
−8.51
0.11


208923_at
CYFIP1
23191
BC005097.1
−8.75
0.11


219371_s_at
KLF2
10365
NM_016270.1
−8.95
0.11


203233_at
IL4R
3566
NM_000418.1
−8.96
0.11


205382_s_at
DF
1675
NM_001928.1
−8.98
0.11


208683_at
CAPN2
824
M23254.1
−9.08
0.11


201160_s_at
CSDA
8531
AL556190
−9.13
0.11


201412_at
LRP10
26020
NM_014045.1
−9.19
0.11


202252_at
RAB13
5872
NM_002870.1
−9.25
0.11


217800_s_at
NDFIP1
80762
NM_030571.1
−9.98
0.11


202241_at
C8FW
10221
NM_025195.1
−10.41
0.11


209191_at
TUBB-5
84617
BC002654.1
−10.60
0.11


200765_x_at
CTNNA1
1495
NM_001903.1
−14.35
0.11


200764_s_at
CTNNA1
1495
AI826881
−15.70
0.11


210844_x_at
CTNNA1
1495
D14705.1
−15.91
0.11
















TABLE 27







Top 40 genes of cluster #5












Probe Set
Gene
Locus Link
Accession
Score
q-value SAM


ID
symbol
number
number
SAM
(%)















206710_s_at
EPB41L3
23136
NM_012307.1
21.03
0.05


207872_s_at
LILRB1
10859
NM_006863.1
19.91
0.05


211776_s_at
EPB41L3
23136
BC006141.1
19.65
0.05


206934_at
SIRPB1
10326
NM_006065.1
19.55
0.05


219788_at
PILRA
29992
NM_013439.1
17.93
0.05


204392_at
CAMK1
8536
NM_003656.2
17.41
0.05


219872_at
DKFZp434L142
51313
NM_016613.1
17.11
0.05


212681_at
EPB41L3
23136
AI770004
17.04
0.05


214590_s_at
UBE2D1
7321
AL545760
15.87
0.05


204254_s_at
VDR
7421
NM_000376.1
15.69
0.05


203767_s_at
STS
412
AU138166
15.64
0.05


207224_s_at
SIGLEC7
27036
NM_016543.1
15.61
0.05


206278_at
PTAFR
5724
D10202.1
15.55
0.05


204619_s_at
CSPG2
1462
BF590263
15.07
0.05


219593_at
PHT2
51296
NM_016582.1
15.04
0.05


220832_at
TLR8
51311
NM_016610.1
14.94
0.05


210146_x_at
LILRB3
11025
AF004231.1
14.91
0.05


222218_s_at
PILRA
29992
AJ400843.1
14.71
0.05


203768_s_at
STS
412
AU138166
14.70
0.05


204858_s_at
ECGF1
1890
NM_001953.2
14.70
0.05


210660_at
LILRB1
10859
AF025529.1
14.70
0.05


211732_x_at
HNMT
3176
BC005907.1
14.69
0.05


217992_s_at
MGC4342
79180
NM_024329.1
14.67
0.05


204487_s_at
KCNQ1
3784
NM_000218.1
14.66
0.05


201642_at
IFNGR2
3460
NM_005534.1
14.58
0.05


220066_at
CARD15
64127
NM_022162.1
14.53
0.05


207104_x_at
LILRB1
10859
NM_006669.1
14.46
0.05


205685_at
CD86
942
BG236280
14.21
0.05


205686_s_at
CD86
942
NM_006889.1
14.15
0.05


203769_s_at
STS
412
NM_000351.2
14.05
0.05


212334_at
GNS
2799
AW167793
14.03
0.05


221578_at
RASSF4
83937
AF260335.1
14.00
0.05


218559_s_at
MAFB
9935
NM_005461.1
13.99
0.05


213624_at
ASM3A
10924
AA873600
13.96
0.05


211135_x_at
LILRB3
11025
AF009644.1
13.91
0.05


208594_x_at
LILRB3
11025
NM_024318.1
13.90
0.05


200866_s_at
PSAP
5660
M32221.1
13.89
0.05


205099_s_at
CCR1
1230
NM_001295.1
13.87
0.05


202895_s_at
EPHB4
140885
D86043.1
13.85
0.05


50221_at
TFEB
7942
AI524138
13.81
0.05
















TABLE 28







Top 40 genes of cluster #6












Probe Set
Gene
Locus Link
Accession
Score
q-value SAM


ID
symbol
number
number
SAM
(%)















221880_s_at
—
—
AI279819
12.39
0.85


51158_at
—
—
AI801973
10.99
0.85


219511_s_at
SNCAIP
9627
NM_005460.1
8.81
0.85


209702_at
FTO
79068
U79260.1
8.51
0.85


221959_at
MGC39325
90362
AK026141.1
8.40
0.85


204984_at
GPC4
2239
NM_001448.1
8.34
0.85


204983_s_at
GPC4
2239
AF064826.1
8.25
0.85


212019_at
DKFZP564M182
26156
AK025446.1
7.56
0.85


215807_s_at
PLXNB1
5364
AV693216
7.42
0.85


219602_s_at
FLJ23403
63895
NM_022068.1
6.93
0.85


218710_at
FLJ20272
55622
NM_017735.1
6.80
0.85


213217_at
ADCY2
108
AU149572
6.78
0.85


219651_at
FLJ10713
55211
NM_018189.1
6.78
0.85


202728_s_at
LTBP1
4052
AI986120
6.64
0.85


206377_at
FOXF2
2295
NM_001452.1
6.60
0.85


219932_at
VLCS-H1
28965
NM_014031.1
6.31
0.85


213260_at
FOXC1
2296
AU145890
6.23
0.85


215623_x_at
SMC4L1
10051
AK002200.1
6.19
0.85


201431_s_at
DPYSL3
1809
NM_001387.1
6.18
0.85


208414_s_at
HOXB4
3214
NM_002146.1
6.17
0.85


218786_at
—
—
NM_016575.1
6.16
0.85


204750_s_at
DSC2
1824
BF196457
6.16
0.85


219036_at
BITE
80321
NM_024491.1
6.13
0.85


215388_s_at
HFL1
3078
X56210.1
6.12
0.85


220898_at
—
—
NM_024972.1
6.08
0.85


215573_at
CAT
847
AU147084
6.04
0.85


204751_x_at
DSC2
1824
NM_004949.1
6.01
0.85


202729_s_at
LTBP1
4052
NM_000627.1
5.97
0.85


213266_at
—
—
BF592982
5.61
0.85


201641_at
BST2
684
NM_004335.2
−5.55
0.85


215193_x_at
HLA-DRB1
3123
AJ297586.1
−5.56
0.85


209619_at
CD74
972
K01144.1
−5.58
0.85


208982_at
PECAM1
5175
AW574504
−5.62
0.85


210982_s_at
HLA-DRA
3122
M60333.1
−5.68
0.85


211990_at
HLA-DPA1
3113
M27487.1
−5.84
0.85


217118_s_at
KIAA0930
23313
AK025608.1
−5.87
0.85


205672_at
XPA
7507
NM_000380.1
−6.10
0.85


217845_x_at
HIG1
25994
NM_014056.1
−6.41
0.85


204319_s_at
RGS10
6001
NM_002925.2
−6.69
0.85


209083_at
CORO1A
11151
U34690.1
−6.97
0.85
















TABLE 29







Top 40 genes of cluster #7












Probe Set
Gene
Locus Link
Accession
Score
q-value SAM


ID
symbol
number
number
SAM
(%)















