METHODS, SYSTEMS, AND KITS FOR EVALUATING MULTIPLE SCLEROSIS

FIELD OF THE INVENTION

The present invention relates to methods, systems, and kits for evaluating multiple sclerosis (MS), and for assisting in the diagnosis, prognosis, and/or treatment of MS.

SEQUENCE LISTING

The contents of the accompanying Sequence Listing are hereby incorporated by reference.

BACKGROUND OF THE INVENTION

Multiple sclerosis (MS) is a disease that affects the central nervous system, and can range from relatively benign to somewhat disabling to devastating. In MS, the myelin surrounding nerve cells is damaged or destroyed, impacting the ability of the nerves to conduct electrical impulses to and from the brain, and leaving scar tissue called sclerosis. These damaged areas are also known as “plaques” or “lesions.” According to the National Multiple Sclerosis Society, there are approximately 400,000 individuals with MS in the United States.

The first symptoms of MS typically appear between the ages of 20 and 40, and include blurred or double vision, red-green color distortion, or even blindness in one eye. Most MS patients experience muscle weakness in their extremities and difficulty with coordination and balance. In severe cases, MS can produce partial or complete paralysis. Paresthesias (numbness, prickling, or “pins and needles”), speech impediments, tremors, and dizziness are frequent symptoms of MS. Approximately half of MS patients experience cognitive impairments.

Diagnosing MS is complicated, because there is no single test that can confirm the presence of MS. The process of diagnosing MS typically involves criteria from the patient's history, a clinical examination, and one or more laboratory tests, with all three often being necessary to rule out other possible causes for symptoms and/or to gather facts sufficient for a diagnosis of MS.

Magnetic resonance imaging (MRI) is a preferred test. An MRI can detect plaques or scarring possibly caused by MS. However, an abnormal MRI does not necessarily indicate MS, as lesions in the brain may be associated with other disorders. Further, spots may also be found in healthy individuals, particularly in healthy older persons. These spots are called UBOs, for unidentified bright objects, and are not related to an ongoing disease process. In addition, a normal MRI does not absolutely rule out the presence MS. About 5% of individuals who are confirmed to have MS on the basis of other criteria, have no brain lesions detectable by MRI. These individuals may have lesions in the spinal cord or may have lesions that cannot be detected by MRI.

A diagnosis of MS might be made based on an evaluation of symptoms, signs, and the results of an MRI, but additional tests may be ordered as well. These include tests of evoked potential, cerebrospinal fluid, and blood.

For example, cerebrospinal fluid is sampled by a lumbar puncture, and is tested for levels of immune system proteins and for the presence of an antibody staining pattern called “oligoclonal bands.” Oligoclonal bands indicate an immune response within the central nervous system and are found in the spinal fluid of 90-95% of individuals with MS. However, oligoclonal bands are also associated with diseases other than MS, and therefore the presence of oligoclonal bands alone is not definitive of MS.

There is likewise no definitive blood test for MS, but blood tests can exclude other possible causes for various neurologic symptoms, such as Lyme disease, collagen-vascular diseases, rare hereditary disorders, and AIDS.

Diagnosing MS generally requires: (1) objective evidence of at least two areas of myelin loss, or demyelinating lesions, “separated in time and space” (lesions occurring in different places within the brain, spinal cord, or optic nerve-at different points in time); and (2) all other diseases that can cause similar neurologic symptoms have been objectively excluded. Until (1) and (2) have been satisfied, a physician does not make a definite diagnosis of MS.

Depending on the clinical problems present when an individual sees a physician, one or more of the tests described above might be performed. Sometimes tests are performed several times over a period of months to help gather the necessary information. A definite MS diagnosis must satisfy the McDonald criteria, named for the distinguished neurologist W. Ian McDonald who sparked society-supported efforts to make the diagnostic process for MS faster and more precise.

There are a few distinct clinical courses for MS, referred to as relapsing-remitting MS, secondary-progressive MS, progressive-relapsing MS, and primary progressive MS. Relapsing-remitting MS is characterized by clearly-defined, acute attacks (relapses), usually with full or partial recovery, and no disease progression between attacks. Secondary-progressive MS is initially relapsing-remitting but then becomes continuously progressive at a variable rate, with or without occasional relapses along the way. The disease-modifying medications are thought to provide benefit for those who continue to have relapses. Primary progressive MS may be characterized by disease progression from the beginning with few or no periods of remission. Progressive-relapsing MS is characterized by disease progression from the beginning, but with clear, acute relapses along the way.

There are several options available for treating individuals diagnosed with MS. Beta-interferon (Avonex, Betaseron, Rebif) has been approved to treat MS. Interferons are also made by the body, mainly to combat viral infections. Interferons have been shown to decrease the worsening or relapse of MS, however disease progression remains unaffected and the side effects of interferons are poorly tolerated. Glatiramer acetate (Copaxone) is a mixture of amino acids that has been shown to decrease the relapse rates of MS by 30%, and appears to also have a positive effect on the overall level of disability. Glatiramer acetate is better tolerated than the interferons and has fewer side effects. Glatiramer acts by binding to major histocompatibility complex class II molecules and competing with MBP and other myelin proteins for such binding and presentation to T cells. Natalizumab (Tysabri) is a monoclonal antibody that binds to alpha-4-integrin on white blood cells and interferes with their movement from the bloodstream into the brain and spinal cord.

An object of the present invention is to provide a blood-based diagnostic test for a more objective, definitive, and rapid diagnosis of MS. Another object of the invention is to provide a diagnostic test for monitoring MS progression, adequacy of treatment, and/or response to treatment.

SUMMARY OF THE INVENTION

The present invention provides methods, systems, and kits for evaluating multiple sclerosis (MS) in a patient. Particularly, the invention provides convenient blood-based, gene-expression tests for evaluating MS, including for diagnosing MS, for excluding MS as a diagnosis, and for monitoring the course of disease or efficacy of treatment.

In one aspect, the invention provides a method for diagnosing MS or excluding MS as a diagnosis for a patient. In this aspect, the invention provides for a confident diagnosis of MS, or a confident exclusion of MS as a diagnosis, and in certain embodiments may help predict a clinical course of the patient's disease and/or a beneficial course of treatment.

In certain embodiments, the method comprises determining a gene expression profile for a blood sample (such as a whole blood sample) of a patient having or suspected of having MS. The gene expression profile contains gene transcript levels (or “expression levels”) for a plurality of genes that are differentially expressed in blood cells of MS patients, and such genes are listed in Tables 1 and 2. Tables 1 and 2 list genes that are differentially expressed in whole blood and PBMCs, respectively, of MS patients, and provide, inter alia, Mean-MS and Mean-control gene expression levels for these differentially expressed genes. In certain embodiments, the gene expression profile contains the expression level in the sample for at least one gene that is also listed in Table 6 (that is, in addition to being listed in Table 1 and/or 2).

In some embodiments, the method comprises determining a gene expression profile for a white blood cell sample (such as a PBMC sample) of a patient having or suspected of having MS. In these embodiments, the gene expression profile contains gene expression levels for a plurality of genes that are differentially expressed in white blood cells of MS patients, and such genes are listed in Table 2. In certain embodiments, the gene expression profile contains the expression level in the sample for at least one gene that is also listed in Table 6 (that is, in addition to being listed in Table 1 and/or 2).

In a second aspect, the invention provides a method for monitoring the course of disease or efficacy of treatment for an MS patient, to thereby provide accurate and objective criteria for determining disease progression and the efficacy of an MS treatment.

In this second aspect, the method comprises determining a gene expression profile, as described above, at various time points after an initial diagnosis of MS. Where the patient is undergoing treatment for MS, the gene expression profiles may include a pre-treatment (or early treatment) gene expression profile and at least one post-treatment gene expression profile of a patient having MS. In some embodiments, the MS patient is undergoing treatment with at least one of Beta-interferon, Glatiramer acetate, and Natalizumab. In certain embodiments, the pre-treatment and post-treatment gene expression profiles are determined for blood samples (such as a whole blood samples) of the patient, or white blood cell samples (such as PBMC samples). The gene expression profiles in accordance with this aspect contain gene expression levels for a plurality of genes that are differentially expressed in blood or in white blood cells of MS patients, and such genes are listed in Table 1 or 2, respectively. In certain embodiments, the gene expression profile contains the expression level in the sample for at least one gene that is also listed in Table 6.

Further, in embodiments where the patient is undergoing treatment with Beta-Interferon, such pre- and post-treatment gene expression profiles may contain gene expression levels for the genes listed in Tables 3 and/or 5, which list genes that are differentially expressed in PBMCs between pre- and post-treatment with Beta-interferon, and which may be correlative of a positive response to treatment. In embodiments where the patient is undergoing treatment with Glatiramer acetate (e.g., Copaxone), the pre- and post-treatment profiles may contain gene expression levels for genes listed in Table 4 and/or 5, which lists genes that are differentially expressed in PBMCs between pre- and post-treatment with Copaxone, and which may be correlative of a positive response to treatment. Table 5 lists genes that are differentially expressed between pre- and post-treatment with either or both of Beta-Interferon and Glatiramer acetate.

The pre-treatment gene expression profile may be compared with the post-treatment gene expression profile, to identify differences between pre-treatment and post-treatment gene expression (e.g., differences between pre-treatment and post-treatment blood transcript levels). These differences may be indicative of the patient's response (positive or negative) to treatment. Alternatively or in addition, the gene expression profiles determined over time, including the pre- and post-treatment profiles, may be compared to MS- and non-MS gene expression profiles (such as those shown in Tables 1 and 2), to determine whether, or to the extent, that the profile becomes more comparable to an MS or non-MS profile. For example, the post-treatment profile may become more or less indicative of an MS profile. Such may be indicative of a patient's positive or negative response to treatment.

In a third aspect, the invention provides a method for preparing a patient gene expression profile for evaluating MS. According to this aspect, the gene expression profile is useful for determining whether the patient has MS, as well as for monitoring the course of the disease, and predicting whether a particular treatment is or will be efficacious. In accordance with this aspect, the method generally comprises quantifying the level of expression, in a patient blood sample, for a plurality of genes listed in one of Tables 1-5.

For example, the gene expression profile may contain the levels of expression in the sample for a plurality of genes listed in Table 1 or Table 2. In some embodiments, at least one of these genes is also listed in Table 6. In accordance with this aspect, the patient may have, or be suspected to have, MS. Such gene expression profiles are useful for classifying samples as MS or non-MS samples in accordance with the first aspect of the invention, or for monitoring the course of the patient's MS over time.

Alternatively, the gene expression profile may contain the levels of expression in the sample for a plurality of genes listed in Table 3, 4, and/or 5. Preferably, at least one of these genes is also listed in Table 6. Such gene expression profiles are useful for predicting whether a particular treatment might be efficacious, or where treatment is already ongoing, determining whether the current treatment is effective.

In still other aspects, the invention provides kits and systems for performing the methods of the invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods, systems, and kits for evaluating multiple sclerosis (MS). The invention provides convenient blood-based, gene-expression tests for evaluating MS in patients. Such patients may be known to have MS, may be suspected of having MS on the basis of one or more MS-like symptoms or results from one or more MS-related clinical exams, or may be beginning or undergoing treatment for MS. In the various aspects of the invention, the invention aids in diagnosing MS, or excluding MS as a diagnosis, monitoring the progression of disease, and predicting or determining efficacy of the various options for MS treatment and care.

Methods For Diagnosing MS

In one aspect, the invention provides a method for diagnosing MS, or for excluding MS as a diagnosis for a patient. The method comprises determining a gene expression profile for a blood sample (such as a whole blood sample) or a white blood cell sample (such as a PBMC sample) of a patient having or suspected of having MS. The gene expression profile prepared according to this aspect of the invention is compared to an MS-profile and/or a non-MS profile, to classify the patient's gene expression profile as an MS profile or a non-MS profile. By classifying the profile as an MS or non-MS profile, a diagnosis of MS may be made, or MS may be excluded as a diagnosis.

Generally, the patient is suspected of having MS. For example, the patient may be suspected of having MS on the basis of neurologic and/or immunologic symptoms consistent with MS, e.g., after an initial physician's exam. The patient may, in some embodiments, be positive for the presence of oligoclonal bands. In these or other embodiments, the patient may have CNS lesions characteristic of MS, which are observable on an MRI. In certain embodiments, the patient has not undergone treatment for MS, but in some embodiments, the patient is already undergoing treatment, such as treatment with Beta-interferon, Glatiramer acetate, and Natalizumab.

Thus, the patient may have one or more presumptive signs of a multiple sclerosis. Presumptive signs of multiple sclerosis include for example, altered sensory, motor, visual or proprioceptive system with at least one of numbness or weakness in one or more limbs, often occurring on one side of the body at a time or the lower half of the body, partial or complete loss of vision, frequently in one eye at a time and often with pain during eye movement, double vision or blurring of vision, tingling or pain in numb areas of the body, electric-shock sensations that occur with certain head movements, tremor, lack of coordination or unsteady gait, fatigue, dizziness, muscle stiffness or spasticity, slurred speech, paralysis, problems with bladder, bowel or sexual function, and mental changes such as forgetfulness or difficulties with concentration, relative to medical standards.

The gene expression profile is determined for a blood sample, such as a whole blood sample or a white blood cell sample, of the patient. The white blood cell sample may be a Peripheral Blood Mononuclear Cell (PBMC) sample of the patient. PBMCs are a mixture of monocytes and lymphocytes. There are several known methods for isolating PBMCs from whole blood. While any suitable method may be employed, in one embodiment, PBMCs are isolated from whole blood samples using density gradient centrifugation. For example, anticoagulated whole blood is layered over a separating medium, and after centrifugation, the following layers are visually observed from top to bottom: plasma/platelets, PBMCs, separating medium and erythrocytes/granulocytes. The PBMC layer may then be removed for RNA isolation. Alternatively, the blood cell sample may be further isolated from whole blood or PBMCs to yield a cell subpopulation, such as a population of lymphocytes (e.g., T-lymphocytes or sub-population thereof). Examples for isolating such sub-populations are known in the art, and include cell sorting, or cell-capturing using antibodies to particular cell-specific markers.

In preparing the gene expression profile of the patient sample(s), RNA is extracted from the collected cells (e.g., using whole blood or PBMC samples) by any known method. For example, RNA may be purified from cells using a variety of standard procedures as described, for example, in RNA Methodologies, A laboratory guide for isolation and characterization, 2nd edition, 1998, Robert E. Farrell, Jr., Ed., Academic Press. In addition, there are various products commercially available for RNA isolation which may be used. Total RNA or polyA+ RNA may be used for preparing gene expression profiles in accordance with the invention.

The gene expression profile (or gene expression signature) is then generated for the samples using any of various techniques known in the art, and described in detail elsewhere herein. Such methods generally include, without limitation, polymerase-based assays, such as RT-PCR (e.g., Taqman™), hybridization-based assays, such as DNA microarray analysis, flap-endonuclease-based assays (e.g., Invader™), as well as direct mRNA capture with branched DNA (QuantiGene™) or Hybrid Capture™ (Digene).

The gene expression profile contains gene expression levels for a plurality of genes that are differentially expressed in blood samples of MS patients, and such genes are disclosed herein. For example, Tables 1 and 2 list genes that are differentially expressed in whole blood and PBMC samples, respectively, of MS patients. As used herein, the term “gene,” refers to a DNA sequence expressed in a sample as an RNA transcript, and may be a full-length gene (protein encoding or non-encoding) or an expressed fragment such as expressed sequence tags or “ESTs.” Thus, the sequences listed in the Tables and Sequence Listing are each independently a full-length gene sequence, whose expression product is present in samples, or is a partial expressed sequence detectable in samples, such as an EST sequence. As used herein, “differentially expressed” means that the level or abundance of an RNA transcript (or abundance of an RNA population sharing a common target sequence, such as splice variant RNAs) is significantly higher or lower in a sample as compared to a reference level. For example, the level of the RNA or RNA population may be higher or lower by at least two-fold as compared to a reference level. The reference level is the level of the same RNA or RNA population in a control sample or control population (e.g., a Mean control level).

Table 1A lists genes that are differentially expressed in whole blood of MS patients, and thus the expression level of these genes or subset thereof may be determined in patient samples to prepare a gene expression profile in accordance with this aspect of the invention. Table 1A refers to these genes by name (title and abbreviation), GeneBank Accession No., and sequence identifier as found in the accompanying Sequence Listing. Table 1A further provides Mean-MS and Mean-control gene expression levels as generated from an exemplary sample set and data set, as well as measures of the statistical association of each differential gene expression level with MS. Table 1B lists these same genes, and expresses the differential RNA levels as fold change (Control/MS), MeanRatio (Control/MS), and Mean Difference (Control-MS).

Thus, in accordance with this aspect, the patient's gene expression profile, which is generated from the patient's blood sample (e.g., a whole blood sample), may contain the levels of expression for at least about 3 genes listed in Table 1. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75, or 100 genes listed in Table 1, such genes being differentially expressed in blood of MS patients over non-MS individuals. In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 1, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 1 and Table 6.

Table 2A lists genes that are differentially expressed in PBMCs of MS patients, and thus the expression level of these genes or subset thereof may be determined in patient samples to prepare a gene expression profile in accordance with this aspect of the invention. Table 2A refers to these genes by name (title and abbreviation), GeneBank Accession No., and sequence identifier as found in the accompanying Sequence Listing. Table 2A further provides the fold change between control and MS samples as generated from an exemplary sample set and data set, as well as measures of the statistical association of each differential gene expression level with MS. Table 2B lists these same genes, and shows the mean control and MS data signals, and indicates the top 42 genes in terms of fold change.

Thus, in accordance with these embodiments, the patient's gene expression profile (generated from whole blood or a white blood cell sample, including a PBMC sample) may contain the levels of expression for at least about 3 genes listed in Table 2. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75 or 100 genes listed in Table 2, such genes being differentially expressed in blood, and particularly PBMCs, of MS patients over non-MS individuals (controls). In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 2, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 2 and Table 6. In some preferred embodiments, one or more, or all, of the genes in Table 2 that are included in the gene expression profile, are in the top 42 genes in terms of fold change between MS and controls, as shown in Table 2.

In certain embodiments, the gene expression profile contains a measure of expression levels for a plurality of genes that are each, independently, expressed in MS samples relative to control samples by a fold change magnitude (up or down) of at least 1.2. In some embodiments, the plurality of genes are differentially expressed in MS samples with respect to control samples (e.g., non-MS sample) by a fold change magnitude of at least 1.5, or at least about 1.7, or at least about 2, or at least about 2.5. Alternatively, the expression levels may differ by at least about 3- or 5-, 10-fold, or more. Tables 1 and 2 list genes by differential levels of expression in control versus MS samples, as determined in whole blood or PBMCs, respectively, and such levels may be used to select genes for profiling in accordance with this paragraph.

The gene expression profile prepared according to this aspect of the invention is compared to an MS-profile and/or a non-MS profile, to classify the patient's gene expression profile as an MS profile or a non-MS profile. In certain embodiments, the non-MS profile is a healthy profile. In these or other embodiments, the MS-profile may be a general MS-profile (e.g., not limited to a clinical MS subtype), or may be a relapsing-remitting MS profile. Tables 1 and 2 present exemplary MS and non-MS profiles, which may be used to classify patient samples. Of course, additional MS and non-MS profiles for classifying samples may be generated from additional MS and control sample sets, using the genes listed in Tables 1 and 2 as described above.

Various classification schemes are known for classifying samples between two or more classes or groups, and these include, without limitation: Naïve Bayes, Support Vector Machines, Nearest Neighbors, Decision Trees, Logistic, Artificial Neural Networks, and Rule-based schemes. In addition, the predictions from multiple models can be combined to generate an overall prediction. For example, a “majority rules” prediction may be generated from the outputs of a Naïve Bayes model, a Support Vector Machine model, and a Nearest Neighbor model.

Thus, a classification algorithm or “class predictor” may be constructed to classify samples. The process for preparing a suitable class predictor is reviewed in R. Simon, Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data, British Journal of Cancer (2003) 89, 1599-1604, which review is hereby incorporated by reference in its entirety.

Generally, the gene expression profile for the patient is compared to both a non-MS profile and an MS profile. Such MS and non-MS profiles may be assembled from gene expression data disclosed herein (Tables 1 and 2), which may be stored in a database and correlated to patient profiles. Thus, MS and non-MS profiles may be assembled from data and matched to a particular patient by, for example, age, race, gender, and/or clinical manifestations of MS. The MS profile may represent a particular clinical course of MS, such as relapsing-remitting MS.

After comparing the patient's gene expression profile to the MS and/or non-MS profile, the sample is classified as, or for example, given a probability of being, an MS profile or a non-MS profile. The classification may be determined computationally based upon known methods as described above. The result of the computation may be displayed on a computer screen or presented in a tangible form, for example, as a probability (e.g., from 0 to 100%) of the patient having MS. The report will aid a physician in diagnosis or treatment of the patient. For example, in certain embodiments of the invention, the patient's gene expression profile will be determined to be an MS profile on the basis of a probability, and the patient will be subsequently treated for MS as appropriate. In other embodiments, the patient's profile will be determined to be a non-MS profile, thereby allowing the physician to exclude MS as a diagnosis for the patient.

In various embodiments, the method according to this aspect of the invention distinguishes a MS-afflicted patient from a non-MS afflicted patient with at least about 50%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater accuracy. In this respect, the method according to this aspect may lend additional or alternative predictive value over standard clinical methods of diagnosing MS, such as for example, absence or presence of lesions on an MRI, testing positive or negative for oligoclonal bands, or the absence or presence of other signs and symptoms of MS such as blurred vision, fatigue, and/or loss of balance.

Methods For Determining Efficacy of Treatment

In a second aspect, the invention is a method for monitoring treatment of an MS patient. While any treatment program may be monitored, including test compounds, in certain embodiments the patient is undergoing treatment with one or more of Beta-Interferon, Glatiramer acetate, and Natalizumab. In this aspect, the invention comprises determining a pre-treatment (or early treatment) gene expression profile and at least one post-treatment gene expression profile for the patient, as already described. The pre-treatment profile may be determined from a sample taken prior to treatment, or may be an early treatment profile determined, for example, for a sample taken within the first six months of treatment. The post-treatment profile(s) may be determined for samples taken anytime after the start of treatment, such as after about three months, after about six months, after about twelve months of treatment, and/or later.

