Patent Publication Number: US-2009222387-A1

Title: Diagnosis, Prognosis and Prediction of Recurrence of Breat Cancer

Description:
TECHNICAL FIELD OF THE INVENTION 
     The present invention relates to methods and compositions for the diagnosis, prognosis, and prediction of breast cancer. More specifically, the invention relates to classification of breast cancer tissue samples based on measuring the expression of a set of marker genes. The set is useful for the identification of clinically important breast cancer subtypes. Methods are disclosed for prediction, diagnosis and prognosis of breast cancer. 
     BACKGROUND OF THE INVENTION AND PRIOR ART 
     Breast cancer is one of the leading causes of cancer death in women in western countries. More specifically breast cancer claims the lives of approximately 40,000 women and is diagnosed in approximately 200,000 women annually in the United States alone. Over the last few decades, adjuvant systemic therapy has led to markedly improved survival in early breast cancer (EBCTCG, 1998 a+b). This clinical experience has led to consensus recommendations offering adjuvant systemic therapy for the vast majority of breast cancer patients (Goldhirsch et al., 2003). In breast cancer a multitude of treatment options are available which can be applied in addition to the routinely performed surgical removal of the tumor and subsequent radiation of the tumor bed. Three main and conceptually different strategies are endocrine treatment, chemotherapy and treatment with targeted therapies. Prerequisite for treatment with endocrine agents is expression of hormone receptors in the tumor tissue i.e. either estrogen, progesterone or both. Several endocrine agents with different mode of action and differences in disease outcome when tested in large patient cohorts are available. Tamoxifen is one of the oldest endocrine drugs that significantly reduced the risk of tumor recurrence. Apparently, even more effective are aromatase inhibitors which belong to a new endocrine drug class. In contrast to tamoxifen which is a competitive inhibitor of estrogen binding aromatase inhibitors block the production of estrogen itself thereby reducing the growth stimulus for estrogen receptor positive tumor cells. Recent clinical trials have demonstrated an even better disease outcome for patients treated with these agents compared to patients treated with tamoxifen. Still, some patients experience a relapse despite endocrine treatment and in particular these patients might benefit from additional therapeutic drugs. Chemotherapy with anthracyclines, taxanes and other agents have been shown to be efficient in reducing disease recurrence in estrogen receptor positive as well as estrogen receptor negative patients. The NSABP-20 study compared tamoxifen alone against tamoxifen plus chemotherapy in node negative estrogen receptor positive patients and showed that the combined treatment was more effective than tamoxifen alone. Recently, a systemically administered antibody directed against the Her2neu antigen on the surface of tumor cells have been shown to reduce the risk of recurrence several fold in a patients with Her2neu over expressing tumors. 
     Yet, most if not all of the different drug treatments have numerous potential adverse effects which can severely impair patients&#39; quality of life (Shapiro and Recht, 2001; Ganz et al., 2002). This makes it mandatory to select the treatment strategy on the basis of a careful risk assessment for the individual patient to avoid over- as well as under treatment. 
     Arguably, the most important histopathological factor for risk stratification in primary breast cancer is the nodal status (Chia et al., 2004; Fisher et al., 1993; Jatoli et al., 1999). Patients with node-negative breast cancer have a favourable long-term prognosis with 10-years survival rates between 67% and 76% even without adjuvant systemic therapies (Fisher et al., 1993; Chia et al., 2004). To further elucidate the prognosis of this substantial subgroup of patients, several other factors such as the age of the patients, tumor size, estrogen receptor status and histological grade are commonly applied to identify those patients with only a minimal risk of recurrence (Chia et al., 2004). Only in these carefully selected patients can adjuvant systemic therapy be omitted without risk of under treatment (Goldhirsch et al., 2003). However, this group with a minimal risk comprises only very few of all node-negative breast cancer patients. An abundance of potential prognostic factors have been analysed in recent years often in studies with varying quality and sometimes conflicting results (Altman and Lyman, 1998). 
     More recently, gene expression profiling studies with DNA microarray technologies were able to show distinct subtypes of breast cancer (Perou et al., 2000). Five major subtypes described as luminal type A, luminal type B, basal like, Her2neu like and normal like tumors were identified by two dimensional hierarchical clustering. Luminal type A and B tumors were mainly estrogen receptor positive and basal like tumors estrogen receptor negative. Importantly, in survival analysis the subtypes showed significantly differences in outcome with the basal like and Her2neu tumors having the worst outcome and with luminal like A patients having the best outcome (Sorlie et al, 2001, 2003). However, this “class discovery” approach based on unsupervised two dimensional hierarchical cluster analysis appeared not to be effective for class prediction. First, by this technique tumor samples are ordered in a row according to the calculated similarity and slight variations of the algorithm or distance metrics can result in large differences of sample orders. In addition, inclusion of a few additional samples can have tremendous influence on sample order so that a robust and reproducible classification is difficult. Furthermore, cluster of genes related to putative clinical relevant tumor subclasses have been identified by visual inspection instead of appropriate statistical evaluation. Consequently, neither discovered classes nor genes selected to characterize them allow reproducible and robust classification. 
     Expression profiles could be linked to prognosis by several investigators using supervised analysis methods that are assumed to be more appropriate for class prediction studies. Van&#39;t Veer et al. identified a prognostic signature consisting of 70 respectively 231 genes in a finding cohort of 78 sporadic breast cancers of node negative women younger than 53 years of age (Van&#39;t Veer et al., 2002; Van de Vijver et al., 2002). They used a case versus control statistics, with development of metastasis within five years defined as case and disease free survival of more than five years as control, and found that the expression values of at least 70 genes could be used to calculate an average “good prognosis” profile. Unknown tumor samples were classified by correlation of the gene expression of these 70 genes to the good prognosis signature. In a subsequent validation study the significance as a predictor of survival was confirmed (Van de Vijver et al., 2002) although a multicenter external validation study showed that the predictor performed less well as previously published (Piccart et al., SABC presentation 2004). Huang et al., 2003 described gene expression predictors of lymph node status and recurrence. They used k-means clustering of 7030 genes with a target of 500 clusters. For all resulting 496 clusters the dominant singular factor was obtained and used as “metagene” in a tree model analysis. They noted that poor outlook with respect to survival is related to the vigorous proliferative ability of the tumor. Aggregates of distinct groups of genes were capable of predicting lymph node status and patient outcome at least in the small cohort which was used in the analysis. Distinct gene expression alterations were found to be associated with different tumor grades (Ma et al., 2003). Grade I and grade III breast tumors exhibit reciprocal gene expression patterns, whereas grade II tumors exhibit a hybrid pattern of grade I and grade III signatures. Similarly, a gene expression signature differentiating grade I versus grade II tumors was found by another group using a high density single colour gene expression platform. Using this signature, which they called “Genomic Grade Index (GGI)” they showed that the GGI could stratify histological grade II tumors into tumors resembling either more genomic grade I or genomic grade III tumors (Sotiriou et al., 2005). ER-alpha (ER) status is an essential determinant of clinical and biological behaviour of human breast cancers. Generally, patients with ESR1-negative tumors tend to have a worse prognosis than patients with ESR1-positive tumors. The underlying reason for this phenomenon is probably the large genetic difference between these two distinct tumor subtypes. Several gene expression studies found that numerous genes are tightly co-regulated with the estrogen receptor and that the estrogen receptor status might be more reliably determined by measuring ESR1 mRNA than the protein by immunohistochemistry (Dressman et al., 2001). In a previous study two prognostic gene expression profiles have been identified for ER-positive and ER-negative tumors, respectively (Wang et al. 2005). The ER status had been determined by ligand binding assay or immuno-histochemistry. Expression values of 60 probe sets measured by Affymetrix HG U133A oligonucleotide gene chips for ER-positive samples and 16 probe sets for ER-negative samples were used to classify separately both tumor types into a high and low risk prognostic class. 
     Gene expression profiling not only has been utilized for identification of prognostic genes but also for development of classification algorithms capable of predicting response of a tumor toward a given drug treatment. Gene signatures and corresponding algorithms have been identified for predicting tumor response toward docetaxel based on a 92 gene predictor (Chang et al. 2003), paclitaxel followed by fluorouracil, doxorubicin and cyclophosphamide using a model based on expression values of 74 genes (Ayers et al. 2004) or tamoxifen using a 44 gene signature (Jansen et al. 2005) and a 62 probe set signature (Loi et al., 2005) respectively. In another study, gene expression profiles of tumors of tamoxifen treated patients were used to define a two-gene ratio supposed to be predictive of disease free survival (Ma et al., 2004). However, neither the 44 gene signature nor the two-gene ratio proposed to predict response to tamoxifen could be validated in a subsequent study (Loi et al., 2005). A multigene assay comprising the measurement of 21 genes (16 breast cancer related genes and 5 housekeeping genes) was shown to predict recurrence of tamoxifen-treated breast cancer (Paik et al. 2004). The genes were selected from a limited list of genes derived from the literature and tested for prognostic and predictive power by expression profiling in patient samples. However, since the genes tested comprise only a minor subset of all genes expressed in breast tumour tissue and the panel of 16 breast cancer related genes is strongly biased in that it predominantly measures the degree of proliferation, it is highly likely, that a more comprehensive gene expression profiling approach will yield a better predictor. 
     Most gene identification methods use per-gene (univariate) statistics such as t-test (Chang et al. 2003), signal to noise ratio (Golub et al. 1999), significance analysis in microarrays SAM (Tusher et al., 2001) or univariate Cox regression (Wang et al. 2005). In recent years, multivariate models have become increasingly popular (Shrunken Centroids (Tibshirani et al., 2001, 2002), KNN (Khan et al. 2002), SVM (Lee 2000, 2001), Artificial Neural Networks (Burke et al., 1995), multivariate Cox Regression (Pawitan et al., 2004; van de Vijver et al., 2002; Li et al., 2003)). The goals remain the same as in the univariate context: to distinguish between two or more different classes and to produce a predictor that can assign a class to a given previously unknown sample while using a minimal set of genes only. Since multivariate models usually allow for geometrically more complex separations, the issue of overfitting the data arises. This is especially a problem if the model has a lot of parameters to be estimated from the training data. Selection of the minimal number of genes needed to successfully capture the nature of the subclasses is also somewhat arbitrary (up to the point of over-fitting the training data) since higher testset accuracy can possibly be achieved by allowing the use of a larger number of genes in the predictor. A disadvantage of most studies using the standard strategy of supervised gene identification is the fact that the corresponding algorithms utilize a high number of genes that are potentially unstable as predictors in the general population. The main reason for this problem can be ascribed to the way how the genes of the classifier are selected. In most cases the number of expression levels measured (p) will exceed the number of patient samples (n) by orders of magnitude (n&lt;&lt;p) so that the selected genes and algorithms are highly prone to over estimating the quality of predictor performance, because the molecular signatures strongly depended on the selection of patients in the gene finding cohort, which may not adequately represent the patient population the classifier is intended for. For instance, with data from the study by van&#39;t Veer and colleagues and a gene finding set of the same size as in the original publication (n=78), only 14 of 70 genes from the published signature were included in more than half of 500 signatures generated after multiple randomisation of the training set, although virtually the same gene finding algorithm was used, namely Pearson correlation with binary patient status (Michiels et al. 2005). Furthermore, samples apparently belonging to a different clinical class, e.g. a sample from a patient with an early distant metastasis and another sample from a patient with no metastasis for many years after diagnosis, still might be very similar with regard to their gene expression pattern. The underlying reasons for the different behaviour of tumors with very similar expression profiles might be subtle and difficult to correlate to gene expression. In any case, all these aspects make it very difficult to extract the most informative genes and to build a high performance classifier. 
     SUMMARY OF THE INVENTION 
     The present invention is based on the unexpected finding that robust classification of breast tumor tissue samples into clinically relevant subgroups can be achieved by predictors that use a small set of specific marker genes. The idea of the invention is to predict the class of a previously unknown tissue sample (i.e. its gene expression profile) hierarchically by separating a number of mutually disjoint groups of classes at a time ( FIG. 1 ). In each node in this tree (where a partial classification is done), only a very small number of genes is used to reliably distinguish the classes or groups of classes until the sample can uniquely be assigned to a single class (the leaves of the tree structure). One embodiment of the method uses a hierarchical binary classification technique (n=2) involving the computation of in-class-probability for each sample point to each class. In another embodiment, the approach is able to cope with an arbitrary number of classes (n&gt;2) at the same time. The whole set of partial classifiers builds the global classifier. The number of genes used in each partial classifier can be as low as 2, but also larger numbers of genes may be used. 
     It is an unexpected finding that the overall predictor is robust in the sense that in a random permutation of the sample-to-class mapping for each partial classifier, the best possible classifier on the original data is significantly better than the best one on randomized data. 
     Compared to the supervised methods mentioned in the previous section, the classification method described in the invention is capable to distinguish between tumours that are genetically very different yet behave very similar with regard to a particular clinical parameter. Furthermore, it uses a much smaller set of genes for class separations and achieves a significantly higher accuracy on test data. In that respect, it out-performs prior classifiers. Special gene sets are provided for the classification of a breast tumor sample into clinically relevant subclasses. 
     The method comprises: 
     a) Measuring the expression of genes in a collection of breast tumor specimens. 
     b) Normalising the raw signal intensities of the gene measurements of each individual array using either signal intensities of housekeeping genes measured on the same array or a global scaling approach, in which all signal intensities of an array multiplied with a factor so that the signal intensities of all arrays of the experiment have the same median (or mean). 
     c) Filtering for those genes that first, are technically well measurable, e.g. with a median signal intensity higher than background signal+3 standard deviations of repeated background measurements and secondly, variable expressed within said specimen collection, e.g. having a coefficient of variation of larger than 5% for log transformed expression values. 
     d) Performing an unsupervised principle component analysis (PCA) on conditions (samples) using the selected genes with appropriate computer programs like GeneSpring® (Silicon Genetics, Redwood City, Calif., USA). 
     e) Displaying the PCA outcome in a two or preferentially three dimensional condition scatter graph using preferentially principal components 1, 2 and 3 ( FIG. 1   a ). 
     f) Visualising categorical clinical information, e.g. estrogen receptor status, presence and absence of metastasis, clinical grade, or histological tumor type, or numerical clinical information, e.g. time to metastasis, time to local recurrence, or age, in the graphical display, e.g. by colouring the respective classes by discrete or continuous colouring, respectively ( FIG. 1   b ). 
     g) Identifying clinically relevant subclasses by I) similar clinical characteristics only, II) by similar clinical characteristics and mutual proximity within the PCA. In accordance to f), similarity in clinical characteristics is visualised by similar colours, so it is easy to extract from the visualisation ( FIG. 1   c ). 
     h) Labelling of the samples according to the identified subclasses. Clinically relevant breast cancer subclasses that have been identified include:
         Estrogen receptor positive breast tumours with a   i. very low likelihood for disease recurrence (FHL++)   ii. low likelihood for disease recurrence (FHL+, FHL++, ESR1++)   iii. high likelihood for disease recurrence (ESR1 LM, ESR1 EM, ESR1 ER)   iv. high likelihood for early disease recurrence (ESR1 ER, ESR1 EM)   v. high likelihood for late disease recurrence (ESR1 LM)   vi. high likelihood for early distant metastasis (ESR1EM), ( FIG. 1   d )   vii. high likelihood for early local recurrence (ESR1 ER)   Estrogen receptor negative breast tumors with a   viii. low likelihood for disease recurrence (ESR-A)   ix. high likelihood for disease recurrence (ESR-B)   x. intermediate likelihood for disease recurrence (ESR-C, ESR-D)       

     i) Identifying genes suitable for classification of said breast cancer subclasses using t-statistics, signal to noise ratio, fishers exact test, support vector machines or any other method previously described to derive separating genes. Special preference is put on genes whose median expression level across all samples in the collection is above the lower quartile of the medians of all genes measured. 
     j) In particular, said subclasses may be characterized on the gene expression level by fitting multivariate normal distributions to each subclass, either with distinctly, partial commonly or commonly chosen or estimated distribution parameters, and selecting a prediction class for a previously unknown sample based on the probability distributions and/or pointwise probability of the gene expression values of the sample under investigation used in the distributions of the training clusters (including, but not limited to e.g. the likeliest cluster). 
     k) Said algorithm may use 2 or more genes or means or medians of gene sets derived prior to classifier training by a grouping procedure such as but not limited to unsupervised clustering or correlation graph analysis. 
     l) Said algorithm may in parts use univariate gene expression distributions and/or values of single genes, medians or means of gene sets previously derived for partial classification. “Estrogen receptor positive” and “estrogen receptor negative”, within the meaning of the invention, relates to the classification of tumors to one of the classes based on methods like immunohistochemistry (IHC), ligand binding assay (DCC) or ESR1 mRNA measurement of preferentially micro-dissected or macro-dissected tumor tissue. 
    