206116_s_at
TPM1
7168
NM_000366.1
15.29
0.11


207854_at
GYPE
2996
NM_002102.1
13.28
0.11


221577_x_at
PLAB
9518
AF003934.1
12.76
0.11


56748_at
TRIM10
10107
X90539
12.56
0.11


205390_s_at
ANK1
286
NM_000037.2
11.78
0.11


204720_s_at
DNAJC6
9829
AV729634
11.68
0.11


206146_s_at
RHAG
6005
AF178841.1
11.40
0.11


216054_x_at
MYL4
4635
X58851
11.18
0.11


210088_x_at
MYL4
4635
M36172.1
11.16
0.11


205391_x_at
ANK1
286
M28880.1
11.09
0.11


207043_s_at
SLC6A9
6536
NM_006934.1
11.08
0.11


218864_at
TNS
7145
AF116610.1
10.98
0.11


203911_at
RAP1GA1
5909
NM_002885.1
10.94
0.11


214530_x_at
EPB41
2035
AF156225.1
10.93
0.11


206647_at
HBZ
3050
NM_005332.2
10.90
0.11


211254_x_at
RHAG
6005
AF031549.1
10.88
0.11


207087_x_at
ANK1
286
NM_020478.1
10.84
0.11


208352_x_at
ANK1
286
NM_020479.1
10.83
0.11


219630_at
MAP17
10158
NM_005764.1
10.71
0.11


208416_s_at
SPTB
6710
NM_000347.2
10.70
0.11


208353_x_at
ANK1
286
NM_020480.1
10.70
0.11


205262_at
KCNH2
3757
NM_000238.1
10.67
0.11


210395_x_at
MYL4
4635
AF116676.1
10.65
0.11


210586_x_at
RHD
6007
AF312679.1
10.64
0.11


210854_x_at
SLC6A8
6535
U17986.1
10.61
0.11


220751_s_at
C5orf4
10826
NM_016348.1
10.60
0.11


216063_at
—
—
N55205
10.60
0.11


217274_x_at
—
—
X52005.1
10.53
0.11


206145_at
RHAG
6005
NM_000324.1
10.51
0.11


213843_x_at
SLC6A8
6535
AW276522
10.48
0.11


206077_at
KEL
3792
NM_000420.1
10.47
0.11


216925_s_at
TAL1
6886
X51990.1
10.42
0.11


221237_s_at
OSBP2
23762
NM_030758.1
10.37
0.11


212804_s_at
DKFZP434C212
26130
AK023841.1
10.27
0.11


207793_s_at
EPB41
2035
NM_004437.1
10.24
0.11


205389_s_at
ANK1
286
AI659683
10.21
0.11


201249_at
SLC2A1
6513
NM_006516.1
10.20
0.11


214433_s_at
SELENBP1
8991
NM_003944.1
10.18
0.11


218978_s_at
MSCP
51312
NM_018586.1
10.13
0.11


201733_at
CLCN3
1182
NM_001829.1
10.12
0.11
















TABLE 30







Top 40 genes of cluster #8














Locus


q-value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















213338_at
RIS1
25907
BF062629
12.86
0.17


201131_s_at
CDH1
999
NM_004360.1
12.12
0.17


209735_at
ABCG2
9429
AF098951.2
11.01
0.17


202073_at
OPTN
10133
AV757675
10.88
0.17


40093_at
LU
4059
X83425
10.45
0.17


212151_at
PBX1
5087
BF967998
10.14
0.17


201333_s_at
ARHGEF12
23365
NM_015313.1
9.95
0.17


210430_x_at
RHD
6007
L08429.1
9.72
0.17


205391_x_at
ANK1
286
M28880.1
9.53
0.17


221237_s_at
OSBP2
23762
NM_030758.1
9.53
0.17


214464_at
CDC42BPA
8476
NM_003607.1
9.44
0.17


220751_s_at
C5orf4
10826
NM_016348.1
9.42
0.17


202364_at
MXI1
4601
NM_005962.1
9.29
0.17


205837_s_at
GYPA
2993
BC005319.1
9.22
0.17


208353_x_at
ANK1
286
NM_020480.1
9.20
0.17


202125_s_at
ALS2CR3
66008
NM_015049.1
9.10
0.17


217572_at
—
—
AA654586
9.06
0.17


211649_x_at
—
—
L14456.1
9.04
0.17


205838_at
GYPA
2993
NM_002099.2
9.04
0.17


202219_at
SLC6A8
6535
NM_005629.1
9.03
0.17


216925_s_at
TAL1
6886
X51990.1
8.98
0.17


203794_at
CDC42BPA
8476
NM_014826.1
8.96
0.17


211820_x_at
GYPA
2993
U00179.1
8.95
0.17


218864_at
TNS
7145
AF116610.1
8.94
0.17


215812_s_at
—
—
U41163
8.90
0.17


202074_s_at
OPTN
10133
NM_021980.1
8.89
0.17


201886_at
WDR23
80344
NM_025230.1
8.86
0.17


216833_x_at
GYPE
2996
U05255.1
8.84
0.17


202124_s_at
ALS2CR3
66008
AV705253
8.84
0.17


216317_x_at
RHCE
6006
X63095.1
8.81
0.17


204467_s_at
SNCA
6622
NM_000345.2
8.80
0.17


207087_x_at
ANK1
286
NM_020478.1
8.78
0.17


213843_x_at
SLC6A8
6535
AW276522
8.78
0.17


210586_x_at
RHD
6007
AF312679.1
8.77
0.17


209890_at
TM4SF9
10098
AF065389.1
8.75
0.17


218853_s_at
DJ473B4
56180
NM_019556.1
8.74
0.17


214433_s_at
SELENBP1
8991
NM_003944.1
8.70
0.17


48031_r_at
C5orf4
10826
H93077
8.70
0.17


208352_x_at
ANK1
286
NM_020479.1
8.69
0.17


203115_at
FECH
2235
AU152635
8.66
0.17
















TABLE 31







Top 40 genes of cluster #9

















q-




Locus


value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















201497_x_at
MYH11
4629
NM_022844.1
89.02
0.18


207961_x_at