The pre-treatment and post-treatment gene expression profiles are prepared from blood samples (e.g., whole blood) or white blood cell samples (such as PBMC samples or subpopulation thereof), isolated from the patient at the selected pre- and post-treatment time points.

The pre- and post-treatment gene expression profiles contain gene expression levels for a plurality of genes that are differentially expressed in blood cells of MS patients, as described in the preceding section with respect to Tables 1, 2, and 6. Thus, in accordance with this aspect, the patient's gene expression profile, which is generated from the patient's blood sample (e.g., a whole blood sample), may contain the levels of expression for at least about 3 genes listed in Table 1. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75, or 100 genes listed in Table 1, such genes being differentially expressed in blood of MS patients over non-MS individuals. In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 1, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 1 and Table 6. Alternatively, the patient's gene expression profile (generated from whole blood or a white blood cell sample, including a PBMC sample) may contain the levels of expression for at least about 3 genes listed in Table 2. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75 or 100 genes listed in Table 2, such genes being differentially expressed in blood, and particularly PBMCs, of MS patients over non-MS individuals (controls). In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 2, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 2 and Table 6. In some preferred embodiments, one or more, or all, of the genes in Table 2 that are included in the gene expression profile, are in the top 42 genes in terms of fold change between MS and controls, as shown in Table 2.

Thus, such gene expression profiles may be useful for monitoring a patient's treatment, to determine whether the post-treatment sample classifies as an MS-sample, to the same, lesser, or greater extent as the pre-treatment sample. Such pre-treatment and post-treatment samples may be classified or scored as MS or non-MS samples as disclosed elsewhere herein.

Alternatively, or in addition, the pre-treatment and post-treatment gene expression profiles may be compared to identify differences in gene expression upon treatment with MS. For example, where the patient is being treated with Beta-interferon, gene expression values may be determined (pre- and post-treatment) for genes (e.g., 3, 5, 7, 10, 15, 20, or 40 genes) listed in Tables 3 and/or 5. In certain embodiments, at least one gene is also listed in Table 6, in addition to being listed in Tables 3 and/or 5. Or, where the patient is being treated with Glatiramer acetate, gene expression values may be determined (pre- and post-treatment) for genes (e.g., 3, 5, 7, 10, 15, 20, or 40 genes) listed in Tables 4 or 5. In certain embodiments, at least one gene is also listed in Table 6, in addition to being listed in Tables 3 and/or 5. Tables 3 and 5 list genes that are differentially expressed in PBMCs between pre- and post-treatment with Beta-interferon. Table 4 and 5 list genes that are differentially expressed in PBMCs between pre- and post-treatment with Copaxone. Table 5 lists genes that are differentially expressed between pre- and post-treatment with each of Beta-Interferon and Glatiramer acetate.

The pre-treatment gene expression profile may then be compared with the post-treatment gene expression profile, to identify differences between pre-treatment and post-treatment gene expression. These differences may be indicative of the patient's response (positive or negative) to treatment.

Many of the genes that are indicative of a patient's response to Beta-interferon may encode cell surface markers, e.g. cell surface markers on immune cells, and several of which are interferon-inducible genes (see Table 3). Accordingly, in some embodiments of the invention, at least one, or at least five, or at least 10 of the genes in the gene expression profile encode a cell-surface marker, some or all of which are interferon-inducible. Such genes are listed in Example 2, herein.

After comparison, the post-treatment gene expression profile may be classified as being indicative of MS, or not being indicative of MS (or being less indicative of MS than the pre-treatment sample), for example due to effective therapy. Alternatively, the post-treatment sample may be more indicative of MS, suggesting that an alternative therapy would be desirable. The analysis in accordance with this aspect may be performed computationally as described. The result of the analysis may be displayed or presented in tangible form to aid in considering further treatment options, such as adjusting or changing the treatment, if needed, and to track the clinical course of the patient's disease.

Methods for Preparing Gene Expression Profiles

Specifically, in accordance with this aspect, the patient's gene expression profile, which is generated from the patient's blood sample (e.g., a whole blood sample), may contain the levels of expression for at least about 3 genes listed in Table 1. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75, or 100 genes listed in Table 1, such genes being differentially expressed in blood of MS patients over non-MS individuals. In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 1, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 1 and Table 6.

Alternatively, the patient's gene expression profile (generated from whole blood or a white blood cell sample, including a PBMC sample) may contain the levels of expression for at least about 3 genes listed in Table 2. In some embodiments, the patient's gene expression profile contains the levels of expression for at least about 5, 7, 10, 12, 15, 20, 25, 40, 50, 75 or 100 genes listed in Table 2, such genes being differentially expressed in blood, and particularly PBMCs, of MS patients over non-MS individuals (controls). In some embodiments, the gene expression profile may contain the levels of expression for all or substantially all genes listed in Table 2, such as at least about 200, 250, or 300 genes. In any of the embodiments described in this paragraph, the gene expression profile may comprise the level of expression of at least one gene that is also listed in Table 6. That is, at least one of the genes is listed in both Table 2 and Table 6. In some preferred embodiments, one or more, or all, of the genes in Table 2 that are included in the gene expression profile, are in the top 42 genes in terms of fold change between MS and controls, as shown in Table 2.

Assay Formats

Gene expression profiles, including patient gene expression profiles and the MS and non-MS profiles as described herein, may be prepared according to any suitable method for measuring gene expression. That is, the profiles may be prepared using any quantitative or semi-quantitative method for determining RNA transcript levels in samples. Such methods include polymerase-based assays, such as RT-PCR, Taqman™, hybridization-based assays, for example using DNA microarrays or other solid support, nucleic acid sequence based amplification (NASBA), flap endonuclease-based assays, as well as direct mRNA capture with branched DNA (QuantiGene™) or Hybrid Capture™ (Digene). The assay format, in addition to determining the gene expression levels for a combination of genes listed in one or more of Tables 1-6, will also allow for the control of, inter alia, intrinsic signal intensity variation between tests. Such controls may include, for example, controls for background signal intensity and/or sample processing, and/or other desirable controls for gene expression quantification across samples. For example, expression levels between samples may be controlled by testing for the expression level of one or more genes that are not differentially expressed in MS patients, or which are generally expressed at similar levels across the population. Such genes may include constitutively expressed genes, many of which are known in the art. Exemplary assay formats for determining gene expression levels, and thus for preparing gene expression profiles and MS- and non-MS profiles are described in this section.

The nucleic acid sample is typically in the form of mRNA or reverse transcribed mRNA (cDNA) isolated from a blood sample, such as a whole blood sample, PBMC sample, or other subpopulation of blood cells (e.g., T-lymphocytes) isolated from the patient's blood. In some embodiments, the nucleic acids in the sample may be cloned or amplified, generally in a manner that does not bias the representation of the transcripts within a sample. In some embodiments, it may be preferable to use total RNA or polyA+ RNA as a source without cloning or amplification, to avoid additional processing steps.

As is apparent to one of skill in the art, nucleic acid samples used in the methods of the invention may be prepared by any available method or process. Methods of isolating total mRNA are well known to those of skill in the art. For example, methods of isolation and purification of nucleic acids are described in detail in Chapter 3 of Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24, Hybridization With Nucleic Acid Probes: Theory and Nucleic Acid Probes, P. Tijssen, Ed., Elsevier Press, New York, 1993. Such samples include RNA samples, but also include cDNA synthesized from a mRNA sample isolated from a cell or tissue of interest (e.g., whole blood or PBMC sample). Such samples also include DNA amplified from the cDNA, and RNA transcribed from the amplified DNA.

In determining a patient's gene expression profile, or in determining an MS- or non-MS profile in accordance with the invention, a hybridization-based assay may be employed. Nucleic acid hybridization involves contacting a probe and a target sample under conditions where the probe and its complementary target sequence (if present) in the sample can form stable hybrid duplexes through complementary base pairing. The nucleic acids that do not form hybrid duplexes may be washed away leaving the hybridized nucleic acids to be detected, typically through detection of an attached detectable label. It is generally recognized that nucleic acids may be denatured by increasing the temperature or decreasing the salt concentration of the buffer containing the nucleic acids. Under low stringency conditions (e.g., low temperature and/or high salt) hybrid duplexes (e.g., DNA:DNA, RNA:RNA, or RNA:DNA) will form even where the annealed sequences are not perfectly complementary. Thus, specificity of hybridization is reduced at lower stringency. Conversely, at higher stringency (e.g., higher temperature or lower salt) successful hybridization tolerates fewer mismatches. One of skill in the art will appreciate that hybridization conditions may be selected to provide any degree of stringency.

In certain embodiments, hybridization is performed at low stringency, such as 6×SSPET at 37° C. (0.005% Triton X-100), to ensure hybridization, and then subsequent washes are performed at higher stringency (e.g., 1×SSPET at 37° C.) to eliminate mismatched hybrid duplexes. Successive washes may be performed at increasingly higher stringency (e.g., down to as low as 0.25×SSPET at 37° C. to 50° C.) until a desired level of hybridization specificity is obtained. Stringency can also be increased by addition of agents such as formamide. Hybridization specificity may be evaluated by comparison of hybridization to the test probes with hybridization to the various controls that may be present, as described below (e.g., expression level control, normalization control, mismatch controls, etc.).

In general, there is a tradeoff between hybridization specificity (stringency) and signal intensity. Thus, in a preferred embodiment, the wash is performed at the highest stringency that produces consistent results and that provides a signal intensity greater than approximately 10% of the background intensity. The hybridized array may be washed at successively higher stringency solutions and read between each wash. Analysis of the data sets thus produced will reveal a wash stringency above which the hybridization pattern is not appreciably altered and which provides adequate signal for the particular oligonucleotide probes of interest.

The hybridized nucleic acids are typically detected by detecting one or more labels attached to the sample nucleic acids. The labels may be incorporated by any of a number of means well known to those of skill in the art. See WO 99/32660.

Numerous hybridization assay formats are known, and which may be used in accordance with the invention. Such hybridization-based formats include solution-based and solid support-based assay formats. Solid supports containing oligonucleotide probes designed to detect differentially expressed genes (e.g., listed in Tables 1-5) can be filters, polyvinyl chloride dishes, particles, beads, microparticles or silicon or glass based chips, etc. Any solid surface to which oligonucleotides can be bound, either directly or indirectly, either covalently or non-covalently, may be used. Bead-based assays are described, for example, in U.S. Pat. Nos. 6,355,431, 6,396,995, and 6,429,027, which are hereby incorporated by reference. Other chip-based assays are described in U.S. Pat. Nos. 6,673,579, 6,733,977, and 6,576,424, which are hereby incorporated by reference.

An exemplary solid support is a high density array or DNA chip, which may contain a particular oligonucleotide probes at predetermined locations on the array. Each predetermined location may contain more than one molecule of the probe, but each molecule within the predetermined location has an identical probe sequence. Such predetermined locations are termed features. Probes corresponding to the genes of Tables 1-5 may be attached to single or multiple solid support structures, e.g., the probes may be attached to a single chip or to multiple chips to comprise a chip set.

Oligonucleotide probe arrays for expression monitoring can be made and used according to any techniques known in the art (see for example, Lockhart et al (1996), Nat Biotechnol 14:1675-1680; McGall et al. (1996), Proc Nat Acad Sci USA 93:13555-13460). Such probe arrays may contain the oligonucleotide probes necessary for determining a patient's gene expression profile, or for preparing MS- and non-MS profiles with population samples. Thus, such arrays may contain oligonucleotide designed to hybridize to at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 50, 70, 100, 200, 300 or more of the genes described herein (e.g., as described in one of Tables 1-5, or as described in any of Tables 1-5). In some embodiments, the array contains probes designed to hybridize to all or nearly all of the genes listed in Tables 1-5. In still other embodiments, arrays are constructed that contain oligonucleotides designed to detect all or nearly all of the genes in Table 1-5 on a single solid support substrate, such as a chip or a set of beads.

Probes based on the sequences of the genes described herein for preparing expression profiles may be prepared by any suitable method. Oligonucleotide probes, for hybridization-based assays, will be of sufficient length or composition (including nucleotide analogs) to specifically hybridize only to appropriate, complementary nucleic acids (e.g., exactly or substantially complementary RNA transcripts or cDNA). Typically the oligonucleotide probes will be at least about 10, 12, 14, 16, 18, 20 or 25 nucleotides in length. In some cases, longer probes of at least 30, 40, or 50 nucleotides may be desirable. In some embodiments, complementary hybridization between a probe nucleic acid and a target nucleic acid embraces minor mismatches (e.g., one, two, or three mismatches) that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target polynucleotide sequence. Of course, the probes may be perfect matches with the intended target probe sequence, for example, the probes may each have a probe sequence that is perfectly complementary to a target sequence (e.g., a sequence of a gene listed in Tables 1-5).

A probe is a nucleic acid capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. A probe may include natural (i.e., A, G, U, C, or T) or modified bases (7-deazaguanosine, inosine, etc.), or locked nucleic acid (LNA). In addition, the nucleotide bases in probes may be joined by a linkage other than a phosphodiester bond, so long as the bond does not interfere with hybridization. Thus, probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages.

When using hybridization-based assays, in may be necessary to control for background signals. The terms “background” or “background signal intensity” refer to hybridization signals resulting from non-specific binding, or other interactions, between the labeled target nucleic acids and components of the oligonucleotide array (e.g., the oligonucleotide probes, control probes, the array substrate, etc.). Background signals may also be produced by intrinsic fluorescence of the array components themselves. A single background signal can be calculated for the entire array, or a different background signal may be calculated for each location of the array. In an exemplary embodiment, background is calculated as the average hybridization signal intensity for the lowest 5% to 10% of the probes in the array. Alternatively, background may be calculated as the average hybridization signal intensity produced by hybridization to probes that are not complementary to any sequence found in the sample (e.g. probes directed to nucleic acids of the opposite sense or to genes not found in the sample such as bacterial genes where the sample is mammalian nucleic acids). Background can also be calculated as the average signal intensity produced by regions of the array that lack any probes at all. Of course, one of skill in the art will appreciate that hybridization signals may be controlled for background using one or a combination of known approached, including one or a combination of approaches described in this paragraph.

The hybridization-based assay will be generally conducted under conditions in which the probe(s) will hybridize to their intended target subsequence, but with only insubstantial hybridization to other sequences or to other sequences, such that the difference may be identified. Such conditions are sometimes called “stringent conditions.” Stringent conditions are sequence-dependent and can vary under different circumstances. For example, longer probe sequences generally hybridize to perfectly complementary sequences (over less than fully complementary sequences) at higher temperatures. Generally, stringent conditions may be selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Exemplary stringent conditions may include those in which the salt concentration is at least about 0.01 to 1.0 M Na⁺ ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides). Desired hybridization conditions may also be achieved with the addition of agents such as formamide or tetramethyl ammonium chloride (TMAC).

When using an array, one of skill in the art will appreciate that an enormous number of array designs are suitable for the practice of this invention. The array will typically include a number of test probes that specifically hybridize to the sequences of interest. That is, the array will include probes designed to hybridize to any region of the genes listed in Tables 1-5, and the accompanying sequence listing. In instances where the gene reference in the Tables is an EST, probes may be designed from that sequence or from other regions of the corresponding full-length transcript that may be available in any of the public sequence databases, such as those herein described. See WO 99/32660 for methods of producing probes for a given gene or genes. In addition, software is commercially available for designing specific probe sequences. Typically, the array will also include one or more control probes, such as probes specific for a constitutively expressed gene, thereby allowing data from different arrays to be normalized or controlled.

The hybridization-based assays may include, in addition to “test probes” (e.g., that bind the target sequences of interest, which are listed in Tables 1-6), the assay may also test for hybridization to one or a combination of control probes. Exemplary control probes include: normalization controls, expression level controls, and mismatch controls. For example, when determining the levels of gene expression in patient or control samples, the expression values may be normalized to control between samples. That is, the levels of gene expression in each sample may be normalized by determining the level of expression of at least one constitutively expressed gene in each sample. In accordance with the invention, the constitutively expressed gene is generally not differentially expressed in samples (blood samples, including whole blood or PBMC samples) of MS patients.

Other useful controls are normalization controls, for example, using probes designed to be complementary to a labeled reference oligonucleotide added to the nucleic acid sample to be assayed. The signals obtained from the normalization controls after hybridization provide a control for variations in hybridization conditions, label intensity, “reading” efficiency and other factors that may cause the signal of a perfect hybridization to vary between arrays. In one embodiment, signals (e.g., fluorescence intensity) read from all other probes in the array are divided by the signal (e.g., fluorescence intensity) from the control probes thereby normalizing the measurements. Exemplary normalization probes are selected to reflect the average length of the other probes (e.g., test probes) present in the array, however, they may be selected to cover a range of lengths. The normalization control(s) may also be selected to reflect the (average) base composition of the other probes in the array. In some embodiments, the assay employs one or a few normalization probes, and they are selected such that they hybridize well (i.e., no secondary structure) and do not hybridize to any potential targets.

The hybridization-based assay may employ expression level controls, for example, probes that hybridize specifically with constitutively expressed genes in the biological sample. Virtually any constitutively expressed gene provides a suitable target for expression level controls. Typically expression level control probes have sequences complementary to subsequences of constitutively expressed “housekeeping genes” including, but not limited to the actin gene, the transferrin receptor gene, the GAPDH gene, and the like.

The hybridization-based assay may also employ mismatch controls for the target sequences, and/or for expression level controls or for normalization controls. Mismatch controls are probes designed to be identical to their corresponding test or control probes, except for the presence of one or more mismatched bases. A mismatched base is a base selected so that it is not complementary to the corresponding base in the target sequence to which the probe would otherwise specifically hybridize. One or more mismatches are selected such that under appropriate hybridization conditions (e.g., stringent conditions) the test or control probe would be expected to hybridize with its target sequence, but the mismatch probe would not hybridize (or would hybridize to a significantly lesser extent). Preferred mismatch probes contain a central mismatch. Thus, for example, where a probe is a 20-mer, a corresponding mismatch probe will have the identical sequence except for a single base mismatch (e.g., substituting a G, a C or a T for an A) at any of positions 6 through 14 (the central mismatch).

Mismatch probes thus provide a control for non-specific binding or cross hybridization to a nucleic acid in the sample other than the target to which the probe is directed. For example, if the target is present, the perfect match probes should provide a more intense signal than the mismatch probes. The difference in intensity between the perfect match and the mismatch probe helps to provide a good measure of the concentration of the hybridized material.

Methods of forming high density arrays of oligonucleotides with a minimal number of synthetic steps are known. The oligonucleotide analogue array can be synthesized on a single or on multiple solid substrates by a variety of methods, including, but not limited to, light-directed chemical coupling, and mechanically directed coupling (see Pirrung, U.S. Pat. No. 5,143,854). In brief, the light-directed combinatorial synthesis of oligonucleotide arrays on a glass surface proceeds using automated phosphoramidite chemistry and chip masking techniques. In one specific implementation, a glass surface is derivatized with a silane reagent containing a functional group, e.g., a hydroxyl or amine group blocked by a photolabile protecting group. Photolysis through a photolithographic mask is used selectively to expose functional groups which are then ready to react with incoming 5′ photoprotected nucleoside phosphoramidites. The phosphoramidites react only with those sites which are illuminated (and thus exposed by removal of the photolabile blocking group). Thus, the phosphoramidites only add to those areas selectively exposed from the preceding step. These steps are repeated until the desired array of sequences have been synthesized on the solid surface. Combinatorial synthesis of different oligonucleotide analogues at different locations on the array is determined by the pattern of illumination during synthesis and the order of addition of coupling reagents.

In addition to the foregoing, additional methods which can be used to generate an array of oligonucleotides on a single substrate are described in PCT Publication Nos. WO 93/09668 and WO 01/23614. High density nucleic acid arrays can also be fabricated by depositing pre-made or natural nucleic acids in predetermined positions. Synthesized or natural nucleic acids are deposited on specific locations of a substrate by light directed targeting and oligonucleotide directed targeting. Another embodiment uses a dispenser that moves from region to region to deposit nucleic acids in specific spots.

The hybdridization-based assay may, as an alternative to purely passive hybridization, employ the methods described in U.S. Pat. No. 6,326,173, which is hereby incorporated by reference. For example, the assay may involve electronically concentrating and hybridizing the nucleic acid sample to the surface of a microchip (e.g., capture sites). This method may allow for rapid concentration and subsequent specific hybridization of template nucleic acid molecules to their complementary anchored amplification primers.

Alternatively, the invention may employ reverse transcription polymerase chain reaction (RT-PCR), which is a sensitive method for the detection of mRNA, including low abundant mRNAs present in clinical samples. The application of fluorescence techniques to RT-PCR combined with suitable instrumentation has led to quantitative RT-PCR methods that combine amplification, detection and quantification in a closed system. Two commonly used quantitative RT-PCR techniques are the Taqman RT-PCR assay (ABI, Foster City, USA) and the Lightcycler assay (Roche, USA).

Thus, in one embodiment of the present invention, the preparation of patient gene expression profiles or the preparation of MS- and non-MS profiles comprises conducting real-time quantitative PCR (TaqMan) with sample-derived RNA and control RNA. Holland, et al., PNAS 88:7276-7280 (1991) describe an assay known as a Taqman assay. The 5′ to 3′ exonuclease activity of Taq polymerase is employed in a polymerase chain reaction product detection system to generate a specific detectable signal concomitantly with amplification. An oligonucleotide probe, non-extendable at the 3′ end, labeled at the 5′ end, and designed to hybridize within the target sequence, is introduced into the polymerase chain reaction assay. Annealing of the probe to one of the polymerase chain reaction product strands during the course of amplification generates a substrate suitable for exonuclease activity. During amplification, the 5′ to 3′ exonuclease activity of Taq polymerase degrades the probe into smaller fragments that can be differentiated from undegraded probe. A version of this assay is also described in Gelfand et al., in U.S. Pat. No. 5,210,015, which is hereby incorporated by reference.

Further, U.S. Pat. No. 5,491,063 to Fisher, et al., which is hereby incorporated by reference, provides a Taqman-type assay. The method of Fisher et al. provides a reaction that results in the cleavage of single-stranded oligonucleotide probes labeled with a light-emitting label wherein the reaction is carried out in the presence of a DNA binding compound that interacts with the label to modify the light emission of the label. The method of Fisher uses the change in light emission of the labeled probe that results from degradation of the probe.