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         FIG. 1   a  depicts the result of an unsupervised principle component analysis of 212 breast tumour samples using variable expressed genes. 
         FIG. 1   b  depicts the result of an unsupervised principle component analysis of 212 breast tumor samples using variable expressed genes coloured according to ESR1 status (1 if signal intensity&gt;1000, 0 if signal intensity ≦1000). 
         FIG. 1   c  depicts the results of an unsupervised principle component analysis of 212 breast tumor samples using variable expressed genes coloured according to time to metastasis (TTM). Samples without metastasis are set to 180 regardless of follow up time. 
         FIG. 1   d  depicts the results of an unsupervised principle component analysis of 212 breast tumor samples using variable expressed genes. A subgroup of estrogen receptor positive tumors with a high likelihood of early metastasis has been labelled (ESR+ EM) based on information provided in  FIGS. 1   b  and  1   c.    
         FIG. 2  depicts an example of a hierarchical classification tree. 
         FIG. 3  depicts the separation scheme used for an embodiment of the invention. 
         FIG. 4  depicts the separation scheme used for an embodiment of the invention with reference numerals. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     The present invention relates to a method of building a classificator for the classification of breast cancer samples into clinically relevant sub-classes, said method comprising 
     (a) collecting data on the expression level of a plurality of genes in a plurality of breast tumor samples, 
     (b) performing an unsupervised principle component analysis on data derived from said data collected under (a), 
     (c) visualizing the outcome of said principle component analysis under (b), 
     (d) visualizing categorical clinical information for individual samples in said visualization of step (c), 
     (e) identifying clinically relevant sub-classes as regions in said visualization of step (d), 
     (f) identifying marker genes and threshold values for expression levels of said marker genes, suitable for classification of said breast cancer samples into said clinically relevant breast cancer classes. 
     The present invention further relates to methods of building a classificator for the classification of breast cancer samples into clinically relevant sub-classes, wherein said classification of said breast cancer samples is in a hierarchical classification tree. 
     Methods of the invention are preferably built exclusively from binary classification steps. 
     According to another aspect of the invention, said data derived from said data collected under step (a) is obtained by normalization of said collected data. 
     According to another aspect of the invention, the method further comprises filtering for genes that are technically well measurable and/or variably expressed in said plurality of breast tumor samples. 
     According to another aspect of the invention said visualization is a visualization of a three-dimensional space, spanned by the first three principle components of said principle component. analysis. 
     Preferably, said visualization of said categorical clinical information is by using a color code, a symbol code and/or a size code. Different categories are assigned different colors, different shapes (i.e. different symbols), or different sizes of the symbols used for visualization of the PCA results. 
     The present invention also relates to a system for building a classificator for the classification breast cancer samples into clinically relevant sub-classes, said system being adapted to perform methods of the invention as described above. 
     Such systems advantageously comprise 
     (a) means for performing an unsupervised principle component analysis on data derived from gene expression data, 
     (b) means for visualizing the outcome of said principle component analysis under (a) in a multidimensional space, 
     (c) means for visualizing categorical clinical information of individual samples in said visualization of (b). 
     Another aspect of the invention relates to a method for the classification of a breast cancer from a sample of said tumor, said method comprising 
     (a) assigning the sample to a first aggregate breast cancer class ( 2 ) if the sample is ESR(+), or to a second aggregate breast cancer class ( 3 ) if the sample is ESR(−), 
     (b) if said sample is in the first aggregate breast cancer class ( 2 ), then
         (i) assigning the sample to a 3rd ( 4 ) or a 4th ( 5 ) aggregate breast cancer class, based on marker gene expression;   (ii) if said sample is in the 3rd aggregate breast cancer class ( 4 ), then assigning the sample to a first ( 8 ) or a second ( 9 ) elementary breast cancer class, based on marker gene expression;.   (iii) if said sample is in the 4th aggregate breast cancer class ( 5 ), then assigning the sample to a third ( 10 ) or a fourth ( 11 ) elementary breast cancer class, based on marker gene expression;       

     (c) if said sample is in the second aggregate breast cancer class ( 3 ), then
         (i) assigning the sample to a fifth ( 6 ) or a 6th ( 7 ) aggregate breast cancer class, based on marker gene expression,   (ii) if said sample is in the fifth aggregate breast cancer class ( 6 ), then assigning the sample to a fifth elementary breast cancer class ( 12 ) or a 7th aggregate breast cancer class ( 13 ), based on marker gene expression,   (iii) if said sample is in said 7th aggregate breast cancer class ( 13 ), then assigning the sample to a 6th ( 16 ) or 7th ( 17 ) elementary breast cancer class   (iv) if said sample is in said 6th aggregate breast cancer class, then assigning said sample to an 8th aggregate breast cancer class ( 14 ) or to a 10th elementary breast cancer class ( 15 ),   (v) if said sample is in said 8th aggregate breast cancer class ( 14 ), then assigning said sample to an 8th ( 18 ) or 9th ( 19 ) elementary breast cancer class.       

     Another aspect of the invention relates to the method described above, wherein 
     (a) said assigning said sample to a 3rd ( 4 ) or 4th ( 5 ) aggregate breast cancer class is based on a bivariate classifier using the expression level of two genes selected from Table 1, 
     (b) said assigning said sample to a first ( 8 ) or second ( 9 ) elementary breast cancer class is based on a bivariate classifier using the expression level of two genes selected from Table 2, 
     (c) said assigning said sample to a 3rd ( 10 ) or 4th ( 11 ) elementary breast cancer class is based on a bivariate classifier using the expression level of two genes selected from Table 3, 
     (d) said assigning said sample to a 5th ( 6 ) or 6th ( 7 ) aggregate breast cancer class is based on a bivariate classifier using the expression level of two genes selected from Table 4, 
     (e) said assigning said sample to a 5th elementary breast cancer class ( 12 ) or a 7th aggregate breast cancer class ( 13 ) is based on a bivariate classifier using the expression level of two genes selected from Table 5, 
     (f) said assigning said sample to a 6th ( 16 ) or 7th ( 17 ) elementary breast cancer class is based on a bivariate classifier using the expression level of two genes selected from Table 6, 
     (g) said assigning said sample to an 8th aggregate breast cancer class ( 14 ) or a 10th elementary breast cancer class ( 15 ) is based on a bivariate classifier using the expression level of two genes selected from Table 7, 
     (h) said assigning said sample to an 8th ( 18 ) or 9th ( 19 ) elementary breast cancer class is based on a bivariate classifier using the expression level of two genes selected from Table 8. 
     Another aspect of the invention relates to the above methods, wherein 
     (a) said assigning said sample to a 3rd ( 4 ) or 4th ( 5 ) aggregate breast cancer class is based on a bivariate classifier using the expression level of two genes selected from the group consisting of 21821_s_at, 213441_x_at, 214404_x_at and 220192_x_at and 208190_s_at, or selected from the group consisting of 219572_at, 204641_at, 207828_s_at and 219918_s_at, or selected from the group consisting of 202580_x_at, 221436 s_at, 202035_s_at, 202036_s_at and 202037_s_at; 
     (b) said assigning said sample to a first ( 8 ) or second ( 9 ) elementary breast cancer class is based on a bivariate classifier using the expression level of 206978_at and 203960_s_at or the absolute expression level of 204502_at and 214433_s_at, or the absolute expression level of 209374_s_at or 206133_at; 
     (c) said assigning said sample to a 3rd ( 10 ) or 4th ( 11 ) elementary breast cancer class is based on a bivariate classifier using the expression level of two genes selected from the group consisting of 209392_at, 210839_at, 209135_at and 210896_s_at, or selected from the group consisting of 219777_at and 213508_at, or selected from the group consisting of 218806_s_at, 218807_at and 208370_s_at; 
     (d) said assigning said sample to a 5th ( 6 ) or 6th ( 7 ) aggregate breast cancer class is based on a bivariate classifier using the absolute expression level of 208747_s_at and 38158s_at, or 216401_x_at and 204222_s_at, or 214768_x_at and 202238_s_at; 
     (e) said assigning said sample to a 5th elementary breast cancer class ( 12 ) or a 7th aggregate breast cancer class ( 13 ) is based on a bivariate classifier using the expression level of 213288_at and 204897_at, or the expression level of two genes selected from the group consisting of 203868_s_at, 203438_at and 203439_s_at, or the expression level of 209374_s_at and 203895_at; 
     (f) said assigning said sample to a 6th ( 16 ) or 7th ( 17 ) elementary breast cancer class is based on a bivariate classifier using the absolute expression level of two genes selected from the group consisting of 218468_s_at, 218469_at, 203438_at and 203439_s_at, or selected from the group consisting of 201656_at, 215177_s_at and 201627_s_at, or selected from 219197_s_at and 209291_at; 
     (g) said assigning said sample to an 8th aggregate breast cancer class ( 14 ) or a 10th elementary breast cancer class ( 15 ) is based on a bivariate classifier using the absolute expression level of two genes selected from the group consisting of 205479_s_at, 211668_s_at, 203797_at, or selected from the group consisting of 212935_at and 212494_at, or selected from the group consisting of 221530_s_at and 202177_at; 
     (h) said assigning said sample to an 8th ( 18 ) or 9th ( 19 ) elementary breast cancer class is based on a bivariate classifier using the absolute expression level of two genes selected from the group consisting of 209714_s_at and 204259_at, or selected from 209200_at and 204041_at, or selected from the group consisting of 202954_at, 208079_s_at, 204092_s_at and 218644_at. 
     Further aspects of the invention are shown in by way of the following examples. 
     EXAMPLES  
     Example 1 
     Isolation of RNA From Tumor Tissue 
     RNA Isolation From Frozen Tumour Tissue Sections 
     Frozen sections were taken for histology and the presence of breast cancer was confirmed in samples from 212 patients. Tumor cell content exceeded 30% in all cases and was above 50% in most cases. Approximately 50 mg of snap frozen breast tumour tissue was crushed in liquid nitrogen. RLT-Buffer (QIAGEN, Hilden, Germany) was added and the homogenate spun through a QIAshredder column (QIAGEN, Hilden, Germany). From the eluate total RNA was isolated by the RNeasy Kit (QIAGEN, Hilden, Germany) according to the manufacturers instruction. RNA yield was determined by UV absorbance and RNA quality was assessed by analysis of ribosomal RNA band integrity on the Agilent Bioanalyzer (Palo Alto, Calif., USA). 
     Example 2 
     Determination of Expression Levels 
     Gene Expression Measurement Utilizing HG-U133A Microarrays of Affymetrix 
     Starting from 5 μg total RNA labelled cRNA was prepared for all 212 tumour samples using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit according to the manufacturer&#39;s instruction. In brief, synthesis of first strand cDNA was done by a T7-linked oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA product was purified and then used as template for an in vitro transcription reaction (IVT) in the presence of biotinylated UTP. Labelled cRNA was hybridized to HG-U133A arrays (Santa Clara, Calif., USA) at 45° C. for 16 h in a hybridization oven at a constant rotation (60 r.p.m.) and then washed and stained with a streptavidin-phycoerythrin conjugate using the GeneChip fluidic station. We scanned the arrays at 560 nm using the GeneArray Scanner G2500A from Hewlett Packard. The readings from the quantitative scanning were analysed using the Microarray Analysis Suit 5.0 (MAS 5.0) from Affymetrix. In the analysis settings the global scaling procedure was chosen which multiplied the output signal intensities of each array to a mean target intensity of 500. Array images were visually inspected for defects and quality controlled using the Refiner Software from GeneData. Routinely we obtained over 50 percent present calls per chip as calculated by MAS 5.0. 
     Example 3 
     Labelling of Breast Cancer Samples into Subclasses After Principle Component Analysis 
     All 212*.chp files generated by MAS 5.0 were converted to *.txt Files and loaded into GeneSpring® software (Silicon Genetics, Redwood City, Calif., USA). An experiment group was created using the following normalisation settings. Values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample. Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out. Next, genes were filtered for quality with regard to the technical measurement. In a first step genes from the default list “all genes”. whose flags in the experiment group were “Present” in at least 10 of the 212 samples were selected for further analysis. Secondly, remaining genes were filtered for variable expression within the experiment group. For that purpose only genes were considered eligible for further analysis when the normalized signal intensity was above 3 or below 0.3 in at least 10 of the 212 samples. Several other cut off values used for filtering of variable genes as well as choosing genes on the basis of coefficient of variation calculations (e.g. &gt;5% for log 2 transformed signal intensities) yielded gene list of similar usefulness for subsequent principal component analysis (PCA). 
     Example 4 
     Classification of Breast Cancer Samples Into Subclasses From Expression Levels of Marker Genes 
     1. The overall classifier on the breast cancer data (n=212 samples (tissue samples) with p˜22k gene expression levels each) was derived in the following steps:
         a) A separation of the samples was carried out by distinguishing estrogen receptor negative and estrogen receptor positive samples by comparing the absolute, relative or standardized expression level of an estrogen related gene with a thresholding value. In an embodiment of the algorithm, the gene ESR1 was used with a threshold of 1000, yielding estrogen receptor state negative (called ESR− from now on) for ESR1 expressions smaller than 1000 and estrogen receptor state positive (called ESR+ from now on) for ESR1 expressions greater or equal to 1000.   b) For the both groups (ESR+ and ESR−) separately, genes with advantageous properties were identified in an unsupervised manner including general quality measures like present calls, minimum expression, minimum median expression, minimum mean expression, standardized variance, normal variance, signal-to-noise ratio and by other means on the raw or processed data (e.g. logarithmized data). In an embodiment of the method, genes were selected to be present in at least 5 samples, to have a minimum mean expression of 250 and a standardized standard deviation exceeding 8% for logarithmised data.   c) For each partial predictor, genes may be used single or in groups, where groups of genes are replaced by one or more quantity derived from the group member genes by linear or nonlinear functions of the member genes, including (but not limited to) means, medians, minimum and maximum values or principal components. In an embodiment of the method, genes sets were “pooled” to increase overall stability and take advantage of redundancy of the underlying genetic network. Clusters of co-expressed genes that had a complete correlation graph in terms of Pearson correlation to a minimum threshold of 0.8 were identified. Each “pool” of genes was replaced by a single value (for each tissue sample) by taking the arithmetic average expression of all genes in the pool.   d) A separation strategy was chosen by grouping sample labels (e.g. ESR− A,B as one group and ESR− C,D as another). The separation may use a strictly hierarchical approach, direct classification or majority decisions using sets of multiple partial classifiers. In an embodiment of the method, a strictly hierarchical separation strategy was chosen as illustrated in  FIG. 3 .   e) Each partial separation inside ESR− and ESR+ uses a multivariate per-class normal distribution to assign a class to an unknown tissue sample as described in items i), j), k) in the Summary of the Invention chapter. In an embodiment of the method, bivariate normal distributions were used to estimate pointwise in-class probabilities of an unknown sample.   f) The parameters of the multivariate distributions can be estimated from the all of the data or a subset thereof using standard statistic methods such as (but not limited to) arithmetic mean (over samples) and covariance (over samples). The parameters of the distribution may be estimated simultaneously (i.e. the value under consideration is expected to be constant over two or more classes) or separately (i.e. the value under consideration is estimated in each class separately). In an embodiment of the method, the mean and the covariance of the distribution were estimated for each class separately.   g) Parameters for the distributions may be selected by exhaustive search, steepest descent or other optimization techniques known to a scientist skilled in the art of mathematics with respect to one or more objectives measuring the performance (quality) of each possible classifier. Parameters include linear and nonlinear mappings of one or more gene expression levels. In an embodiment of the method, exhaustive search with respect to the selection of two different gene pools in the meaning of item c) was performed with the objective of minimizing the arithmetic mean of 100 ten-fold cross validation test set misclassification rates. If this objective did not yield a unique (partial) classifier, cross entropy (misclassification error) was computed for the predicted and true classes of the test set samples, and the predictor with the lowest cross entropy was chosen.   h) With the optimal set of genes determined by g), parameters of the final partial classifier distribution may be estimated in a way described in f) using either the full or a partial set of available samples. In an embodiment of the method, mean and covariance of the bivariate normal distribution was estimated for each class separately by using all samples bearing the labels under discussion in the partial classifier.       

     For the separation of (ESR1− A, ESR1− B) against (ESR1− C, ESR1− D), the following partial classifier is used:
         i) With g 1  being the mean of the binary logarithm of the absolute expression levels of genes 218211_s_at, 213441_x_at, 214404_x_at, and 220192_x_at, and g 2  being the binary logarithm of the absolute expression level of gene 208190_s_at, evaluate       

     
       
         
           
             
               
                 
                     
                    
                   
                     
                       p 
                       1 
                     
                     := 
                     
                       
                         1 
                         
                           
                             
                               
                                 ( 
                                 
                                   2 
                                   · 
                                   π 
                                 
                                 ) 
                               
                               2 
                             
                             · 
                             
                                
                               
                                 det 
                                  
                                 
                                     
                                 
                                  
                                 
                                   Σ 
                                   1 
                                 
                               
                                
                             
                           
                         
                       
                       · 
                       
                         exp 
                          
                         
                           ( 
                           
                             
                               
                                 
                                   - 
                                   
                                     1 
                                     2 
                                   
                                 
                                 · 
                                 
                                   
                                     ( 
                                     
                                       g 
                                       - 
                                       
                                         μ 
                                         1 
                                       
                                     
                                     ) 
                                   
                                   t 
                                 
                               
                                
                               
                                 Σ 
                                 1 
                                 
                                   - 
                                   1 
                                 
                               
                                
                               g 
                             
                             - 
                             
                               μ 
                               1 
                             
                           
                           ) 
                         
                       
                     
                   
                 
               
             
             
               
                 
                     
                    
                   
                     
                       p 
                       2 
                     
                     := 
                     
                       
                         1 
                         
                           
                             
                               
                                 ( 
                                 
                                   2 
                                   · 
                                   π 
                                 
                                 ) 
                               
                               2 
                             
                             · 
                             
                                
                               
                                 det 
                                  
                                 
                                     
                                 
                                  
                                 
                                   Σ 
                                   2 
                                 
                               
                                
                             
                           
                         
                       
                       · 
                       
                         exp 
                          
                         
                           ( 
                           
                             
                               
                                 - 
                                 
                                   1 
                                   2 
                                 
                               
                               · 
                               
                                 
                                   ( 
                                   
                                     g 
                                     - 
                                     
                                       μ 
                                       2 
                                     
                                   
                                   ) 
                                 
                                 t 
                               
                             
                              
                             
                               
                                 Σ 
                                 2 
                                 
                                   - 
                                   1 
                                 
                               
                                
                               
                                 ( 
                                 
                                   g 
                                   - 
                                   
                                     μ 
                                     2 
                                   
                                 
                                 ) 
                               
                             
                           
                           ) 
                         
                       
                     
                   
                 
               
             
             
               
                 
                     
                    
                   with 
                 
               
             
             
               
                 
                   
                     g 
                     := 
                     
                       ( 
                       
                         
                           
                             
                               g 
                               1 
                             
                           
                         
                         
                           
                             
                               g 
                               2 
                             
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       μ 
                       1 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             7.69 
                           
                         
                         
                           
                             10.39 
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       μ 
                       2 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             10.53 
                           
                         
                         
                           
                             9.96 
                           
                         
                       
                       ) 
                     
                   
                   , 
                 
               
             
             
               
                 
                   
                     
                       Σ 
                       1 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             0.80 
                           
                           
                             
                               - 
                               0.073 
                             
                           
                         
                         
                           
                             
                               - 
                               0.073 
                             
                           
                           
                             0.32 
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       Σ 
                       2 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             1.37 
                           
                           
                             0.71 
                           
                         
                         
                           
                             0.71 
                           
                           
                             0.92 
                           
                         
                       
                       ) 
                     
                   
                 
               
             
           
         
       
         
         
           
             If p 1 &gt;p 2 , we assign the unknown sample to the first group of clusters, ESR1− A, ESR1− B, and if not, to the second group of clusters, ESR1− C, ESR1− D. 
             ii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression values of 219572_at, g 2 : mean of binary logarithms of raw expression values of 204641_at, 207828_s_at, and 219918_s_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       8.06 
                     
                   
                   
                     
                       9.78 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       9.57 
                     
                   
                   
                     
                       8.48 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.48 
                     
                     
                       0.0078 
                     
                   
                   
                     
                       0.0078 
                     
                     
                       0.41 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.44 
                     
                     
                       0.17 
                     
                   
                   