MYH11
4629
NM_022870.1
26.72
0.18


212358_at
CLIPR-59
25999
AL117468.1
20.92
0.18


206135_at
ST18
9705
NM_014682.1
19.69
0.18


212298_at
NRP1
8829
BE620457
18.71
0.18


206682_at
CLECSF13
10462
NM_006344.1
15.32
0.18


203060_s_at
PAPSS2
9060
AF074331.1
15.04
0.18


203058_s_at
PAPSS2
9060
AW299958
14.73
0.18


205987_at
CD1C
911
NM_001765.1
12.82
0.18


221019_s_at
COLEC12
81035
NM_030781.1
12.69
0.18


204885_s_at
MSLN
10232
NM_005823.2
12.36
0.18


209396_s_at
CHI3L1
1116
M80927.1
12.06
0.18


219694_at
FLJ11127
54491
NM_019018.1
11.59
0.18


205076_s_at
CRA
10903
NM_006697.1
11.49
0.18


209395_at
CHI3L1
1116
M80927.1
11.07
0.18


219308_s_at
AK5
26289
NM_012093.1
10.88
0.18


207194_s_at
ICAM4
3386
NM_001544.2
10.76
0.18


204787_at
Z39IG
11326
NM_007268.1
10.23
0.18


200665_s_at
SPARC
6678
NM_003118.1
10.18
0.18


201506_at
TGFBI
7045
NM_000358.1
9.99
0.18


212912_at
RPS6KA2
6196
AI992251
9.82
0.18


203939_at
NT5E
4907
NM_002526.1
9.67
0.18


205330_at
MN1
4330
NM_002430.1
9.24
0.18


202481_at
SDR1
9249
NM_004753.1
8.92
0.18


212771_at
LOC221061
221061
AU150943
8.85
0.18


210889_s_at
FCGR2B
2213
M31933.1
8.82
0.18


218876_at
CGI-38
51673
NM_016140.1
8.45
0.18


203329_at
PTPRM
5797
NM_002845.1
8.25
0.18


204197_s_at
RUNX3
864
NM_004350.1
−8.25
0.18


200984_s_at
CD59
966
NM_000611.1
−8.33
0.18


218414_s_at
NDE1
54820
NM_017668.1
−8.42
0.18


213779_at
EMU1
129080
AL031186
−8.56
0.18


204198_s_at
RUNX3
864
AA541630
−8.85
0.18


211026_s_at
MGLL
11343
BC006230.1
−9.01
0.18


219218_at
FLJ23058
79749
NM_024696.1
−9.61
0.18


206788_s_at
CBFB
865
AF294326.1
−9.73
0.18


218927_s_at
CHST12
55501
NM_018641.1
−9.82
0.18


211031_s_at
CYLN2
7461
BC006259.1
−10.24
0.18


202370_s_at
CBFB
865
NM_001755.1
−13.01
0.18


200675_at
CD81
975
NM_004356.1
−14.28
0.18
















TABLE 32







Top 40 genes of cluster #10

















q-




Locus


value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















219145_at
FLJ11939
79732
NM_024679.1
12.59
0.21


202551_s_at
CRIM1
51232
BG546884
11.82
0.21


47560_at
FLJ11939
79732
AI525402
11.75
0.21


209763_at
NRLN1
91851
AL049176
8.99
0.21


200671_s_at
SPTBN1
6711
NM_003128.1
8.75
0.21


213488_at
FLJ00133
25992
AL050143.1
8.75
0.21


204004_at
—
—
AI336206
8.74
0.21


205933_at
SETBP1
26040
NM_015559.1
8.63
0.21


213506_at
F2RL1
2150
BE965369
8.53
0.21


41577_at
PPP1R16B
26051
AB020630
8.52
0.21


209679_s_at
LOC57228
57228
BC003379.1
8.51
0.21


212558_at
GDAP1L1
78997
BF508662
8.43
0.21


207788_s_at
SCAM-1
10174
NM_005775.1
8.42
0.21


204083_s_at
TPM2
7169
NM_003289.1
8.21
0.21


209487_at
RBPMS
11030
D84109.1
8.19
0.21


207836_s_at
RBPMS
11030
NM_006867.1
8.14
0.21


209282_at
PRKD2
25865
AF309082.1
8.14
0.21


209436_at
SPON1
10418
AB018305.1
8.12
0.21


204484_at
PIK3C2B
5287
NM_002646.1
8.11
0.21


212750_at
PPP1R16B
26051
AB020630.1
8.09
0.21


205330_at
MN1
4330
NM_002430.1
8.03
0.21


209576_at
GNAI1
2770
AL049933.1
8.02
0.21


220377_at
C14orf110
29064
NM_014151.1
7.91
0.21


203756_at
P164RHOGEF
9828
NM_014786.1
7.89
0.21


200672_x_at
SPTBN1
6711
NM_003128.1
7.88
0.21


212827_at
IGHM
3507
X17115.1
7.86
0.21


209437_s_at
SPON1
10418
AB051390.1
7.74
0.21


204917_s_at
MLLT3
4300
AV756536
7.59
0.21


204540_at
EEF1A2
1917
NM_001958.1
7.57
0.21


208614_s_at
FLNB
2317
M62994.1
7.40
0.21


204581_at
CD22
933
NM_001771.1
7.29
0.21


218086_at
NPDC1
56654
NM_015392.1
7.25
0.21


209488_s_at
RBPMS
11030
D84109.1
7.21
0.21


218899_s_at
BAALC
79870
NM_024812.1
7.11
0.21


203796_s_at
BCL7A
605
AI950380
7.05
0.21


212071_s_at
SPTBN1
6711
BE968833
6.93
0.21


206111_at
RNASE2
6036
NM_002934.1
−7.00
0.21


209906_at
C3AR1
719
U62027.1
−7.34
0.21


205382_s_at
DF
1675
NM_001928.1
−7.63
0.21


214575_s_at
AZU1
566
NM_001700.1
−7.95
0.21
















TABLE 33







Top 40 genes of cluster #11














Locus


q-value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















209079_x_at
PCDHGC3
5098
AF152318.1