The TaqMan detection assays offer certain advantages. First, the methodology makes possible the handling of large numbers of samples efficiently and without cross-contamination and is therefore adaptable for robotic sampling. As a result, large numbers of test samples can be processed in a very short period of time using the TaqMan assay. Another advantage of the TaqMan system is the potential for multiplexing. Since different fluorescent reporter dyes can be used to construct probes, the expression of several different genes associated with MS could be assayed in the same PCR reaction, thereby reducing the labor costs that would be incurred if each of the tests were performed individually. Thus, the TaqMan assay format is preferred where the patient's gene expression profile, and the corresponding MS- and non-MS profiles comprise the expression levels of about 20 of fewer, or about 10 or fewer, or about 7 of fewer, or about 5 genes (e.g., genes listed in Tables 1-6).

Alternatively, the assay format may employ the methodologies described in Direct Multiplexed Measurement of Gene Expression with Color-Coded Probe Pairs, Nature Biotechnology (Mar. 7, 2008), which describes the nCounter™ Analysis System (nanoString Technologies). This system captures and counts individual mRNA transcripts by a molecular bar-coding technology, and is commercialized by Nanostring.

In other embodiments, the invention employs detection and quantification of RNA levels in real-time using nucleic acid sequence based amplification (NASBA) combined with molecular beacon detection molecules. NASBA is described for example, in Compton J., Nucleic acid sequence-based amplification, Nature 1991; 350(6313): 91-2. NASBA is a singe-step isothermal RNA-specific amplification method. Generally, the method involves the following steps: RNA template is provided to a reaction mixture, where the first primer attaches to its complementary site at the 3′ end of the template; reverse transcriptase synthesizes the opposite, complementary DNA strand; RNAse H destroys the RNA template (RNAse H only destroys RNA in RNA-DNA hybrids, but not single-stranded RNA); the second primer attaches to the 3′ end of the DNA strand, and reverse transcriptase synthesizes the second strand of DNA; and T7 RNA polymerase binds double-stranded DNA and produces a complementary RNA strand which can be used again in step 1, such that the reaction is cyclic.

In yet other embodiments, the assay format is a flap endonuclease-based format, such as the Invader™ assay (Third Wave Technologies). In the case of using the invader method, an invader probe containing a sequence specific to the region 3′ to a target site, and a primary probe containing a sequence specific to the region 5′ to the target site of a template and an unrelated flap sequence, are prepared. Cleavase is then allowed to act in the presence of these probes, the target molecule, as well as a FRET probe containing a sequence complementary to the flap sequence and an auto-complementary sequence that is labeled with both a fluorescent dye and a quencher. When the primary probe hybridizes with the template, the 3′ end of the invader probe penetrates the target site, and this structure is cleaved by the Cleavase resulting in dissociation of the flap. The flap binds to the FRET probe and the fluorescent dye portion is cleaved by the Cleavase resulting in emission of fluorescence.

In yet other embodiments, the assay format employs direct mRNA capture with branched DNA (QuantiGene™, Panomics) or Hybrid Capture™ (Digene).

The design of appropriate probes for hybridizing to a particular target nucleic acid, and as configured for any appropriate nucleic acid detection assay, is well known.

Computer Systems

In another aspect, the invention is a computer system that contains a database, on a computer-readable medium, of mean gene expression values determined in an MS patient population and in a non-MS patient population. These gene expression values are determined in blood samples, such as whole blood cell samples or white blood cell samples (e.g., PBMC samples), and for genes selected from one or more of Tables 1-5. The database may include gene expression measurements for at least one or a plurality of genes that are also listed in Table 6. The database may include, for each gene, Mean-MS and Mean-Control (e.g., non-MS or healthy) gene expression levels, as well as various statistical measures, including measures of value dispersion (e.g., Standard Variation), fold change (e.g., between control and MS populations), and statistical significance (statistical association with MS). Various such measures are shown in the accompanying Tables, and such measures may be employed in the computer systems of the invention. Further, the MS patient population may include patients being treated with Beta-interferon, Glatiramer acetate, and/or Natalizumab, and such treatment and other clinical information may be included in the database such that an appropriate gene expression profile may be assembled for use with the diagnostic methods of the invention. Generally, profiles may be assembled based upon parameters to be selected and input by a user, with these parameters including one or more of age, race, gender, MS treatment, and clinical manifestation and course of MS.

In certain embodiments, the database contains mean gene expression values for at least about 5, 7, 10, 20, 40, 50, or 100 genes selected from any one, or a combination of, Tables 1-6. In some embodiments, the database may contain mean gene expression values for more than about 100 genes, or about 300 genes, or about 400 genes selected from Tables 1-6. In one embodiment, the database contains mean gene expression values for all or substantially all the genes listed in Tables 1-6. The database may include gene expression measurements for at least one or a plurality of genes that are also listed in Table 6.

The computer system of the invention may be programmed to compare (e.g., in response to user inputs) a gene expression profile to a non-MS gene expression profile and/or an MS-gene expression profile stored and/or generated from the database, to determine whether the gene expression profile is itself an MS-profile or a non-MS profile. For example, the computer system may be programmed to perform any of the known classification schemes for classifying gene expression profiles. Various classification schemes are known for classifying samples, and these include, without limitation: Naïve Bayes, Support Vector Machines, Nearest Neighbors, Decision Trees, Logistic, Artificial Neural Networks, and Rule-based schemes. The computer system may employ a classification algorithm or “class predictor” as described in R. Simon, Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data, British Journal of Cancer (2003) 89, 1599-1604, which is hereby incorporated by reference in its entirety.

The computer system of the invention may comprise a user interface, allowing a user to input gene expression values for comparison to an MS and/or non-MS gene expression profile, or gene expression profile previously generated for the patient. The patient's gene expression values may be input from a location remote from the database.

The computer system may further comprise a display, for presenting and/or displaying a result, such as a profile assembled from the database, or the result of a comparison (or classification) between input gene expression values and an MS and non-MS profiles. Such results may further be provided in a tangible form (e.g., as a printed report).

The computer system of the invention may further comprise relational databases containing sequence information, for instance, for the genes of Tables 1-5. For example, the database may contain information associated with a given gene, or patient sample, such as descriptive information about the gene associated with the sequence information, or descriptive information concerning the clinical status of the patient. The database may be designed to include different parts, for instance a sequence database and a gene expression database. Methods for the configuration and construction of such databases and computer-readable media to which such databases are saved are widely available, for instance, see U.S. Pat. No. 5,953,727, which is hereby incorporated by reference in its entirety.

The databases of the invention may be linked to an outside or external database (e.g., on the world wide web) such as GenBank (ncbi.nlm.nih.gov/entrez.index.html); KEGG (genome.ad.jp/kegg); SPAD (grt.kuyshu-u.ac.jp/spad/index.html); HUGO (gene.ucl.ac.uk/hugo); Swiss-Prot (expasy.ch.sprot); Prosite (expasy.ch/tools/scnpsitl.html); OMIM (ncbi.nlm.nih.gov/omim); and GDB (gdb.org). In certain embodiments, the external database is GenBank and the associated databases maintained by the National Center for Biotechnology Information (NCBI) (ncbi.nlm.nih.gov).

Any appropriate computer platform, user interface, etc. may be used to perform the necessary comparisons between sequence information, gene expression information (e.g., gene expression profiles) and any other information in the database or information provided as an input. For example, a large number of computer workstations are available from a variety of manufacturers, such has those available from Silicon Graphics. Client/server environments, database servers and networks are also widely available and appropriate platforms for the databases described herein.

The databases of the invention may be used to produce, among other things, electronic Northerns that allow the user to determine the samples in which a given gene is expressed and to allow determination of the abundance or expression level of the given gene.

Diagnostic Kits

The invention further provides a kit or array containing nucleic acid primers and/or probes for determining the level of expression in a patient sample of a plurality of genes listed in Tables 1-5. The kit may consist essentially of primers and/or probes related to evaluating MS in a sample, and primers and/or probes related to necessary or meaningful assay controls (such as expression level controls and normalization controls, as described herein under “Assay Formats”). The kit for evaluating MS may comprise nucleic acid probes and/or primers designed to detect the expression level of ten or more genes associated with MS, such as the genes listed in Tables 1, 2, 3, 4, and/or 5. The kit may include a set of probes and/or primers designed to detect or quantify the expression levels of at least 5, 7, 10, or 20 genes listed in one or more of Tables 1, 2, 3, 4, and/or 5. In certain embodiments, the kit includes at least one probe and/or primer for quantifying expression of at least one or a plurality of genes that are also listed in Table 6. The primers and/or probes may be designed to detect gene expression levels in accordance with any assay format, including those described herein under the heading “Assay Format.” Exemplary assay formats include polymerase-based assays, such as RT-PCR, Taqman™, hybridization-based assays, for example using DNA microarrays or other solid support, nucleic acid sequence based amplification (NASBA), flap endonuclease-based assays.

In accordance with this aspect, the probes and primers may comprise antisense nucleic acids or oligonucleotides that are wholly or partially complementary to the diagnostic targets described herein (e.g., Tables 1-6). The probes and primers will be designed to detect the particular diagnostic target via an available nucleic acid detection assay format, which are well known in the art. The kits of the invention may comprise probes and/or primers designed to detect the diagnostic targets via detection methods that include amplification, endonuclease cleavage, and hybridization.

Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the compounds of the present invention and practice the claimed methods.

EXAMPLES

MS and control (non-MS) gene expression profiles were identified by hybridization of RNA samples (from whole blood or PBMC samples) to microarrays.

Total RNA isolated from PBMC samples of 11 MS patients and 8 healthy controls was hybridized to a U133A/B chip set (Affymetrix).

Total RNA isolated from whole blood of 62 MS patients and 64 healthy controls was hybridized to a U133 Plus 2.0 chip (Affymetrix). These patients had at least one diagnosis of relapsing remitting MS.

Samples were processed as follows.

For PBMC isolation and subsequent RNA isolation, whole blood was collected into Vacutainer tubes (BD) containing an anticoagulant such as heparin. Peripheral blood mononuclear cells (PBMCs) were isolated by ficoll-hypaque density gradient centrifugation. Total RNA was isolated using standard RNA isolation kits (Qiagen).

For whole blood and subsequent RNA isolation, approximately 2.5 ml of whole blood was collected into each of 2-4 PAXgene tubes (BD/PreAnalytiX) using a blood collection set (BD Safety-Lok™ Blood Collection Set with butterfly needle), per PAXgene tube) following the protocol recommended by the manufacture. The PAXgene tubes were inverted 8-10 times to ensure proper mixture of blood with RNA stabilization solution. Total RNA was isolated using the PAXgene 96 Blood RNA Kit (Qiagen).

Following RNA isolation, the RNA was checked for quality, quantity and purity. Total RNA was evaluated for Quality by using the Agilent Bioanalyzer. RNA preps were quantified by measuring the absorbance at A260 and purity was assessed based on the ratio of the absorbance at A260/A280.

Hybridization of total RNA to microarrays, and following analysis of the data, produced the following MS and non-MS gene expression profiles (or “signatures”).

Table 1A lists genes that are differentially expressed in whole blood of MS patients, and provides an exemplary MS and non-MS profile for such genes. Table 1A refers to these genes by name (title and abbreviation), GeneBank Accession No., and sequence identifier as found in the accompanying Sequence Listing. Table 1A further provides Mean-MS and Mean-control gene expression levels as generated from the sample and data set, as well as measures of the statistical association of each differential gene expression level with MS. Table 1B lists these same genes, and expresses the differential RNA levels as fold change (Control/MS).

Table 2A lists genes that are differentially expressed in PBMCs of MS patients, and provides an exemplary MS and non-MS profile for such genes. Table 2A refers to these genes by name (title and abbreviation), GeneBank Accession No., and sequence identifier as found in the accompanying Sequence Listing. Table 2A further provides the fold change between control and MS samples as generated from this exemplary sample and data set, as well as measures of the statistical association of each differential gene expression level with MS. Table 2B lists these same genes, and shows the mean control and MS data signals, and indicates the top 42 genes in terms of fold change.

Tables 3 and 5 list genes that are differentially expressed in PBMCs between pre- and post-treatment with Beta-interferon. Table 4 and 5 list genes that are differentially expressed in PBMCs between pre- and post-treatment with Copaxone. Table 5 lists genes that are differentially expressed between pre- and post-treatment with each of Beta-Interferon and Glatiramer acetate.

The identification of such gene signatures, is illustrated in the following examples.

Example 1
Genes that are Differentially Expressed Between MS and Normal Samples Using a False Discovery Rate P-Value of 0.001.

The procedure to derive the list of differentially expressed genes in Table 2 was as follows.

A Genesis® (GeneLogic proprietary software) Comparative Analysis was performed using normal white blood cell (WBC) samples as the reference set and MS WBC samples as the experimental set. Parameters were as follows:

- Log with Floor=0,
- 95% Confidence level,
- Unequal Variance,
- Exclude Expression with Call Values of “Unknown” or “No Value,”
- Sample Set Expression Lower and Upper Percentiles of 25 and 75,
- MAS5.0 Affymetrix Summarization,
- Exclude gene fragments absent in all samples,

No other analysis filters were used. The analysis yielded 25,340 gene fragments. Fold Change, t-test p-value, and all sample expression values for each of these 25,340 fragments were exported from Genesis. All MAS5 logged expression values from Genesis for the 25,340 gene fragments for all 19 samples were uploaded into Partek Genomics Suite(R) software. A Benjamini and Hochberg False Discovery Rate correction was performed using a p-value cutoff of 0.001. This yielded a set of 339 non-control gene fragments listed in Table 2. Annotations for gene sets were based on UniGene assignments using the Gene Logic GeneIndex Build 33.

A correlation heatmap was calculated and visualized using Stat->Correlate->Similarity Matrix. Parameters=Pearson, All Combinations (19×19). The default heatmap showed the following. First, the normal (Control) group is cohesive and highly correlated. Second, the MS within-group correlations were higher than the Normal within-group correlations, except for three MS samples. These three MS samples were not as highly correlated to the remainder of the MS samples as the correlations for the majority of this group's intersample correlations. However, the three samples in question are also not highly correlated to each other, indicating absence of “batch” effect for contiguous GID's. Third, the Normal vs. MS correlations indicate robust differences even before gene selection, a sign that many genes are differentially expressed between the groups. Fourth, correlations are at levels consistent with what is expected. No outliers.

The data was transposed in Partek to allow for Principal Components Analysis (PCA). A categorical factor variable was added to the transposed data for coloring the PCA visual by terms “MS” and “Normal”. PCA Parameters: Correlation Dispersion Matrix, Normalized Eigenvector Scaling. Review of PCA showed: the variance explained by the plot is relatively larger than expected such that a robust response is expected upon hypothesis testing for individual genes. Even without prior gene selection, both groups separate well on the 1^stprincipal component, indicating a robust separation of samples. Further, the number of fragments p<0.01 (unadjusted) was 4,146, and the number of fragments p<0.01 (unadjusted) and with a fold change of >=2 was 386. This number of changing fragments indicates a high degree of regulation that is likely to be biologically real.

Comparison of the genes and gene fragments listed in Table 2 between baseline MS samples and control blood samples identifies a differentiating signature.

Thus, genes were further identified on the basis of stringent statistical differentiation thresholding, for example, using a fold-change cut-off to identify gene fragments with expression intensity in MS WBC that is either less than half or more than twice the expression intensity in normal WBC. This rationale is based on the consideration that it is more practical to detect changes in clinical samples when the range of the difference between disease and normal is large.

The procedure to derive the list of gene fragments with a fold change of at least 2 was as follows. A Genesis® Comparative Analysis was performed using normal WBC samples as the reference set and MS WBC samples as the experimental set. Parameters were as follows:

- Log with Floor=0,
- 95% Confidence level,
- Unequal Variance,
- Exclude expression with call values of “unknown” or “no value,”
- MAS5.0 Affymetrix Summarization,
- Include only gene fragments that do not have Affymetrix “Present” Call in 100% of Samples in either sample set,
- Sample set expression lower and upper percentiles of 25 and 75,
- Fold-change magnitude of +/−2.0,
- Raw p-value threshold of 0.05.

This analysis yielded a set of 182 genes, which are listed in Table 2. Annotations for gene sets were based on UniGene assignments using the Gene Logic GeneIndex Build 33.

Thus comparison of the genes listed in Table 2 between baseline MS samples and control blood samples identifies a differentiating signature.

Example 2
Genes that are Differentially Expressed Between Pre- and Post-Avonex Treatment MS Samples

Expression changes in WBC after treatment can be used as a pharmacodynamic measure of exposure to drugs, and thus as a measure of adequate dosing. They may also be a measure of therapeutic response. In the context of neutralizing antibodies to a biologic therapy, it can also be used as a functional measure activity of the drug. Presence of neutralizing antibodies to beta-interferons is known to inhibit response to therapy in patients with MS. Consequently, a Genesis® Comparative Analysis was performed using pre-Avonex treatment WBC samples as the reference set and post-Avonex treatment MS samples WBC samples as the experimental set. Parameters were as follows:

- Log with Floor=0,
- 95% confidence level,
- Unequal Variance,
- Exclude expression with call values of “Unknown” or “No Value,”
- MAS5.0 Affymetrix Summarization,
- Include only gene fragments that do not have Affymetrix “Present” Call in 100% of samples in either sample set,
- Sample set expression lower and upper percentiles of 25 and 75,
- Fold-change magnitude of +/−1.3,
- Raw p-value threshold of 0.05.

This analysis yielded the set of 111 genes listed in Table 3. Gene expression values for the genes listed in Table 3 provide a gene signature associated with drug exposure and response to treatment, or worsening of disease.

Further, many interferon-inducible genes were identified as markers for adequate treatment monitoring, and these include:

IFI44L
interferon-induced protein 44-like

RSAD2
radical S-adenosyl methionine domain containing 2

RSAD2
radical S-adenosyl methionine domain containing 2

IFI44
interferon-induced protein 44

MX1
myxovirus (influenza virus) resistance 1,

interferon-inducible protein p78 (mouse

LOC650557
similar to HLA class II histocompatibility

antigen, DQ(W1.1) beta chain precursor

IFIT3
interferon-induced protein with tetratricopeptide repeats 3

LY6E
lymphocyte antigen 6 complex, locus E

ISG15
ISG15 ubiquitin-like modifier

BIRC4BP
XIAP associated factor-1

LOC129607
hypothetical protein LOC129607

IFI44
interferon-induced protein 44

APOBEC3A
apolipoprotein B mRNA editing enzyme,

catalytic polypeptide-like 3A

MS4A4A
membrane-spanning 4-domains, subfamily A, member 4

IFIT2
interferon-induced protein with tetratricopeptide repeats 2

IFIT3
interferon-induced protein with tetratricopeptide repeats 3

PARP14
poly (ADP-ribose) polymerase family, member 14

IFI6
interferon, alpha-inducible protein 6

Example 3
Genes that are Differentially Expressed Between Pre- and Post-Copaxone Treatment MS Samples

Parameters were the same as for Example 2. This analysis yielded the set of 229 gene listed in Table 4. Annotations for gene sets were based on UniGene assignments using the Gene Logic GeneIndex Build 33. Gene expression values for the genes listed in Table 4 provide a gene signature associated with drug exposure and response to treatment, or worsening of disease.

Example 4
Genes that are Differentially Expressed Between Pre- and Post-Copaxone Treatment MS Samples and Between Pre- and Post-Avonex Treatment MS Samples

Avonex and Copaxone have distinct mechanisms of molecular action. Beta-interferon (Avonex) is a protein made by the body, thought primarily to combat viral infections. Glatiramer acetate (Copaxone) is a mixture of amino acids that bind to major histocompatibility complex class II molecules and competition with MBP and other myelin proteins for such binding and presentation to T cells. Genes that are altered in expression after treatment with both agents may represent a common signature of therapeutic benefit. Table 5 lists the genes that are common to both Table 3 and Table 4. Parameters were the same as for Example 2.

This analysis yielded the set of 36 gene fragments listed in Table 5. Annotations for gene sets were based on UniGene assignments using the Gene Logic GeneIndex Build 33.

Gene expression values for the genes listed in Table 5 provide a gene signature associated with drug exposure and response to treatment, or worsening of disease.

All patents or publications disclosed herein are incorporated by reference in their entireties.