                     
                       0.17 
                     
                     
                       0.99 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             iii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : mean of binary logarithms of raw expression values of 202580_x_at and 221436_s_at, g 2 : mean of binary logarithms of raw expression values of 202035_s_at, 202036_s_at and 202037_s_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       9.49 
                     
                   
                   
                     
                       10.76 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.12 
                     
                   
                   
                     
                       8.18 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.37 
                     
                     
                       10.76 
                     
                   
                   
                     
                       0.37 
                     
                     
                       
                         - 
                         0.33 
                       
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.66 
                     
                     
                       
                         - 
                         0.28 
                       
                     
                   
                   
                     
                       
                         - 
                         0.28 
                       
                     
                     
                       2.33 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             For the separation of (ESR1− A) against (ESR1− B), the following partial classifier is used: 
             i) With g 1  being the binary logarithm of the absolute expression level of 206978_at and g 2  being the binary logarithm of the absolute expression level of 203960_s_at evaluate 
           
         
       
    
     
       
         
           
             
               
                 
                     
                    
                   
                     
                       p 
                       1 
                     
                     := 
                     
                       
                         1 
                         
                           
                             
                               
                                 ( 
                                 
                                   2 
                                   · 
                                   π 
                                 
                                 ) 
                               
                               2 
                             
                             · 
                             
                                
                               
                                 det 
                                  
                                 
                                     
                                 
                                  
                                 
                                   Σ 
                                   1 
                                 
                               
                                
                             
                           
                         
                       
                       · 
                       
                         exp 
                          
                         
                           ( 
                           
                             
                               
                                 - 
                                 
                                   1 
                                   2 
                                 
                               
                               · 
                               
                                 
                                   ( 
                                   
                                     g 
                                     - 
                                     
                                       μ 
                                       1 
                                     
                                   
                                   ) 
                                 
                                 t 
                               
                             
                              
                             
                               
                                 Σ 
                                 1 
                                 
                                   - 
                                   1 
                                 
                               
                                
                               
                                 ( 
                                 
                                   g 
                                   - 
                                   
                                     μ 
                                     1 
                                   
                                 
                                 ) 
                               
                             
                           
                           ) 
                         
                       
                     
                   
                 
               
             
             
               
                 
                     
                    
                   
                     
                       p 
                       2 
                     
                     := 
                     
                       
                         1 
                         
                           
                             
                               
                                 ( 
                                 
                                   2 
                                   · 
                                   π 
                                 
                                 ) 
                               
                               2 
                             
                             · 
                             
                                
                               
                                 det 
                                  
                                 
                                     
                                 
                                  
                                 
                                   Σ 
                                   2 
                                 
                               
                                
                             
                           
                         
                       
                       · 
                       
                         exp 
                          
                         
                           ( 
                           
                             
                               
                                 - 
                                 
                                   1 
                                   2 
                                 
                               
                               · 
                               
                                 
                                   ( 
                                   
                                     g 
                                     - 
                                     
                                       μ 
                                       2 
                                     
                                   
                                   ) 
                                 
                                 t 
                               
                             
                              
                             
                               
                                 Σ 
                                 2 
                                 
                                   - 
                                   1 
                                 
                               
                                
                               
                                 ( 
                                 
                                   g 
                                   - 
                                   
                                     μ 
                                     2 
                                   
                                 
                                 ) 
                               
                             
                           
                           ) 
                         
                       
                     
                   
                 
               
             
             
               
                 
                     
                    
                   with 
                 
               
             
             
               
                 
                   
                     g 
                     := 
                     
                       ( 
                       
                         
                           
                             
                               g 
                               1 
                             
                           
                         
                         
                           
                             
                               g 
                               2 
                             
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       μ 
                       1 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             8.68 
                           
                         
                         
                           
                             8.61 
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       μ 
                       2 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             7.48 
                           
                         
                         
                           
                             8.29 
                           
                         
                       
                       ) 
                     
                   
                   , 
                 
               
             
             
               
                 
                   
                     
                       Σ 
                       1 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             0.56 
                           
                           
                             
                               - 
                               0.20 
                             
                           
                         
                         
                           
                             
                               - 
                               0.20 
                             
                           
                           
                             0.55 
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       Σ 
                       2 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             0.23 
                           
                           
                             
                               - 
                               0.034 
                             
                           
                         
                         
                           
                             
                               - 
                               0.034 
                             
                           
                           
                             0.18 
                           
                         
                       
                       ) 
                     
                   
                 
               
             
           
         
       
         
         
           
             If p 1 &gt;p 2 , we assign the unknown sample to the first cluster, ESR1− A, and if not, to the second cluster, ESR1− B. 
             ii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 204502_at, g 2 : binary logarithm of raw expression value of 214433_s_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       9.36 
                     
                   
                   
                     
                       9.92 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.58 
                     
                   
                   
                     
                       9.06 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.25 
                     
                     
                       
                         - 
                         0.32 
                       
                     
                   
                   
                     
                       
                         - 
                         0.32 
                       
                     
                     
                       1.47 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.22 
                     
                     
                       
                         - 
                         0.26 
                       
                     
                   
                   
                     
                       
                         - 
                         0.26 
                       
                     
                     
                       0.87 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             iii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 209374_s_at, g 2 : binary logarithm of raw expression value of 206133_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       12.48 
                     
                   
                   
                     
                       8.90 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       9.90 
                     
                   
                   
                     
                       7.71 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       2.11 
                     
                     
                       
                         - 
                         0.075 
                       
                     
                   
                   
                     
                       
                         - 
                         0.075 
                       
                     
                     
                       0.67 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       2.97 
                     
                     
                       
                         - 
                         0.44 
                       
                     
                   
                   
                     
                       
                         - 
                         0.44 
                       
                     
                     
                       0.40 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             For the separation of (ESR1− C) against (ESR1− D), the following partial classifier is used: 
             i) With g 1  being the mean of the binary logarithms of the absolute expression levels of 209392_at and 210839_s_at and g 2  being the mean of the binary logarithms of the absolute expression level of209135_at and 210896_s_at, evaluate 
           
         
       
    
     
       
         
           
             
               
                 
                     
                    
                   
                     
                       p 
                       1 
                     
                     := 
                     
                       
                         1 
                         
                           
                             
                               
                                 ( 
                                 
                                   2 
                                   · 
                                   π 
                                 
                                 ) 
                               
                               2 
                             
                             · 
                             
                                
                               
                                 det 
                                  
                                 
                                     
                                 
                                  
                                 
                                   Σ 
                                   1 
                                 
                               
                                
                             
                           
                         
                       
                       · 
                       
                         exp 
                          
                         
                           ( 
                           
                             
                               
                                 - 
                                 
                                   1 
                                   2 
                                 
                               
                               · 
                               
                                 
                                   ( 
                                   
                                     g 
                                     - 
                                     
                                       μ 
                                       1 
                                     
                                   
                                   ) 
                                 
                                 t 
                               
                             
                              
                             
                               
                                 Σ 
                                 1 
                                 
                                   - 
                                   1 
                                 
                               
                                
                               
                                 ( 
                                 
                                   g 
                                   - 
                                   
                                     μ 
                                     1 
                                   
                                 
                                 ) 
                               
                             
                           
                           ) 
                         
                       
                     
                   
                 
               
             
             
               
                 
                     
                    
                   
                     
                       p 
                       2 
                     
                     := 
                     
                       
                         1 
                         
                           
                             
                               
                                 ( 
                                 
                                   2 
                                   · 
                                   π 
                                 
                                 ) 
                               
                               2 
                             
                             · 
                             
                                
                               
                                 det 
                                  
                                 
                                     
                                 
                                  
                                 
                                   Σ 
                                   2 
                                 
                               
                                
                             
                           
                         
                       
                       · 
                       
                         exp 
                          
                         
                           ( 
                           
                             
                               
                                 - 
                                 
                                   1 
                                   2 
                                 
                               
                               · 
                               
                                 
                                   ( 
                                   
                                     g 
                                     - 
                                     
                                       μ 
                                       2 
                                     
                                   
                                   ) 
                                 
                                 t 
                               
                             
                              
                             
                               
                                 Σ 
                                 2 
                                 
                                   - 
                                   1 
                                 
                               
                                
                               
                                 ( 
                                 
                                   g 
                                   - 
                                   
                                     μ 
                                     2 
                                   
                                 
                                 ) 
                               
                             
                           
                           ) 
                         
                       
                     
                   
                 
               
             
             
               
                 
                     
                    
                   with 
                 
               
             
             
               
                 
                   
                     g 
                     := 
                     
                       ( 
                       
                         
                           
                             
                               g 
                               1 
                             
                           
                         
                         
                           
                             
                               g 
                               2 
                             
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       μ 
                       1 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             11.25 
                           
                         
                         
                           
                             8.84 
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       μ 
                       2 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             8.85 
                           
                         
                         
                           
                             10.10 
                           
                         
                       
                       ) 
                     
                   
                   , 
                 
               
             
             
               
                 
                   
                     
                       Σ 
                       1 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             0.18 
                           
                           
                             0.26 
                           
                         
                         
                           
                             0.26 
                           
                           
                             0.64 
                           
                         
                       
                       ) 
                     
                   
                   , 
                   
                     
                       Σ 
                       2 
                     
                     := 
                     
                       ( 
                       
                         
                           
                             0.97 
                           
                           
                             
                               - 
                               0.052 
                             
                           
                         
                         
                           
                             
                               - 
                               0.052 
                             
                           
                           
                             0.85 
                           
                         
                       
                       ) 
                     
                   
                 
               
             
           
         
       
         
         
           
             If p 1 &gt;p 2 , we assign the unknown sample to the first cluster, ESR1− C, and if not, to the second cluster, ESR1− D. 
             ii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 219777_at, g 2 : binary logarithm of raw expression value of 213508_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       9.89 
                     
                   
                   
                     
                       9.06 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.10 
                     
                   
                   
                     
                       10.10 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.13 
                     
                     
                       0.11 
                     
                   
                   
                     
                       0.11 
                     
                     
                       0.13 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       1.03 
                     
                     
                       0.065 
                     
                   
                   
                     
                       0.065 
                     
                     
                       0.75 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             iii) Another choice for genes, μ 1 , μ 2 , Σ 1  and Σ 2  is g 1 : mean of binary logarithms of raw expression values of 218806_s_at and 218807_at, g 2 : binary logarithm of raw expression value of 208370_s_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       8.03 
                     
                   
                   
                     
                       10.00 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       9.47 
                     
                   
                   
                     
                       9.20 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.13 
                     
                     
                       0.15 
                     
                   
                   
                     
                       0.15 
                     
                     
                       0.23 
                     
                   
                 
                 ) 
               
             
             , 
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.62 
                     
                     
                       0.022 
                     
                   
                   
                     
                       0.022 
                     
                     
                       0.41 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             For the separation of (ESR1++, ESR1+ ER, ESR1+ EM) against (ESR1+ FHL+, ESR1+ FHL++, ESR1+ LM), the following partial classifier is used: 
             i) With g 1  being the binary logarithm of the absolute expression level of 208747_s_at and g 2  being the binary logarithm of the absolute expression level of 38158_at, evaluate 
           
         
       
    
     
       
         
           
             
               p 
               1 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         1 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               1 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         1 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             1 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           
             
               p 
               2 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         2 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               2 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         2 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             2 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           with 
         
       
       
         
           
             
               g 
               := 
               
                 ( 
                 
                   
                     
                       
                         g 
                         1 
                       
                     
                   
                   
                     
                       
                         g 
                         2 
                       
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       10.82 
                     
                   
                   
                     
                       8.28 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       12.37 
                     
                   
                   
                     
                       7.54 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       1.13 
                     
                     
                       
                         - 
                         0.10 
                       
                     
                   
                   
                     
                       
                         - 
                         0.10 
                       
                     
                     
                       0.37 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.23 
                     
                     
                       0.072 
                     
                   
                   
                     
                       0.072 
                     
                     
                       0.33 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             If p 1 &gt;p 2 , we assign the unknown sample to the first group of clusters, ESR1++, ESR1+ ER, ESR1+ EM, and if not, to the second group of clusters, ESR1+ FHL+, ESR1+ FHL++, ESR1+ LM. 
             ii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression values of 216401_x_at, g 2 : binary logarithm of raw expression values of 204222_s_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       6.27 
                     
                   
                   
                     
                       7.41 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       9.73 
                     
                   
                   
                     
                       8.43 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       3.79 
                     
                     
                       0.050 
                     
                   
                   
                     
                       0.050 
                     
                     
                       0.28 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       1.43 
                     
                     
                       0.13 
                     
                   
                   
                     
                       0.13 
                     
                     
                       0.23 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             iii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression values of 214768_x_at, g 2 : binary logarithm of raw expression values of 202238_s_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       7.88 
                     
                   
                   
                     
                       9.73 
                     
                   
                 
                 ) 
               
             
             , 
             
                 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       10.05 
                     
                   
                   
                     
                       10.91 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       1.36 
                     
                     
                       
                         - 
                         0.15 
                       
                     
                   
                   
                     
                       
                         - 
                         0.15 
                       
                     
                     
                       0.97 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       1.18 
                     
                     
                       
                         - 
                         0.14 
                       
                     
                   
                   
                     
                       
                         - 
                         0.14 
                       
                     
                     
                       0.34 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             For the separation of (ESR1++) against (ESR1+ ER, ESR1+ EM), the following partial classifier is used: 
             i) With g 1  being the binary logarithm of the absolute expression level of 213288_at and g 2  being the binary logarithm of the absolute expression level of 204897_at, evaluate 
           
         
       
    
     
       
         
           
             
               p 
               1 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         1 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               1 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         1 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             1 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           
             
               p 
               2 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         2 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               2 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         2 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             2 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           with 
         
       
       
         
           
             
               g 
               := 
               
                 ( 
                 
                   
                     
                       
                         g 
                         1 
                       
                     
                   
                   
                     
                       
                         g 
                         2 
                       
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       8.89 
                     
                   
                   
                     
                       7.73 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       9.24 
                     
                   
                   
                     
                       8.51 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.15 
                     
                     
                       0.025 
                     
                   
                   
                     
                       0.025 
                     
                     
                       0.32 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.85 
                     
                     
                       
                         - 
                         0.29 
                       
                     
                   
                   
                     
                       
                         - 
                         0.29 
                       
                     
                     
                       0.49 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             If p 1 &gt; 2 , we assign the unknown sample to the first cluster, ESR1++, and if not, to the second group of clusters, ESR1+ ER, ESR1+ EM. 
             ii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 203868_s_at, g 2 : mean of binary logarithms of raw expression values of 203438_at and 203439_s_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       7.70 
                     
                   
                   
                     
                       11.04 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.68 
                     
                   
                   
                     
                       10.18 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.24 
                     
                     
                       0.00063 
                     
                   
                   
                     
                       0.00063 
                     
                     
                       1.24 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.28 
                     
                     
                       0.067 
                     
                   
                   
                     
                       0.067 
                     
                     
                       2.46 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             iii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 209374_s_at, g 2 : binary logarithm of raw expression value of 203895_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       7.47 
                     
                   
                   
                     
                       6.55 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.96 
                     
                   
                   
                     
                       7.90 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       1.32 
                     
                     
                       0.30 
                     
                   
                   
                     
                       0.30 
                     
                     
                       1.04 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       2.25 
                     
                     
                       
                         - 
                         0.46 
                       
                     
                   
                   
                     
                       
                         - 
                         0.46 
                       
                     
                     
                       1.70 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             For the separation of (ESR1+ ER) against (ESR1+ EM), the following partial classifier is used: 
             i) With g 1  being the mean of the binary logarithms of the absolute expression level of 218468_s_at and 218469_at and g 2  being the mean of the binary logarithms of the absolute expression level of 203438_at and 203439_s_at, evaluate 
           
         
       
    
     
       
         
           
             
               p 
               1 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         1 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               1 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         1 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             1 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           
             
               p 
               2 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         2 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               2 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         2 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             2 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           with 
         
       
       
         
           
             
               g 
               := 
               
                 ( 
                 
                   
                     
                       
                         g 
                         1 
                       
                     
                   
                   
                     
                       
                         g 
                         2 
                       
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       7.40 
                     
                   
                   
                     
                       11.08 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.66 
                     
                   
                   
                     
                       9.06 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       1.24 
                     
                     
                       0.41 
                     
                   
                   
                     
                       0.41 
                     
                     
                       1.73 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.77 
                     
                     
                       0.48 
                     
                   
                   
                     
                       0.48 
                     
                     
                       1.09 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             If p 1 &gt;p 2 , we assign the unknown sample to the first cluster, ESR1+ ER, and if not, to the second cluster, ESR1+ EM. 
             ii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : mean of binary logarithms of raw expression values of 201656_at and 215177_s_at, g 2 : binary logarithm of raw expression value of 201627_s_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       8.94 
                     
                   
                   
                     
                       8.77 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.17 
                     
                   
                   
                     
                       9.78 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.32 
                     
                     
                       
                         - 
                         0.031 
                       
                     
                   
                   
                     
                       
                         - 
                         0.031 
                       
                     
                     
                       0.38 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.66 
                     
                     
                       0.14 
                     
                   
                   
                     
                       0.14 
                     
                     
                       0.76 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             iii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 219197_s_at, g 2 : binary logarithm of raw expression value of 209291_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       11.69 
                     
                   
                   
                     
                       9.34 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       9.76 
                     
                   
                   
                     
                       7.75 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       1.69 
                     
                     
                       
                         - 
                         0.55 
                       
                     
                   
                   
                     
                       
                         - 
                         0.55 
                       
                     
                     
                       2.12 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       1.60 
                     
                     
                       
                         - 
                         0.29 
                       
                     
                   
                   
                     
                       
                         - 
                         0.29 
                       
                     
                     
                       1.02 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             For the separation of (ESR1+ FHL+, ESR1+ FHL++) against (ESR1+ LM), the following partial classifier is used: 
             i) With g 1  being the mean of the binary logarithms of the absolute expression level of 205479_s_at and 211668_s_at and g 2  being the binary logarithm of the absolute expression level of 203797_at, evaluate 
           
         
       
    
     
       
         
           
             
               p 
               1 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         1 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               1 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         1 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             1 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           
             
               p 
               2 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         2 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               2 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         2 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             2 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           with 
         
       
       
         
           
             
               g 
               := 
               
                 ( 
                 
                   
                     
                       
                         g 
                         1 
                       
                     
                   
                   
                     
                       
                         g 
                         2 
                       
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       9.19 
                     
                   
                   
                     
                       8.61 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       10.01 
                     
                   
                   
                     
                       8.08 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.38 
                     
                     
                       0.11 
                     
                   
                   