−2.72
1.48


207076_s_at
ASS
445
NM_000050.1
−2.74
1.48


218825_at
EGFL7
51162
NM_016215.1
−2.74
1.48


201522_x_at
SNRPN
6638
NM_003097.2
−2.74
1.48


201601_x_at
IFITM1
8519
NM_003641.1
−2.75
1.48


206042_x_at
SNRPN
6638
NM_022804.1
−2.80
1.48


209583_s_at
MOX2
4345
AF063591.1
−2.81
1.48


204385_at
KYNU
8942
NM_003937.1
−2.84
1.48


218805_at
IAN4L1
55340
NM_018384.1
−2.90
1.48


214953_s_at
APP
351
X06989.1
−2.90
1.48


203859_s_at
PALM
5064
NM_002579.1
−2.97
1.48


203542_s_at
BTEB1
687
BF438302
−2.97
1.48


212171_x_at
VEGF
7422
H95344
−3.03
1.48


218237_s_at
SLC38A1
81539
NM_030674.1
−3.05
1.48


219777_at
hIAN2
79765
NM_024711.1
−3.07
1.48


201656_at
ITGA6
3655
NM_000210.1
−3.13
1.48


208886_at
H1F0
3005
BC000145.1
−3.17
1.48


203139_at
DAPK1
1612
NM_004938.1
−3.18
1.48


31874_at
GAS2L1
10634
Y07846
−3.21
1.48


218966_at
MYO5C
55930
NM_018728.1
−3.22
1.48


216033_s_at
FYN
2534
S74774.1
−3.23
1.48


218589_at
P2RY5
10161
NM_005767.1
−3.24
1.48


217838_s_at
EVL
51466
NM_016337.1
−3.25
1.48


201279_s_at
DAB2
1601
BC003064.1
−3.26
1.48


200762_at
DPYSL2
1808
NM_001386.1
−3.29
1.48


209723_at
SERPINB9
5272
BC002538.1
−3.34
1.48


205101_at
MHC2TA
4261
NM_000246.1
−3.37
1.48


208873_s_at
DP1
7905
BC000232.1
−3.43
1.48


211675_s_at
HIC
29969
AF054589.1
−3.49
1.48


200665_s_at
SPARC
6678
NM_003118.1
−3.50
1.48


213848_at
DUSP7
1849
AI655015
−3.54
1.48


215116_s_at
DNM1
1759
AF035321.1
−3.56
1.48


203217_s_at
SIAT9
8869
NM_003896.1
−3.56
1.48


209543_s_at
CD34
947
M81104.1
−3.57
1.48


201425_at
ALDH2
217
NM_000690.1
−3.63
1.48


201559_s_at
CLIC4
25932
AF109196.1
−4.00
1.48


221223_x_at
CISH
1154
NM_013324.2
−4.36
1.48


212658_at
LHFPL2
10184
N66633
−4.43
1.48


204401_at
KCNN4
3783
NM_002250.1
−4.70
1.48


201560_at
CLIC4
25932
NM_013943.1
−4.95
1.48
















TABLE 34







Top 40 genes of cluster #12












Probe Set
Gene
Locus Link
Accession
Score
q-value SAM


ID
symbol
number
number
SAM
(%)















210997_at
HGF
3082
M77227.1
25.95
0.13


210998_s_at
HGF
3082
M77227.1
24.77
0.13


205110_s_at
FGF13
2258
NM_004114.1
24.76
0.13


210794_s_at
MEG3
55384
AF119863.1
23.54
0.13


204537_s_at
GABRE
2564
NM_004961.2
22.89
0.13


205614_x_at
MST1
4485
NM_020998.1
20.74
0.13


205663_at
PCBP3
54039
NM_020528.1
20.42
0.13


202260_s_at
STXBP1
6812
NM_003165.1
19.36
0.13


216320_x_at
MST1
4485
U37055
18.72
0.13


203074_at
ANXA8
244
NM_001630.1
18.42
0.13


206634_at
SIX3
6496
NM_005413.1
16.41
0.13


210755_at
HGF
3082
U46010.1
16.11
0.13


203397_s_at
GALNT3
2591
BF063271
15.29
0.13


212732_at
MEG3
55384
AI950273
15.24
0.13


207895_at
NAALADASEL
10004
NM_005468.1
14.64
0.13


218043_s_at
AZ2
64343
NM_022461.1
14.17
0.13


209961_s_at
HGF
3082
M60718.1
13.51
0.13


209815_at
na
349352
U43148.1
12.71
0.13


201276_at
RAB5B
5869
AF267863.1
12.44
0.13


212509_s_at
—
—
BF968134
12.27
0.13


207650_x_at
PTGER1
5731
NM_000955.1
11.92
0.13


209960_at
HGF
3082
X16323.1
11.88
0.13


200770_s_at
LAMC1
3915
J03202.1
11.57
0.13


212204_at
DKFZP564G2022
25963
AF132733.1
11.55
0.13


207031_at
BAPX1
579
NM_001189.1
11.44
0.13


211663_x_at
PTGDS
5730
M61900.1
11.33
0.13


206105_at
FMR2
2334
NM_002025.1
11.28
0.13


214203_s_at
PRODH
5625
AA074145
11.27
0.13


200654_at
P4HB
5034
J02783.1
11.24
0.13


200656_s_at
P4HB
5034
NM_000918.1
11.23
0.13


210140_at
CST7
8530
AF031824.1
11.16
0.13


200935_at
CALR
811
NM_004343.2
11.12
0.13


204153_s_at
MFNG
4242
NM_002405.1
−11.33
0.13


202599_s_at
NRIP1
8204
NM_003489.1
−11.33
0.13


200931_s_at
VCL
7414
NM_014000.1
−11.57
0.13


204362_at
SCAP2
8935
NM_003930.1
−11.76
0.13


202600_s_at
NRIP1
8204
AI824012
−11.86
0.13


204152_s_at
MFNG
4242
AI738965
−12.02
0.13


203236_s_at
LGALS9
3965
NM_009587.1
−18.14
0.13


204425_at
ARHGAP4
393
NM_001666.1
−21.49
0.13
















TABLE 35







Top 40 genes of cluster #13












Probe Set
Gene
Locus Link
Accession
Score
q-value SAM


ID
symbol
number
number
SAM
(%)