TABLE 1A

SEQ

Genbank
ID

Bonferroni
Stepup

Mean
Mean

Gene Title
Gene Symbol
Acc. No.
NO.
p-value
(p-value)
(p-value)
T
(CONTROL)
(MS)

FK506 binding protein 5
FKBP5
NM_004117
0813
4.95E−20
2.71E−15
2.71E−15
−10.9889
78.0882
190.055

FK506 binding protein 5
FKBP5
W86302
1003
9.38E−18
5.13E−13
2.56E−13
−10.0535
473.34
934.916

FK506 binding protein 5
FKBP5
AI753747
0255
3.80E−17
2.08E−12
6.93E−13
−9.80302
1184.25
2126.26

cyclin D3
CCND3
NM_001760
0778
9.21E−13
5.04E−08
1.26E−08
−7.96208
2021.6
2569.7

tetraspanin 14
TSPAN14
NM_030927
0958
8.54E−12
4.67E−07
9.09E−08
−7.54226
436.935
543.259

chemokine (C—X—C motif)
CXCR4
AF348491
0158
9.97E−12
5.45E−07
9.09E−08
−7.51268
1798.6
2290.67

receptor 4

Rho GTPase activating
ARHGAP27
AI814329
0276
1.22E−11
6.65E−07
9.50E−08
−7.47481
47.2712
91.2659

protein 27

integrin, beta 2
ITGB2
L78790
0728
1.83E−11
1.00E−06
1.25E−07
−7.39644
3519.18
4443.09

(complement component 3

receptor 3 and 4 subunit)

adrenergic, beta, receptor
ADRBK1
M80776
0738
4.17E−11
2.28E−06
2.53E−07
−7.23859
275.479
414.407

kinase 1

solute carrier family 6
SLC6A6
NM_003043
0797
5.34E−11
2.92E−06
2.72E−07
−7.1906
125.121
202.558

(neurotransmitter

transporter, taurine),

member 6

Rho GTPase activating
ARHGAP18
BE501862
0576
5.47E−11
2.99E−06
2.72E−07
7.18598
237.506
168.061

protein 18

DNA-damage-inducible
DDIT4
NM_019058
0928
6.90E−11
3.77E−06
3.14E−07
−7.1411
247.135
427.375

transcript 4

chromodomain helicase
CHD9
AW300405
0505
7.89E−11
4.31E−06
3.32E−07
7.11505
241.321
194.754

DNA binding protein 9

polypyrimidine tract
PTBP1
AA679988
0041
9.27E−11
5.07E−06
3.54E−07
−7.08362
140.67
188.645

binding protein 1

DEAD (Asp-Glu-Ala-Asp)
DDX6
NM_004397
0822
9.71E−11
5.31E−06
3.54E−07
7.07456
59.5517
43.1658

box polypeptide 6

transmembrane 9
TM9SF1
BE899402
0606
1.17E−10
6.40E−06
4.00E−07
−7.03808
95.4238
120.952

superfamily member 1

structural maintenance of
SMC3
AI373676
0193
1.62E−10
8.88E−06
4.76E−07
6.97411
277.737
200.67

chromosomes 3

chromosome 6 open
C6orf166
AI742378
0253
1.71E−10
9.35E−06
4.76E−07
−6.96395
84.0063
129.545

reading frame 166

salvador homolog 1
SAV1
AJ292969
0315
1.74E−10
9.52E−06
4.76E−07
6.96043
122.391
92.8185

(Drosophila)

heat shock 70 kDa protein
HSPA5
AF216292
0145
1.74E−10
9.52E−06
4.76E−07
−6.96042
1512.26
1749.33

5 (glucose-regulated

protein, 78 kDa)

MFNG O-fucosylpeptide
MFNG
AI738965
0249
2.02E−10
1.10E−05
5.26E−07
−6.93133
171.014
235.075

3-beta-N-

acetylglucosaminyltransferase

ankyrin repeat and BTB
ABTB1
BF115480
0622
2.50E−10
1.37E−05
6.20E−07
−6.88974
39.5212
65.1926

(POZ) domain containing 1

leukotriene B4 receptor
LTB4R
U33448
0980
4.64E−10
2.54E−05
1.06E−06
−6.76716
127.687
245.457

myeloid cell leukemia
MCL1
BF594446
0650
4.65E−10
2.54E−05
1.06E−06
−6.76677
182.812
295.014

sequence 1 (BCL2-

related)

Friend leukemia virus
FLI1
M93255
0741
5.83E−10
3.19E−05
1.27E−06
−6.72202
620.183
755.664

integration 1

unc-93 homolog B1
UNC93B1
AW001274
0460
7.24E−10
3.96E−05
1.52E−06
−6.67888
130.118
217.625

(C. elegans)

mindbomb homolog 1
MIB1
W80418
1001
8.62E−10
4.71E−05
1.71E−06
6.64405
230.686
181.53

(Drosophila)

period homolog 1
PER1
NM_002616
0790
8.86E−10
4.85E−05
1.71E−06
−6.63854
54.7084
86.7084

(Drosophila)

splicing factor,
SFRS17A
M99578
0743
9.08E−10
4.96E−05
1.71E−06
−6.63372
89.447
111.808

arginine/serine-rich 17A

zinc finger and BTB
ZBTB16
NM_006006
0849
9.49E−10
5.19E−05
1.73E−06
−6.62487
122.114
211.501

domain containing 16

ER lipid raft associated 1
ERLIN1
NM_006459
0862
9.95E−10
5.44E−05
1.76E−06
−6.61532
49.7838
68.0357

PHD finger protein 3
PHF3
AW189430
0482
1.05E−09
5.75E−05
1.80E−06
6.60417
170.33
132.083

toll-like receptor 2
TLR2
NM_003264
0801
1.15E−09
6.29E−05
1.85E−06
−6.58638
1897.07
2567.42

paxillin
PXN
D86862
0710
1.17E−09
6.39E−05
1.85E−06
−6.58298
92.9515
193.438

RAB GTPase activating
RABGAP1L
AB019490
0087
1.21E−09
6.62E−05
1.85E−06
6.57615
286.939
191.152

protein 1-like

proline rich 14
PRR14
BE788667
0599
1.25E−09
6.82E−05
1.85E−06
−6.57015
122.602
235.313

Fc fragment of IgA,
FCAR
D87858
0712
1.25E−09
6.86E−05
1.85E−06
−6.56901
97.3093
155.905

receptor for

tripeptidyl peptidase I
TPP1
AA602532
0032
1.76E−09
9.62E−05
2.53E−06
−6.50075
200.439
264.395

signal-regulatory protein
SIRPA
D86043
0709
1.85E−09
0.000101
2.59E−06
−6.49062
69.319
119.932

alpha

insulin-like growth factor 2
IGF2BP3
AU160004
0441
2.08E−09
0.000114
2.84E−06
6.46737
35.8267
21.3437

mRNA binding protein 3

RAN binding protein 3
RANBP3
AI689052
0244
2.52E−09
0.000138
3.36E−06
−6.42824
128.056
158.814

tankyrase, TRF1-
TNKS2
BF060683
0615
2.84E−09
0.000155
3.69E−06
6.4041
346.06
256.529

interacting ankyrin-related

ADP-ribose polymerase 2

transmembrane 9
TM9SF4
AI418892
0200
3.11E−09
0.00017
3.87E−06
−6.38564
167.867
208.305

superfamily protein

member 4

CCR4-NOT transcription
CNOT1
BC040523
0561
3.12E−09
0.00017
3.87E−06
−6.38501
70.5108
91.1365

complex, subunit 1

trophoblast-derived
TncRNA
AV659198
0443
3.26E−09
0.000178
3.93E−06
−6.37561
80.5859
112.859

noncoding RNA

CD83 molecule
CD83
NM_004233
0816
3.31E−09
0.000181
3.93E−06
6.37304
119.09
91.3124

Transcribed locus
—
AI032730
0160
3.49E−09
0.000191
4.05E−06
6.36222
195.488
149.453

TBC1 domain family,
TBC1D2B
BF195608
0625
3.90E−09
0.000213
4.23E−06
−6.33953
288.317
340.68

member 28

hypothetical protein
FLJ10038
NM_017976
0918
3.91E−09
0.000214
4.23E−06
6.33873
86.1568
69.6291

FLJ10038

procollagen-proline, 2-
P4HB
AK075503
0362
3.93E−09
0.000215
4.23E−06
−6.33781
289.177
412.473

oxoglutarate 4-

dioxygenase (proline 4-

hydroxylase), beta

polypeptide

Ewing sarcoma breakpoint
EWSR1 ///
AF327066
0156
3.95E−09
0.000216
4.23E−06
−6.3368
331.762
417.378

region 1 /// Friend
FLI1

leukemia virus integration 1

Rab interacting lysosomal
RILPL2
AI810244
0275
4.09E−09
0.000224
4.30E−06
−6.32963
726.676
871.377

protein-like 2

RAB5C, member RAS
RAB5C
AF141304
0136
4.41E−09
0.000241
4.54E−06
−6.31423
663.073
848.044

oncogene family

SMAD specific E3
SMURF2
AY014180
0532
4.48E−09
0.000245
4.54E−06
6.31098
417.357
352.415

ubiquitin protein ligase 2

diacylglycerol lipase, beta
DAGLB
BE795104
0600
5.78E−09
0.000316
5.75E−06
−6.2587
76.1839
103.52

—
—
AW275093
0495
6.77E−09
0.00037
6.61E−06
6.22634
37.8503
25.7363

cisplatin resistance-
CROP
AW089673
0478
7.20E−09
0.000394
6.80E−06
6.21366
1253.96
1024.1

associated overexpressed

protein

CUG triplet repeat, RNA
CUGBP2
AI652861
0231
7.22E−09
0.000395
6.80E−06
−6.21313
439.059
508.726

binding protein 2

cleft lip and palate
CLPTM1
BC004865
0551
7.52E−09
0.000411
6.86E−06
−6.20462
269.664
340.303

associated

transmembrane protein 1

plasminogen activator,
PLAUR
AY029180
0533
7.53E−09
0.000412
6.86E−06
−6.20442
407.032
590.904

urokinase receptor

SH3 domain and
SH3TC1
NM_018986
0926
7.68E−09
0.00042
6.89E−06
−6.20022
156.867
208.68

tetratricopeptide repeats 1

CCAAT/enhancer binding
CEBPD
AV655640
0442
7.96E−09
0.000435
7.02E−06
−6.19304
66.2588
101.6

protein (C/EBP), delta

myotrophin
MTPN
AL533334
0410
8.33E−09
0.000455
7.23E−06
6.18357
2922.38
2651.39

diacylglycerol kinase, zeta
DGKZ
NM_003646
0806
8.88E−09
0.000486
7.50E−06
−6.17031
495.581
742.687

104 kDa

coiled-coil domain
CCDC95
AA743390
0052
9.01E−09
0.000492
7.50E−06
−6.16737
114.613
146.782

containing 95

golgi autoantigen, golgin
GOLGA8B
AI829170
0286
9.05E−09
0.000495
7.50E−06
6.16637
85.2551
49.0105

subfamily a, 8B

O-linked N-
OGT
U77413
0990
9.95E−09
0.000544
8.02E−06
−6.14688
276.547
320.452

acetylglucosamine

(GlcNAc) transferase

(UDP-N-

acetylgluco-

samine:polypeptide-N-

acetylglucosaminyl

transferase)

alpha thalassemia/mental
ATRX ///
AI650257
0227
1.01E−08
0.00055
8.02E−06
6.14467
408.475
331.005

retardation syndrome X-
LOC728849

linked (RAD54 homolog,

S. cerevisiae) /// similar to

transcriptional regulator

ATRX isoform 1

mitogen-activated protein
MAP2K1
AI571419
0217
1.01E−08
0.000554
8.02E−06
−6.14319
404.667
463.791

kinase kinase 1

Glutathione S-transferase
GSTK1
AV722006
0451
1.16E−08
0.000636
9.08E−06
6.11454
19.2432
11.7156

kappa 1

ATP-binding cassette,
ABCC1
NM_004996
0833
1.27E−08
0.000694
9.77E−06
−6.09625
116.754
144.306

sub-family C

(CFTR/MRP), member 1

chromosome 19 open
C19orf6
AI805266
0270
1.32E−08
0.000719
9.99E−06
−6.0888
83.2411
131.22

reading frame 6

potassium channel
KCTD5
AA872593
0073
1.34E−08
0.000732
1.00E−05
−6.08503
69.8096
86.2762

tetramerisation domain

containing 5

Transcribed locus
—
AI767751
0265
1.60E−08
0.000873
1.18E−05
6.04842
71.4585
56.7931

leukotriene B4 receptor
LTB4R
U41070
0982
1.65E−08
0.0009
1.20E−05
−6.04214
138.048
192.488

TSC22 domain family,
TSC22D3
NM_004089
0811
1.75E−08
0.000955
1.26E−05
−6.02976
544.464
834.605

member 3

peroxiredoxin 6
PRDX6
NM_004905
0831
1.78E−08
0.000971
1.26E−05
6.02632
877.551
731.524

6-phosphofructo-2-
PFKFB2
AB044805
0093
1.86E−08
0.00102
1.30E−05
−6.01598
29.4293
42.6113

kinase/fructose-2,6-

biphosphatase 2

chromobox homolog 4 (Pc
CBX4
NM_003655
0807
1.88E−08
0.001028
1.30E−05
−6.01429
72.9469
113.789

class homolog,

Drosophila)

GTPase, IMAP family
GIMAP5
AL080068
0378
1.99E−08
0.001088
1.36E−05
6.00246
95.8797
62.4753

member 5

surfeit 4
SURF4
AF078866
0123
2.03E−08
0.00111
1.37E−05
−5.99814
226.218
267.996

PHD finger protein 12
PHF12
AL161953
0399
2.12E−08
0.001158
1.41E−05
−5.98937
30.8623
52.3356

CCAAT/enhancer binding
CEBPD
NM_005195
0837
2.29E−08
0.001253
1.51E−05
−5.97285
2487.99
3256.48

protein (C/EBP), delta

prion protein (p27-30)
PRNP
AV725328
0453
2.37E−08
0.001297
1.54E−05
−5.96555
110.316
135.332

(Creutzfeldt-Jakob

disease, Gerstmann-

Strausler-Scheinker

syndrome, fatal familial

insomnia)

phosphoinositide-3-
PIK3R5
NM_014308
0883
2.40E−08
0.001313
1.54E−05
−5.96298
182.242
221.794

kinase, regulatory subunit

5, p101

myotubularin related
MTMR1
AK001816
0322
2.49E−08
0.001362
1.57E−05
−5.9552
65.8114
89.0136

protein 1

SLAIN motif family,
SLAIN2
AI979301
0310
2.49E−08
0.001363
1.57E−05
5.95515
209.516
151.766

member 2

C-type lectin domain
CLEC1B
NM_016509
0902
2.90E−08
0.001584
1.80E−05
5.92338
93.1775
59.0062

family 1, member B

tetratricopeptide repeat
TTC7A
BE205790
0568
3.05E−08
0.001666
1.87E−05
−5.91278
37.0092
50.8386

domain 7A

suppressor of Ty 16
SUPT16H
AK024072
0341
3.08E−08
0.001685
1.87E−05
5.91033
263.419
187.951

homolog (S. cerevisiae)

SERPINE1 mRNA binding
SERBP1
BC003049
0547
3.25E−08
0.001778
1.92E−05
5.89903
1399.78
1212.41

protein 1

RNA binding motif protein
RBM14
AF315633
0153
3.26E−08
0.001782
1.92E−05
−5.89857
39.9955
59.7803

14

T-cell acute lymphocytic
TAL1
NM_003189
0800
3.28E−08
0.001794
1.92E−05
5.89718
206.228
138.234

leukemia 1

Ras association
RAPH1
AA194149
0014
3.30E−08
0.001805
1.92E−05
5.89586
48.0791
34.1444

(RAlGDS/AF-6) and

pleckstrin homology

domains 1

disabled homolog 2,
DAB2
N21202
0744
3.55E−08
0.001939
2.01E−05
5.88069
97.375
73.5883

mitogen-responsive

phosphoprotein

(Drosophila)

v-ets erythroblastosis virus
ETS1
NM_005238
0840
3.55E−08
0.00194
2.01E−05
−5.8806
52.905
74.8306

E26 oncogene homolog 1

(avian)

elastin microfibril
EMILIN2
AL552384
0416
3.58E−08
0.001958
2.01E−05
−5.87865
39.6291
58.0146

interfacer 2

myosin IXB
MYO9B
NM_004145
0815
3.60E−08
0.001968
2.01E−05
−5.87757
63.7389
105.347

DnaJ (Hsp40) homolog,
DNAJC13
BC043583
0562
3.70E−08
0.002021
2.04E−05
5.87194
25.7886
18.3726

subfamily C, member 13

acyl-Coenzyme A binding
ACBD5
BC025309
0560
3.93E−08
0.002151
2.15E−05
5.85869
84.7927
62.1417

domain containing 5

Ras association
RAPH1
AA194149
0014
4.25E−08
0.002321
2.30E−05
5.84254
31.6578
22.9448

(RAlGDS/AF-6) and

pleckstrin homology

domains 1

C-type lectin domain
CLEC4E
BC000715
0538
4.41E−08
0.002412
2.35E−05
−5.8344
829.005
1208.34

family 4, member E

Fc fragment of IgA,
FCAR
U43677
0983
4.43E−08
0.002424
2.35E−05
−5.8333
63.8877
101.844

receptor for

ATPase, Ca++
ATP2A3
AA877910
0076
4.84E−08
0.002649
2.52E−05
−5.81444
72.7871
103.656

transporting, ubiquitous

methionine
MAT2A
NM_005911
0848
4.90E−08
0.002681
2.52E−05
−5.8119
97.8356
120.978

adenosyltransferase II,

alpha

general transcription factor
GTF2A1
NM_015859
0891
4.94E−08
0.002701
2.52E−05
5.81025
49.1129
30.3493

IIA, 1, 19/37 kDa

DAZ associated protein 2
DAZAP2
AL534321
0411
4.96E−08
0.002711
2.52E−05
−5.80949
1687.13
2024.25

chromosome 1 open
C1orf38
AB035482
0091
4.98E−08
0.002723
2.52E−05
−5.80855
1388.6
1760.08

reading frame 38

arrestin domain containing 1
ARRDC1
AK001822
0323
5.37E−08
0.002936
2.69E−05
−5.79252
226.097
291.039

RAD23 homolog B
RAD23B
AL527365
0409
5.42E−08
0.002966
2.70E−05
−5.79036
500.181
673.845

(S. cerevisiae)

chromosome 19 open
C19orf6
AC004528
0097
5.59E−08
0.003057
2.75E−05
−5.78388
95.6151
147.154

reading frame 6

procollagen-proline, 2-
P4HB
J02783
0716
5.81E−08
0.003178
2.84E−05
−5.77559
1504.99
1750.23

oxoglutarate 4-

dioxygenase (proline 4-

hydroxylase), beta

polypeptide

period homolog 1
PER1
AF022991
0108
6.03E−08
0.003298
2.92E−05
−5.76764
72.7414
94.1226

(Drosophila)

galactosylceramidase
GALC
D25284
0705
6.24E−08
0.003413
2.99E−05
−5.76034
55.0178
65.2393

CDNA FLJ33748 fis, clone
—
H75391
0715
6.38E−08
0.00349
3.03E−05
5.75554
58.2421
42.1421

BRCAN2000148

glucosamine (N-acetyl)-6-
GNS
NM_002076
0782
6.49E−08
0.00355
3.06E−05
−5.75189
94.4501
134.182

sulfatase (Sanfilippo

disease IIID)

non-POU domain
NONO
L14599
0721
6.55E−08
0.00358
3.06E−05
−5.75007
523.202
604.536

containing, octamer-

binding

zinc finger protein 117
ZNF117
NM_024498
0946
6.86E−08
0.003749
3.18E−05
5.74018
140.903
101.407

activin A receptor, type IB
ACVR1B
AL117643
0384
7.04E−08
0.003851
3.24E−05
−5.73445
173.827
206.214

minichromosome
MCM3AP
AK022303
0333
7.15E−08
0.00391
3.26E−05
−5.73118
30.2496
41.9715

maintenance complex

component 3 associated

protein

natural killer-tumor
NKTR
AA732581
0048
7.29E−08
0.003984
3.28E−05
5.72714
151.814
110.341

recognition sequence

sorbin and SH3 domain
SORBS3
MM_005775
0844
7.34E−08
0.004013
3.28E−05
−5.72558
27.3042
44.7622

containing 3

phosphoinositide-3-kinase
PIK3IP1
BE042976
0563
7.42E−08
0.004058
3.28E−05
−5.7232
535.676
693.49

interacting protein 1

CDNA FLJ34061 fis, clone
—
BG430133
0695
7.44E−08
0.004065
3.28E−05
5.72283
40.264
27.4554

FCBBF3000462

heterogeneous nuclear
HNRNPC
AV725195
0452
8.11E−08
0.004435
3.53E−05
5.7041
1949.64
1687.13

ribonucleoprotein C

(C1/C2)

calnexin
CANX
AI761759
0258
8.14E−08
0.004453
3.53E−05
−5.70324
426.358
492.788

inositol polyphosphate-5-
INPP5D
U53470
0985
8.34E−08
0.004561
3.59E−05
−5.69807
246.284
314.816

phosphatase, 145 kDa

hepatocellular carcinoma-
HCRP1
AK025343
0356
8.40E−08
0.00459
3.59E−05
−5.69672
56.4645
71.8341

related HCRP1

solute carrier family 12
SLC12A9
BC000154
0535
9.12E−08
0.004986
3.83E−05
−5.6789
66.7681
99.8859

(potassium/chloride

transporters), member 9

suppression of
ST14
U20428
0979
9.16E−08
0.005011
3.83E−05
−5.67782
22.546
32.7603

tumorigenicity 14 (colon

carcinoma)

plasminogen activator,
PLAUR
U08839
0975
9.17E−08
0.005016
3.83E−05
−5.67761
524.092
709.03

urokinase receptor

TAF8 RNA polymerase II,
TAF8
BU618741
0703
9.40E−08
0.005138
3.89E−05
−5.67241
59.63
73.0919

TATA box binding protein

(TBP)-associated factor,

43 kDa

chemokine (C—X—C motif)
CXCR4
L01639
0719
9.54E−08
0.005218
3.90E−05
−5.66907
1512.58
1818.68

receptor 4

N-acetylglucosamine-1-
GNPTG
AF302786
0151
9.56E−08
0.005226
3.90E−05
−5.66876
178.91
206.84

phosphate transferase,

gamma subunit

protein associated with
PATL1
AA359612
0018
9.69E−08
0.005298
3.92E−05
−5.66579
72.1086
87.181

topoisomerase II homolog

1 (yeast)

galactosidase, beta 1
GLB1
NM_000404
0758
1.04E−07
0.005679
4.18E−05
−5.6508
511.828
593.578

PDZ and LIM domain 2
PDLIM2
NM_021630
0934
1.05E−07
0.005739
4.19E−05
−5.64853
541.251
633.673

(mystique)

(clone 1NIB-4) normalized
—
BQ002274
0702
1.08E−07
0.005882
4.26E−05
−5.64319
20.177
30.5449

cDNA library sequence

transmembrane protein 43
TMEM43
W74580
1000
1.10E−07
0.006007
4.32E−05
−5.63862
440.535
521.401

exosome component 1
EXOSC1
BC012538
0559
1.11E−07
0.006085
4.35E−05
5.63584
38.3959
29.0411

transducin-like enhancer
TLE4
AL358975
0400
1.15E−07
0.006276
4.45E−05
−5.62913
204.851
242.919

of split 4 (E(sp1) homolog,

Drosophila)

plectin 1, intermediate
PLEC1
Z54367
1015
1.20E−07
0.006555
4.62E−05
−5.61971
95.9978
135.448

filament binding protein

500 kDa

FIP1 like 1 (S. cerevisiae)
FIP1L1
NM_030917
0957
1.23E−07
0.006726
4.70E−05
5.61413
201.771
180.087

blocked early in transport
BET1L
NM_016526
0903
1.25E−07
0.006853
4.74E−05
−5.61006
12.5373
29.2921