                     
                       0.11 
                     
                     
                       0.28 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.62 
                     
                     
                       0.25 
                     
                   
                   
                     
                       0.25 
                     
                     
                       0.22 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             If p 1 &gt;p 2 , we assign the unknown sample to the first group of clusters, ESR1+ FHL+, ESR1+ FHL++, and if not, to the second cluster, ESR1+ LM. 
             ii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 212935_at, g 2 : binary logarithm of raw expression value of 212494_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       8.49 
                     
                   
                   
                     
                       9.15 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       9.30 
                     
                   
                   
                     
                       8.59 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.92 
                     
                     
                       0.11 
                     
                   
                   
                     
                       0.11 
                     
                     
                       0.29 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       1.04 
                     
                     
                       0.31 
                     
                   
                   
                     
                       0.31 
                     
                     
                       0.097 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             iii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 221530_s_at, g 2 : binary logarithm of raw expression value of 202177_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       10.79 
                     
                   
                   
                     
                       9.23 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       10.13 
                     
                   
                   
                     
                       8.55 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.25 
                     
                     
                       0.026 
                     
                   
                   
                     
                       0.026 
                     
                     
                       0.23 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.081 
                     
                     
                       
                         - 
                         0.11 
                       
                     
                   
                   
                     
                       
                         - 
                         0.11 
                       
                     
                     
                       0.19 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             For the separation of (ESR1+ FHL++) against (ESR1+ FHL+), the following partial classifier is used: 
             i) With g 1  being the binary logarithm of the absolute expression level of 209714_s_at and g 2  being the binary logarithm of the absolute expression level of 204259_at, evaluate 
           
         
       
    
     
       
         
           
             
               p 
               1 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         1 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               1 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         1 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             1 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           
             
               p 
               2 
             
             := 
             
               
                 1 
                 
                   
                     
                       
                         ( 
                         
                           2 
                           - 
                           π 
                         
                         ) 
                       
                       2 
                     
                     - 
                     
                        
                       
                         
                           det 
                            
                           Σ 
                         
                         2 
                       
                        
                     
                   
                 
               
               · 
               
                 exp 
                  
                 
                   ( 
                   
                     
                       
                         - 
                         
                           1 
                           2 
                         
                       
                       · 
                       
                         
                           ( 
                           
                             g 
                             - 
                             
                               μ 
                               2 
                             
                           
                           ) 
                         
                         t 
                       
                     
                      
                     
                       
                         Σ 
                         2 
                         
                           - 
                           1 
                         
                       
                        
                       
                         ( 
                         
                           g 
                           - 
                           
                             μ 
                             2 
                           
                         
                         ) 
                       
                     
                   
                   ) 
                 
               
             
           
         
       
       
         
           with 
         
       
       
         
           
             
               g 
               := 
               
                 ( 
                 
                   
                     
                       
                         g 
                         1 
                       
                     
                   
                   
                     
                       
                         g 
                         2 
                       
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       7.48 
                     
                   
                   
                     
                       10.03 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.12 
                     
                   
                   
                     
                       9.20 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.17 
                     
                     
                       
                         - 
                         0.074 
                       
                     
                   
                   
                     
                       
                         - 
                         0.074 
                       
                     
                     
                       0.21 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.31 
                     
                     
                       0.33 
                     
                   
                   
                     
                       0.33 
                     
                     
                       1.16 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             If p 1 &gt;p 2 , we assign the unknown sample to the first cluster, ESR1+ FHL++, and if not, to the second cluster, ESR1+ FHL+. 
             ii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : binary logarithm of raw expression value of 209200_at, g 2 : binary logarithm of raw expression value of 204041_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       9.07 
                     
                   
                   
                     
                       11.61 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.52 
                     
                   
                   
                     
                       10.20 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.24 
                     
                     
                       0.18 
                     
                   
                   
                     
                       0.18 
                     
                     
                       0.34 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.19 
                     
                     
                       
                         - 
                         0.011 
                       
                     
                   
                   
                     
                       
                         - 
                         0.101 
                       
                     
                     
                       2.29 
                     
                   
                 
                 ) 
               
             
           
         
       
         
         
           
             iii) Another choice for genes, μ 1 , μ 2 , Σ 1 , and Σ 2  is g 1 : mean of binary logarithms of raw expression values of 202954_at, 208079_s_at, and 204092_s_at, g 2 : binary logarithm of raw expression value of 218644_at, and 
           
         
       
    
     
       
         
           
             
               
                 μ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       7.52 
                     
                   
                   
                     
                       8.15 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 μ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       8.24 
                     
                   
                   
                     
                       8.34 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 1 
               
               := 
               
                 ( 
                 
                   
                     
                       0.16 
                     
                     
                       
                         - 
                         0.049 
                       
                     
                   
                   
                     
                       
                         - 
                         0.049 
                       
                     
                     
                       0.073 
                     
                   
                 
                 ) 
               
             
             , 
             
               
 
             
              
             
               
                 Σ 
                 2 
               
               := 
               
                 ( 
                 
                   
                     
                       0.25 
                     
                     
                       
                         - 
                         0.099 
                       
                     
                   
                   
                     
                       
                         - 
                         0.099 
                       
                     
                     
                       0.31 
                     
                   
                 
                 ) 
               
             
           
         
       
     
     2. Classification of an unknown sample is done by measuring the gene expression levels of some or all of the genes used in the partial classifiers (including an estrogen receptor related gene), determining the estrogen receptor state and then using one or more partial classifiers to subsequently assign the given unknown probe to one or more class or groups of classes using the partial classifiers obtained on a training set in step 1. 
     It is to be understood that alternative marker genes can be used for classification according to the present invention, in particular if said alternative marker genes show a similar expression pattern as show those used in the examples above. Alternative marker genes useful in methods and systems of the invention are listed in Tables 1-8 below. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Genes useful for separation of ESR1-A, ESR1-B &lt;-&gt; ESR1-C, ESR1-D 
               
            
           
           
               
               
               
               
            
               
                 Affymetrix 
                 GenBank 
                   
                   
               
               
                 Probe Set ID 
                 Accession 
               
               
                 HG U133A 
                 No 
                 Gene Symbol 
                 Unigene ID 
               
               
                   
               
               
                 55616_at 
                 AI703342 
                 CAB2 
                 Hs.91668 
               
               
                 51158_at 
                 AI801973 
                 — 
                 Hs.27373 
               
               
                 32094_at 
                 AB017915 
                 CHST3 
                 Hs.158304 
               
               
                 222258_s_at 
                 AF015043.1 
                 SH3BP4 
                 Hs.17667 
               
               
                 222039_at 
                 AA292789 
                 LOC146909 
                 Hs.433234 
               
               
                 221922_at 
                 AW195581 
                 LGN 
                 Hs.278338 
               
               
                 221880_s_at 
                 AI279819 
                 — 
                 Hs.27373 
               
               
                 221811_at 
                 BF033007 
                 CAB2 
                 Hs.91668 
               
               
                 221521_s_at 
                 BC003186.1 
                 LOC51659 
                 Hs.433180 
               
               
                 221505_at 
                 AW612574 
                 LANPL 
                 Hs.71331 
               
               
                 221436_s_at 
                 NM_031299 
                 GRCC8 
                 Hs.30114 
               
               
                 221185_s_at 
                 NM_025111 
                 DKFZp434B227 
                 Hs.334483 
               
               
                 221024_s_at 
                 NM_030777 
                 SLC2A10 
                 Hs.305971 
               
               
                 220651_s_at 
                 NM_018518 
                 MCM10 
                 Hs.198363 
               
               
                 220625_s_at 
                 AF115403.1 
                 ELF5 
                 Hs.11713 
               
               
                 220559_at 
                 NM_001426 
                 EN1 
                 Hs.271977 
               
               
                 220425_x_at 
                 NM_017578 
                 ROPN1 
                 Hs.194093 
               
               
                 220192_x_at 
                 NM_012391 
                 PDEF 
                 Hs.79414 
               
               
                 219959_at 
                 NM_017947 
                 HMCS 
                 Hs.157986 
               
               
                 219918_s_at 
                 NM_018123 
                 ASPM 
                 Hs.121028 
               
               
                 219768_at 
                 NM_024626 
                 FLJ22418 
                 Hs.36563 
               
               
                 219735_s_at 
                 NM_014553 
                 LBP-9 
                 Hs.114747 
               
               
                 219582_at 
                 NM_024576 
                 FLJ21079 
                 Hs.16512 
               
               
                 219572_at 
                 NM_017954 
                 FLJ20761 
                 Hs.107872 
               
               
                 219498_s_at 
                 NM_018014 
                 BCL11A 
                 Hs.130881 
               
               
                 219497_s_at 
                 NM_022893 
                 BCL11A 
                 Hs.130881 
               
               
                 219157_at 
                 NM_007246 
                 KLHL2 
                 Hs.122967 
               
               
                 219148_at 
                 NM_018492 
                 TOPK 
                 Hs.104741 
               
               
                 218918_at 
                 NM_020379 
                 MAN1C1 
                 Hs.8910 
               
               
                 218870_at 
                 NM_018460 
                 ARHGAP15 
                 Hs.177812 
               
               
                 218807_at 
                 NM_006113 
                 VAV3 
                 Hs.267659 
               
               
                 218806_s_at 
                 AF118887.1 
                 VAV3 
                 Hs.267659 
               
               
                 218782_s_at 
                 NM_014109 
                 PRO2000 
                 Hs.222088 
               
               
                 218726_at 
                 NM_018410 
                 DKFZp762E1312 
                 Hs.104859 
               
               
                 218665_at 
                 NM_012193 
                 FZD4 
                 Hs.19545 
               
               
                 218542_at 
                 NM_018131 
                 C10orf3 
                 Hs.14559 
               
               
                 218502_s_at 
                 NM_014112 
                 TRPS1 
                 Hs.26102 
               
               
                 218353_at 
                   
                 RGS5 
                 Hs.274368 
               
               
                 218331_s_at 
                 NM_017782 
                 FLJ20360 
                 Hs.26434 
               
               
                 218298_s_at 
                 NM_024952 
                 FLJ20950 
                 Hs.285673 
               
               
                 218211_s_at 
                 NM_024101 
                 MLPH 
                 Hs.297405 
               
               
                 218009_s_at 
                 NM_003981 
                 PRC1 
                 Hs.344037 
               
               
                 217989_at 
                 NM_016245 
                 RetSDR2 
                 Hs.12150 
               
               
                 217901_at 
                 BF031829 
                 — 
                 Hs.348710 
               
               
                 216836_s_at 
                 X03363.1 
                 ERBB2 
                 Hs.323910 
               
               
                 216092_s_at 
                 AL365347.1 
                 SLC7A8 
                 Hs.22891 
               
               
                 215945_s_at 
                 BC005016.1 
                 TRIM2 
                 Hs.12372 
               
               
                 215726_s_at 
                 M22976.1 
                 CYB5 
                 Hs.83834 
               
               
                 215034_s_at 
                 AI189753 
                 TM4SF1 
                 Hs.409060 
               
               
                 214667_s_at 
                 AK026607.1 
                 PIG11 
                 Hs.433813 
               
               
                 214404_x_at 
                 AI307915 
                 PDEF 
                 Hs.79414 
               
               
                 213441_x_at 
                 AI745526 
                 PDEF 
                 Hs.79414 
               
               
                 213260_at 
                 AU145890 
                 — 
                 Hs.284186 
               
               
                 213226_at 
                 AI346350 
                 PMSCL1 
                 Hs.91728 
               
               
                 213122_at 
                 AI096375 
                 KIAA1750 
                 Hs.173094 
               
               
                 213060_s_at 
                 U58515.1 
                 CHI3L2 
                 Hs.154138 
               
               
                 212771_at 
                 AU150943 
                 LOC221061 
                 Hs.66762 
               
               
                 212730_at 
                 AK026420.1 
                 DMN 
                 Hs.10587 
               
               
                 212708_at 
                 AV721987 
                 — 
                 Hs.184779 
               
               
                 212594_at 
                 N92498 
                 — 
                 Hs.326248 
               
               
                 212510_at 
                 AA135522 
                 KIAA0089 
                 Hs.82432 
               
               
                 212458_at 
                 AW138902 
                 LOC200734 
                 Hs.173108 
               
               
                 212256_at 
                 BE906572 
                 GALNT10 
                 Hs.107260 
               
               
                 211709_s_at 
                 BC005810.1 
                 SCGF 
                 Hs.425339 
               
               
                 211657_at 
                 M18728.1 
                 CEACAM6 
                 Hs.73848 
               
               
                 210933_s_at 
                 BC004908.1 
                 MGC4655 
                 Hs.381638 
               
               
                 210761_s_at 
                 AB008790.1 
                 GRB7 
                 Hs.86859 
               
               
                 210605_s_at 
                 BC003610.1 
                 MFGE8 
                 Hs.3745 
               
               
                 210559_s_at 
                 D88357.1 
                 CDC2 
                 Hs.334562 
               
               
                 209897_s_at 
                 AF055585.1 
                 SLIT2 
                 Hs.29802 
               
               
                 209842_at 
                 AI367319 
                 SOX10 
                 Hs.44317 
               
               
                 209747_at 
                 J03241.1 
                 TGFB3 
                 Hs.2025 
               
               
                 209504_s_at 
                 AF081583.1 
                 PLEKHB1 
                 Hs.380812 
               
               
                 209396_s_at 
                 M80927.1 
                 CHI3L1 
                 Hs.75184 
               
               
                 209395_at 
                 M80927.1 
                 CHI3L1 
                 Hs.75184 
               
               
                 209387_s_at 
                 M90657.1 
                 TM4SF1 
                 Hs.351316 
               
               
                 209366_x_at 
                 M22865.1 
                 CYB5 
                 Hs.83834 
               
               
                 209173_at 
                 AF088867.1 
                 AGR2 
                 Hs.91011 
               
               
                 209071_s_at 
                 AF159570.1 
                 RGS5 
                 Hs.24950 
               
               
                 209070_s_at 
                 AI183997 
                 RGS5 
                 Hs.24950 
               
               
                 208998_at 
                 U94592.1 
                 UCP2 
                 Hs.80658 
               
               
                 208190_s_at 
                 NM_015925 
                 LISCH7 
                 Hs.95697 
               
               
                 208103_s_at 
                 NM_030920 
                 LANPL 
                 Hs.71331 
               
               
                 208072_s_at 
                 NM_003648 
                 DGKD 
                 Hs.115907 
               
               
                 208009_s_at 
                 NM_014448 
                 ARHGEF16 
                 Hs.87435 
               
               
                 207843_x_at 
                 NM_001914 
                 CYB5 
                 Hs.83834 
               
               
                 207828_s_at 
                 NM_005196 
                 CENPF 
                 Hs.77204 
               
               
                 207357_s_at 
                 NM_017540 
                 GALNT10 
                 Hs.107260 
               
               
                 206560_s_at 
                 NM_006533 
                 MIA 
                 Hs.279651 
               
               
                 205453_at 
                 NM_002145 
                 HOXB2 
                 Hs.2733 
               
               
                 205405_at 
                 NM_003966 
                 SEMA5A 
                 Hs.27621 
               
               
                 205240_at 
                 NM_013296 
                 LGN 
                 Hs.278338 
               
               
                 205044_at 
                 NM_014211 
                 GABRP 
                 Hs.70725 
               
               
                 204855_at 
                 NM_002639 
                 SERPINB5 
                 Hs.55279 
               
               
                 204825_at 
                 NM_014791 
                 MELK 
                 Hs.184339 
               
               
                 204822_at 
                 NM_003318 
                 TTK 
                 Hs.169840 
               
               
                 204751_x_at 
                 NM_004949 
                 DSC2 
                 Hs.239727 
               
               
                 204641_at 
                 NM_002497 
                 NEK2 
                 Hs.153704 
               
               
                 204613_at 
                 NM_002661 
                 PLCG2 
                 Hs.75648 
               
               
                 204288_s_at 
                 NM_021069 
                 ARGBP2 
                 Hs.379795 
               
               
                 204285_s_at 
                 AI857639 
                 PMAIP1 
                 Hs.96 
               
               
                 204259_at 
                 NM_002423 
                 MMP7 
                 Hs.2256 
               
               
                 204153_s_at 
                 NM_002405 
                 MFNG 
                 Hs.31939 
               
               
                 204146_at 
                 BE966146 
                 PIR51 
                 Hs.24596 
               
               
                 204030_s_at 
                 NM_014575 
                 SCHIP1 
                 Hs.61490 
               
               
                 204015_s_at 
                 BC002671.1 
                 DUSP4 
                 Hs.2359 
               
               
                 203764_at 
                 NM_014750 
                 DLG7 
                 Hs.77695 
               
               
                 203706_s_at 
                 NM_003507 
                 FZD7 
                 Hs.173859 
               
               
                 203705_s_at 
                 AI333651 
                 FZD7 
                 Hs.173859 
               
               
                 203693_s_at 
                 NM_001949 
                 E2F3 
                 Hs.1189 
               
               
                 203592_s_at 
                 NM_005860 
                 FSTL3 
                 Hs.433827 
               
               
                 203570_at 
                 NM_005576 
                 LOXL1 
                 Hs.65436 
               
               
                 203362_s_at 
                 NM_002358 
                 MAD2L1 
                 Hs.79078 
               
               
                 203358_s_at 
                 NM_004456 
                 EZH2 
                 Hs.77256 
               
               
                 203343_at 
                 NM_003359 
                 UGDH 
                 Hs.28309 
               
               
                 203214_x_at 
                 NM_001786 
                 CDC2 
                 Hs.334562 
               
               
                 203213_at 
                 AL524035 
                 CDC2 
                 Hs.334562 
               
               
                 202996_at 
                 NM_021173 
                 POLD4 
                 Hs.82520 
               
               
                 202991_at 
                 NM_006804 
                 STARD3 
                 Hs.77628 
               
               
                 202948_at 
                 NM_000877 
                 IL1R1 
                 Hs.82112 
               
               
                 202870_s_at 
                 NM_001255 
                 CDC20 
                 Hs.82906 
               
               
                 202752_x_at 
                 NM_012244 
                 SLC7A8 
                 Hs.22891 
               
               
                 202747_s_at 
                 NM_004867 
                 ITM2A 
                 Hs.17109 
               
               
                 202746_at 
                 AL021786 
                 ITM2A 
                 Hs.17109 
               
               
                 202589_at 
                 NM_001071 
                 TYMS 
                 Hs.29475 
               
               
                 202580_x_at 
                 NM_021953 
                 FOXM1 
                 Hs.239 
               
               
                 202412_s_at 
                 AW499935 
                 USP1 
                 Hs.35086 
               