205529_s_at
CBFA2T1 (ETO)
862
NM_004349.1
60.36
0.14


205528_s_at
CBFA2T1 (ETO)
862
X79990.1
56.08
0.14


216831_s_at
CBFA2T1 (ETO)
862
AF018283.1
26.62
0.14


213194_at
ROBO1
6091
BF059159
24.74
0.14


204811_s_at
CACNA2D2
9254
NM_006030.1
23.53
0.14


206940_s_at
POU4F1
5457
NM_006237.1
21.42
0.14


210744_s_at
IL5RA
3568
M75914.1
21.09
0.14


211517_s_at
IL5RA
3568
M96651.1
20.92
0.14


211341_at
POU4F1
5457
L20433.1
20.66
0.14


204990_s_at
ITGB4
3691
NM_000213.1
20.55
0.14


212097_at
CAV1
857
AU147399
20.47
0.14


216832_at
CBFA2T1
862
AF018283.1
17.51
0.14


206128_at
ADRA2C
152
AI264306
16.87
0.14


204874_x_at
BAIAP3
8938
NM_003933.2
16.41
0.14


203065_s_at
CAV1
857
NM_001753.2
16.07
0.14


212496_s_at
KIAA0876
23030
AW237172
15.75
0.14


212492_s_at
KIAA0876
23030
AW237172
15.66
0.14


218613_at
DKFZp761K1423
55358
NM_018422.1
14.20
0.14


206622_at
TRH
7200
NM_007117.1
13.63
0.14


216356_x_at
BAIAP3
8938
AB018277.1
13.48
0.14


201621_at
NBL1
4681
NM_005380.1
13.45
0.14


213894_at
LOC221981
221981
BF447246
13.05
0.14


203088_at
FBLN5
10516
NM_006329.1
12.93
0.14


204396_s_at
GPRK5
2869
NM_005308.1
12.66
0.14


201655_s_at
HSPG2
3339
M85289.1
12.62
0.14


218742_at
HPRN
64428
NM_022493.1
12.59
0.14


214920_at
LOC221981
221981
R33964
12.55
0.14


219686_at
HSA250839
55351
NM_018401.1
12.44
0.14


204073_s_at
C11orf9
745
NM_013279.1
12.35
0.14


209822_s_at
VLDLR
7436
L22431.1
12.29
0.14


206793_at
PNMT
5409
NM_002686.1
12.27
0.14


211685_s_at
NCALD
83988
AF251061.1
12.16
0.14


214946_x_at
FLJ10824
55747
AV728658
12.03
0.14


210010_s_at
SLC25A1
6576
U25147.1
11.84
0.14


203741_s_at
ADCY7
113
NM_001114.1
−11.89
0.14


208885_at
LCP1
3936
J02923.1
−12.03
0.14


204494_s_at
LOC56905
56905
AW516789
−12.21
0.14


208091_s_at
DKFZP564K0822
81552
NM_030796.1
−13.52
0.14


220560_at
C11orf21
29125
NM_014144.1
−14.30
0.14


221581_s_at
WBSCR5
7462
AF257135.1
−17.67
0.14









Table 36: Top40 genes of cluster #14
(No significant genes identified.)







TABLE 37







Top 40 genes of cluster #15














Locus


q-value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















206676_at
CEACAM8
1088
M33326.1
7.20
1.66


204661_at
CDW52
1043
NM_001803.1
−3.44
1.07


211182_x_at
RUNX1
861
AF312387.1
−3.46
1.07


212827_at
IGHM
3507
X17115.1
−3.47
1.07


203542_s_at
BTEB1
687
BF438302
−3.49
1.07


214835_s_at
SUCLG2
8801
AF131748.1
−3.51
1.07


209905_at
HOXA9
3205
AI246769
−3.56
1.07


201867_s_at
TBL1X
6907
NM_005647.1
−3.59
1.07


204069_at
MEIS1
4211
NM_002398.1
−3.61
1.07


205600_x_at
HOXB5
3215
AI052747
−3.62
1.07


208962_s_at
FADS1
3992
BE540552
−3.63
1.07


205453_at
HOXB2
3212
NM_002145.1
−3.69
1.07


219256_s_at
FLJ20356
54436
NM_018986.1
−3.74
1.07


218627_at
FLJ11259
55332
NM_018370.1
−3.76
1.07


201719_s_at
EPB41L2
2037
NM_001431.1
−3.77
1.07


213150_at
HOXA10
3206
NM_018951.1
−3.77
1.07


209374_s_at
IGHM
3507
BC001872.1
−3.89
1.07


210365_at
RUNX1
861
D43967.1
−3.90
1.07


214651_s_at
HOXA9
3205
U41813.1
−3.92
1.07


218552_at
FLJ10948
55268
NM_018281.1
−3.94
1.07


212906_at
na
283158
BE044440
−3.97
1.07


213147_at
HOXA10
3206
NM_018951.1
−3.98
1.07


213400_s_at
TBL1X
6907
AV753028
−4.01
1.07


200765_x_at
CTNNA1
1495
NM_001903.1
−4.02
1.07


202391_at
BASP1
10409
NM_006317.1
−4.07
1.07


217226_s_at
PMX1
5396
M95929.1
−4.09
1.07


217800_s_at
NDFIP1
80762
NM_030571.1
−4.26
1.07


201841_s_at
HSPB1
3315
NM_001540.2
−4.34
1.07


202236_s_at
SLC16A1
6566
NM_003051.1
−4.34
1.07


212314_at
KIAA0746
23231
AB018289.1
−4.43
1.07


215772_x_at
SUCLG2
8801
AL050226.1
−4.44
1.07


218847_at
IMP-2
10644
NM_006548.1
−4.46
1.07


212311_at
KIAA0746
23231
AB018289.1
−4.56
1.07


212459_x_at
SUCLG2
8801
BF593940
−4.63
1.07


209191_at
TUBB-5
84617
BC002654.1
−4.63
1.07


220974_x_at
BA108L7.2
81855
NM_030971.1
−4.75
1.07


217853_at
TEM6
64759
NM_022748.1
−5.09
1.07


218501_at
ARHGEF3
50650
NM_019555.1
−5.11
1.07


40489_at
DRPLA
1822
D31840
−5.57
1.07


221737_at
GNA12
2768
NM_007353.1
−5.84
1.07
















TABLE 38







Top 40 genes of cluster #16

















q-




Locus


value


Probe Set
Gene
Link
Accession
Score
SAM


ID
symbol
number
number
SAM
(%)