1 homolog (S. cerevisiae)-

like

SMEK homolog 1,
SMEK1
NM_017936
0917
1.26E−07
0.006873
4.74E−05
5.60944
91.0002
70.0335

suppressor of mek1

(Dictyostelium)

nuclear casein kinase and
NUCKS1
AW515443
0516
1.28E−07
0.006977
4.78E−05
5.60618
1001.36
797.94

cyclin-dependent kinase

substrate 1

myosin IXB
MYO9B
AF143684
0137
1.29E−07
0.007064
4.81E−05
−5.60349
301.367
426.587

zinc finger RNA binding
ZFR
AI459274
0207
1.33E−07
0.007252
4.90E−05
5.59779
90.3366
66.8956

protein

chromosome 8 open
C8orf42
AI632224
0222
1.35E−07
0.007362
4.94E−05
5.5945
19.8855
12.7616

reading frame 42

retinol saturase (all-trans-
RETSAT
AK098125
0364
1.35E−07
0.007405
4.94E−05
−5.59324
38.949
52.5054

retinol 13,14-reductase)

protein kinase, AMP-
PRKAB2
NM_005399
0841
1.50E−07
0.008186
5.39E−05
5.57142
44.2835
33.7496

activated, beta 2 non-

catalytic subunit

U2 small nuclear RNA
U2AF2
NM_007279
0875
1.50E−07
0.008188
5.39E−05
−5.57136
111.086
152.14

auxiliary factor 2

WD repeat domain 1
WDR1
AF274954
0150
1.58E−07
0.008627
5.64E−05
−5.55997
413.045
580.746

PTK2 protein tyrosine
PTK2
AL037339
0368
1.61E−07
0.008819
5.67E−05
5.55518
73.6126
59.6382

kinase 2

solute carrier family 16,
SLC16A3
AL513917
0404
1.62E−07
0.008831
5.67E−05
−5.55488
372.042
569.693

member 3

(monocarboxylic acid

transporter 4)

tripartite motif-containing 8
TRIM8
NM_030912
0956
1.62E−07
0.008848
5.67E−05
5.55447
781.843
658.669

Full-length cDNA clone
—
AW953794
0525
1.74E−07
0.009534
6.05E−05
−5.53815
27.1676
38.0869

CS0DF032YA11 of Fetal

brain of Homo sapiens

(human)

speckle-type POZ protein
SPOP
NM_003563
0805
1.75E−07
0.009565
6.05E−05
5.53745
917.406
826.599

BCL2-associated X
BAX
U19599
0977
1.77E−07
0.009659
6.07E−05
−5.53531
114.446
151.371

protein

high mobility group AT-
HMGA1
AF176039
0141
1.80E−07
0.009863
6.16E−05
−5.53073
22.5906
40.0994

hook 1

Transcribed locus
—
BE348304
0572
1.84E−07
0.010055
6.25E−05
5.52651
55.2633
42.0568

transmembrane and
TMCO3
NM_017905
0914
1.89E−07
0.010358
6.39E−05
−5.52001
68.6431
86.2412

coiled-coil domains 3

C-type lectin domain
CLEC4E
NM_014358
0885
1.99E−07
0.010891
6.67E−05
−5.50901
152.544
201.687

family 4, member E

chromosome 7 open
C7orf27
AK024482
0345
2.00E−07
0.010939
6.67E−05
−5.50806
101.071
132.536

reading frame 27

suppressor of zeste 12
SUZ12 ///
AI924660
0297
2.03E−07
0.011081
6.69E−05
5.50523
295.079
253.21

homolog (Drosophila) ///
SUZ12P

suppressor of zeste 12

homolog pseudogene

unc-93 homolog B1
UNC93B1
NM_030930
0959
2.03E−07
0.011114
6.69E−05
−5.50458
89.4778
132.242

(C. elegans)

Transcribed locus,
—
AI738675
0248
2.09E−07
0.011409
6.83E−05
−5.49882
394.226
504.553

strongly similar to

XP_529518.1

PREDICTED: hypothetical

protein XP_529518 [Pan

troglodytes]

differentially expressed in
DEF6
NM_022047
0937
2.17E−07
0.011852
7.06E−05
−5.49046
287.062
338.604

FDCP 6 homolog (mouse)

KIAA0146
KIAA0146
AI363213
0191
2.21E−07
0.01207
7.14E−05
−5.48646
80.4881
111.914

BCL6 co-repressor
BCOR
AF317392
0154
2.23E−07
0.012214
7.16E−05
5.48386
111.082
75.8345

KIAA0319-like
KIAA0319L
W58365
0999
2.24E−07
0.012251
7.16E−05
−5.48318
368.026
488.272

—
—
AK000677
0317
2.26E−07
0.012378
7.20E−05
5.48093
62.6473
48.142

ADP-dependent
ADPGK
BC006112
0557
2.32E−07
0.012687
7.33E−05
−5.47549
135.74
160.824

glucokinase

TSC22 domain family,
TSC22D3
AL110191
0382
2.34E−07
0.012819
7.37E−05
−5.47322
3412.5
4338.52

member 3

nemo-like kinase
NLK
NM_016231
0897
2.37E−07
0.012956
7.40E−05
5.47089
86.344
73.4371

amyloid beta (A4)
APLP2
AW001847
0461
2.40E−07
0.013111
7.41E−05
−5.46827
677.954
884.114

precursor-like protein 2

phospholipase D family,
PLD3
NM_012268
0878
2.41E−07
0.013179
7.41E−05
−5.46712
190.559
273.424

member 3

Transcribed locus
—
BF114745
0621
2.41E−07
0.01319
7.41E−05
5.46695
103.561
92.2368

ER lipid raft associated 1
ERLIN1
AL568449
0419
2.47E−07
0.013486
7.53E−05
−5.46206
340.054
398.739

Transcribed locus
—
H24473
0713
2.58E−07
0.014086
7.83E−05
5.45246
26.6195
19.7937

procollagen-proline, 2-
P4HB
NM_000918
0762
2.66E−07
0.014538
8.03E−05
−5.44549
795.05
902.135

oxoglutarate 4-

dioxygenase (proline 4-

hydroxylase), beta

polypeptide

calreticulin
CALR
BE251303
0570
2.71E−07
0.014816
8.14E−05
−5.44132
356.88
465.235

PTK2B protein tyrosine
PTK2B
NM_004103
0812
2.73E−07
0.014902
8.14E−05
−5.44003
101.943
153.102

kinase 2 beta

KIAA0892
KIAA0892
AC003030
0096
2.77E−07
0.01513
8.19E−05
−5.43668
15.0909
27.2329

angiotensin II receptor-
AGTRAP
AF165187
0139
2.77E−07
0.015159
8.19E−05
−5.43627
577.465
745.496

associated protein

Transcribed locus
—
AW244016
0490
2.85E−07
0.015562
8.37E−05
−5.43047
108.711
161.89

Full length insert cDNA
—
AF086041
0124
2.90E−07
0.015846
8.40E−05
5.42647
73.6103
50.4274

clone YX53E08

suppression of
ST14
NM_021978
0936
2.90E−07
0.015869
8.40E−05
−5.42615
36.3457
56.3781

tumorigenicity 14 (colon

carcinoma)

serologically defined colon
SDCCAG1
BC006001
0556
2.92E−07
0.015938
8.40E−05
5.42519
413.226
349.695

cancer antigen 1

Cbp/p300-interacting
CITED2
NM_006079
0852
2.92E−07
0.015952
8.40E−05
−5.425
256.843
305.525

transactivator, with

Glu/Asp-rich carboxy-

terminal domain, 2

ankyrin repeat and FYVE
ANKFY1
NM_016376
0901
2.94E−07
0.016093
8.43E−05
−5.42305
86.1838
107.681

domain containing 1

interleukin 13 receptor,
IL13RA1
NM_001560
0773
2.97E−07
0.016254
8.43E−05
−5.42085
640.164
787.654

alpha 1

EH domain binding protein
EHBP1L1
AA149545
0012
2.98E−07
0.016276
8.43E−05
−5.42055
260.818
334.559

1-like 1

Rho GTPase activating
ARHGAP4
NM_001666
0777
3.01E−07
0.016452
8.48E−05
−5.41817
204.777
266.516

protein 4

Transcribed locus
—
AW298731
0504
3.03E−07
0.016586
8.49E−05
−5.41638
27.4913
49.2688

Ras and Rab interactor 3
RIN3
AW027923
0470
3.07E−07
0.016787
8.49E−05
−5.4137
162.083
222.874

CDNA clone
—
N57510
0749
3.07E−07
0.016793
8.49E−05
5.41363
127.327
110.056

IMAGE: 5313062

Homo sapiens, clone
—
AV735241
0455
3.08E−07
0.016816
8.49E−05
5.41333
171.32
145.168

IMAGE: 3345917, mRNA

pro-platelet basic protein
PPBP
R64130
0963
3.13E−07
0.017119
8.60E−05
5.40937
4143.9
2480.31

(chemokine (C—X—C motif)

ligand 7)

cell division cycle 2-like 1
CDC2L1 ///
NM_001787
0779
3.18E−07
0.017373
8.69E−05
−5.40611
167.96
197.461

(PITSLRE proteins) /// cell
CDC2L2

division cycle 2-like 2

(PITSLRE proteins)

cysteine conjugate-beta
CCBL2
BC000819
0540
3.28E−07
0.017938
8.92E−05
5.39902
322.023
274.341

lyase 2

sema domain,
SEMA4A
NM_022367
0939
3.36E−07
0.018372
9.09E−05
−5.39372
362.638
494.889

immunoglobulin domain

(Ig), transmembrane

domain (TM) and short

cytoplasmic domain,

(semaphorin) 4A

Rho GDP dissociation
ARHGDIA
D13989
0704
3.41E−07
0.018624
9.14E−05
−5.3907
98.9323
215.826

inhibitor (GDI) alpha

Wolf-Hirschhorn syndrome
WHSC1L1
NM_017778
0912
3.41E−07
0.01864
9.14E−05
5.3905
68.4864
57.256

candidate 1-like 1

tissue factor pathway
TFPI
AF021834
0107
3.46E−07
0.018898
9.22E−05
5.38745
21.9809
12.7738

inhibitor (lipoprotein-

associated coagulation

inhibitor)

zinc finger protein 271
ZNF271
AF159567
0138
3.56E−07
0.019471
9.43E−05
5.38082
179.018
149.631

Wiskott-Aldrich syndrome
WAS
NM_000377
0757
3.57E−07
0.019512
9.43E−05
−5.38036
184.107
410.974

(eczema-

thrombocytopenia)

EH domain binding protein 1
EHBP1
BF116032
0624
3.63E−07
0.019842
9.54E−05
5.37662
96.9949
68.9836

solute carrier family 6
SLC6A6
U16120
0976
3.71E−07
0.020295
9.65E−05
−5.37161
60.7858
85.2317

(neurotransmitter

transporter, taurine),

member 6

ADAM metallopeptidase
ADAM8
AI814527
0277
3.72E−07
0.020315
9.65E−05
−5.37139
120.008
221.72

domain 8

zinc finger protein 36, C3H
ZFP36L2
AI356398
0189
3.73E−07
0.020368
9.65E−05
−5.37081
563.157
986.407

type-like 2

RAB27B, member RAS
RAB27B
BF438386
0637
3.77E−07
0.020613
9.72E−05
5.36815
187.305
137.411

oncogene family

versican
VCAN
D32039
0706
3.79E−07
0.020739
9.74E−05
−5.36679
1066.01
1372.33

Interleukin 8
IL8
AJ239383
0313
4.33E−07
0.02365
0.000108
−5.33753
75.0461
119.62

leukocyte immunoglobulin-
LILRA2
U82277
0993
4.81E−07
0.026298
0.000116
−5.31382
349.215
498.426

like receptor, subfamily A

(with TM domain),

member 2

immunoglobulin heavy
IGH@ ///
S55735
0965
5.11E−07
0.027913
0.000122
−5.30048
2641.16
4723.74

locus /// immunoglobulin
IGHA1 ///

heavy constant alpha 1 ///
IGHA2 ///

immunoglobulin heavy
LOC100126583

constant alpha 2 (A2m

marker) /// hypothetical

LOC100126583

regulator of G-protein
RGS14
AF037194
0109
5.12E−07
0.027979
0.000122
−5.29995
80.6164
117.832

signaling 14

F-box protein 9
FBXO9
AK095315
0363
5.15E−07
0.028176
0.000122
5.29838
1081.96
798.526

septin 9
9-Sep
NM_006640
0865
5.17E−07
0.028263
0.000122
−5.29769
87.4231
164.873

myeloid cell leukemia
MCL1
NM_021960
0935
5.40E−07
0.029511
0.000126
−5.288
3409.06
4155.72

sequence 1 (BCL2-

related)

poly(A) polymerase alpha
PAPOLA
BF797555
0662
5.74E−07
0.031378
0.00013
5.27423
1470.85
1208.87

Transcribed locus
—
AI492388
0212
6.97E−07
0.038094
0.00015
−5.23055
216.947
349.917

Rho GDP dissociation
ARHGDIA
AI571798
0218
7.40E−07
0.040446
0.000155
−5.21702
94.6544
217.268

inhibitor (GDI) alpha

guanine nucleotide
GNAZ
NM_002073
0781
7.49E−07
0.040958
0.000155
5.21417
138.429
84.1772

binding protein (G

protein), alpha z

polypeptide

ATPase, Ca++
ATP2A3
AF068220
0120
8.34E−07
0.04561
0.000168
−5.18981
95.5902
142.894

transporting, ubiquitous

prostaglandin-
PTGS1
BE613133
0580
9.28E−07
0.050719
0.000182
5.1657
276.922
176.715

endoperoxide synthase 1

(prostaglandin G/H

synthase and

cyclooxygenase)

ankyrin repeat and BTB
ABTB1
AW511257
0514
9.52E−07
0.052074
0.000185
−5.15971
39.4124
61.2487

(POZ) domain containing 1

folate receptor 1 (adult)
FOLR1
AF000381
0102
1.38E−06
0.075578
0.000238
5.07454
1958.77
1397.2

Fc fragment of IgA,
FCAR
NM_002000
0780
1.45E−06
0.079201
0.000246
−5.06377
177.357
246.89

receptor for

G-protein signaling
GPSM3
BG111168
0671
1.76E−06
0.095967
0.00028
−5.01948
477.969
796.568

modulator 3 (AGS3-like,

C. elegans)

Spermatid perinuclear
STRBP
AK024960
0353
1.93E−06
0.105266
0.000299
4.99807
44.2908
29.796

RNA binding protein

enoyl Coenzyme A
ECHDC3
NM_024693
0948
2.10E−06
0.114859
0.000316
−4.97782
61.4091
98.8895

hydratase domain

containing 3

heterogeneous nuclear
HNRNPC
NM_004500
0824
2.17E−06
0.118742
0.000322
4.97009
1575.25
1401.51

ribonucleoprotein C

(C1/C2)

colony stimulating factor 3
CSF3R
NM_000760
0761
2.36E−06
0.128959
0.000344
−4.95087
3038.28
4004.48

receptor (granulocyte)

myosin, light chain 6,
MYL6
BE734356
0594
2.45E−06
0.134031
0.000356
4.94187
5732.33
4706.58

alkali, smooth muscle and

non-muscle

strawberry notch homolog
SBNO2
AC005390
0100
2.72E−06
0.148716
0.000383
−4.91756
126.198
194.376

2 (Drosophila)

DEAD (Asp-Glu-Ala-Asp)
DDX17
AA521056
0025
2.79E−06
0.152295
0.000387
4.91199
3247.14
2585.45

box polypeptide 17

amyotrophic lateral
ALS2CR12
AI057333
0163
3.30E−06
0.180188
0.000423
4.8725
92.0138
46.3901

sclerosis 2 (juvenile)

chromosome region,

candidate 12

egl nine homolog 2
EGLN2
AW057545
0472
3.41E−06
0.186485
0.000434
−4.8644
46.7042
81.0448

(C. elegans)

WD and tetratricopeptide
WDTC1
AK001734
0321
3.74E−06
0.204421
0.000464
−4.84273
143.089
215.035

repeats 1

CD74 molecule, major
CD74
M28590
0733
3.99E−06
0.218102
0.000477
−4.82741
393.178
654.678

histocompatibility

complex, class II invariant

chain

glycoprotein VI (platelet)
GP6
AB043821
0092
4.78E−06
0.261363
0.000537
4.78445
95.1473
61.4523

dual specificity
DUSP1
AA530892
0027
4.79E−06
0.261693
0.000537
−4.78415
107.394
209.5

phosphatase 1

transcription factor binding
TFE3
AY034078
0534
4.79E−06
0.262114
0.000537
−4.78376
58.8061
97.4688

to IGHM enhancer 3

gelsolin (amyloidosis,
GSN
BE675337
0587
4.83E−06
0.2639
0.000538
−4.78215
77.2986
118.847

Finnish type)

guanine nucleotide
GNG11
NM_004126
0814
4.83E−06
0.264071
0.000538
4.78199
548.288
339.78

binding protein (G

protein), gamma 11

CD6 molecule
CD6
NM_006725
0867
5.60E−06
0.306414
0.000594
−4.74649
92.2557
150.98

nerve growth factor
NGFRAP1
NM_014380
0886
6.87E−06
0.375513
0.000699
4.69768
691.606
498.72

receptor (TNFRSF16)

associated protein 1

selectin P ligand
SELPLG
AI741056
0250
7.68E−06
0.419967
0.000755
−4.67069
2721.41
3268.22

CD44 molecule (Indian
CD44
AF098641
0127
7.70E−06
0.420973
0.000756
−4.67012
371.069
433.064

blood group)

ORAI calcium release-
ORAI2
BF939788
0663
7.87E−06
0.430403
0.000771
−4.66476
59.2229
93.4356

activated calcium

modulator 2

prosaposin (variant
PSAP
M32221
0734
8.14E−06
0.444966
0.000787
−4.65671
5511.12
6507.81

Gaucher disease and

variant metachromatic

leukodystrophy)

cortactin
CTTN
NM_005231
0839
8.54E−06
0.467172
0.000808
4.64491
182.112
121.169

CD6 molecule
CD6
U66145
0988
9.03E−06
0.493658
0.00084
−4.63152
108.146
166.093

potassium voltage-gated
KCNAB2
AF044253
0112
9.05E−06
0.494828
0.00084
−4.63095
32.1399
55.8352

channel, shaker-related

subfamily, beta member 2

tyrosine 3-
YWHAZ
NM_003406
0803
1.07E−05
0.585411
0.000955
4.58999
3462.95
2974.74

monooxygenase/tryptophan

5-monooxygenase

activation protein, zeta

polypeptide

prefoldin subunit 5
PFDN5
NM_002624
0793
1.11E−05
0.608358
0.000981
4.58059
1086.43
759.973

zinc finger E-box binding
ZEB2
AV739670
0456
1.26E−05
0.687237
0.00107
4.5507
90.1064
58.9124

homeobox 2

lymphocyte-specific
LSP1
NM_002339
0784
1.80E−05
0.983838
0.001356
−4.46201
2289.02
2996.22

protein 1

GM2 ganglioside activator
GM2A
AL513583
0403
1.94E−05
1
0.001433
−4.44336
295.155
407.539

B-cell CLL/lymphoma 3
BCL3
AI829875
0287
2.01E−05
1
0.001474
−4.43457
73.2591
122.329

signal-regulatory protein
SIRPA
AC004832
0099
2.15E−05
1
0.00155
−4.41809
66.2175
114.978

alpha

chromosome 21 open
C21orf7
NM_020152
0932
2.42E−05
1
0.00169
4.3876
280.123
180.541

reading frame 7

arachidonate 12-
ALOX12
NM_000697
0760
2.59E−05
1
0.001773
4.37069
142.898
92.6631

lipoxygenase

immunoglobulin heavy
IGHD
AJ275469
0314
2.75E−05
1
0.001841
−4.35534
115.496
181.147

constant delta

signal-regulatory protein
SIRPA
NM_004648
0827
2.87E−05
1
0.001899
−4.34524
277.486
340.134

alpha

talin 1
TLN1
NM_006289
0857
3.03E−05
1
0.001968
−4.33118
677.305
962.298

versican
VCAN
R94644
0964
3.18E−05
1
0.002032
−4.31901
1312.01
1597.22

leukocyte immunoglobulin-
LILRA4
AF041261
0110
3.36E−05
1
0.002112
−4.30455
50.1417
71.7018

like receptor, subfamily A

(with TM domain),

member 4

dual specificity
DUSP1
NM_004417
0823
3.50E−05
1
0.002177
−4.2941
2510.99
3381.13

phosphatase 1

leukocyte immunoglobulin-
LILRA2
U82278
0994
3.51E−05
1
0.002177
−4.29389
1033.51
1293.64

like receptor, subfamily A

(with TM domain),

member 2

leukocyte immunoglobulin-
LILRA2
U82276
0992
3.94E−05
1
0.002317
−4.26416
899.494
1137.99

like receptor, subfamily A

(with TM domain),

member 2

colony stimulating factor 3
CSF3R
NM_172313
0960
4.66E−05
1
0.002581
−4.22109
3895.82
4816.3

receptor (granulocyte)

immunoglobulin lambda
IGL@
D87021
0711
4.82E−05
1
0.002642
−4.21222
44.8257
78.8501

locus

opioid growth factor
OGFR
AF172449
0140
5.54E−05
1
0.002911
−4.17619
54.9759
81.4231

receptor

BCL2-associated
BAG1
NM_004323
0820
5.83E−05
1
0.003012
4.16308
3331.77
2495.07

athanogene

tetraspanin 5
TSPAN5
AF065389
0119
6.55E−05
1
0.003253
4.13256
1141.55
805.081

platelet factor 4
PF4
NM_002619
0791
7.11E−05
1
0.003433
4.11123
2982.12
2052.36

(chemokine (C—X—C motif)

ligand 4)

Fc fragment of IgA,
FCAR
U56237
0986
7.24E−05
1
0.003466
−4.10642
22.6711
32.7601

receptor for

transketolase (Wernicke-
TKT
BF696840
0656
7.66E−05
1
0.003582
−4.09169
2569.82
3111.72