               
                 202345_s_at 
                 NM_001444 
                 FABP5 
                 Hs.153179 
               
               
                 202342_s_at 
                 NM_015271 
                 TRIM2 
                 Hs.12372 
               
               
                 202236_s_at 
                 NM_003051 
                 SLC16A1 
                 Hs.75231 
               
               
                 202037_s_at 
                 NM_003012 
                 SFRP1 
                 Hs.7306 
               
               
                 202036_s_at 
                 AF017987.1 
                 SFRP1 
                 Hs.7306 
               
               
                 202035_s_at 
                 AI332407 
                 SFRP1 
                 Hs.7306 
               
               
                 201819_at 
                 NM_005505 
                 SCARB1 
                 Hs.180616 
               
               
                 201564_s_at 
                 NM_003088 
                 FSCN1 
                 Hs.118400 
               
               
                 201292_at 
                 NM_001067.1 
                 TOP2A 
                 Hs.156346 
               
               
                 201291_s_at 
                 NM_001067.1 
                 TOP2A 
                 Hs.156346 
               
               
                 201117_s_at 
                 NM_001873 
                 CPE 
                 Hs.75360 
               
               
                 201116_s_at 
                 AI922855 
                 CPE 
                 Hs.75360 
               
               
                 200824_at 
                 NM_000852 
                 GSTP1 
                 Hs.226795 
               
               
                 200783_s_at 
                 NM_005563 
                 STMN1 
                 Hs.406269 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Genes useful for separation of ESR1-A &lt;-&gt; ESR1-B 
               
            
           
           
               
               
               
               
            
               
                 Affymetrix 
                 GenBank 
                   
                   
               
               
                 Probe Set ID HG 
                 Accession 
               
               
                 U133A 
                 No 
                 Gene Symbol 
                 Unigene ID 
               
               
                   
               
               
                 38149_at 
                 D29642 
                 KIAA0053 
                 Hs.1528 
               
               
                 34210_at 
                 N90866 
                 CDW52 
                 Hs.276770 
               
               
                 219812_at 
                 NM_024070 
                 MGC2463 
                 Hs.323634 
               
               
                 219716_at 
                 NM_030641 
                 APOL6 
                 Hs.257352 
               
               
                 219630_at 
                 NM_005764 
                 DD96 
                 Hs.271473 
               
               
                 219243_at 
                 NM_018326 
                 HIMAP4 
                 Hs.30822 
               
               
                 219157_at 
                 NM_007246 
                 KLHL2 
                 Hs.122967 
               
               
                 217236_x_at 
                 S74639.1 
                 IGHM 
                 Hs.153261 
               
               
                 215603_x_at 
                 AI344075 
                 GGT2 
                 Hs.289098 
               
               
                 215189_at 
                 X99142.1 
                 KRTHB6 
                 Hs.278658 
               
               
                 214916_x_at 
                 BG340548 
                 IGHM 
                 Hs.153261 
               
               
                 214777_at 
                 BG482805 
                 IGKC 
                 Hs.406565 
               
               
                 214765_s_at 
                 AK024677.1 
                 ASAHL 
                 Hs.264330 
               
               
                 214620_x_at 
                 BF038548 
                 PAM 
                 Hs.83920 
               
               
                 214617_at 
                 AI445650 
                 PRF1 
                 Hs.411106 
               
               
                 214433_s_at 
                 NM_003944.1 
                 SELENBP1 
                 Hs.334841 
               
               
                 214339_s_at 
                 AA744529 
                 MAP4K1 
                 Hs.95424 
               
               
                 214239_x_at 
                 AI560455 
                 LOC284106 
                 Hs.184669 
               
               
                 213958_at 
                 AW134823 
                 CD6 
                 Hs.81226 
               
               
                 213603_s_at 
                 BE138888 
                 RAC2 
                 Hs.367740 
               
               
                 213551_x_at 
                 AI744229 
                 LOC284106 
                 Hs.184669 
               
               
                 213539_at 
                 NM_000732.1 
                 CD3D 
                 Hs.95327 
               
               
                 213193_x_at 
                 AL559122 
                 TRB@ 
                 Hs.303157 
               
               
                 213036_x_at 
                 Y15724 
                 ATP2A3 
                 Hs.5541 
               
               
                 213004_at 
                 AF007150.1 
                 ANGPTL2 
                 Hs.8025 
               
               
                 213001_at 
                 AF007150.1 
                 ANGPTL2 
                 Hs.8025 
               
               
                 212914_at 
                 AV648364 
                 CBX7 
                 Hs.356416 
               
               
                 212588_at 
                 AI809341 
                 PTPRC 
                 Hs.170121 
               
               
                 212587_s_at 
                 AI809341 
                 PTPRC 
                 Hs.170121 
               
               
                 212538_at 
                 AL576253 
                 zizimini 1 
                 Hs.8021 
               
               
                 212415_at 
                 D50918.1 
                 6-Sep 
                 Hs.90998 
               
               
                 212314_at 
                 AB018289.1 
                 KIAA0746 
                 Hs.49500 
               
               
                 212311_at 
                 AB018289.1 
                 KIAA0746 
                 Hs.49500 
               
               
                 212233_at 
                 AL523076 
                 — 
                 Hs.82503 
               
               
                 211998_at 
                 NM_005324.1 
                 H3F3B 
                 Hs.180877 
               
               
                 211902_x_at 
                 L34703.1 
                 TRA@ 
                 Hs.74647 
               
               
                 211796_s_at 
                 AF043179.1 
                 TRB@ 
                 Hs.303157 
               
               
                 211795_s_at 
                 AF198052.1 
                 FYB 
                 Hs.58435 
               
               
                 211742_s_at 
                 BC005926.1 
                 EVI2B 
                 Hs.5509 
               
               
                 211639_x_at 
                 L23518.1 
                 IGHM 
                 Hs.153261 
               
               
                 211417_x_at 
                 L20493.1 
                 — 
                 Hs.352120 
               
               
                 211339_s_at 
                 D13720.1 
                 ITK 
                 Hs.211576 
               
               
                 211277_x_at 
                 BC004369.1 
                 APP 
                 Hs.177486 
               
               
                 211138_s_at 
                 BC005297.1 
                 KMO 
                 Hs.107318 
               
               
                 210972_x_at 
                 M15565.1 
                 TRA@ 
                 Hs.74647 
               
               
                 210915_x_at 
                 M15564.1 
                 TRB@ 
                 Hs.303157 
               
               
                 210629_x_at 
                 AF000425.1 
                 LST1 
                 Hs.380427 
               
               
                 210140_at 
                 AF031824.1 
                 CST7 
                 Hs.143212 
               
               
                 210031_at 
                 J04132.1 
                 CD3Z 
                 Hs.97087 
               
               
                 210029_at 
                 M34455.1 
                 INDO 
                 Hs.840 
               
               
                 209919_x_at 
                 L20490.1 
                 GGTL4 
                 Hs.352119 
               
               
                 209879_at 
                 AI741056 
                 SELPLG 
                 Hs.79283 
               
               
                 209846_s_at 
                 BC002832.1 
                 BTN3A2 
                 Hs.87497 
               
               
                 209827_s_at 
                 NM_004513.1 
                 IL16 
                 Hs.82127 
               
               
                 209671_x_at 
                 M12423.1 
                 TRA@ 
                 Hs.74647 
               
               
                 209670_at 
                 M12959.1 
                 TRA@ 
                 Hs.74647 
               
               
                 209606_at 
                 L06633.1 
                 PSCDBP 
                 Hs.270 
               
               
                 209499_x_at 
                 BF448647 
                 TNFSF13 
                 Hs.54673 
               
               
                 209374_s_at 
                 BC001872.1 
                 IGHM 
                 Hs.153261 
               
               
                 209355_s_at 
                 AB000889.1 
                 PPAP2B 
                 Hs.432840 
               
               
                 209351_at 
                 BC002690.1 
                 KRT14 
                 Hs.355214 
               
               
                 209205_s_at 
                 BC003600.1 
                 LMO4 
                 Hs.3844 
               
               
                 209083_at 
                 U34690.1 
                 CORO1A 
                 Hs.109606 
               
               
                 208284_x_at 
                 NM_013421 
                 GGT1 
                 Hs.401847 
               
               
                 208078_s_at 
                 NM_030751 
                 TCF8 
                 Hs.232068 
               
               
                 207238_s_at 
                 NM_002838 
                 PTPRC 
                 Hs.170121 
               
               
                 207131_x_at 
                 NM_013430 
                 GGT1 
                 Hs.401847 
               
               
                 206978_at 
                 NM_000647 
                 CCR2 
                 Hs.395 
               
               
                 206666_at 
                 NM_002104 
                 GZMK 
                 Hs.3066 
               
               
                 206227_at 
                 NM_003613 
                 CILP 
                 Hs.151407 
               
               
                 206150_at 
                 NM_001242 
                 TNFRSF7 
                 Hs.355307 
               
               
                 206133_at 
                 NM_017523 
                 HSXIAPAF1 
                 Hs.139262 
               
               
                 206118_at 
                 NM_003151 
                 STAT4 
                 Hs.80642 
               
               
                 206082_at 
                 NM_006674 
                 P5-1 
                 Hs.1845 
               
               
                 205977_s_at 
                 NM_005232 
                 EPHA1 
                 Hs.89839 
               
               
                 205965_at 
                 NM_006399 
                 BATF 
                 Hs.41691 
               
               
                 205890_s_at 
                 NM_006398 
                 UBD 
                 Hs.44532 
               
               
                 205842_s_at 
                 AF001362.1 
                 JAK2 
                 Hs.115541 
               
               
                 205831_at 
                 NM_001767 
                 CD2 
                 Hs.89476 
               
               
                 205821_at 
                 NM_007360 
                 D12S2489E 
                 Hs.74085 
               
               
                 205798_at 
                 NM_002185 
                 IL7R 
                 Hs.362807 
               
               
                 205692_s_at 
                 NM_001775 
                 CD38 
                 Hs.66052 
               
               
                 205569_at 
                 NM_014398 
                 LAMP3 
                 Hs.10887 
               
               
                 205456_at 
                 NM_000733 
                 CD3E 
                 Hs.3003 
               
               
                 205306_x_at 
                 AI074145 
                 KMO 
                 Hs.107318 
               
               
                 205120_s_at 
                 U29586.1 
                 SGCB 
                 Hs.77501 
               
               
                 205060_at 
                 NM_003631 
                 PARG 
                 Hs.91390 
               
               
                 204951_at 
                 NM_004310 
                 ARHH 
                 Hs.109918 
               
               
                 204949_at 
                 NM_002162 
                 ICAM3 
                 Hs.99995 
               
               
                 204912_at 
                 NM_001558 
                 IL10RA 
                 Hs.327 
               
               
                 204891_s_at 
                 NM_005356 
                 LCK 
                 Hs.1765 
               
               
                 204855_at 
                 NM_002639 
                 SERPINB5 
                 Hs.55279 
               
               
                 204834_at 
                 NM_006682 
                 FGL2 
                 Hs.351808 
               
               
                 204774_at 
                 NM_014210 
                 EVI2A 
                 Hs.70499 
               
               
                 204677_at 
                 NM_001795 
                 CDH5 
                 Hs.76206 
               
               
                 204661_at 
                 NM_001803 
                 CDW52 
                 Hs.276770 
               
               
                 204655_at 
                 NM_002985 
                 CCL5 
                 Hs.241392 
               
               
                 204638_at 
                 NM_001611 
                 ACP5 
                 Hs.1211 
               
               
                 204613_at 
                 NM_002661 
                 PLCG2 
                 Hs.75648 
               
               
                 204502_at 
                 NM_015474 
                 SAMHD1 
                 Hs.23889 
               
               
                 204416_x_at 
                 NM_001645 
                 APOC1 
                 Hs.268571 
               
               
                 204279_at 
                 NM_002800 
                 PSMB9 
                 Hs.381081 
               
               
                 204205_at 
                 NM_021822 
                 APOBEC3G 
                 Hs.250619 
               
               
                 204192_at 
                 NM_001774 
                 CD37 
                 Hs.153053 
               
               
                 204141_at 
                 NM_001069 
                 TUBB 
                 Hs.336780 
               
               
                 204118_at 
                 NM_001778 
                 CD48 
                 Hs.901 
               
               
                 204116_at 
                 NM_000206 
                 IL2RG 
                 Hs.84 
               
               
                 203960_s_at 
                 NM_016126 
                 LOC51668 
                 Hs.46967 
               
               
                 203951_at 
                 NM_001299 
                 CNN1 
                 Hs.21223 
               
               
                 203923_s_at 
                 NM_000397 
                 CYBB 
                 Hs.88974 
               
               
                 203853_s_at 
                 NM_012296 
                 GAB2 
                 Hs.30687 
               
               
                 203793_x_at 
                 NM_007144 
                 ZNF144 
                 Hs.184669 
               
               
                 203760_s_at 
                 U44403.1 
                 SLA 
                 Hs.75367 
               
               
                 203233_at 
                 NM_000418 
                 IL4R 
                 Hs.75545 
               
               
                 203052_at 
                 NM_000063 
                 C2 
                 Hs.2253 
               
               
                 202957_at 
                 NM_005335 
                 HCLS1 
                 Hs.14601 
               
               
                 202902_s_at 
                 NM_004079 
                 CTSS 
                 Hs.181301 
               
               
                 202664_at 
                 AI005043 
                 — 
                 Hs.24143 
               
               
                 202575_at 
                 NM_001878 
                 CRABP2 
                 Hs.183650 
               
               
                 202528_at 
                 NM_000403 
                 GALE 
                 Hs.76057 
               
               
                 202409_at 
                 X07868 
                 — 
                 Hs.251664 
               
               
                 202307_s_at 
                 NM_000593 
                 TAP1 
                 Hs.180062 
               
               
                 202273_at 
                 NM_002609 
                 PDGFRB 
                 Hs.76144 
               
               
                 202240_at 
                 NM_005030 
                 PLK 
                 Hs.433619 
               
               
                 202147_s_at 
                 NM_001550 
                 IFRD1 
                 Hs.7879 
               
               
                 202146_at 
                 AA747426 
                 IFRD1 
                 Hs.7879 
               
               
                 201858_s_at 
                 J03223.1 
                 PRG1 
                 Hs.1908 
               
               
                 201694_s_at 
                 NM_001964 
                 EGR1 
                 Hs.326035 
               
               
                 201693_s_at 
                 AV733950 
                 EGR1 
                 Hs.326035 
               
               
                 201497_x_at 
                 NM_022844 
                 MYH11 
                 Hs.78344 
               
               
                 201450_s_at 
                 NM_022037 
                 TIA1 
                 Hs.239489 
               
               
                 201313_at 
                 NM_001975 
                 ENO2 
                 Hs.146580 
               
               
                 200824_at 
                 NM_000852 
                 GSTP1 
                 Hs.226795 
               
               
                 200632_s_at 
                 NM_006096 
                 NDRG1 
                 Hs.75789 
               
               
                 1405_i_at 
                 M21121 
                 CCL5 
                 Hs.241392 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Genes useful for separation of ESR1-C &lt;-&gt; ESR1-D 
               
            
           
           
               
               
               
               
            
               
                 Affymetrix 
                   
                   
                   
               
               
                 Probe Set ID 
                 GenBank 
               
               
                 HG U133A 
                 Accession No 
                 Gene Symbol 
                 Unigene ID 
               
               
                   
               
               
                 58780_s_at 
                 R42449 
                 FLJ10357 
                 Hs.22451 
               
               
                 55616_at 
                 AI703342 
                 CAB2 
                 Hs.91668 
               
               
                 38149_at 
                 D29642 
                 KIAA0053 
                 Hs.1528 
               
               
                 37117_at 
                 Z83838 
                 ARHGAP8 
                 Hs.102336 
               
               
                 34210_at 
                 N90866 
                 CDW52 
                 Hs.276770 
               
               
                 221811_at 
                 BF033007 
                 CAB2 
                 Hs.91668 
               
               
                 221601_s_at 
                 AI084226 
                 TOSO 
                 Hs.58831 
               
               
                 220625_s_at 
                 AF115403.1 
                 ELF5 
                 Hs.11713 
               
               
                 220425_x_at 
                 NM_017578 
                 ROPN1 
                 Hs.194093 
               
               
                 220326_s_at 
                 NM_018071 
                 FLJ10357 
                 Hs.22451 
               
               
                 220192_x_at 
                 NM_012391 
                 PDEF 
                 Hs.79414 
               
               
                 219812_at 
                 NM_024070 
                 MGC2463 
                 Hs.323634 
               
               
                 219777_at 
                 NM_024711 
                 hIAN2 
                 Hs.105468 
               
               
                 219471_at 
                 NM_025113 
                 C13orf18 
                 Hs.288708 
               
               
                 219411_at 
                 NM_024712 
                 ELMO3 
                 Hs.105861 
               
               
                 219395_at 
                 NM_024939 
                 FLJ21918 
                 Hs.282093 
               
               
                 219388_at 
                 NM_024915 
                 FLJ13782 
                 Hs.257924 
               
               
                 219304_s_at 
                 NM_025208 
                 SCDGF-B 
                 Hs.112885 
               
               
                 219143_s_at 
                 NM_017793 
                 FLJ20374 
                 Hs.8562 
               
               
                 219127_at 
                 NM_024320 
                 MGC11242 
                 Hs.36529 
               
               
                 219010_at 
                 NM_018265 
                 FLJ10901 
                 Hs.73239 
               
               
                 218959_at 
                 NM_017409 
                 HOXC10 
                 Hs.44276 
               
               
                 218913_s_at 
                 NM_016573 
                 GMIP 
                 Hs.49427 
               
               
                 218856_at 
                 NM_016629 
                 TNFRSF21 
                 Hs.159651 
               
               
                 218816_at 
                 NM_018214 
                 LANO 
                 Hs.35091 
               
               
                 218807_at 
                 NM_006113 
                 VAV3 
                 Hs.267659 
               
               
                 218806_s_at 
                 AF118887.1 
                 VAV3 
                 Hs.267659 
               
               
                 218805_at 
                 NM_018384 
                 IAN4L1 
                 Hs.26194 
               
               
                 218678_at 
                 NM_024609 
                 FLJ21841 
                 Hs.29076 
               
               
                 218507_at 
                 NM_013332 
                 HIG2 
                 Hs.61762 
               
               
                 218380_at 
                 NM_021730 
                 PP1044 
                 Hs.7212 
               
               
                 218211_s_at 
                 NM_024101 
                 MLPH 
                 Hs.297405 
               
               
                 218186_at 
                 NM_020387 
                 RAB25 
                 Hs.150826 
               