220057_at
GAGED2
9503
NM_020411.1
22.48
0.27


219360_s_at
TRPM4
54795
NM_017636.1
21.22
0.27


219414_at
CLSTN2
64084
NM_022131.1
16.98
0.27


220116_at
KCNN2
3781
NM_021614.1
16.31
0.27


216370_s_at
TKTL1
8277
Z49258
15.76
0.27


205550_s_at
BRE
9577
NM_004899.1
15.55
0.27


211566_x_at
BRE
9577
U19178.1
15.11
0.27


214183_s_at
TKTL1
8277
X91817.1
14.70
0.27


209031_at
IGSF4
23705
NM_014333.1
13.62
0.27


212645_x_at
BRE
9577
AL566299
13.32
0.27


209030_s_at
IGSF4
23705
NM_014333.1
13.30
0.27


213791_at
PENK
5179
NM_006211.1
13.25
0.27


206508_at
TNFSF7
970
NM_001252.1
12.46
0.27


219506_at
FLJ23221
79630
NM_024579.1
12.31
0.27


211421_s_at
RET
5979
M31213.1
12.03
0.27


203241_at
UVRAG
7405
NM_003369.1
11.99
0.27


213908_at
LOC339005
339005
AI824078
11.94
0.27


207911_s_at
TGM5
9333
NM_004245.1
11.78
0.27


214190_x_at
GGA2
23062
AI799984
11.49
0.27


204561_x_at
APOC2
344
NM_000483.2
11.38
0.27


209663_s_at
ITGA7
3679
AF072132.1
11.27
0.27


214259_s_at
AKR7A2
8574
AW074911
11.14
0.27


205472_s_at
DACH
1602
NM_004392.1
10.91
0.27


216331_at
ITGA7
3679
AK022548.1
10.89
0.27


220010_at
KCNE1L
23630
NM_012282.1
10.78
0.27


213484_at
na
151521
AI097640
10.73
0.27


204497_at
ADCY9
115
AB011092.1
10.48
0.27


215771_x_at
RET
5979
X15786.1
10.33
0.27


209032_s_at
IGSF4
23705
AF132811.1
10.32
0.27


219714_s_at
CACNA2D3
55799
NM_018398.1
10.21
0.27


219463_at
C20orf103
24141
NM_012261.1
10.21
0.27


202139_at
AKR7A2
8574
NM_003689.1
9.87
0.27


219143_s_at
FLJ20374
54913
NM_017793.1
9.66
0.27


205996_s_at
AK2
204
NM_013411.1
9.60
0.27


219288_at
HT021
57415
NM_020685.1
9.57
0.27


215663_at
MBNL1
4154
BC005296.1
9.42
0.27


213361_at
PCTAIRE2BP
23424
AW129593
9.23
0.27


210658_s_at
GGA2
23062
BC000284.1
8.73
0.27


213772_s_at
GGA2
23062
BF196572
8.59
0.27


212174_at
AK2
204
AK023758.1
8.59
0.27
















TABLE 39







PAM genes of prognostically important clusters (#13, #12, #9, #16,


#10, #4, #15, #4 and #15, and FLT3ITD)











Probe Set
Gene
Locus Link
Accession



ID
symbol
number
number
Abnormality





205529_s_at
CBFA2T1 (ETO)
862
NM_004349.1
AML and t (8; 21)


205528_s_at
CBFA2T1 (ETO)
862
X79990.1
AML and t (8; 21)


213194_at
ROBO1
6091
BF059159
AML and t (8; 21)


210997_at
HGF
3082
M77227.1
AML and t (15; 17)


210998_s_at
HGF
3082
M77227.1
AML and t (15; 17)


205110_s_at
FGF13
2258
NM_004114.1
AML and t (15; 17)


201497_x_at
MYH11
4629
NM_022844.1
AML and inv (16)


214183_s_at
TKTL1
8277
X91817.1
11q23 (cluster 16)


216370_s_at
TKTL1
8277
Z49258
11q23 (cluster 16)


220057_at
GAGED2
9503
NM_020411.1
11q23 (cluster 16)


209031_at
IGSF4
23705
NM_014333.1
11q23 (cluster 16)


209030_s_at
IGSF4
23705
NM_014333.1
11q23 (cluster 16)


219360_s_at
TRPM4
54795
NM_017636.1
11q23 (cluster 16)


216331_at
ITGA7
3679
AK022548.1
11q23 (cluster 16)


206508_at
TNFSF7
970
NM_001252.1
11q23 (cluster 16)


204561_x_at
APOC2
344
NM_000483.2
11q23 (cluster 16)


200989_at
HIF1A
3091
NM_001530.1
11q23 (cluster 16)


219506_at
FLJ23221
79630
NM_024579.1
11q23 (cluster 16)


213791_at
PENK
5179
NM_006211.1
11q23 (cluster 16)


205472_s_at
DACH
1602
NM_004392.1
11q23 (cluster 16)


209629_s_at
NXT2
55916
AF201942.1
11q23 (cluster 16)


219288_at
HT021
57415
NM_020685.1
11q23 (cluster 16)


205471_s_at
DACH
1602
AW772082
11q23 (cluster 16)


219463_at
C20orf103
24141
NM_012261.1
11q23 (cluster 16)


209628_at
NXT2
55916
AK023289.1
11q23 (cluster 16)


215571_at
—
—
AK021495.1
11q23 (cluster 16)


209663_s_at
ITGA7
3679
AF072132.1
11q23 (cluster 16)


220010_at
KCNE1L
23630
NM_012282.1
11q23 (cluster 16)


204885_s_at
MSLN
10232
NM_005823.2
11q23 (cluster 16)


207911_s_at
TGM5
9333
NM_004245.1
11q23 (cluster 16)


209032_s_at
IGSF4
23705
AF132811.1
11q23 (cluster 16)


206277_at
P2RY2
5029
NM_002564.1
11q23 (cluster 16)


211421_s_at
RET
5979
M31213.1
11q23 (cluster 16)


203241_at
UVRAG
7405
NM_003369.1
11q23 (cluster 16)


209616_s_at
CES1
1066
S73751.1
11q23 (cluster 16)


219714_s_at
CACNA2D3
55799
NM_018398.1
11q23 (cluster 16)


213908_at
LOC339005
339005
AI824078
11q23 (cluster 16)


217520_x_at
na
219392
BG396614
11q23 (cluster 16)


202551_s_at
CRIM1
51232
BG546884
EVI (cluster 10)


213506_at
F2RL1
2150
BE965369
EVI (cluster 10)


206111_at
RNASE2
6036
NM_002934.1
EVI (cluster 10)


214575_s_at
AZU1
566
NM_001700.1
EVI (cluster 10)


209679_s_at
LOC57228
57228
BC003379.1
EVI (cluster 10)


41577_at
PPP1R16B
26051
AB020630
EVI (cluster 10)


212750_at
PPP1R16B
26051
AB020630.1
EVI (cluster 10)


204540_at
EEF1A2
1917
NM_001958.1
EVI (cluster 10)


205330_at
MN1
4330
NM_002430.1
EVI (cluster 10)


200671_s_at
SPTBN1
6711
NM_003128.1
EVI (cluster 10)


207788_s_at
SCAM-1
10174
NM_005775.1
EVI (cluster 10)


209576_at
GNAI1
2770
AL049933.1
EVI (cluster 10)


218086_at
NPDC1
56654
NM_015392.1
EVI (cluster 10)


204484_at
PIK3C2B
5287
NM_002646.1
EVI (cluster 10)


219145_at
FLJ11939
79732
NM_024679.1
EVI (cluster 10)


212820_at
RC3
23312
AB020663.1
EVI (cluster 10)


204004_at
—
—
AI336206
EVI (cluster 10)


209487_at
RBPMS
11030
D84109.1
EVI (cluster 10)


209543_s_at
CD34
947
M81104.1
EVI (cluster 10)