Korsakoff syndrome)

heterogeneous nuclear
HNRNPC
AA664258
0039
8.17E−05
1
0.003762
4.07462
1778.78
1539.09

ribonucleoprotein C

(C1/C2)

tumor necrosis factor
TNFRSF10C
NM_003841
0808
8.60E−05
1
0.003866
−4.06101
1233.42
1735.81

receptor superfamily,

member 10c, decoy

without an intracellular

domain

clusterin
CLU
M25915
0732
0.000109
1
0.00464
3.99777
917.982
586.775

Interleukin 8
IL8
L34164
0723
0.000115
1
0.004824
−3.98299
68.9562
113.762

chromosome Y open
CYorf15A
AW468885
0510
0.000124
1
0.005062
3.96438
61.848
33.1275

reading frame 15A

insulin-like growth factor 1
IGF1R
BF347362
0633
0.000127
1
0.005152
−3.95765
22.2597
31.1978

receptor

Immunoglobulin heavy
IGHG1
M24668
0731
0.000144
1
0.005654
−3.92265
42.8722
66.9195

constant gamma 1 (G1m

marker)

adducin 3 (gamma)
ADD3
AI763123
0262
0.000155
1
0.005926
3.90373
2119.65
1920.44

GM2 ganglioside activator
GM2A
M76477
0737
0.000176
1
0.006491
−3.86822
21.724
39.5498

small EDRK-rich factor 2
SERF2
BE568651
0579
0.000179
1
0.00656
3.86335
4954.6
4192.08

neurofilament, light
NEFL
AL537457
0413
0.000179
1
0.006562
3.86307
31.9431
23.1309

polypeptide 68 kDa

hypothetical protein
LOC284701
AL137733
0398
0.000218
1
0.007625
−3.80903
64.9496
112.816

LOC284701

interferon regulatory factor 7
IRF7
NM_004030
0810
0.000231
1
0.007884
−3.79395
409.493
623.352

CTD (carboxy-terminal
CTDSPL
NM_005808
0846
0.000235
1
0.00799
3.78905
93.671
62.2121

domain, RNA polymerase

II, polypeptide A) small

phosphatase-like

immunoglobulin heavy
IGHA1 ///
U92706
0997
0.000252
1
0.008417
−3.76895
86.7125
132.558

constant alpha 1 ///
IGHG1 ///

immunoglobulin heavy
IGHG3 ///

constant gamma 1 (G1m
IGHM ///

marker) /// immunoglobulin
IGHV4-31

heavy constant gamma 3

(G3m marker) ///

immunoglobulin heavy

constant mu ///

immunoglobulin heavy

variable 4-31

calreticulin
CALR
NM_004343
0821
0.00026
1
0.008592
−3.76047
79.4426
119.207

profilin 1
PFN1
NM_005022
0834
0.000262
1
0.008638
−3.75833
6953.19
7641.43

GM2 ganglioside activator
GM2A
M76477
0737
0.000299
1
0.009457
−3.72107
162.01
213.128

Immunoglobulin heavy
IGHA1
AW519168
0517
0.000324
1
0.009983
−3.69913
152.921
219.57

constant alpha 1

BCL2-associated
BAG1
AF116273
0132
0.000352
1
0.010602
3.67548
3286.14
2540.18

athanogene

integrin, beta 2
ITGB2
NM_000211
0756
0.000355
1
0.010648
−3.67283
5760.57
6367.25

(complement component 3

receptor 3 and 4 subunit)

integral membrane protein
ITM2B
AF092128
0126
0.000477
1
0.013182
−3.58869
10431.6
11336.4

2B

myeloid cell leukemia
MCL1
AI275690
0180
0.000503
1
0.013715
−3.5734
6463.22
7020.98

sequence 1 (BCL2-

related)

GNAS complex locus
GNAS
AA650558
0038
0.000515
1
0.013953
3.56649
1501.58
1173

tubulin, beta 1
TUBB1
N63244
0750
0.000816
1
0.019091
3.4314
2271.09
1745.37

ribosomal protein L23
RPL23
NM_000978
0767
0.000818
1
0.019126
3.43065
2085.23
1502.85

peroxiredoxin 6
PRDX6
BE869583
0604
0.000914
1
0.020772
3.39769
3442.93
2661.75

neurofilament, light
NEFL
BF055311
0613
0.00094
1
0.021238
3.38918
82.1
61.5983

polypeptide 68 kDa

immunoglobulin kappa
IGK@ /// IGKC
AW575927
0518
0.001341
1
0.027148
−3.28165
4837.67
5839.72

constant ///
/// IGKV1-5 ///

immunoglobulin kappa
IGKV2-24

variable 1-5 ///

immunoglobulin kappa

variable 2-24 ///

immunoglobulin kappa

locus

cystatin C (amyloid
CST3
NM_000099
0755
0.001346
1
0.027219
−3.28039
3566.07
4248.09

angiopathy and cerebral

hemorrhage)

ribosomal protein L7
RPL7
NM_000971
0766
0.001461
1
0.028666
3.25511
6070.42
4837.24

interferon induced
IFITM1
AA749101
0057
0.001797
1
0.033003
−3.19088
7152.48
8178.72

transmembrane protein 1

(9-27)

ribosomal protein L36a ///
LOC729362 ///
NM_021029
0933
0.001813
1
0.03322
3.18807
4537.53
3218.25

similar to large subunit
RPL36A

ribosomal protein L36a

SUB1 homolog (S. cerevisiae)
SUB1
BE784583
0598
0.001896
1
0.034265
3.17412
1392.33
1081.88

guanylate kinase 1
GUK1
BC006249
0558
0.001983
1
0.035305
3.15989
4000.02
3171.59

Pre-B-cell colony
PBEF1
AA873350
0074
0.002161
1
0.037276
−3.13274
3292.91
3867.52

enhancing factor 1

prostaglandin-
PTGS1
NM_000962
0764
0.002218
1
0.037809
3.12446
103.535
79.4279

endoperoxide synthase 1

(prostaglandin G/H

synthase and

cyclooxygenase)

F-box protein 7
FBXO7
NM_012179
0877
0.002317
1
0.038996
3.11068
6069.43
5014.48

hemoglobin, alpha 1 ///
HBA1 /// HBA2
AF105974
0128
0.002367
1
0.039561
3.10384
6124.77
4656.14

hemoglobin, alpha 2

hemoglobin, alpha 1
HBA1
BC005931
0555
0.00239
1
0.039846
3.10074
6143.06
4645.89

immunoglobulin lambda
IGL@ /// IGLJ3
X57812
1008
0.002707
1
0.043327
−3.06075
3476.47
4451

locus /// immunoglobulin
/// IGLV2-14 ///

lambda variable 4-3 ///
IGLV3-25 ///

immunoglobulin lambda
IGLV4-3

variable 3-25 ///

immunoglobulin lambda

variable 2-14 ///

immunoglobulin lambda

joining 3

major histocompatibility
HLA-G
M90686
0740
0.002992
1
0.046215
−3.02834
5755.57
7193.31

complex, class I, G

SUB1 homolog (S. cerevisiae)
SUB1
BG231551
0678
0.003023
1
0.046448
3.02497
2004.47
1599.13

chemokine (C—X3—C motif)
CX3CR1
U20350
0978
0.003112
1
0.04726
3.0156
2713.44
2373.65

receptor 1

metastasis associated
MALAT1
AF132202
0134
0.003436
1
0.050486
−2.98318
6262.75
7016.01

lung adenocarcinoma

transcript 1 (non-protein

coding)

metastasis associated
MALAT1
BG534952
0699
0.00728
1
0.08193
2.72885
6776.17
6030.81

lung adenocarcinoma

transcript 1 (non-protein

coding)

tubulin, beta 2A
TUBB2A
NM_001069
0768
0.017717
1
0.144043
2.40355
1238.52
689.685

solute carrier family 25,
SLC25A37
BG251467
0679
0.019789
1
0.154414
2.36091
7684.14
6998.66

member 37

solute carrier family 25,
SLC25A37
BG251467
0679
0.037867
1
0.228447
2.09875
4732.41
4047.49

member 37

GNAS complex locus
GNAS
NM_016592
0905
0.060396
1
0.298237
1.89518
6053.88
5672.78

metastasis associated
MALAT1
BE708432
0592
0.097547
1
0.387215
1.66947
15502.2
14795.3

lung adenocarcinoma

transcript 1 (non-protein

coding)

TABLE 1B

MeanDiff

Genbank
SEQ ID
MeanRatio
(CONTROL −
FoldChange

Gene Title
Gene Symbol
Acc. No.
NO.
(CONTROL/MS)
MS)
(CONTROL/MS)
Probe Set ID

FK506 binding protein 5
FKBP5
NM_004117
0813
0.410872
−111.966
−2.43385
204560_at

FK506 binding protein 5
FKBP5
W86302
1003
0.506291
−461.576
−1.97515
224856_at

FK506 binding protein 5
FKBP5
AI753747
0255
0.556963
−942.013
−1.79545
224840_at

cyclin D3
CCND3
NM_001760
0778
0.786706
−548.102
−1.27112
201700_at

tetraspanin 14
TSPAN14
NM_030927
0958
0.804285
−106.324
−1.24334
221002_s_at

chemokine (C—X—C motif)
CXCR4
AF348491
0158
0.785186
−492.069
−1.27358
211919_s_at

receptor 4

Rho GTPase activating
ARHGAP27
AI814329
0276
0.51795
−43.9948
−1.93069
227057_at

protein 27

integrin, beta 2
ITGB2
L78790
0728
0.792057
−923.911
−1.26254
1555349_a_at

(complement component 3

receptor 3 and 4 subunit)

adrenergic, beta, receptor
ADRBK1
M80776
0738
0.664754
−138.928
−1.50432
201401_s_at

kinase 1

solute carrier family 6
SLC6A6
NM_003043
0797
0.617703
−77.4371
−1.6189
205920_at

(neurotransmitter

transporter, taurine),

member 6

Rho GTPase activating
ARHGAP18
BE501862
0576
1.41321
69.4447
1.41321
225173_at

protein 18

DNA-damage-inducible
DDIT4
NM_019058
0928
0.578263
−180.24
−1.72932
202887_s_at

transcript 4

chromodomain helicase
CHD9
AW300405
0505
1.23911
46.5668
1.23911
229586_at

DNA binding protein 9

polypyrimidine tract
PTBP1
AA679988
0041
0.745687
−47.9749
−1.34105
212016_s_at

binding protein 1

DEAD (Asp-Glu-Ala-Asp)
DDX6
NM_004397
0822
1.3796
16.3859
1.3796
204909_at

box polypeptide 6

transmembrane 9
TM9SF1
BE899402
0606
0.788937
−25.5286
−1.26753
209149_s_at

superfamily member 1

structural maintenance of
SMC3
AI373676
0193
1.38405
77.0678
1.38405
209258_s_at

chromosomes 3

chromosome 6 open
C6orf166
AI742378
0253
0.64847
−45.5391
−1.54209
223143_s_at

reading frame 166

salvador homolog 1
SAV1
AJ292969
0315
1.3186
29.5723
1.3186
234491_s_at

(Drosophila)

heat shock 70 kDa protein
HSPA5
AF216292
0145
0.864477
−237.075
−1.15677
211936_at

5 (glucose-regulated

protein, 78 kDa)

MFNG O-fucosylpeptide
MFNG
AI738965
0249
0.727485
−64.0613
−1.3746
204152_s_at

3-beta-N-

acetylglucosaminyltransferase

ankyrin repeat and BTB
ABTB1
BF115480
0622
0.606222
−25.6714
−1.64956
242567_at

(POZ) domain containing 1

leukotriene B4 receptor
LTB4R
U33448
0980
0.520201
−117.77
−1.92234
216388_s_at

myeloid cell leukemia
MCL1
BF594446
0650
0.619672
−112.202
−1.61376
200796_s_at

sequence 1 (BCL2-

related)

Friend leukemia virus
FLI1
M93255
0741
0.820712
−135.481
−1.21845
210786_s_at

integration 1

unc-93 homolog B1 (C. elegans)
UNC93B1
AW001274
0460
0.597899
−87.5072
−1.67252
225869_s_at

mindbomb homolog 1
MIB1
W80418
1001
1.27079
49.1563
1.27079
224726_at

(Drosophila)

period homolog 1
PER1
NM_002616
0790
0.630947
−32
−1.58492
202861_at

(Drosophila)

splicing factor,
SFRS17A
M99578
0743
0.800003
−22.3614
−1.25
210269_s_at

arginine/serine-rich 17A

zinc finger and BTB
ZBTB16
NM_006006
0849
0.577369
−89.3868
−1.73199
205883_at

domain containing 16

ER lipid raft associated 1
ERLIN1
NM_006459
0862
0.73173
−18.2519
−1.36662
202444_s_at

PHD finger protein 3
PHF3
AW189430
0482
1.28957
38.2468
1.28957
217951_s_at

toll-like receptor 2
TLR2
NM_003264
0801
0.738901
−670.351
−1.35336
204924_at

paxillin
PXN
D86862
0710
0.480522
−100.487
−2.08107
211823_s_at

RAB GTPase activating
RABGAP1L
AB019490
0087
1.5011
95.7868
1.5011
215342_s_at

protein 1-like

proline rich 14
PRR14
BE788667
0599
0.521016
−112.711
−1.91933
1559397_s_at

Fc fragment of IgA,
FCAR
D87858
0712
0.62416
−58.5952
−1.60215
211816_x_at

receptor for

tripeptidyl peptidase I
TPP1
AA602532
0032
0.758102
−63.9567
−1.31908
214196_s_at

signal-regulatory protein
SIRPA
D86043
0709
0.577984
−50.6133
−1.73015
202895_s_at

alpha

insulin-like growth factor 2
IGF2BP3
AU160004
0441
1.67856
14.483
1.67856
203819_s_at

mRNA binding protein 3

RAN binding protein 3
RANBP3
AI689052
0244
0.806327
−30.7581
−1.24019
202639_s_at

tankyrase, TRF1-
TNKS2
BF060683
0615
1.34901
89.5309
1.34901
222562_s_at

interacting ankyrin-related

ADP-ribose polymerase 2

transmembrane 9
TM9SF4
AI418892
0200
0.805871
−40.4381
−1.24089
212194_s_at

superfamily protein

member 4

CCR4-NOT transcription
CNOT1
BC040523
0561
0.773683
−20.6257
−1.29252
1554052_at

complex, subunit 1

trophoblast-derived
TncRNA
AV659198
0443
0.714038
−32.2735
−1.40049
238320_at

noncoding RNA

CD83 molecule
CD83
NM_004233
0816
1.30421
27.778
1.30421
204440_at

Transcribed locus
—
AI032730
0160
1.30802
46.0351
1.30802
244679_at

TBC1 domain family,
TBC1D2B
BF195608
0625
0.846298
−52.3633
−1.18162
212796_s_at

member 2B

hypothetical protein
FLJ10038
NM_017976
0918
1.23737
16.5277
1.23737
205511_at

FLJ10038

procollagen-proline, 2-
P4HB
AK075503
0362
0.70108
−123.296
−1.42637
1564494_s_at

oxoglutarate 4-

dioxygenase (proline 4-

hydroxylase), beta

polypeptide

Ewing sarcoma breakpoint
EWSR1 ///
AF327066
0156
0.794872
−85.6159
−1.25806
211825_s_at

region 1 /// Friend
FLI1

leukemia virus integration 1

Rab interacting lysosomal
RILPL2
AI810244
0275
0.833939
−144.701
−1.19913
227983_at

protein-like 2

RAB5C, member RAS
RAB5C
AF141304
0136
0.781885
−184.971
−1.27896
201156_s_at

oncogene family

SMAD specific E3
SMURF2
AY014180
0532
1.18427
64.941
1.18427
205596_s_at

ubiquitin protein ligase 2

diacylglycerol lipase, beta
DAGLB
BE795104
0600
0.735937
−27.3357
−1.35881
225833_at

—
—
AW275093
0495
1.4707
12.114
1.4707
242929_at

cisplatin resistance-
CROP
AW089673
0478
1.22445
229.86
1.22445
208835_s_at

associated overexpressed

protein

CUG triplet repeat, RNA
CUGBP2
AI652861
0231
0.863056
−69.6671
−1.15867
227178_at

binding protein 2

cleft lip and palate
CLPTM1
BC004865
0551
0.792422
−70.6394
−1.26195
211136_s_at

associated

transmembrane protein 1

plasminogen activator,
PLAUR
AY029180
0533
0.688829
−183.872
−1.45174
211924_s_at

urokinase receptor

SH3 domain and
SH3TC1
NM_018986
0926
0.751709
−51.8135
−1.3303
219256_s_at

tetratricopeptide repeats 1

CCAAT/enhancer binding
CEBPD
AV655640
0442
0.652156
−35.3408
−1.53337
213006_at

protein (C/EBP), delta

myotrophin
MTPN
AL533334
0410
1.10221
270.99
1.10221
224656_s_at

diacylglycerol kinase, zeta
DGKZ
NM_003646
0806
0.667281
−247.106
−1.49862
207556_s_at

104 kDa

coiled-coil domain
CCDC95
AA743390
0052
0.780837
−32.1692
−1.28068
227286_at

containing 95

golgi autoantigen, golgin
GOLGA8B
AI829170
0286
1.73953
36.2445
1.73953
208797_s_at

subfamily a, 8B

O-linked N-
OGT
U77413
0990
0.86299
−43.9052
−1.15876
207563_s_at

acetylglucosamine

(GlcNAc) transferase

(UDP-N-

acetylglucosamine:polypeptide-

N-

acetylglucosaminyl

transferase)

alpha thalassemia/mental
ATRX ///
AI650257
0227
1.23404
77.4692
1.23404
208859_s_at

retardation syndrome X-
LOC728849

linked (RAD54 homolog,

S. cerevisiae) /// similar to

transcriptional regulator

ATRX isoform 1

mitogen-activated protein
MAP2K1
AI571419
0217
0.87252
−59.124
−1.14611
202670_at

kinase kinase 1

Glutathione S-transferase
GSTK1
AV722006
0451
1.64253
7.52765
1.64253
243325_at

kappa 1

ATP-binding cassette,
ABCC1
NM_004996
0833
0.809071
−27.5522
−1.23599
202805_s_at

sub-family C

(CFTR/MRP), member 1

chromosome 19 open
C19orf6
AI805266
0270
0.634364
−47.9788
−1.57638
213986_s_at

reading frame 6

potassium channel
KCTD5
AA872593
0073
0.809141
−16.4666
−1.23588
222645_s_at

tetramerisation domain

containing 5

Transcribed locus
—
AI767751
0265
1.25823
14.6655
1.25823
228084_at

leukotriene B4 receptor
LTB4R
U41070
0982
0.717178
−54.4399
−1.39435
210128_s_at

TSC22 domain family,
TSC22D3
NM_004089
0811
0.652362
−290.14
−1.53289
207001_x_at

member 3

peroxiredoxin 6
PRDX6
NM_004905
0831
1.19962
146.027
1.19962
200845_s_at

6-phosphofructo-2-
PFKFB2
AB044805
0093
0.690646
−13.182
−1.44792
209992_at

kinase/fructose-2,6-

biphosphatase 2

chromobox homolog 4 (Pc
CBX4
NM_003655
0807
0.641073
−40.8418
−1.55988
206724_at

class homolog,

Drosophila)

GTPase, IMAP family
GIMAP5
AL080068
0378
1.53468
33.4044
1.53468
215352_at

member 5

surfeit 4
SURF4
AF078866
0123
0.84411
−41.7779
−1.18468
222979_s_at

PHD finger protein 12
PHF12
AL161953
0399
0.5897
−21.4733
−1.69578
234939_s_at

CCAAT/enhancer binding
CEBPD
NM_005195
0837
0.764013
−768.486
−1.30888
203973_s_at

protein (C/EBP), delta

prion protein (p27-30)
PRNP
AV725328
0453
0.815149
−25.0163
−1.22677
215707_s_at

(Creutzfeldt-Jakob

disease, Gerstmann-

Strausler-Scheinker

syndrome, fatal familial

insomnia)

phosphoinositide-3-
PIK3R5
NM_014308
0883
0.821673
−39.5518
−1.21703
220566_at

kinase, regulatory subunit

5, p101

myotubularin related
MTMR1
AK001816
0322
0.739341
−23.2022
−1.35256
214975_s_at

protein 1

SLAIN motif family,
SLAIN2
AI979301
0310
1.38052
57.75
1.38052
224854_s_at

member 2

C-type lectin domain
CLEC1B
NM_016509
0902
1.57911
34.1712
1.57911
220496_at

family 1, member B

tetratricopeptide repeat
TTC7A
BE205790
0568
0.727973
−13.8295
−1.37368
224924_at

domain 7A

suppressor of Ty 16
SUPT16H
AK024072
0341
1.40153
75.4675
1.40153
233827_s_at

homolog (S. cerevisiae)

SERPINE1 mRNA binding
SERBP1
BC003049
0547
1.15454
187.371
1.15454
209669_s_at

protein 1

RNA binding motif protein
RBM14
AF315633
0153
0.669042
−19.7848
−1.49467
1555639_a_at

14

T-cell acute lymphocytic
TAL1
NM_003189
0800
1.49187
67.9937
1.49187
206283_s_at

leukemia 1

Ras association
RAPH1
AA194149
0014
1.40811
13.9347
1.40811
225188_at

(RalGDS/AF-6) and

pleckstrin homology

domains 1

disabled homolog 2,
DAB2
N21202
0744
1.32324
23.7867
1.32324
201278_at

mitogen-responsive

phosphoprotein

(Drosophila)

v-ets erythroblastosis virus
ETS1
NM_005238
0840
0.706997
−21.9256
−1.41443
214447_at