               
                 218180_s_at 
                 NM_022772 
                 EPS8R2 
                 Hs.55016 
               
               
                 218145_at 
                 NM_021158 
                 C20orf97 
                 Hs.26802 
               
               
                 217904_s_at 
                 NM_012104 
                 BACE 
                 Hs.49349 
               
               
                 217767_at 
                 NM_000064 
                 C3 
                 Hs.284394 
               
               
                 217236_x_at 
                 S74639.1 
                 IGHM 
                 Hs.153261 
               
               
                 216836_s_at 
                 X03363.1 
                 ERBB2 
                 Hs.323910 
               
               
                 216381_x_at 
                 AL035413 
                 AKR7A3 
                 Hs.284236 
               
               
                 216033_s_at 
                 S74774.1 
                 FYN 
                 Hs.169370 
               
               
                 215785_s_at 
                 AL161999.1 
                 CYFIP2 
                 Hs.258503 
               
               
                 215726_s_at 
                 M22976.1 
                 CYB5 
                 Hs.83834 
               
               
                 215471_s_at 
                 AJ242502.1 
                 MAP7 
                 Hs.146388 
               
               
                 214617_at 
                 AI445650 
                 PRF1 
                 Hs.411106 
               
               
                 214581_x_at 
                 BE568134 
                 TNFRSF21 
                 Hs.159651 
               
               
                 214505_s_at 
                 AF220153.1 
                 FHL1 
                 Hs.239069 
               
               
                 214439_x_at 
                 AF043899.1 
                 BIN1 
                 Hs.193163 
               
               
                 214404_x_at 
                 AI307915 
                 PDEF 
                 Hs.79414 
               
               
                 214175_x_at 
                 BE043700 
                 RIL 
                 Hs.424312 
               
               
                 214038_at 
                 AI984980 
                 CCL8 
                 Hs.271387 
               
               
                 213620_s_at 
                 AA126728 
                 ICAM2 
                 Hs.433303 
               
               
                 213603_s_at 
                 BE138888 
                 RAC2 
                 Hs.367740 
               
               
                 213539_at 
                 NM_000732.1 
                 CD3D 
                 Hs.95327 
               
               
                 213508_at 
                 AA142942 
                 — 
                 Hs.356665 
               
               
                 213457_at 
                 BF739959 
                 — 
                 Hs.379414 
               
               
                 213441_x_at 
                 AI745526 
                 PDEF 
                 Hs.79414 
               
               
                 213375_s_at 
                 N80918 
                 CG018 
                 Hs.22174 
               
               
                 213338_at 
                 BF062629 
                 RIS1 
                 Hs.35861 
               
               
                 213193_x_at 
                 AL559122 
                 TRB@ 
                 Hs.303157 
               
               
                 213160_at 
                 D86964.1 
                 DOCK2 
                 Hs.17211 
               
               
                 213005_s_at 
                 D79994.1 
                 KANK 
                 Hs.77546 
               
               
                 212827_at 
                 X17115.1 
                 IGHM 
                 Hs.153261 
               
               
                 212728_at 
                 AB033058.1 
                 DLG3 
                 Hs.11101 
               
               
                 212589_at 
                 BG168858 
                 RRAS2 
                 Hs.206097 
               
               
                 212588_at 
                 AI809341 
                 PTPRC 
                 Hs.170121 
               
               
                 212587_s_at 
                 AI809341 
                 PTPRC 
                 Hs.170121 
               
               
                 212458_at 
                 AW138902 
                 LOC200734 
                 Hs.173108 
               
               
                 212382_at 
                 AK021980.1 
                 — 
                 Hs.289068 
               
               
                 212187_x_at 
                 NM_000954.1 
                 PTGDS 
                 Hs.8272 
               
               
                 211796_s_at 
                 AF043179.1 
                 TRB@ 
                 Hs.303157 
               
               
                 211795_s_at 
                 AF198052.1 
                 FYB 
                 Hs.58435 
               
               
                 211748_x_at 
                 BC005939.1 
                 PTGDS 
                 Hs.8272 
               
               
                 211742_s_at 
                 BC005926.1 
                 EVI2B 
                 Hs.5509 
               
               
                 211663_x_at 
                 M61900.1 
                 PTGDS 
                 Hs.8272 
               
               
                 211564_s_at 
                 BC003096.1 
                 RIL 
                 Hs.424312 
               
               
                 211527_x_at 
                 M27281.1 
                 VEGF 
                 Hs.73793 
               
               
                 211339_s_at 
                 D13720.1 
                 ITK 
                 Hs.211576 
               
               
                 211071_s_at 
                 BC006471.1 
                 AF1Q 
                 Hs.75823 
               
               
                 211056_s_at 
                 BC006373.1 
                 SRD5A1 
                 Hs.552 
               
               
                 210959_s_at 
                 AF113128.1 
                 SRD5A1 
                 Hs.552 
               
               
                 210915_x_at 
                 M15564.1 
                 TRB@ 
                 Hs.303157 
               
               
                 210896_s_at 
                 AF306765.1 
                 ASPH 
                 Hs.283664 
               
               
                 210839_s_at 
                 D45421.1 
                 ENPP2 
                 Hs.174185 
               
               
                 210761_s_at 
                 AB008790.1 
                 GRB7 
                 Hs.86859 
               
               
                 210547_x_at 
                 L21181.1 
                 ICA1 
                 Hs.167927 
               
               
                 210513_s_at 
                 AF091352.1 
                 VEGF 
                 Hs.73793 
               
               
                 210399_x_at 
                 U27336.1 
                 FUT6 
                 Hs.32956 
               
               
                 210356_x_at 
                 BC002807.1 
                 MS4A1 
                 Hs.89751 
               
               
                 210347_s_at 
                 AF080216.1 
                 BCL11A 
                 Hs.130881 
               
               
                 210298_x_at 
                 AF098518.1 
                 FHL1 
                 Hs.239069 
               
               
                 209842_at 
                 AI367319 
                 SOX10 
                 Hs.44317 
               
               
                 209687_at 
                 U19495.1 
                 CXCL12 
                 Hs.385710 
               
               
                 209670_at 
                 M12959.1 
                 TRA@ 
                 Hs.74647 
               
               
                 209633_at 
                 L07590.1 
                 PPP2R3A 
                 Hs.28219 
               
               
                 209606_at 
                 L06633.1 
                 PSCDBP 
                 Hs.270 
               
               
                 209584_x_at 
                 AF165520.1 
                 APOBEC3C 
                 Hs.8583 
               
               
                 209583_s_at 
                 AF063591.1 
                 MOX2 
                 Hs.79015 
               
               
                 209522_s_at 
                 BC000723.1 
                 CRAT 
                 Hs.12068 
               
               
                 209496_at 
                 BC000069.1 
                 RARRES2 
                 Hs.37682 
               
               
                 209392_at 
                 L35594.1 
                 ENPP2 
                 Hs.174185 
               
               
                 209366_x_at 
                 M22865.1 
                 CYB5 
                 Hs.83834 
               
               
                 209343_at 
                 BC002449.1 
                 FLJ13612 
                 Hs.24391 
               
               
                 209337_at 
                 AF063020.1 
                 PSIP2 
                 Hs.82110 
               
               
                 209293_x_at 
                 U16153.1 
                 ID4 
                 Hs.34853 
               
               
                 209291_at 
                 NM_001546.1 
                 ID4 
                 Hs.34853 
               
               
                 209213_at 
                 BC002511.1 
                 CBR1 
                 Hs.88778 
               
               
                 209200_at 
                 N22468 
                 MEF2C 
                 Hs.78995 
               
               
                 209199_s_at 
                 N22468 
                 MEF2C 
                 Hs.78995 
               
               
                 209135_at 
                 AF289489.1 
                 ASPH 
                 Hs.283664 
               
               
                 209083_at 
                 U34690.1 
                 CORO1A 
                 Hs.109606 
               
               
                 209016_s_at 
                 BC002700.1 
                 KRT7 
                 Hs.23881 
               
               
                 209008_x_at 
                 U76549.1 
                 KRT8 
                 Hs.242463 
               
               
                 208983_s_at 
                 M37780.1 
                 PECAM1 
                 Hs.78146 
               
               
                 208881_x_at 
                 BC005247.1 
                 IDI1 
                 Hs.76038 
               
               
                 208370_s_at 
                 NM_004414 
                 DSCR1 
                 Hs.184222 
               
               
                 208083_s_at 
                 NM_000888 
                 ITGB6 
                 Hs.57664 
               
               
                 207843_x_at 
                 NM_001914 
                 CYB5 
                 Hs.83834 
               
               
                 207842_s_at 
                 NM_007359 
                 MLN51 
                 Hs.83422 
               
               
                 207808_s_at 
                 NM_000313 
                 PROS1 
                 Hs.64016 
               
               
                 207540_s_at 
                 NM_003177 
                 SYK 
                 Hs.74101 
               
               
                 207339_s_at 
                 NM_002341 
                 LTB 
                 Hs.890 
               
               
                 207238_s_at 
                 NM_002838 
                 PTPRC 
                 Hs.170121 
               
               
                 206666_at 
                 NM_002104 
                 GZMK 
                 Hs.3066 
               
               
                 206560_s_at 
                 NM_006533 
                 MIA 
                 Hs.279651 
               
               
                 206481_s_at 
                 NM_001290 
                 LDB2 
                 Hs.4980 
               
               
                 206469_x_at 
                 NM_012067 
                 AKR7A3 
                 Hs.284236 
               
               
                 206364_at 
                 NM_014875 
                 KIF14 
                 Hs.3104 
               
               
                 206303_s_at 
                 AF191653.1 
                 NUDT4 
                 Hs.355399 
               
               
                 206150_at 
                 NM_001242 
                 TNFRSF7 
                 Hs.355307 
               
               
                 205980_s_at 
                 NM_015366 
                 ARHGAP8 
                 Hs.102336 
               
               
                 205968_at 
                 NM_002252 
                 KCNS3 
                 Hs.47584 
               
               
                 205961_s_at 
                 NM_004682 
                 PSIP2 
                 Hs.82110 
               
               
                 205926_at 
                 NM_004843 
                 WSX1 
                 Hs.132781 
               
               
                 205831_at 
                 NM_001767 
                 CD2 
                 Hs.89476 
               
               
                 205821_at 
                 NM_007360 
                 D12S2489E 
                 Hs.74085 
               
               
                 205798_at 
                 NM_002185 
                 IL7R 
                 Hs.362807 
               
               
                 205455_at 
                 NM_002447 
                 MST1R 
                 Hs.2942 
               
               
                 205405_at 
                 NM_003966 
                 SEMA5A 
                 Hs.27621 
               
               
                 205267_at 
                 NM_006235 
                 POU2AF1 
                 Hs.2407 
               
               
                 205079_s_at 
                 NM_003829 
                 MPDZ 
                 Hs.169378 
               
               
                 205049_s_at 
                 NM_001783 
                 CD79A 
                 Hs.79630 
               
               
                 205044_at 
                 NM_014211 
                 GABRP 
                 Hs.70725 
               
               
                 205024_s_at 
                 NM_002875 
                 RAD51 
                 Hs.343807 
               
               
                 204951_at 
                 NM_004310 
                 ARHH 
                 Hs.109918 
               
               
                 204949_at 
                 NM_002162 
                 ICAM3 
                 Hs.99995 
               
               
                 204942_s_at 
                 NM_000695 
                 ALDH3B2 
                 Hs.87539 
               
               
                 204912_at 
                 NM_001558 
                 IL10RA 
                 Hs.327 
               
               
                 204784_s_at 
                 NM_022443 
                 MLF1 
                 Hs.85195 
               
               
                 204731_at 
                 NM_003243 
                 TGFBR3 
                 Hs.342874 
               
               
                 204683_at 
                 NM_000873 
                 ICAM2 
                 Hs.433303 
               
               
                 204679_at 
                 NM_002245 
                 KCNK1 
                 Hs.79351 
               
               
                 204678_s_at 
                 U90065.1 
                 KCNK1 
                 Hs.79351 
               
               
                 204675_at 
                 NM_001047 
                 SRD5A1 
                 Hs.552 
               
               
                 204661_at 
                 NM_001803 
                 CDW52 
                 Hs.276770 
               
               
                 204615_x_at 
                 NM_004508 
                 IDI1 
                 Hs.76038 
               
               
                 204613_at 
                 NM_002661 
                 PLCG2 
                 Hs.75648 
               
               
                 204563_at 
                 NM_000655 
                 SELL 
                 Hs.82848 
               
               
                 204562_at 
                 NM_002460 
                 IRF4 
                 Hs.82132 
               
               
                 204446_s_at 
                 NM_000698 
                 ALOX5 
                 Hs.89499 
               
               
                 204442_x_at 
                 NM_003573 
                 LTBP4 
                 Hs.85087 
               
               
                 204396_s_at 
                 NM_005308 
                 GPRK5 
                 Hs.211569 
               
               
                 204345_at 
                 NM_001856 
                 COL16A1 
                 Hs.26208 
               
               
                 204220_at 
                 NM_004877 
                 GMFG 
                 Hs.5210 
               
               
                 204198_s_at 
                 AA541630 
                 RUNX3 
                 Hs.170019 
               
               
                 204197_s_at 
                 NM_004350 
                 RUNX3 
                 Hs.170019 
               
               
                 204192_at 
                 NM_001774 
                 CD37 
                 Hs.153053 
               
               
                 204153_s_at 
                 NM_002405 
                 MFNG 
                 Hs.31939 
               
               
                 204118_at 
                 NM_001778 
                 CD48 
                 Hs.901 
               
               
                 204116_at 
                 NM_000206 
                 IL2RG 
                 Hs.84 
               
               
                 204099_at 
                 NM_003078 
                 SMARCD3 
                 Hs.71622 
               
               
                 204083_s_at 
                 NM_003289 
                 TPM2 
                 Hs.300772 
               
               
                 204061_at 
                 NM_005044 
                 PRKX 
                 Hs.147996 
               
               
                 203936_s_at 
                 NM_004994 
                 MMP9 
                 Hs.151738 
               
               
                 203921_at 
                 NM_004267 
                 CHST2 
                 Hs.8786 
               
               
                 203911_at 
                 NM_002885 
                 RAP1GA1 
                 Hs.433797 
               
               
                 203685_at 
                 NM_000633 
                 BCL2 
                 Hs.79241 
               
               
                 203666_at 
                 NM_000609 
                 CXCL12 
                 Hs.237356 
               
               
                 203549_s_at 
                 NM_000237 
                 LPL 
                 Hs.180878 
               
               
                 203548_s_at 
                 BF672975 
                 LPL 
                 Hs.180878 
               
               
                 203281_s_at 
                 NM_003335 
                 UBE1L 
                 Hs.16695 
               
               
                 203216_s_at 
                 NM_004999 
                 MYO6 
                 Hs.22564 
               
               
                 202991_at 
                 NM_006804 
                 STARD3 
                 Hs.77628 
               
               
                 202957_at 
                 NM_005335 
                 HCLS1 
                 Hs.14601 
               
               
                 202931_x_at 
                 NM_004305 
                 BIN1 
                 Hs.193163 
               
               
                 202902_s_at 
                 NM_004079 
                 CTSS 
                 Hs.181301 
               
               
                 202890_at 
                 T62571 
                 MAP7 
                 Hs.146388 
               
               
                 202889_x_at 
                 T62571 
                 MAP7 
                 Hs.146388 
               
               
                 202862_at 
                 NM_000137 
                 FAH 
                 Hs.73875 
               
               
                 202790_at 
                 NM_001307 
                 CLDN7 
                 Hs.278562 
               
               
                 202555_s_at 
                 NM_005965 
                 MYLK 
                 Hs.211582 
               
               
                 202275_at 
                 NM_000402 
                 G6PD 
                 Hs.80206 
               
               
                 202147_s_at 
                 NM_001550 
                 IFRD1 
                 Hs.7879 
               
               
                 202146_at 
                 AA747426 
                 IFRD1 
                 Hs.7879 
               
               
                 202037_s_at 
                 NM_003012 
                 SFRP1 
                 Hs.7306 
               
               
                 202036_s_at 
                 AF017987.1 
                 SFRP1 
                 Hs.7306 
               
               
                 202035_s_at 
                 AI332407 
                 SFRP1 
                 Hs.7306 
               
               
                 201952_at 
                 NM_001627.1 
                 ALCAM 
                 Hs.10247 
               
               
                 201951_at 
                 NM_001627.1 
                 ALCAM 
                 Hs.10247 
               
               
                 201858_s_at 
                 J03223.1 
                 PRG1 
                 Hs.1908 
               
               
                 201849_at 
                 NM_004052 
                 BNIP3 
                 Hs.79428 
               
               
                 201688_s_at 
                 BE974098 
                 TPD52 
                 Hs.2384 
               
               
                 201650_at 
                 NM_002276 
                 KRT19 
                 Hs.182265 
               
               
                 201644_at 
                 NM_003313 
                 TSTA3 
                 Hs.404119 
               
               
                 201596_x_at 
                 NM_000224 
                 KRT18 
                 Hs.406013 
               
               
                 201540_at 
                 NM_001449 
                 FHL1 
                 Hs.239069 
               
               
                 201497_x_at 
                 NM_022844 
                 MYH11 
                 Hs.78344 
               
               
                 201211_s_at 
                 AF061337.1 
                 DDX3 
                 Hs.380774 
               
               
                 201058_s_at 
                 NM_006097 
                 MYL9 
                 Hs.9615 
               
               
                 201030_x_at 
                 NM_002300 
                 LDHB 
                 Hs.234489 
               
               
                 200962_at 
                 AI348010 
                 — 
                 Hs.250367 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Genes useful for separation of ESR1++, 
               
               
                 ESRl+ ER. ESR1+ EM &lt;-&gt; ESR1+ FHL++. 
               