205382_s_at
DF
1675
NM_001928.1
EVI (cluster 10)


47560_at
FLJ11939
79732
AI525402
EVI (cluster 10)


212827_at
IGHM
3507
X17115.1
EVI (cluster 10)


217977_at
SEPX1
51734
NM_016332.1
EVI (cluster 10)


212558_at
GDAP1L1
78997
BF508662
EVI (cluster 10)


206429_at
F2RL1
2150
NM_005242.2
EVI (cluster 10)


220377_at
C14orf110
29064
NM_014151.1
EVI (cluster 10)


206851_at
RNASE3
6037
NM_002935.1
EVI (cluster 10)


212012_at
D2S448
7837
AF200348.1
EVI (cluster 10)


210844_x_at
CTNNA1
1495
D14705.1
cEBPalpha (cluster4)


200765_x_at
CTNNA1
1495
NM_001903.1
cEBPalpha (cluster4)


200764_s_at
CTNNA1
1495
AI826881
cEBPalpha (cluster4)


214551_s_at
CD7
924
NM_006137.2
cEBPalpha (cluster4)


214049_x_at
CD7
924
AI829961
cEBPalpha (cluster4)


216191_s_at
TRD@
6964
X72501.1
cEBPalpha (cluster4)


217143_s_at
TRD@
6964
X06557.1
cEBPalpha (cluster4)


216286_at
—
—
AV760769
cEBPalpha (cluster4)


206232_s_at
B4GALT6
9331
NM_004775.1
cEBPalpha (cluster4)


202241_at
C8FW
10221
NM_025195.1
cEBPalpha (cluster4)


219383_at
FLJ14213
79899
NM_024841.1
cEBPalpha (cluster4)


209191_at
TUBB-5
84617
BC002654.1
cEBPalpha (cluster4)


213830_at
TRD@
6964
AW007751
cEBPalpha (cluster4)


206676_at
CEACAM8
1088
M33326.1
cEBPalpha (cluster15)


210244_at
CAMP
820
U19970.1
cEBPalpha (cluster15)


202018_s_at
LTF
4057
NM_002343.1
cEBPalpha (cluster15)


217853_at
TEM6
64759
NM_022748.1
cEBPalpha (cluster15)


204417_at
GALC
2581
NM_000153.1
cEBPalpha (cluster15)


204039_at
CEBPA
1050
NM_004364.1
cEBPalpha (cluster15)


211810_s_at
GALC
2581
D25284.1
cEBPalpha (cluster15)


210762_s_at
DLC1
10395
AF026219.1
cEBPalpha (cluster15)


217800_s_at
NDFIP1
80762
NM_030571.1
cEBPalpha (cluster15)


206726_at
PGDS
27306
NM_014485.1
cEBPalpha (cluster15)


202236_s_at
SLC16A1
6566
NM_003051.1
cEBPalpha (cluster15)


202016_at
MEST
4232
NM_002402.1
cEBPalpha (cluster15)


212531_at
LCN2
3934
NM_005564.1
cEBPalpha (cluster15)


218847_at
IMP-2
10644
NM_006548.1
cEBPalpha (cluster15)


205692_s_at
CD38
952
NM_001775.1
cEBPalpha (cluster15)


212459_x_at
SUCLG2
8801
BF593940
cEBPalpha (cluster15)


201841_s_at
HSPB1
3315
NM_001540.2
cEBPalpha (cluster15)


207329_at
MMP8
4317
NM_002424.1
cEBPalpha (cluster15)


220974_x_at
BA108L7.2
81855
NM_030971.1
cEBPalpha (cluster15)


207384_at
PGLYRP
8993
NM_005091.1
cEBPalpha (cluster15)


209191_at
TUBB-5
84617
BC002654.1
cEBPalpha (cluster15)


202391_at
BASP1
10409
NM_006317.1
cEBPalpha (cluster15)


215772_x_at
SUCLG2
8801
AL050226.1
cEBPalpha (cluster15)


212314_at
KIAA0746
23231
AB018289.1
cEBPalpha (cluster15)


221737_at
GNA12
2768
NM_007353.1
cEBPalpha (cluster15)


214651_s_at
HOXA9
3205
U41813.1
cEBPalpha (cluster15)


218501_at
ARHGEF3
50650
NM_019555.1
cEBPalpha (cluster15)


202747_s_at
ITM2A
9452
NM_004867.1
cEBPalpha (cluster15)


213400_s_at
TBL1X
6907
AV753028
cEBPalpha (cluster15)


214049_x_at
CD7
924
AI829961
cEBPalpha (cluster15)


209374_s_at
IGHM
3507
BC001872.1
cEBPalpha (cluster15)


212311_at
KIAA0746
23231
AB018289.1
cEBPalpha (cluster15)


40489_at
DRPLA
1822
D31840
cEBPalpha (cluster15)


205453_at
HOXB2
3212
NM_002145.1
cEBPalpha (cluster15)


214551_s_at
CD7
924
NM_006137.2
cEBPalpha (cluster15)


206660_at
IGLL1
3543
NM_020070.1
cEBPalpha (cluster15)


210844_x_at
CTNNA1
1495
D14705.1
CEBPalpha (cluster4 and 15)


200765_x_at
CTNNA1
1495
NM_001903.1
CEBPalpha (cluster4 and 15)


200764_s_at
CTNNA1
1495
AI826881
CEBPalpha (cluster4 and 15)


214551_s_at
CD7
924
NM_006137.2
CEBPalpha (cluster4 and 15)


214049_x_at
CD7
924
AI829961
CEBPalpha (cluster4 and 15)


209191_at
TUBB-5
84617
BC002654.1
CEBPalpha (cluster4 and 15)


217800_s_at
NDFIP1
80762
NM_030571.1
CEBPalpha (cluster4 and 15)


217143_s_at
TRD@
6964
X06557.1
CEBPalpha (cluster4 and 15)


216191_s_at
TRD@
6964
X72501.1
CEBPalpha (cluster4 and 15)