E26 oncogene homolog 1

(avian)

elastin microfibril
EMILIN2
AL552384
0416
0.683088
−18.3855
−1.46394
242288_s_at

interfacer 2

myosin IXB
MYO9B
NM_004145
0815
0.605039
−41.608
−1.65279
208452_x_at

DnaJ (Hsp40) homolog,
DNAJC13
BC043583
0562
1.40365
7.41601
1.40365
1560020_at

subfamily C, member 13

acyl-Coenzyme A binding
ACBD5
BC025309
0560
1.36451
22.651
1.36451
1568877_a_at

domain containing 5

Ras association
RAPH1
AA194149
0014
1.37974
8.71298
1.37974
225189_s_at

(RalGDS/AF-6) and

pleckstrin homology

domains 1

C-type lectin domain
CLEC4E
BC000715
0538
0.686069
−379.336
−1.45758
222934_s_at

family 4, member E

Fc fragment of IgA,
FCAR
U43677
0983
0.627309
−37.9565
−1.59411
211307_s_at

receptor for

ATPase, Ca++
ATP2A3
AA877910
0076
0.702202
−30.8685
−1.42409
213042_s_at

transporting, ubiquitous

methionine
MAT2A
NM_005911
0848
0.808703
−23.1428
−1.23655
200769_s_at

adenosyltransferase II,

alpha

general transcription factor
GTF2A1
NM_015859
0891
1.61825
18.7636
1.61825
206521_s_at

IIA, 1, 19/37 kDa

DAZ associated protein 2
DAZAP2
AL534321
0411
0.83346
−337.118
−1.19982
212595_s_at

chromosome 1 open
C1orf38
AB035482
0091
0.788942
−371.48
−1.26752
210785_s_at

reading frame 38

arrestin domain containing 1
ARRDC1
AK001822
0323
0.77686
−64.9423
−1.28723
226405_s_at

RAD23 homolog B
RAD23B
AL527365
0409
0.742279
−173.664
−1.3472
201222_s_at

(S. cerevisiae)

chromosome 19 open
C19orf6
AC004528
0097
0.649764
−51.5385
−1.53902
212574_x_at

reading frame 6

procollagen-proline, 2-
P4HB
J02783
0716
0.859883
−245.237
−1.16295
200654_at

oxoglutarate 4-

dioxygenase (proline 4-

hydroxylase), beta

polypeptide

period homolog 1
PER1
AF022991
0108
0.772837
−21.3812
−1.29393
36829_at

(Drosophila)

galactosylceramidase
GALC
D25284
0705
0.843323
−10.2215
−1.18579
211810_s_at

CDNA FLJ33748 fis, clone
—
H75391
0715
1.38204
16.1
1.38204
1559515_at

BRCAN2000148

glucosamine (N-acetyl)-6-
GNS
NM_002076
0782
0.703894
−39.7323
−1.42067
203676_at

sulfatase (Sanfilippo

disease IIID)

non-POU domain
NONO
L14599
0721
0.865461
−81.334
−1.15545
208698_s_at

containing, octamer-

binding

zinc finger protein 117
ZNF117
NM_024498
0946
1.38949
39.4965
1.38949
207605_x_at

activin A receptor, type IB
ACVR1B
AL117643
0384
0.842946
−32.3868
−1.18632
213198_at

minichromosome
MCM3AP
AK022303
0333
0.720718
−11.7219
−1.38751
215581_s_at

maintenance complex

component 3 associated

protein

natural killer-tumor
NKTR
AA732581
0048
1.37587
41.4737
1.37587
231235_at

recognition sequence

sorbin and SH3 domain
SORBS3
NM_005775
0844
0.609982
−17.4581
−1.63939
207788_s_at

containing 3

phosphoinositide-3-kinase
PIK3IP1
BE042976
0563
0.772434
−157.815
−1.29461
221757_at

interacting protein 1

CDNA FLJ34061 fis, clone
—
BG430133
0695
1.46652
12.8086
1.46652
1565614_at

FCBBF3000462

heterogeneous nuclear
HNRNPC
AV725195
0452
1.15559
262.504
1.15559
214737_x_at

ribonucleoprotein C

(C1/C2)

calnexin
CANX
AI761759
0258
0.865197
−66.4295
−1.15581
208852_s_at

inositol polyphosphate-5-
INPP5D
U53470
0985
0.782311
−68.532
−1.27826
203331_s_at

phosphatase, 145 kDa

hepatocellular carcinoma-
HCRP1
AK025343
0356
0.78604
−15.3697
−1.2722
216174_at

related HCRP1

solute carrier family 12
SLC12A9
BC000154
0535
0.668443
−33.1179
−1.49601
223994_s_at

(potassium/chloride

transporters), member 9

suppression of
ST14
U20428
0979
0.688211
−10.2143
−1.45304
216905_s_at

tumorigenicity 14 (colon

carcinoma)

plasminogen activator,
PLAUR
U08839
0975
0.739167
−184.938
−1.35287
210845_s_at

urokinase receptor

TAF8 RNA polymerase II,
TAF8
BU618741
0703
0.815823
−13.4618
−1.22576
1556178_x_at

TATA box binding protein

(TBP)-associated factor,

43 kDa

chemokine (C—X—C motif)
CXCR4
L01639
0719
0.831693
−306.096
−1.20237
209201_x_at

receptor 4

N-acetylglucosamine-1-
GNPTG
AF302786
0151
0.864971
−27.9294
−1.15611
224887_at

phosphate transferase,

gamma subunit

protein associated with
PATL1
AA359612
0018
0.827113
−15.0724
−1.20902
235235_s_at

topoisomerase II homolog

1 (yeast)

galactosidase, beta 1
GLB1
NM_000404
0758
0.862277
−81.7493
−1.15972
201576_s_at

PDZ and LIM domain 2
PDLIM2
NM_021630
0934
0.854149
−92.4219
−1.17076
219165_at

(mystique)

(clone 1NIB-4) normalized
—
BQ002274
0702
0.660567
−10.368
−1.51385
1556314_a_at

cDNA library sequence

transmembrane protein 43
TMEM43
W74580
1000
0.844907
−80.8659
−1.18356
217795_s_at

exosome component 1
EXOSC1
BC012538
0559
1.32212
9.35476
1.32212
1559044_at

transducin-like enhancer
TLE4
AL358975
0400
0.843292
−38.0674
−1.18583
216997_x_at

of split 4 (E(sp1) homolog,

Drosophila)

plectin 1, intermediate
PLEC1
Z54367
1015
0.708741
−39.4505
−1.41095
216971_s_at

filament binding protein

500 kDa

FIP1 like 1 (S. cerevisiae)
FIP1L1
NM_030917
0957
1.12041
21.6845
1.12041
221007_s_at

blocked early in transport
BET1L
NM_016526
0903
0.428008
−16.7549
−2.3364
220470_at

1 homolog (S. cerevisiae)-

like

SMEK homolog 1,
SMEK1
NM_017936
0917
1.29938
20.9668
1.29938
220369_at

suppressor of mek1

(Dictyostelium)

nuclear casein kinase and
NUCKS1
AW515443
0516
1.25494
203.425
1.25494
229353_s_at

cyclin-dependent kinase

substrate 1

myosin IXB
MYO9B
AF143684
0137
0.706462
−125.22
−1.4155
217297_s_at

zinc finger RNA binding
ZFR
AI459274
0207
1.35041
23.441
1.35041
33148_at

protein

chromosome 8 open
C8orf42
AI632224
0222
1.55823
7.12392
1.55823
226778_at

reading frame 42

retinol saturase (all-trans-
RETSAT
AK098125
0364
0.74181
−13.5564
−1.34805
1566472_s_at

retinol 13,14-reductase)

protein kinase, AMP-
PRKAB2
NM_005399
0841
1.31212
10.5339
1.31212
214474_at

activated, beta 2 non-

catalytic subunit

U2 small nuclear RNA
U2AF2
NM_007279
0875
0.730157
−41.0539
−1.36957
218382_s_at

auxiliary factor 2

WD repeat domain 1
WDR1
AF274954
0150
0.711232
−167.701
−1.40601
210935_s_at

PTK2 protein tyrosine
PTK2
AL037339
0368
1.23432
13.9745
1.23432
208820_at

kinase 2

solute carrier family 16,
SLC16A3
AL513917
0404
0.653057
−197.651
−1.53126
202855_s_at

member 3

(monocarboxylic acid

transporter 4)

tripartite motif-containing 8
TRIM8
NM_030912
0956
1.187
123.174
1.187
221012_s_at

Full-length cDNA clone
—
AW953794
0525
0.713306
−10.9193
−1.40192
230968_at

CS0DF032YA11 of Fetal

brain of Homo sapiens

(human)

speckle-type POZ protein
SPOP
NM_003563
0805
1.10986
90.8075
1.10986
204640_s_at

BCL2-associated X
BAX
U19599
0977
0.756064
−36.9248
−1.32264
211833_s_at

protein

high mobility group AT-
HMGA1
AF176039
0141
0.563365
−17.5088
−1.77505
210457_x_at

hook 1

Transcribed locus
—
BE348304
0572
1.31402
13.2065
1.31402
237554_at

transmembrane and
TMCO3
NM_017905
0914
0.795943
−17.5981
−1.25637
220240_s_at

coiled-coil domains 3

C-type lectin domain
CLEC4E
NM_014358
0885
0.75634
−49.143
−1.32216
219859_at

family 4, member E

chromosome 7 open
C7orf27
AK024482
0345
0.762591
−31.4652
−1.31132
225437_s_at

reading frame 27

suppressor of zeste 12
SUZ12 ///
AI924660
0297
1.16535
41.8695
1.16535
213971_s_at

homolog (Drosophila) ///
SUZ12P

suppressor of zeste 12

homolog pseudogene

unc-93 homolog B1 (C. elegans)
UNC93B1
NM_030930
0959
0.676621
−42.7644
−1.47793
220998_s_at

Transcribed locus,
—
AI738675
0248
0.781337
−110.327
−1.27986
240064_at

strongly similar to

XP_529518.1

PREDICTED: hypothetical

protein XP_529518 [Pan

troglodytes]

differentially expressed in
DEF6
NM_022047
0937
0.84778
−51.5421
−1.17955
221293_s_at

FDCP 6 homolog (mouse)

KIAA0146
KIAA0146
AI363213
0191
0.719196
−31.4259
−1.39044
228325_at

BCL6 co-repressor
BCOR
AF317392
0154
1.4648
35.2478
1.4648
223916_s_at

KIAA0319-like
KIAA0319L
W58365
0999
0.753732
−120.246
−1.32673
222468_at

—
—
AK000677
0317
1.3013
14.5053
1.3013
233876_at

ADP-dependent
ADPGK
BC006112
0557
0.844025
−25.0846
−1.1848
224455_s_at

glucokinase

TSC22 domain family,
TSC22D3
AL110191
0382
0.786558
−926.021
−1.27136
208763_s_at

member 3

nemo-like kinase
NLK
NM_016231
0897
1.17576
12.9069
1.17576
218318_s_at

amyloid beta (A4)
APLP2
AW001847
0461
0.766817
−206.16
−1.30409
214875_x_at

precursor-like protein 2

phospholipase D family,
PLD3
NM_012268
0878
0.696935
−82.8652
−1.43485
201050_at

member 3

Transcribed locus
—
BF114745
0621
1.12277
11.3237
1.12277
235459_at

ER lipid raft associated 1
ERLIN1
AL568449
0419
0.852824
−58.6846
−1.17257
202441_at

Transcribed locus
—
H24473
0713
1.34485
6.82582
1.34485
229951_x_at

procollagen-proline, 2-
P4HB
NM_000918
0762
0.881299
−107.084
−1.13469
200656_s_at

oxoglutarate 4-

dioxygenase (proline 4-

hydroxylase), beta

polypeptide

calreticulin
CALR
BE251303
0570
0.767097
−108.355
−1.30362
212953_x_at

PTK2B protein tyrosine
PTK2B
NM_004103
0812
0.665846
−51.1597
−1.50185
203111_s_at

kinase 2 beta

KIAA0892
KIAA0892
AC003030
0096
0.554142
−12.142
−1.80459
216926_s_at

angiotensin II receptor-
AGTRAP
AF165187
0139
0.774605
−168.031
−1.29098
1555736_a_at

associated protein

Transcribed locus
—
AW244016
0490
0.671508
−53.1796
−1.48918
227762_at

Full length insert cDNA
—
AF086041
0124
1.45973
23.1829
1.45973
1556812_a_at

clone YX53E08

suppression of
ST14
NM_021978
0936
0.644679
−20.0323
−1.55116
202005_at

tumorigenicity 14 (colon

carcinoma)

serologically defined colon
SDCCAG1
BC006001
0556
1.18167
63.5301
1.18167
1569594_a_at

cancer antigen 1

Cbp/p300-interacting
CITED2
NM_006079
0852
0.840662
−48.6818
−1.18954
207980_s_at

transactivator, with

Glu/Asp-rich carboxy-

terminal domain, 2

ankyrin repeat and FYVE
ANKFY1
NM_016376
0901
0.800364
−21.4969
−1.24943
219868_s_at

domain containing 1

interleukin 13 receptor,
IL13RA1
NM_001560
0773
0.812748
−147.49
−1.23039
201887_at

alpha 1

EH domain binding protein
EHBP1L1
AA149545
0012
0.779588
−73.7409
−1.28273
91703_at

1-like 1

Rho GTPase activating
ARHGAP4
NM_001666
0777
0.768348
−61.7389
−1.30149
204425_at

protein 4

Transcribed locus
—
AW298731
0504
0.557986
−21.7775
−1.79216
239249_at

Ras and Rab interactor 3
RIN3
AW027923
0470
0.727238
−60.7916
−1.37507
219456_s_at

CDNA clone
—
N57510
0749
1.15693
17.2711
1.15693
234998_at

IMAGE: 5313062

Homo sapiens, clone
—
AV735241
0455
1.18015
26.1526
1.18015
225055_at

IMAGE: 3345917, mRNA

pro-platelet basic protein
PPBP
R64130
0963
1.67072
1663.59
1.67072
214146_s_at

(chemokine (C—X—C motif)

ligand 7)

cell division cycle 2-like 1
CDC2L1 ///
NM_001787
0779
0.850597
−29.5012
−1.17564
207428_x_at

(PITSLRE proteins) /// cell
CDC2L2

division cycle 2-like 2

(PITSLRE proteins)

cysteine conjugate-beta
CCBL2
BC000819
0540
1.1738
47.6813
1.1738
209472_at

lyase 2

sema domain,
SEMA4A
NM_022367
0939
0.732766
−132.251
−1.36469
219259_at

immunoglobulin domain

(Ig), transmembrane

domain (TM) and short

cytoplasmic domain,

(semaphorin) 4A

Rho GDP dissociation
ARHGDIA
D13989
0704
0.45839
−116.893
−2.18155
201167_x_at

inhibitor (GDI) alpha

Wolf-Hirschhorn syndrome
WHSC1L1
NM_017778
0912
1.19614
11.2303
1.19614
218173_s_at

candidate 1-like 1

tissue factor pathway
TFPI
AF021834
0107
1.72078
9.20714
1.72078
210664_s_at

inhibitor (lipoprotein-

associated coagulation

inhibitor)

zinc finger protein 271
ZNF271
AF159567
0138
1.1964
29.3872
1.1964
211009_s_at

Wiskott-Aldrich syndrome
WAS
NM_000377
0757
0.447977
−226.867
−2.23226
205400_at

(eczema-

thrombocytopenia)

EH domain binding protein 1
EHBP1
BF116032
0624
1.40606
28.0113
1.40606
212650_at

solute carrier family 6
SLC6A6
U16120
0976
0.713183
−24.4459
−1.40216
205921_s_at

(neurotransmitter

transporter, taurine),

member 6

ADAM metallopeptidase
ADAM8
AI814527
0277
0.541261
−101.711
−1.84754
205179_s_at

domain 8

zinc finger protein 36, C3H
ZFP36L2
AI356398
0189
0.570918
−423.25
−1.75157
201367_s_at

type-like 2

RAB27B, member RAS
RAB27B
BF438386
0637
1.3631
49.8935
1.3631
228708_at

oncogene family

versican
VCAN
D32039
0706
0.776785
−306.325
−1.28736
211571_s_at

Interleukin 8
IL8
AJ239383
0313
0.627373
−44.5734
−1.59395
217281_x_at

leukocyte immunoglobulin-
LILRA2
U82277
0993
0.700637
−149.21
−1.42727
211102_s_at

like receptor, subfamily A

(with TM domain),

member 2

immunoglobulin heavy
IGH@ ///
S55735
0965
0.559124
−2082.58
−1.78851
217022_s_at

locus /// immunoglobulin
IGHA1 ///

heavy constant alpha 1 ///
IGHA2 ///

immunoglobulin heavy
LOC100126583

constant alpha 2 (A2m

marker) /// hypothetical

LOC100126583

regulator of G-protein
RGS14
AF037194
0109
0.684164
−37.2156
−1.46164
211021_s_at

signaling 14

F-box protein 9
FBXO9
AK095315
0363
1.35494
283.431
1.35494
1566509_s_at

septin 9
9-Sep
NM_006640
0865
0.530246
−77.4496
−1.88592
207425_s_at

myeloid cell leukemia
MCL1
NM_021960
0935
0.820331
−746.654
−1.21902
200798_x_at

sequence 1 (BCL2-

related)

poly(A) polymerase alpha
PAPOLA
BF797555
0662
1.21671
261.98
1.21671
212718_at

Transcribed locus
—
AI492388
0212
0.619996
−132.97
−1.61291
228854_at

Rho GDP dissociation
ARHGDIA
AI571798
0218
0.435657
−122.614
−2.29538
213606_s_at

inhibitor (GDI) alpha

guanine nucleotide
GNAZ
NM_002073
0781
1.6445
54.2522
1.6445
204993_at

binding protein (G

protein), alpha z

polypeptide

ATPase, Ca++
ATP2A3
AF068220
0120
0.668956
−47.3043
−1.49487
207521_s_at

transporting, ubiquitous

prostaglandin-
PTGS1
BE613133
0580
1.56705
100.206
1.56705
238669_at

endoperoxide synthase 1

(prostaglandin G/H

synthase and

cyclooxygenase)

ankyrin repeat and BTB
ABTB1
AW511257
0514
0.643482
−21.8363
−1.55405
228848_at

(POZ) domain containing 1

folate receptor 1 (adult)
FOLR1
AF000381
0102
1.40192
561.562
1.40192
211074_at

Fc fragment of IgA,
FCAR
NM_002000
0780
0.718362
−69.5336
−1.39206
207674_at

receptor for

G-protein signaling
GPSM3
BG111168
0671
0.600035
−318.6
−1.66657
214847_s_at

modulator 3 (AGS3-like,

C. elegans)

Spermatid perinuclear
STRBP
AK024960
0353
1.48647
14.4948
1.48647
233251_at

RNA binding protein

enoyl Coenzyme A
ECHDC3
NM_024693
0948
0.620987
−37.4804
−1.61034
219298_at

hydratase domain

containing 3

heterogeneous nuclear
HNRNPC
NM_004500
0824
1.12397
173.739
1.12397
200014_s_at

ribonucleoprotein C

(C1/C2)

colony stimulating factor 3
CSF3R
NM_000760
0761
0.75872
−966.201
−1.31801
203591_s_at

receptor (granulocyte)

myosin, light chain 6,
MYL6
BE734356
0594
1.21794
1025.74
1.21794
212082_s_at

alkali, smooth muscle and

non-muscle

strawberry notch homolog
SBNO2
AC005390
0100
0.649244
−68.1785
−1.54025
215760_s_at

2 (Drosophila)

DEAD (Asp-Glu-Ala-Asp)
DDX17
AA521056
0025
1.25593
661.69
1.25593
230180_at

box polypeptide 17

amyotrophic lateral
ALS2CR12
AI057333
0163
1.98348
45.6236
1.98348
239458_at

sclerosis 2 (juvenile)

chromosome region,

candidate 12

egl nine homolog 2 (C. elegans)
EGLN2
AW057545
0472
0.576276
−34.3406
−1.73528
223083_s_at

WD and tetratricopeptide
WDTC1
AK001734
0321
0.665423
−71.9458
−1.5028
216036_x_at

repeats 1

CD74 molecule, major
CD74
M28590
0733
0.600568
−261.5
−1.66509
1567628_at

histocompatibility

complex, class II invariant

chain

glycoprotein VI (platelet)
GP6
AB043821
0092
1.54831
33.695
1.54831
220336_s_at

dual specificity
DUSP1
AA530892
0027
0.512623
−102.105
−1.95075
201044_x_at

phosphatase 1

transcription factor binding
TFE3
AY034078
0534
0.603333
−38.6627
−1.65746
1565347_s_at

to IGHM enhancer 3

gelsolin (amyloidosis,
GSN
BE675337
0587
0.650402
−41.5488
−1.53751
214040_s_at

Finnish type)

guanine nucleotide
GNG11
NM_004126
0814
1.61366
208.508
1.61366
204115_at

binding protein (G

protein), gamma 11

CD6 molecule
CD6
NM_006725
0867
0.611045
−58.7246
−1.63654
208602_x_at

nerve growth factor
NGFRAP1
NM_014380
0886
1.38676
192.886
1.38676
217963_s_at

receptor (TNFRSF16)

associated protein 1

selectin P ligand
SELPLG
AI741056
0250
0.832688
−546.812
−1.20093
209879_at

CD44 molecule (Indian
CD44
AF098641
0127
0.856847
−61.9943
−1.16707
210916_s_at

blood group)

ORAI calcium release-
ORAI2
BF939788
0663
0.633836
−34.2127
−1.57769
218811_at

activated calcium

modulator 2

prosaposin (variant
PSAP
M32221
0734
0.846847
−996.693
−1.18085
200866_s_at

Gaucher disease and

variant metachromatic

leukodystrophy)

cortactin
CTTN
NM_005231
0839
1.50296
60.9429
1.50296
201059_at

CD6 molecule
CD6
U66145
0988
0.651121
−57.9464
−1.53581
211893_x_at

potassium voltage-gated
KCNAB2
AF044253
0112
0.575621
−23.6953
−1.73725
211791_s_at

channel, shaker-related

subfamily, beta member 2

tyrosine 3-
YWHAZ
NM_003406
0803
1.16412
488.217
1.16412
200639_s_at

monooxygenase/tryptophan

5-monooxygenase

activation protein, zeta

polypeptide

prefoldin subunit 5
PFDN5
NM_002624
0793
1.42957
326.46
1.42957
207132_x_at

zinc finger E-box binding
ZEB2
AV739670
0456
1.5295
31.1939
1.5295
233031_at

homeobox 2

lymphocyte-specific
LSP1
NM_002339
0784
0.76397
−707.2
−1.30895
203523_at

protein 1

GM2 ganglioside activator
GM2A
AL513583
0403
0.724236
−112.384
−1.38076
212737_at