               
                 ESR1+ FHL+. ESR1+ LM 
               
            
           
           
               
               
               
               
            
               
                 Affymetrix 
                 GenBank 
                   
                   
               
               
                 Probe Set ID HG 
                 Accession 
               
               
                 U133A 
                 No 
                 Gene Symbol 
                 Unigene ID 
               
               
                   
               
               
                 38158_at 
                 D79987 
                 ESPL1 
                 Hs.153479 
               
               
                 221900_at 
                 AI806793 
                 COL8A2 
                 Hs.353001 
               
               
                 221731_x_at 
                 J02814.1 
                 CSPG2 
                 Hs.81800 
               
               
                 221730_at 
                 NM_000393.1 
                 COL5A2 
                 Hs.82985 
               
               
                 221729_at 
                 NM_000393.1 
                 COL5A2 
                 Hs.82985 
               
               
                 221671_x_at 
                 M63438.1 
                 IGKC 
                 Hs.406565 
               
               
                 221651_x_at 
                 BC005332.1 
                 IGKC 
                 Hs.406565 
               
               
                 221541_at 
                 AL136861.1 
                 DKF2P434B044 
                 Hs.262958 
               
               
                 221530_s_at 
                 AB044088.1 
                 BHLHB3 
                 Hs.33829 
               
               
                 221447_s_at 
                 NM_031302 
                 LOC83468 
                 Hs.159993 
               
               
                 219806_s_at 
                 NM_020179 
                 FN5 
                 Hs.259737 
               
               
                 219561_at 
                 NM_016429 
                 COPZ2 
                 Hs.37482 
               
               
                 219134_at 
                 NM_022159 
                 ETL 
                 Hs.57958 
               
               
                 219091_s_at 
                 NM_024756 
                 ENDOGLYX1 
                 Hs.127216 
               
               
                 218039_at 
                 NM_016359 
                 ANKT 
                 Hs.279905 
               
               
                 218009_s_at 
                 NM_003981 
                 PRC1 
                 Hs.344037 
               
               
                 217890_s_at 
                 NM_018222 
                 PARVA 
                 Hs.44077 
               
               
                 217525_at 
                 AW305097 
                 — 
                 Hs.418738 
               
               
                 217480_x_at 
                 M20812 
                 — 
               
               
                 217428_s_at 
                 X98568 
                 — 
               
               
                 217378_x_at 
                 X51887 
                 — 
               
               
                 217281_x_at 
                 AJ239383.1 
                 IGHG3 
                 Hs.300697 
               
               
                 217157_x_at 
                 AF103530.1 
                 IGKC 
                 Hs.381418 
               
               
                 217148_x_at 
                 AJ249377.1 
                 IGLJ3 
                 Hs.102950 
               
               
                 217022_s_at 
                 S55735.1 
                 MGC27165 
                 Hs.153261 
               
               
                 216984_x_at 
                 D84143.1 
                 IGLJ3 
                 Hs.102950 
               
               
                 216576_x_at 
                 AF103529.1 
                 — 
                 Hs.381417 
               
               
                 216401_x_at 
                 AJ408433 
                 — 
               
               
                 216207_x_at 
                 AW408194 
                 IGKV1D-13 
                 Hs.390427 
               
               
                 215646_s_at 
                 R94644 
                 — 
                 Hs.81800 
               
               
                 215446_s_at 
                 L16895 
                 LOX 
                 Hs.348385 
               
               
                 215388_s_at 
                 X56210.1 
                 HFL2 
                 Hs.296941 
               
               
                 215379_x_at 
                 AV698647 
                 IGLJ3 
                 Hs.405944 
               
               
                 215176_x_at 
                 AW404894 
                 IGKC 
                 Hs.406565 
               
               
                 215121_x_at 
                 AA680302 
                 IGLJ3 
                 Hs.102950 
               
               
                 215051_x_at 
                 BF213829 
                 AIF1 
                 Hs.76364 
               
               
                 214973_x_at 
                 AJ275469 
                 IGHG3 
                 Hs.300697 
               
               
                 214916_x_at 
                 BG340548 
                 IGHM 
                 Hs.153261 
               
               
                 214836_x_at 
                 BG536224 
                 IGKC 
                 Hs.406565 
               
               
                 214768_x_at 
                 BG540628 
                 IGKC 
                 Hs.406565 
               
               
                 214677_x_at 
                 X57812.1 
                 IGLJ3 
                 Hs.102950 
               
               
                 214669_x_at 
                 BG485135 
                 IGKC 
                 Hs.406565 
               
               
                 213800_at 
                 X04697.1 
                 HF1 
                 Hs.250651 
               
               
                 213790_at 
                 W46291 
                 — 
                 Hs.352537 
               
               
                 213502_x_at 
                 X03529 
                 LOC91316 
                 Hs.350074 
               
               
                 213194_at 
                 BF059159 
                 ROBO1 
                 Hs.301198 
               
               
                 213139_at 
                 AI572079 
                 SNAI2 
                 Hs.93005 
               
               
                 213095_x_at 
                 AF299327.1 
                 AIF1 
                 Hs.76364 
               
               
                 213071_at 
                 AI146848 
                 DPT 
                 Hs.80552 
               
               
                 213068_at 
                 AI146848 
                 DPT 
                 Hs.80552 
               
               
                 213004_at 
                 AF007150.1 
                 ANGPTL2 
                 Hs.8025 
               
               
                 212865_s_at 
                 BF449063 
                 COL14A1 
                 Hs.403836 
               
               
                 212764_at 
                 U19969.1 
                 TCF8 
                 Hs.232068 
               
               
                 212713_at 
                 R72286 
                 MFAP4 
                 Hs.296049 
               
               
                 212671_s_at 
                 BG397856 
                 HLA-DQA1 
                 Hs.198253 
               
               
                 212609_s_at 
                 U79271.1 
                 SDCCAG8 
                 Hs.300642 
               
               
                 212592_at 
                 AV733266 
                 IGJ 
                 Hs.76325 
               
               
                 212489_at 
                 AI983428 
                 COL5A1 
                 Hs.146428 
               
               
                 212488_at 
                 AI983428 
                 COL5A1 
                 Hs.146428 
               
               
                 212419_at 
                 AL049949.1 
                 FLJ90798 
                 Hs.28264 
               
               
                 212298_at 
                 BE620457 
                 NRP1 
                 Hs.69285 
               
               
                 212188_at 
                 AF052169.1 
                 LOC115207 
                 Hs.109438 
               
               
                 211896_s_at 
                 AF138302.1 
                 DCN 
                 Hs.433989 
               
               
                 211813_x_at 
                 AF138303.1 
                 DCN 
                 Hs.433989 
               
               
                 211798_x_at 
                 AB001733.1 
                 IGLJ3 
                 Hs.102950 
               
               
                 211645_x_at 
                 M85256.1 
                 IGKC 
                 Hs.406565 
               
               
                 211644_x_at 
                 L14458.1 
                 IGKC 
                 Hs.406565 
               
               
                 211643_x_at 
                 L14457.1 
                 IGKC 
                 Hs.406565 
               
               
                 211637_x_at 
                 L23516.1 
                 IGHM 
                 Hs.153261 
               
               
                 211571_s_at 
                 D32039.1 
                 CSPG2 
                 Hs.81800 
               
               
                 211368_s_at 
                 U13700.1 
                 CASP1 
                 Hs.2490 
               
               
                 210982_s_at 
                 M60333.1 
                 HLA-DRA 
                 Hs.76807 
               
               
                 210904_s_at 
                 U81380.2 
                 IL13RA1 
                 Hs.285115 
               
               
                 210839_s_at 
                 D45421.1 
                 ENPP2 
                 Hs.174185 
               
               
                 210072_at 
                 U88321.1 
                 CCL19 
                 Hs.50002 
               
               
                 209901_x_at 
                 U19713.1 
                 AIF1 
                 Hs.76364 
               
               
                 209687_at 
                 U19495.1 
                 CXCL12 
                 Hs.385710 
               
               
                 209542_x_at 
                 M29644.1 
                 IGF1 
                 Hs.85112 
               
               
                 209541_at 
                 NM_000618.1 
                 IGF1 
                 Hs.85112 
               
               
                 209540_at 
                 NM_000618.1 
                 IGF1 
                 Hs.85112 
               
               
                 209496_at 
                 BC000069.1 
                 RARRES2 
                 Hs.37682 
               
               
                 209436_at 
                 AB018305.1 
                 SPON1 
                 Hs.5378 
               
               
                 209392_at 
                 L35594.1 
                 ENPP2 
                 Hs.174185 
               
               
                 209374_s_at 
                 BC001872.1 
                 IGHM 
                 Hs.153261 
               
               
                 209335_at 
                 AI281593 
                 DCN 
                 Hs.433989 
               
               
                 209138_x_at 
                 M87790.1 
                 IGLJ3 
                 Hs.102950 
               
               
                 209047_at 
                 AL518391 
                 AQP1 
                 Hs.76152 
               
               
                 208937_s_at 
                 D13889.1 
                 ID1 
                 Hs.75424 
               
               
                 208850_s_at 
                 AL558479 
                 THY1 
                 Hs.125359 
               
               
                 208747_s_at 
                 M18767.1 
                 C1S 
                 Hs.169756 
               
               
                 208131_s_at 
                 NM_000961 
                 PTGIS 
                 Hs.302085 
               
               
                 208079_s_at 
                 NM_003158 
                 STK6 
                 Hs.250822 
               
               
                 207542_s_at 
                 NM_000385 
                 AQP1 
                 Hs.76152 
               
               
                 207480_s_at 
                 NM_020149 
                 MEIS2 
                 Hs.104105 
               
               
                 207266_x_at 
                 NM_016837 
                 RBMS1 
                 Hs.241567 
               
               
                 207238_s_at 
                 NM_002838 
                 PTPRC 
                 Hs.170121 
               
               
                 206584_at 
                 NM_015364 
                 LY96 
                 Hs.69328 
               
               
                 206102_at 
                 NM_021067 
                 KIAA0186 
                 Hs.36232 
               
               
                 206101_at 
                 NM_001393 
                 ECM2 
                 Hs.35094 
               
               
                 205941_s_at 
                 AI376003 
                 COL10A1 
                 Hs.179729 
               
               
                 205898_at 
                 U20350.1 
                 CX3CR1 
                 Hs.78913 
               
               
                 205392_s_at 
                 NM_004166 
                 CCL14 
                 Hs.20144 
               
               
                 205226_at 
                 NM_006207 
                 PDGFRL 
                 Hs.170040 
               
               
                 204964_s_at 
                 NM_005086 
                 SSPN 
                 Hs.183428 
               
               
                 204963_at 
                 AL136756.1 
                 SSPN 
                 Hs.183428 
               
               
                 204955_at 
                 NM_006307 
                 SRPX 
                 Hs.15154 
               
               
                 204927_at 
                 NM_003475 
                 C11orf13 
                 Hs.72925 
               
               
                 204897_at 
                 NM_000958.1 
                 PTGER4 
                 Hs.199248 
               
               
                 204619_s_at 
                 BF590263 
                 CSPG2 
                 Hs.81800 
               
               
                 204451_at 
                 NM_003505 
                 FZD1 
                 Hs.94234 
               
               
                 204359_at 
                 NM_013231 
                 FLRT2 
                 Hs.48998 
               
               
                 204298_s_at 
                 NM_002317 
                 LOX 
                 Hs.432618 
               
               
                 204222_s_at 
                 NM_006851 
                 GLIPR1 
                 Hs.64639 
               
               
                 204115_at 
                 NM_004126 
                 GNG11 
                 Hs.83381 
               
               
                 204092_s_at 
                 NM_003600 
                 STK6 
                 Hs.250822 
               
               
                 204052_s_at 
                 NM_003014 
                 SFRP4 
                 Hs.105700 
               
               
                 204051_s_at 
                 AW089415 
                 SFRP4 
                 Hs.105700 
               
               
                 204036_at 
                 AW269335 
                 EDG2 
                 Hs.75794 
               
               
                 203989_x_at 
                 NM_001992 
                 F2R 
                 Hs.128087 
               
               
                 203854_at 
                 NM_000204 
                 IF 
                 Hs.36602 
               
               
                 203748_x_at 
                 NM_016839 
                 RBMS1 
                 Hs.241567 
               
               
                 203666_at 
                 NM_000609 
                 CXCL12 
                 Hs.237356 
               
               
                 203325_s_at 
                 AI130969 
                 COL5A1 
                 Hs.146428 
               
               
                 203324_s_at 
                 NM_001233 
                 CAV2 
                 Hs.139851 
               
               
                 203323_at 
                 BF197655 
                 — 
                 Hs.397414 
               
               
                 203088_at 
                 NM_006329 
                 FBLN5 
                 Hs.11494 
               
               
                 203083_at 
                 NM_003247 
                 THBS2 
                 Hs.108623 
               
               
                 203065_s_at 
                 NM_001753 
                 CAV1 
                 Hs.74034 
               
               
                 202995_s_at 
                 NM_006486 
                 FBLN1 
                 Hs.79732 
               
               
                 202994_s_at 
                 Z95331 
                 FBLN1 
                 Hs.79732 
               
               
                 202954_at 
                 NM_007019 
                 UBE2C 
                 Hs.93002 
               
               
                 202766_s_at 
                 NM_000138 
                 FBN1 
                 Hs.750 
               
               
                 202723_s_at 
                 AW117498 
                 FOXO1A 
                 Hs.170133 
               
               
                 202705_at 
                 NM_004701 
                 CCNB2 
                 Hs.194698 
               
               
                 202503_s_at 
                 NM_014736 
                 KIAA0101 
                 Hs.81892 
               
               
                 202465_at 
                 NM_002593 
                 PCOLCE 
                 Hs.202097 
               
               
                 202381_at 
                 NM_003816 
                 ADAM9 
                 Hs.2442 
               
               
                 202311_s_at 
                 NM_000088.1 
                 COL1A1 
                 Hs.434012 
               
               
                 202283_at 
                 NM_002615 
                 SERPINF1 
                 Hs.173594 
               
               
                 202238_s_at 
                 NM_006169 
                 NNMT 
                 Hs.364345 
               
               
                 202095_s_at 
                 NM_001168 
                 BIRC5 
                 Hs.1578 
               
               
                 202075_s_at 
                 NM_006227 
                 PLTP 
                 Hs.283007 
               
               
                 201787_at 
                 NM_001996 
                 FBLN1 
                 Hs.79732 
               
               
                 201431_s_at 
                 NM_001387 
                 DPYSL3 
                 Hs.74566 
               
               
                 201430_s_at 
                 W72516 
                 DPYSL3 
                 Hs.74566 
               
               
                 201325_s_at 
                 NM_001423 
                 EMP1 
                 Hs.79368 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Genes useful for separation of ESR1++ &lt;-&gt; ESR1+ ER, ESR1+ EM 
               
            
           
           
               
               
               
               
            
               
                 Affymetrix 
                 GenBank 
                   
                   
               
               
                 Probe Set ID HG 
                 Accession 
               
               
                 U133A 
                 No 
                 Gene Symbol 
                 Unigene ID 
               
               
                   
               
               
                 40016_g_at 
                 AB002301 
                 KIAA0303 
                 Hs.432631 
               
               
                 221824_s_at 
                 AA770170 
                 MGC26766 
                 Hs.288156 
               
               
                 218051_s_at 
                 NM_022908 
                 FLJ12442 
                 Hs.84753 
               
               
                 218002_s_at 
                 NM_004887 
                 CXCL14 
                 Hs.24395 
               
               
                 217875_s_at 
                 NM_020182 
                 TMEPAI 
                 Hs.83883 
               
               
                 213539_at 
                 NM_000732.1 
                 CD3D 
                 Hs.95327 
               
               
                 213288_at 
                 AI761250 
                 — 
                 Hs.90797 
               
               
                 213193_x_at 
                 AL559122 
                 TRB@ 
                 Hs.303157 
               
               
                 212588_at 
                 AI809341 
                 PTPRC 
                 Hs.170121 
               
               
                 211996_s_at 
                 BG256504 
                 — 
                 Hs.110613 
               
               
                 210958_s_at 
                 BC003646.1 
                 KIAA0303 
                 Hs.432631 
               
               
                 210916_s_at 
                 AF098641.1 
                 — 
                 Hs.306278 
               
               
                 210915_x_at 
                 M15564.1 
                 TRB@ 
                 Hs.303157 
               
               
                 210096_at 
                 J02871.1 
                 CYP4B1 
                 Hs.687 
               
               
                 210072_at 
                 U88321.1 
                 CCL19 
                 Hs.50002 
               
               
                 209374_s_at 
                 BC001872.1 
                 IGHM 
                 Hs.153261 
               
               
                 205831_at 
                 NM_001767 
                 CD2 
                 Hs.89476 
               
               
                 204897_at 
                 NM_000958.1 
                 PTGER4 
                 Hs.199248 
               
               
                 204655_at 
                 NM_002985 
                 CCL5 
                 Hs.241392 
               
               
                 204118_at 
                 NM_001778 
                 CD48 
                 Hs.901 
               
               
                 203895_at 
                 AL535113 
                 — 
                 Hs.348724 
               
               
                 203868_s_at 
                 NM_001078 
                 VCAM1 
                 Hs.109225 
               
               
                 203439_s_at 
                 BC000658.1 
                 STC2 
                 Hs.155223 
               
               
                 203438_at 
                 AI435828 
                 STC2 
                 Hs.155223 
               
               
                 202644_s_at 
                 NM_006290 
                 TNFAIP3 
                 Hs.211600 
               
               
                 201422_at 
                 NM_006332 
                 IFI30 
                 Hs.14623 
               
               
                 201369_s_at 
                 NM_006887 
                 ZFP36L2 
                 Hs.78909 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Genes useful for separation of ESR1+ ER &lt;-&gt; ESR1+ EM 
               
            
           
           
               
               
               
               
            
               
                 Affymetrix 
                 GenBank 
                   
                   
               
               
                 Probe Set ID HG 
                 Accession 
                   
                 Unigene 
               
               
                 U133A 
                 No 
                 Gene Symbol 
                 ID 
               
               
                   
               
               
                 38158_at 
                 D79987 
                 ESPL1 
                 Hs.153479 
               
               
                 219197_s_at 
                 AI424243 
                 SCUBE2 
                 Hs.105790 
               
               
                 218613_at 
                 NM_018422 
                 DKFZp761K1423 
                 Hs.236438 
               
               
                 218469_at 
                 NM_013372 
                 CKTSF1B1 
                 Hs.40098 
               
               
                 218468_s_at 
                 AF154054.1 
                 CKTSF1B1 
                 Hs.40098 
               
               
                 217022_s_at 
                 S55735.1 
                 MGC27165 
                 Hs.153261 
               
               
                 216320_x_at 
                 U37055 
                 — 
                 Hs.349110 
               
               
                 215177_s_at 
                 AV733308 
                 ITGA6 
                 Hs.227730 
               
               
                 212741_at 
                 AA923354 
                 MAOA 
                 Hs.183109 
               
               
                 210559_s_at 
                 D88357.1 
                 CDC2 
                 Hs.334562 
               
               
                 209460_at 
                 AF237813.1 
                 NPD009 
                 Hs.283675 
               
               
                 209459_s_at 
                 AF237813.1 
                 NPD009 
                 Hs.283675 
               
               
                 209291_at 
                 NM_001546.1 
                 ID4 
                 Hs.34853 
               