219615_s_at
KCNK5
8645
NM_003740.1
FLT3 ITD


204341_at
TRIM16
10626
NM_006470.1
FLT3 ITD


201664_at
SMC4L1
10051
AL136877.1
FLT3 ITD


201663_s_at
SMC4L1
10051
NM_005496.1
FLT3 ITD


213110_s_at
COL4A5
1287
AW052179
FLT3 ITD


213844_at
HOXA5
3202
NM_019102.1
FLT3 ITD


204082_at
PBX3
5090
NM_006195.1
FLT3 ITD


203151_at
MAP1A
4130
AW296788
FLT3 ITD


211269_s_at
IL2RA
3559
K03122.1
FLT3 ITD


203708_at
PDE4B
5142
NM_002600.1
FLT3 ITD


210425_x_at
GOLGIN-67
23015
AF164622.1
FLT3 ITD


212070_at
GPR56
9289
AL554008
FLT3 ITD


205366_s_at
HOXB6
3216
NM_018952.1
FLT3 ITD


214039_s_at
LAPTM4B
55353
T15777
FLT3 ITD


203897_at
LOC57149
57149
BE963444
FLT3 ITD


215806_x_at
TRGC2
6967
M13231.1
FLT3 ITD


209813_x_at
—
—
M16768.1
FLT3 ITD


216920_s_at
TRGC2
6967
M27331.1
FLT3 ITD


206945_at
LCT
3938
NM_002299.1
FLT3 ITD


208029_s_at
LAPTM4B
55353
NM_018407.1
FLT3 ITD


215288_at
TRPC2
7221
AI769824
FLT3 ITD


203373_at
SOCS2
8835
NM_003877.1
FLT3 ITD


209905_at
HOXA9
3205
AI246769
FLT3 ITD


215623_x_at
SMC4L1
10051
AK002200.1
FLT3 ITD


211144_x_at
TRGC2
6967
M30894.1
FLT3 ITD


220813_at
CYSLTR2
57105
NM_020377.1
FLT3 ITD


208767_s_at
LAPTM4B
55353
AW149681
FLT3 ITD


205227_at
IL1RAP
3556
NM_002182.1
FLT3 ITD


209014_at
MAGED1
9500
AF217963.1
FLT3 ITD


206341_at
IL2RA
3559
NM_000417.1
FLT3 ITD


205453_at
HOXB2
3212
NM_002145.1
FLT3 ITD


209392_at
ENPP2
5168
L35594.1
FLT3 ITD


219304_s_at
SCDGF-B
80310
NM_025208.1
FLT3 ITD


208798_x_at
GOLGIN-67
23015
AF204231.1
FLT3 ITD


211302_s_at
PDE4B
5142
L20966.1
FLT3 ITD


210839_s_at
ENPP2
5168
D45421.1
FLT3 ITD


205600_x_at
HOXB5
3215
AI052747
FLT3 ITD


208414_s_at
HOXB4
3214
NM_002146.1
FLT3 ITD


208797_s_at
GOLGIN-67
23015
AI829170
FLT3 ITD


210123_s_at
CHRNA7
1139
U62436.1
FLT3 ITD


206289_at
HOXA4
3201
NM_002141.1
FLT3 ITD


201069_at
MMP2
4313
NM_004530.1
FLT3 ITD


213217_at
ADCY2
108
AU149572
FLT3 ITD


214651_s_at
HOXA9
3205
U41813.1
FLT3 ITD


211402_x_at
NR6A1
2649
AF004291.1
FLT3 ITD


204044_at
QPRT
23475
NM_014298.2
FLT3 ITD


204438_at
MRC1
4360
NM_002438.1
FLT3 ITD


206042_x_at
SNRPN
6638
NM_022804.1
FLT3 ITD


214953_s_at
APP
351
X06989.1
FLT3 ITD


201427_s_at
SEPP1
6414
NM_005410.1
FLT3 ITD


209193_at
PIM1
5292
M24779.1
FLT3 ITD


219218_at
FLJ23058
79749
NM_024696.1
FLT3 ITD


200923_at
LGALS3BP
3959
NM_005567.2
FLT3 ITD


210424_s_at
GOLGIN-67
23015
AF163441.1
FLT3 ITD


219602_s_at
FLJ23403
63895
NM_022068.1
FLT3 ITD


201522_x_at
SNRPN
6638
NM_003097.2
FLT3 ITD

## Claims

1. A method for determining the prognosis for an AML-affected subject, said method comprising the steps of:
determining, in a sample obtained from the subject, a level of expression of each of at least MYH11, CLIPR-59, ST18, NRP1 and CLECSF13 from cluster #9, corresponding to the AML class of inv(16);
establishing the similarity of expression levels between the at least MYH11, CLIPR-59, ST18, NRP1 and CLECSF13 in the AML-affected subject and the at least MYH11, CLIPR-59, ST18, NRP1 and CLECSF13 in subjects selected from the inv(16) class; and
assigning to the AML-affected subject a prognosis based on the established similarity of expression levels between the at least MYH11, CLIPR-59, ST18, NRP1 and CLECSF13 in the AML-affected subject and the at least MYH11, CLIPR-59, ST18, NRP1 and CLECSF13 in subjects selected from the inv(16) class.

2. A method for determining the prognosis for an AML-affected subject, said method comprising the steps of:
determining, in a sample obtained from the subject, a level of expression of each of at least HGF, FGF13, MEG3, GABRE and MST1 from cluster #12, corresponding to the AML class of t(15; 17);
establishing the similarity of expression levels between the at least HGF, FGF13, MEG3, GABRE and MST1 in the AML-affected subject and the at least HGF, FGF13, MEG3, GABRE and MST1 in subjects selected from the t(15; 17) class; and
assigning to the AML-affected subject a prognosis based on the established similarity of expression levels between the at least HGF, FGF13, MEG3, GABRE and MST1 in the AML-affected subject and the at least HGF, FGF13, MEG3, GABRE and MST1 in subjects selected from the t(15; 17) class.

3. A method for determining the prognosis for an AML-affected subject, said method comprising the steps of:
determining, in a sample obtained from the subject, a level of expression of each of at least CBFA2T1, ROBO1, CACNA2D2, POU4F1 and IL5RA from cluster #13, corresponding to the AML class of t(8;21);
establishing the similarity of expression levels between the at least CBFA2T1, ROBO1, CACNA2D2, POU4F1 and IL5RA in the AML-affected subject and the at least CBFA2T1, ROBO1, CACNA2D2, POU4F1 and IL5RA in subjects selected from the t(8;21) class; and
assigning to the AML-affected subject a prognosis based on the established similarity of expression levels between the at least CBFA2T1, ROBO1, CACNA2D2, POU4F1 and IL5RA in the AML-affected subject and the at least CBFA2T1, ROBO1, CACNA2D2, POU4F1 and IL5RA in subjects selected from the t(8;21) class.

4. The method according to claim 2, wherein determining the level of expression is performed with a gene chip.

5. The method according to claim 2, wherein the level of expression of each of at least eight cluster-specific genes from cluster #12 is determined.

6. The method according to claim 3, wherein determining the level of expression is performed with a gene chip.

7. The method according to claim 3, wherein the level of expression of each of at least eight cluster-specific genes from cluster #13 is determined.

8. The method according to claim 1, wherein determining the level of expression is performed with a gene chip.

9. The method according to claim 1, wherein the level of expression of each of at least eight cluster-specific genes from cluster #9 is determined.