               
                 207414_s_at 
                 NM_002570 
                 PACE4 
                 Hs.170414 
               
               
                 206102_at 
                 NM_021067 
                 KIAA0186 
                 Hs.36232 
               
               
                 203439_s_at 
                 BC000658.1 
                 STC2 
                 Hs.155223 
               
               
                 203438_at 
                 AI435828 
                 STC2 
                 Hs.155223 
               
               
                 203355_s_at 
                 NM_015310 
                 EFA6R 
                 Hs.6763 
               
               
                 203214_x_at 
                 NM_001786 
                 CDC2 
                 Hs.334562 
               
               
                 203213_at 
                 AL524035 
                 CDC2 
                 Hs.334562 
               
               
                 201656_at 
                 NM_000210 
                 ITGA6 
                 Hs.227730 
               
               
                 201627_s_at 
                 NM_005542 
                 INSIG1 
                 Hs.56205 
               
               
                 201037_at 
                 NM_002627 
                 PFKP 
                 Hs.99910 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Genes useful for separation of ESR1+ FHL++, 
               
               
                 ESR1+ FHL+ &lt;-&gt; ESR1+ LM 
               
            
           
           
               
               
               
               
            
               
                 Affymetrix 
                 GenBank 
                   
                   
               
               
                 Probe Set ID HG 
                 Accession 
               
               
                 U133A 
                 No 
                 Gene Symbol 
                 Unigene ID 
               
               
                   
               
               
                 222379_at 
                 AI002715 
                 — 
                 Hs.172047 
               
               
                 222250_s_at 
                 AK001363.1 
                 DKFZP434B168 
                 Hs.48604 
               
               
                 222043_at 
                 AI982754 
                 CLU 
                 Hs.75106 
               
               
                 222037_at 
                 AI859865 
                 — 
                 Hs.319215 
               
               
                 221872_at 
                 AI669229 
                 RARRES1 
                 Hs.82547 
               
               
                 221796_at 
                 AA707199 
                 NTRK2 
                 Hs.47860 
               
               
                 221653_x_at 
                 BC004395.1 
                 APOL2 
                 Hs.241412 
               
               
                 221645_s_at 
                 M27877.1 
                 ZNF83 
                 Hs.305953 
               
               
                 221530_s_at 
                 AB044088.1 
                 BHLHB3 
                 Hs.33829 
               
               
                 221521_s_at 
                 BC003186.1 
                 LOC51659 
                 Hs.433180 
               
               
                 221188_s_at 
                 NM_014430 
                 CIDEB 
                 Hs.299867 
               
               
                 220240_s_at 
                 NM_017905 
                 C13orf11 
                 Hs.27337 
               
               
                 219935_at 
                 NM_007038 
                 ADAMTS5 
                 Hs.58324 
               
               
                 219918_s_at 
                 NM_018123 
                 ASPM 
                 Hs.121028 
               
               
                 219777_at 
                 NM_024711 
                 hIAN2 
                 Hs.105468 
               
               
                 219304_s_at 
                 NM_025208 
                 SCDGF-B 
                 Hs.112885 
               
               
                 219077_s_at 
                 NM_016373 
                 WWOX 
                 Hs.519 
               
               
                 218976_at 
                 NM_021800 
                 JDP1 
                 Hs.260720 
               
               
                 218901_at 
                 NM_020353 
                 PLSCR4 
                 Hs.182538 
               
               
                 218819_at 
                 NM_012141 
                 DDX26 
                 Hs.58570 
               
               
                 218322_s_at 
                 NM_016234 
                 FACL5 
                 Hs.11638 
               
               
                 218236_s_at 
                 NM_005813 
                 PRKCN 
                 Hs.143460 
               
               
                 218039_at 
                 NM_016359 
                 ANKT 
                 Hs.279905 
               
               
                 218009_s_at 
                 NM_003981 
                 PRC1 
                 Hs.344037 
               
               
                 217784_at 
                 BE384482 
                 YKT6 
                 Hs.296244 
               
               
                 217763_s_at 
                 NM_006868 
                 RAB31 
                 Hs.223025 
               
               
                 217762_s_at 
                 BE789881 
                 RAB31 
                 Hs.223025 
               
               
                 217179_x_at 
                 X79782.1 
                 IGL@ 
                 Hs.405944 
               
               
                 217148_x_at 
                 AJ249377.1 
                 IGLJ3 
                 Hs.102950 
               
               
                 216984_x_at 
                 D84143.1 
                 IGLJ3 
                 Hs.102950 
               
               
                 216384_x_at 
                 AF257099 
                 — 
               
               
                 216320_x_at 
                 U37055 
                 — 
                 Hs.349110 
               
               
                 215603_x_at 
                 AI344075 
                 GGT2 
                 Hs.289098 
               
               
                 215504_x_at 
                 AF131777.1 
                 — 
                 Hs.183475 
               
               
                 214594_x_at 
                 BG252666 
                 ATP8B1 
                 Hs.406187 
               
               
                 214097_at 
                 AW024383 
                 RPS21 
                 Hs.356317 
               
               
                 214016_s_at 
                 AL558875 
                 SFPQ 
                 Hs.180610 
               
               
                 213693_s_at 
                 AI610869 
                 MUC1 
                 Hs.89603 
               
               
                 213577_at 
                 AA639705 
                 SQLE 
                 Hs.71465 
               
               
                 213554_s_at 
                 BG257762 
                 H41 
                 Hs.283690 
               
               
                 213158_at 
                 AL049423.1 
                 — 
                 Hs.16193 
               
               
                 213156_at 
                 AL049423.1 
                 — 
                 Hs.16193 
               
               
                 212981_s_at 
                 BF791738 
                 — 
                 Hs.107479 
               
               
                 212935_at 
                 AB002360.1 
                 MCF2L 
                 Hs.25515 
               
               
                 212915_at 
                 AL569804 
                 SEMACAP3 
                 Hs.177635 
               
               
                 212914_at 
                 AV648364 
                 CBX7 
                 Hs.356416 
               
               
                 212865_s_at 
                 BF449063 
                 COL14A1 
                 Hs.403836 
               
               
                 212774_at 
                 AJ223321 
                 ZNF238 
                 Hs.69997 
               
               
                 212494_at 
                 AB028998.1 
                 TENC1 
                 Hs.6147 
               
               
                 212444_at 
                 AA156240 
                 — 
                 Hs.288660 
               
               
                 212417_at 
                 BF058944 
                 SCAMP1 
                 Hs.31218 
               
               
                 212259_s_at 
                 BF344265 
                 HPIP 
                 Hs.8068 
               
               
                 212236_x_at 
                 Z19574 
                 KRT17 
                 Hs.2785 
               
               
                 212141_at 
                 X74794.1 
                 MCM4 
                 Hs.154443 
               
               
                 211698_at 
                 AF349444.1 
                 CRI1 
                 Hs.75847 
               
               
                 211695_x_at 
                 AF348143.1 
                 MUC1 
                 Hs.89603 
               
               
                 211668_s_at 
                 K03226.1 
                 PLAU 
                 Hs.77274 
               
               
                 211597_s_at 
                 AB059408.1 
                 HOP 
                 Hs.13775 
               
               
                 211430_s_at 
                 M87789.1 
                 IGHG3 
                 Hs.300697 
               
               
                 211417_x_at 
                 L20493.1 
                 — 
                 Hs.352120 
               
               
                 210605_s_at 
                 BC003610.1 
                 MFGE8 
                 Hs.3745 
               
               
                 210559_s_at 
                 D88357.1 
                 CDC2 
                 Hs.334562 
               
               
                 210235_s_at 
                 U22815.1 
                 PPFIA1 
                 Hs.183648 
               
               
                 209948_at 
                 U61536.1 
                 KCNMB1 
                 Hs.93841 
               
               
                 209919_x_at 
                 L20490.1 
                 GGTL4 
                 Hs.352119 
               
               
                 209906_at 
                 U62027.1 
                 C3AR1 
                 Hs.155935 
               
               
                 209897_s_at 
                 AF055585.1 
                 SLIT2 
                 Hs.29802 
               
               
                 209791_at 
                 AL049569 
                 PADI2 
                 Hs.33455 
               
               
                 209708_at 
                 AY007239.1 
                 DKFZP564G202 
                 Hs.6909 
               
               
                 209542_x_at 
                 M29644.1 
                 IGF1 
                 Hs.85112 
               
               
                 209541_at 
                 NM_000618.1 
                 IGF1 
                 Hs.85112 
               
               
                 209540_at 
                 NM_000618.1 
                 IGF1 
                 Hs.85112 
               
               
                 209505_at 
                 AI951185 
                 NR2F1 
                 Hs.374991 
               
               
                 209351_at 
                 BC002690.1 
                 KRT14 
                 Hs.355214 
               
               
                 209291_at 
                 NM_001546.1 
                 ID4 
                 Hs.34853 
               
               
                 209040_s_at 
                 U17496.1 
                 PSMB8 
                 Hs.180062 
               
               
                 209016_s_at 
                 BC002700.1 
                 KRT7 
                 Hs.23881 
               
               
                 208932_at 
                 BC001416.1 
                 PPP4C 
                 Hs.2903 
               
               
                 208767_s_at 
                 AW149681 
                 LAPTM4B 
                 Hs.296398 
               
               
                 208284_x_at 
                 NM_013421 
                 GGT1 
                 Hs.401847 
               
               
                 208029_s_at 
                 NM_018407 
                 LAPTM4B 
                 Hs.296398 
               
               
                 207961_x_at 
                 NM_022870 
                 MYH11 
                 Hs.78344 
               
               
                 207847_s_at 
                 NM_002456 
                 MUC1 
                 Hs.89603 
               
               
                 207480_s_at 
                 NM_020149 
                 MEIS2 
                 Hs.104105 
               
               
                 207131_x_at 
                 NM_013430 
                 GGT1 
                 Hs.401847 
               
               
                 206385_s_at 
                 NM_020987 
                 ANK3 
                 Hs.75893 
               
               
                 206049_at 
                 NM_003005 
                 SELP 
                 Hs.73800 
               
               
                 205882_x_at 
                 AI818488 
                 ADD3 
                 Hs.324470 
               
               
                 205875_s_at 
                 NM_016381 
                 TREX1 
                 Hs.278408 
               
               
                 205786_s_at 
                 NM_000632 
                 ITGAM 
                 Hs.172631 
               
               
                 205668_at 
                 NM_002349 
                 LY75 
                 Hs.153563 
               
               
                 205614_x_at 
                 NM_020998 
                 MST1 
                 Hs.349110 
               
               
                 205518_s_at 
                 NM_003570 
                 CMAH 
                 Hs.24697 
               
               
                 205479_s_at 
                 NM_002658 
                 PLAU 
                 Hs.77274 
               
               
                 205450_at 
                 NM_002637 
                 PHKA1 
                 Hs.2393 
               
               
                 205253_at 
                 NM_002585 
                 PBX1 
                 Hs.155691 
               
               
                 205159_at 
                 AV756141 
                 CSF2RB 
                 Hs.285401 
               
               
                 205157_s_at 
                 NM_000422 
                 KRT17 
                 Hs.2785 
               
               
                 205051_s_at 
                 NM_000222 
                 KIT 
                 Hs.81665 
               
               
                 204971_at 
                 NM_005213 
                 CSTA 
                 Hs.2621 
               
               
                 204894_s_at 
                 NM_003734 
                 AOC3 
                 Hs.198241 
               
               
                 204787_at 
                 NM_007268 
                 Z39IG 
                 Hs.8904 
               
               
                 204686_at 
                 NM_005544 
                 IRS1 
                 Hs.96063 
               
               
                 204641_at 
                 NM_002497 
                 NEK2 
                 Hs.153704 
               
               
                 204542_at 
                 NM_006456 
                 STHM 
                 Hs.288215 
               
               
                 204455_at 
                 NM_001723 
                 BPAG1 
                 Hs.198689 
               
               
                 204446_s_at 
                 NM_000698 
                 ALOX5 
                 Hs.89499 
               
               
                 204416_x_at 
                 NM_001645 
                 APOC1 
                 Hs.268571 
               
               
                 204359_at 
                 NM_013231 
                 FLRT2 
                 Hs.48998 
               
               
                 204348_s_at 
                 NM_013410 
                 AK3 
                 Hs.274691 
               
               
                 204115_at 
                 NM_004126 
                 GNG11 
                 Hs.83381 
               
               
                 204026_s_at 
                 NM_007057 
                 ZWINT 
                 Hs.42650 
               
               
                 204006_s_at 
                 NM_000570 
                 FCGR3B 
                 Hs.372679 
               
               
                 203954_x_at 
                 NM_001306 
                 CLDN3 
                 Hs.25640 
               
               
                 203953_s_at 
                 BE791251 
                 CLDN3 
                 Hs.25640 
               
               
                 203892_at 
                 NM_006103 
                 WFDC2 
                 Hs.2719 
               
               
                 203851_at 
                 NM_002178 
                 IGFBP6 
                 Hs.274313 
               
               
                 203797_at 
                 AF039555.1 
                 VSNL1 
                 Hs.2288 
               
               
                 203749_s_at 
                 AI806984 
                 RARA 
                 Hs.361071 
               
               
                 203726_s_at 
                 NM_000227 
                 LAMA3 
                 Hs.83450 
               
               
                 203698_s_at 
                 NM_001463 
                 FRZB 
                 Hs.153684 
               
               
                 203697_at 
                 U91903.1 
                 FRZB 
                 Hs.153684 
               
               
                 203590_at 
                 NM_006141 
                 DNCLI2 
                 Hs.194625 
               
               
                 203324_s_at 
                 NM_001233 
                 CAV2 
                 Hs.139851 
               
               
                 203214_x_at 
                 NM_001786 
                 CDC2 
                 Hs.334562 
               
               
                 203213_at 
                 AL524035 
                 CDC2 
                 Hs.334562 
               
               
                 203108_at 
                 NM_003979 
                 RAI3 
                 Hs.194691 
               
               
                 203065_s_at 
                 NM_001753 
                 CAV1 
                 Hs.74034 
               
               
                 203059_s_at 
                 NM_004670 
                 PAPSS2 
                 Hs.274230 
               
               
                 203038_at 
                 NM_002844 
                 PTPRK 
                 Hs.79005 
               
               
                 202870_s_at 
                 NM_001255 
                 CDC20 
                 Hs.82906 
               
               
                 202765_s_at 
                 AI264196 
                 FBN1 
                 Hs.750 
               
               
                 202760_s_at 
                 NM_007203 
                 AKAP2 
                 Hs.42322 
               
               
                 202705_at 
                 NM_004701 
                 CCNB2 
                 Hs.194698 
               
               
                 202555_s_at 
                 NM_005965 
                 MYLK 
                 Hs.211582 
               
               
                 202504_at 
                 NM_012101 
                 TRIM29 
                 Hs.82237 
               
               
                 202503_s_at 
                 NM_014736 
                 KIAA0101 
                 Hs.81892 
               
               
                 202242_at 
                 NM_004615 
                 TM4SF2 
                 Hs.82749 
               
               
                 202177_at 
                 NM_000820 
                 MGC5560 
                 Hs.207251 
               
               
                 201820_at 
                 NM_000424 
                 KRT5 
                 Hs.433845 
               
               
                 201787_at 
                 NM_001996 
                 FBLN1 
                 Hs.79732 
               
               
                 201753_s_at 
                 NM_019903 
                 ADD3 
                 Hs.324470 
               
               
                 201752_s_at 
                 AI763123 
                 ADD3 
                 Hs.324470 
               
               
                 201497_x_at 
                 NM_022844 
                 MYH11 
                 Hs.78344 
               
               
                 201461_s_at 
                 NM_004759 
                 MAPKAPK2 
                 Hs.75074 
               
               
                 201428_at 
                 NM_001305 
                 CLDN4 
                 Hs.5372 
               
               
                 201224_s_at 
                 AU147713 
                 SRRM1 
                 Hs.18192 
               
               
                 201212_at 
                 D55696.1 
                 LGMN 
                 Hs.18069 
               
               
                 201195_s_at 
                 AB018009.1 
                 SLC7A5 
                 Hs.184601 
               
               
                 201034_at 
                 BE545756 
                 ADD3 
                 Hs.324470 
               
               
                 200841_s_at 
                 AI475965 
                 EPRS 
                 Hs.55921 
               
               
                 200770_s_at 
                 J03202.1 
                 LAMC1 
                 Hs.214982 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Genes useful for separation of ESR1+ FHL++ &lt;-&gt; ESR+ FHL+ 
               
            
           
           
               
               
               
               
            
               
                 Affymetrix 
                 GenBank 
                   
                   
               
               
                 Probe Set ID HG 
                 Accession 
               
               
                 U133A 
                 No 
                 Gene Symbol 
                 Unigene ID 
               
               
                   
               
               
                 218644_at 
                 NM_016445 
                 PLEK2 
                 Hs.39957 
               
               
                 218451_at 
                 NM_022842 
                 CDCP1 
                 Hs.146170 
               
               
                 213364_s_at 
                 AI052536 
                 — 
                 Hs.31834 
               
               
                 212914_at 
                 AV648364 
                 CBX7 
                 Hs.356416 
               
               
                 210052_s_at 
                 AF098158.1 
                 C20orf1 
                 Hs.9329 
               
               
                 209714_s_at 
                 AF213033.1 
                 CDKN3 
                 Hs.84113 
               
               
                 209505_at 
                 AI951185 
                 NR2F1 
                 Hs.374991 
               
               
                 209200_at 
                 N22468 
                 MEF2C 
                 Hs.78995 
               
               
                 208079_s_at 
                 NM_003158 
                 STK6 
                 Hs.250822 
               
               
                 206754_s_at 
                 NM_000767 
                 CYP2B6 
                 Hs.1360 
               
               
                 204679_at 
                 NM_002245 
                 KCNK1 
                 Hs.79351 
               
               
                 204678_s_at 
                 U90065.1 
                 KCNK1 
                 Hs.79351 
               
               
                 204259_at 
                 NM_002423 
                 MMP7 
                 Hs.2256 
               
               
                 204092_s_at 
                 NM_003600 
                 STK6 
                 Hs.250822 
               
               
                 204041_at 
                 NM_000898 
                 MAOB 
                 Hs.82163 
               
               
                 202954_at 
                 NM_007019 
                 UBE2C 
                 Hs.93002 
               
               
                 201292_at 
                 NM_001067.1 
                 TOP2A 
                 Hs.156346 
               
               
                 201291_s_at 
                 NM_001067.1 
                 TOP2A 
                 Hs.156346 
               
               
                   
               
            
           
         
       
     
     LITERATURE 
     
         
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