B-cell CLL/lymphoma 3
BCL3
AI829875
0287
0.59887
−49.0698
−1.66981
204907_s_at

signal-regulatory protein
SIRPA
AC004832
0099
0.575913
−48.7608
−1.73637
217024_x_at

alpha

chromosome 21 open
C21orf7
NM_020152
0932
1.55157
99.5819
1.55157
221211_s_at

reading frame 7

arachidonate 12-
ALOX12
NM_000697
0760
1.54212
50.2344
1.54212
207206_s_at

lipoxygenase

immunoglobulin heavy
IGHD
AJ275469
0314
0.637582
−65.6509
−1.56843
214973_x_at

constant delta

signal-regulatory protein
SIRPA
NM_004648
0827
0.815813
−62.6483
−1.22577
202896_s_at

alpha

talin 1
TLN1
NM_006289
0857
0.703842
−284.992
−1.42077
203254_s_at

versican
VCAN
R94644
0964
0.821433
−285.21
−1.21738
215646_s_at

leukocyte immunoglobulin-
LILRA4
AF041261
0110
0.699309
−21.5601
−1.42998
210313_at

like receptor, subfamily A

(with TM domain),

member 4

dual specificity
DUSP1
NM_004417
0823
0.742647
−870.146
−1.34654
201041_s_at

phosphatase 1

leukocyte immunoglobulin-
LILRA2
U82278
0994
0.798914
−260.133
−1.2517
211100_x_at

like receptor, subfamily A

(with TM domain),

member 2

leukocyte immunoglobulin-
LILRA2
U82276
0992
0.79042
−238.501
−1.26515
211101_x_at

like receptor, subfamily A

(with TM domain),

member 2

colony stimulating factor 3
CSF3R
NM_172313
0960
0.808882
−920.479
−1.23627
1553297_a_at

receptor (granulocyte)

immunoglobulin lambda
IGL@
D87021
0711
0.568492
−34.0245
−1.75904
216560_x_at

locus

opioid growth factor
OGFR
AF172449
0140
0.675188
−26.4472
−1.48107
211513_s_at

receptor

BCL2-associated
BAG1
NM_004323
0820
1.33534
836.698
1.33534
202387_at

athanogene

tetraspanin 5
TSPAN5
AF065389
0119
1.41793
336.467
1.41793
209890_at

platelet factor 4
PF4
NM_002619
0791
1.45302
929.754
1.45302
206390_x_at

(chemokine (C—X—C motif)

ligand 4)

Fc fragment of IgA,
FCAR
U56237
0986
0.692035
−10.089
−1.44501
211306_s_at

receptor for

transketolase (Wernicke-
TKT
BF696840
0656
0.825852
−541.902
−1.21087
208699_x_at

Korsakoff syndrome)

heterogeneous nuclear
HNRNPC
AA664258
0039
1.15573
239.689
1.15573
212626_x_at

ribonucleoprotein C

(C1/C2)

tumor necrosis factor
TNFRSF10C
NM_003841
0808
0.710572
−502.391
−1.40732
206222_at

receptor superfamily,

member 10c, decoy

without an intracellular

domain

clusterin
CLU
M25915
0732
1.56445
331.206
1.56445
208792_s_at

Interleukin 8
IL8
L34164
0723
0.606145
−44.8057
−1.64977
211650_x_at

chromosome Y open
CYorf15A
AW468885
0510
1.86697
28.7205
1.86697
236694_at

reading frame 15A

insulin-like growth factor 1
IGF1R
BF347362
0633
0.713503
−8.93807
−1.40154
243358_at

receptor

Immunoglobulin heavy
IGHG1
M24668
0731
0.640653
−24.0473
−1.56091
211633_x_at

constant gamma 1 (G1m

marker)

adducin 3 (gamma)
ADD3
AI763123
0262
1.10373
199.209
1.10373
201752_s_at

GM2 ganglioside activator
GM2A
M76477
0737
0.549282
−17.8258
−1.82056
209727_at

small EDRK-rich factor 2
SERF2
BE568651
0579
1.18189
762.518
1.18189
224625_x_at

neurofilament, light
NEFL
AL537457
0413
1.38097
8.81215
1.38097
221805_at

polypeptide 68 kDa

hypothetical protein
LOC284701
AL137733
0398
0.575711
−47.8667
−1.73698
234664_at

LOC284701

interferon regulatory factor 7
IRF7
NM_004030
0810
0.656921
−213.859
−1.52225
208436_s_at

CTD (carboxy-terminal
CTDSPL
NM_005808
0846
1.50567
31.4589
1.50567
201906_s_at

domain, RNA polymerase

II, polypeptide A) small

phosphatase-like

immunoglobulin heavy
IGHA1 ///
U92706
0997
0.654147
−45.8457
−1.52871
216557_x_at

constant alpha 1 ///
IGHG1 ///

immunoglobulin heavy
IGHG3 ///

constant gamma 1 (G1m
IGHM ///

marker) /// immunoglobulin
IGHV4-31

heavy constant gamma 3

(G3m marker) ///

immunoglobulin heavy

constant mu ///

immunoglobulin heavy

variable 4-31

calreticulin
CALR
NM_004343
0821
0.666427
−39.7641
−1.50054
200935_at

profilin 1
PFN1
NM_005022
0834
0.909933
−688.243
−1.09898
200634_at

GM2 ganglioside activator
GM2A
M76477
0737
0.760155
−51.1178
−1.31552
35820_at

Immunoglobulin heavy
IGHA1
AW519168
0517
0.696459
−66.6484
−1.43583
215118_s_at

constant alpha 1

BCL2-associated
BAG1
AF116273
0132
1.29366
745.959
1.29366
211475_s_at

athanogene

integrin, beta 2
ITGB2
NM_000211
0756
0.904719
−606.678
−1.10532
202803_s_at

(complement component 3

receptor 3 and 4 subunit)

integral membrane protein
ITM2B
AF092128
0126
0.920192
−904.73
−1.08673
217732_s_at

2B

myeloid cell leukemia
MCL1
AI275690
0180
0.920558
−557.764
−1.0863
200797_s_at

sequence 1 (BCL2-

related)

GNAS complex locus
GNAS
AA650558
0038
1.28011
328.574
1.28011
217673_x_at

tubulin, beta 1
TUBB1
N63244
0750
1.30121
525.72
1.30121
230690_at

ribosomal protein L23
RPL23
NM_000978
0767
1.38751
582.376
1.38751
200888_s_at

peroxiredoxin 6
PRDX6
BE869583
0604
1.29349
781.185
1.29349
200844_s_at

neurofilament, light
NEFL
BF055311
0613
1.33283
20.5017
1.33283
221916_at

polypeptide 68 kDa

immunoglobulin kappa
IGK@ /// IGKC
AW575927
0518
0.828408
−1002.05
−1.20713
224795_x_at

constant ///
/// IGKV1-5 ///

immunoglobulin kappa
IGKV2-24

variable 1-5 ///

immunoglobulin kappa

variable 2-24 ///

immunoglobulin kappa

locus

cystatin C (amyloid
CST3
NM_000099
0755
0.839452
−682.022
−1.19125
201360_at

angiopathy and cerebral

hemorrhage)

ribosomal protein L7
RPL7
NM_000971
0766
1.25494
1233.19
1.25494
200717_x_at

interferon induced
IFITM1
AA749101
0057
0.874523
−1026.24
−1.14348
214022_s_at

transmembrane protein 1

(9-27)

ribosomal protein L36a ///
LOC729362 ///
NM_021029
0933
1.40994
1319.28
1.40994
201406_at

similar to large subunit
RPL36A

ribosomal protein L36a

SUB1 homolog (S. cerevisiae)
SUB1
BE784583
0598
1.28695
310.449
1.28695
224586_x_at

guanylate kinase 1
GUK1
BC006249
0558
1.2612
828.435
1.2612
200075_s_at

Pre-B-cell colony
PBEF1
AA873350
0074
0.851427
−574.61
−1.1745
243296_at

enhancing factor 1

prostaglandin-
PTGS1
NM_000962
0764
1.30351
24.1075
1.30351
205127_at

endoperoxide synthase 1

(prostaglandin G/H

synthase and

cyclooxygenase)

F-box protein 7
FBXO7
NM_012179
0877
1.21038
1054.96
1.21038
201178_at

hemoglobin, alpha 1 ///
HBA1 /// HBA2
AF105974
0128
1.31542
1468.63
1.31542
209458_x_at

hemoglobin, alpha 2

hemoglobin, alpha 1
HBA1
BC005931
0555
1.32226
1497.18
1.32226
211745_x_at

immunoglobulin lambda
IGL@ /// IGLJ3
X57812
1008
0.781053
−974.535
−1.28032
214677_x_at

locus /// immunoglobulin
/// IGLV2-14 ///

lambda variable 4-3 ///
IGLV3-25 ///

immunoglobulin lambda
IGLV4-3

variable 3-25 ///

immunoglobulin lambda

variable 2-14 ///

immunoglobulin lambda

joining 3

major histocompatibility
HLA-G
M90686
0740
0.800128
−1437.74
−1.2498
211530_x_at

complex, class I, G

SUB1 homolog (S. cerevisiae)
SUB1
BG231551
0678
1.25347
405.331
1.25347
212857_x_at

chemokine (C—X3—C motif)
CX3CR1
U20350
0978
1.14315
339.788
1.14315
205898_at

receptor 1

metastasis associated
MALAT1
AF132202
0134
0.892637
−753.262
−1.12028
223940_x_at

lung adenocarcinoma

transcript 1 (non-protein

coding)

metastasis associated
MALAT1
BG534952
0699
1.12359
745.361
1.12359
224567_x_at

lung adenocarcinoma

transcript 1 (non-protein

coding)

tubulin, beta 2A
TUBB2A
NM_001069
0768
1.79577
548.832
1.79577
204141_at

solute carrier family 25,
SLC25A37
BG251467
0679
1.09794
685.472
1.09794
222529_at

member 37

solute carrier family 25,
SLC25A37
BG251467
0679
1.16922
684.917
1.16922
222528_s_at

member 37

GNAS complex locus
GNAS
NM_016592
0905
1.06718
381.104
1.06718
200981_x_at

metastasis associated
MALAT1
BE708432
0592
1.04778
706.89
1.04778
1558678_s_at

lung adenocarcinoma

transcript 1 (non-protein

coding)

TABLE 2A

t-Test
Fold Change

Log10

Known
Genbank
SEQ

p-Value
Signed

Mean

Fragment
Genes: Gene
Accession
ID
Sequence Clusters:
(MS vs
Magnitude (MS
FC
(Control

Name
Symbol
No.
NO.
Cluster Title
Control)
vs. Control)
Magnitude
Samples)

214847_s_at
GPSM3
BG111168
0671
“G-protein signalling
1.29E−11
1.82
1.82
2.2

modulator 3 (AGS3-like,

C. elegans)”

227510_x_at

AL037917
0369
Transcribed locus
1.41E−10
6.2
6.2
2.29

223578_x_at
MALAT1
AF113016
0131
Metastasis associated
1.55E−10
3.4
3.4
1.83

lung adenocarcinoma

transcript 1 (non-coding

RNA)

232431_at

AI934556
0302
“Glucocorticoid receptor
4.46E−10
−2.75
2.75
2.52

alpha mRNA, variant 3′

UTR”

219878_s_at
KLF13
NM_015995
0892
Kruppel-like factor 13
8.23E−10
13.42
13.42
0.4

214352_s_at
KRAS
BF673699
0652
V-Ki-ras2 Kirsten rat
1.04E−09
2.25
2.25
2.06

sarcoma viral oncogene

homolog

228582_x_at
MALAT1
AI475544
0211
Metastasis associated
1.06E−09
9.68
9.68
2.39

lung adenocarcinoma

transcript 1 (non-coding

RNA)

243981_at

AI763206
0263
Transcribed locus
1.42E−09
−2.43
2.43
2.5

201753_s_at
ADD3
NM_019903
0931
Adducin 3 (gamma)
1.95E−09
−1.85
1.85
3.16

211074_at
FOLR1
AF000381
0102
Folate receptor 1 (adult)
3.38E−09
2.39
2.39
2.16

225956_at
LOC153222
AL565238
0417
Adult retina protein
3.62E−09
−1.48
1.48
2.87

223161_at
KIAA1147
AA029331
0003
KIAA1147
4.65E−09
2.34
2.34
2.27

218389_s_at
APH1A
NM_016022
0894
Anterior pharynx defective
4.69E−09
1.51
1.51
2.26

1 homolog A (C. elegans)

236924_at
GLMN
AA814383
0065
“Glomulin, FKBP
7.55E−09
−2.5
2.5
2.05

associated protein”

226148_at
ZBTB44
AU144305
0422
Zinc finger and BTB
1.05E−08
−1.78
1.78
2.96

domain containing 44

219696_at
FLJ20054
NM_019049
0927
Hypothetical protein
1.10E−08
−1.47
1.47
2.18

FLJ20054

223940_x_at

AF132202
0134

1.32E−08
2.92
2.92
2.45

225889_at
AEBP2
BF475280
0639
AE binding protein 2
1.37E−08
−1.88
1.88
2.69

214697_s_at
ROD1
AW190873
0485
ROD1 regulator of
1.71E−08
2.27
2.27
1.9

differentiation 1 (S. pombe)

208610_s_at
SRRM2
AI655799
0233
Serine/arginine repetitive
2.18E−08
3.16
3.16
1.72

matrix 2

241751_at
OFD1
AW292752
0498
Oral-facial-digital
2.26E−08
−2.4
2.4
2.17

syndrome 1

204049_s_at
PHACTR2
NM_014721
0889
Phosphatase and actin
3.26E−08
−1.7
1.7
2.33

regulator 2

225377_at
C9orf86
BE783949
0597
Chromosome 9 open
3.78E−08
1.9
1.9
2.27

reading frame 86

225139_at
RBM35B
AW070424
0473
RNA binding motif protein
3.81E−08
−1.6
1.6
3

35B

216177_at
LOC391132
AW582267
0519
Similar to 60S ribosomal
3.88E−08
−1.88
1.88
2.19

protein L29 (P23)

242232_at

AI652864
0232

4.50E−08
2.15
2.15
1.7

200734_s_at
ARF3
BG341906
0689
ADP-ribosylation factor 3
4.57E−08
1.78
1.78
2.25

211716_x_at
ARHGDIA
BC005851
0554
Rho GDP dissociation
4.64E−08
1.66
1.66
2.62

inhibitor (GDI) alpha

215460_x_at
BRD1
AL080149
0380
Bromodomain containing 1
4.65E−08
−1.39
1.39
2.25

222576_s_at
EIF2C1
AW071829
0475
“Eukaryotic translation
4.71E−08
1.88
1.88
2.14

initiation factor 2C, 1”

230141_at
ARID4A
AI640594
0226
AT rich interactive domain
5.62E−08
−1.88
1.88
2.19

4A (RBP1-like)

227740_at
UHMK1
AW173222
0481
U2AF homology motif
5.74E−08
2.45
2.45
2.37

(UHM) kinase 1

204805_s_at
H1FX
NM_006026
0851
“H1 histone family,
6.56E−08
2.3
2.3
2.26

member X”

208624_s_at
EIF4G1
BE966878
0610
“Eukaryotic translation
6.81E−08
1.41
1.41
1.88

initiation factor 4 gamma,

1”

243612_at
NSD1
AL526448
0408
Nuclear receptor binding
7.09E−08
−2.61
2.61
2.19

SET domain protein 1

201167_x_at
ARHGDIA
D13989
0704
Rho GDP dissociation
7.24E−08
2.48
2.48
1.72

inhibitor (GDI) alpha

241786_at

AI380514
0198
Transcribed locus
7.33E−08
−2.3
2.3
2.61

238430_x_at
SLFN5
AI923675
0295
Schlafen family member 5
7.41E−08
2.67
2.67
2.57

202102_s_at
BRD4
BF718610
0657
Bromodomain containing 4
7.45E−08
1.54
1.54
2.32

201737_s_at
MARCH6
NM_005885
0847
Membrane-associated
8.45E−08
−1.77
1.77
2.53

ring finger (C3HC4) 6

229926_at

AI633738
0225
Transcribed locus
8.49E−08
−1.61
1.61
2.04

230961_at

BE856980
0603

9.10E−08
−2.05
2.05
2.07

201996_s_at
SPEN
AL524033
0406
“Spen homolog,
9.12E−08
2.59
2.59
1.55

transcriptional regulator

(Drosophila)”

231858_x_at
DKFZp761E198
BC004895
0552
DKFZp761E198 protein
9.89E−08
1.83
1.83
2.02

200608_s_at
RAD21
NM_006265
0855
RAD21 homolog (S. pombe)
9.99E−08
−1.44
1.44
2.61

201168_x_at
ARHGDIA
NM_004309
0818
Rho GDP dissociation
1.00E−07
1.81
1.81
2.37

inhibitor (GDI) alpha

224631_at
ZFP91
AA758013
0058
Zinc finger protein 91
1.00E−07
1.92
1.92
2.02

homolog (mouse)

225563_at
PAN3
AI970788
0309
PAN3 polyA specific
1.05E−07
−1.62
1.62
3.03

ribonuclease subunit

homolog (S. cerevisiae)

222133_s_at
PHF20L1
AK022280
0332
PHD finger protein 20-like 1
1.09E−07
−1.61
1.61
2.12

237768_x_at

AA825925
0066

1.10E−07
−2.29
2.29
2.57

208677_s_at
BSG
AL550657
0415
Basigin (Ok blood group)
1.16E−07
2.21
2.21
1.92

224572_s_at
IRF2BP2
BG485163
0697
Interferon regulatory factor
1.36E−07
2.35
2.35
2.63

2 binding protein 2

221899_at
PFAAP5
AI809961
0274
Phosphonoformate
1.37E−07
−1.92
1.92
2.5

immuno-associated

protein 5

224969_at
ATXN7L3
AL390158
0401
Ataxin 7-like 3
1.45E−07
1.65
1.65
2.32

229389_at
ATG16L2
AA741058
0050
ATG16 autophagy related
1.46E−07
3
3
2.32

16-like 2 (S. cerevisiae)

242134_at

AI733194
0247
Transcribed locus
1.50E−07
2.2
2.2
1.72

224676_at
TMED4
AI472339
0208
Transmembrane emp24
1.52E−07
2.09
2.09
2.45

protein transport domain

containing 4

224568_x_at
MALAT1
AW005982
0462
Metastasis associated
1.60E−07
3.14
3.14
2.28

lung adenocarcinoma

transcript 1 (non-coding

RNA)

218659_at
ASXL2
NM_018263
0923
Additional sex combs like
1.65E−07
−1.46
1.46
2.88

2 (Drosophila)

203497_at
PPARBP
NM_004774
0829
PPAR binding protein
1.68E−07
−1.57
1.57
2.4

204285_s_at
PMAIP1
AI857639
0288
Phorbol-12-myristate-13-
1.74E−07
2.56
2.56
1.82

acetate-induced protein 1

213015_at

BF448315
0638
“ARTC1 mRNA, complete
1.93E−07
2.51
2.51
1.95

sequence”

224567_x_at
MALAT1
BG534952
0699
Metastasis associated
1.95E−07
2.79
2.79
2.47

lung adenocarcinoma

transcript 1 (non-coding

RNA)

222790_s_at
RSBN1
AK022166
0330
Round spermatid basic
2.00E−07
−2.2
2.2
2.87

protein 1

207057_at
SLC16A7
NM_004731
0828
“Solute carrier family 16,
2.09E−07
4.01
4.01
1.41

member 7

(monocarboxylic acid

transporter 2)”

212852_s_at
TROVE2
AL538601
0414
“TROVE domain family,
2.09E−07
−1.44
1.44
2.61

member 2”

238761_at

BE645241
0581

2.13E−07
−2.49
2.49
2.86

214198_s_at
DGCR2
AU150824
0430
DiGeorge syndrome
2.16E−07
−1.66
1.66
2.25

critical region gene 2

202809_s_at
INTS3
NM_023015
0943
Integrator complex subunit 3
2.18E−07
−1.26
1.26
2.19

236072_at

N64578
0751
Transcribed locus
2.23E−07
−2.3
2.3
1.91

225827_at
EIF2C2
AI832074
0288
“Eukaryotic translation
2.28E−07
2.51
2.51
2.14

initiation factor 2C, 2”

241775_at

AW298119
0502
“CDNA FLJ26437 fis,
2.37E−07
−2.2
2.2
2.5

clone KDN02067”

215706_x_at
ZYX
BC002323
0543
Zyxin
2.42E−07
1.68
1.68
2.6

201730_s_at
TPR
BF110993
0619
Translocated promoter
2.44E−07
1.77
1.77
2.29

region (to activated MET

oncogene)

226447_at
ASH1L
BG290742
0687
“Ash1 (absent, small, or
2.55E−07
−1.52
1.52
2.6

homeotic)-like

(Drosophila)”

200623_s_at
CALM3
MM_005184
0836
“Calmodulin 3
2.82E−07
1.87
1.87
2.33

(phosphorylase kinase,

delta)”

215990_s_at
BCL6
S67779
0966
B-cell CLL/lymphoma 6
2.92E−07
1.96
1.96
1.8

(zinc finger protein 51)

212007_at
UBXD2
AI927512
0301
UBX domain containing 2
3.02E−07
1.5
1.5
2.05

225885_at
EEA1
AI336848
0183
Early endosome antigen 1
3.04E−07
−1.63
1.63
2.5

212629_s_at
PKN2
AI633689
0224
Protein kinase N2
3.06E−07
1.66
1.66
1.83

216971_s_at
PLEC1
Z54367
1015
“Plectin 1, intermediate
3.10E−07
3.34
3.34
1.55

filament binding protein

500 kDa”

225289_at
STAT3
AI139252
0174
Signal transducer and
3.15E−07
1.58
1.58
2.62

activator of transcription 3

(acute-phase response

factor)

217713_x_at

AA126763
0008

3.42E−07
−1.62
1.62
2.22

225361_x_at
FAM122B
AI348001
0187
Family with sequence
3.69E−07
−1.44
1.44
2.8

similarity 122B

242920_at

AW590838
0520

3.89E−07
−2.63
2.63
2.52

227754_at

AV700815
0447
“CDNA FLJ10417 fis,
3.93E−07
−2.01
2.01
2.24

clone NT2RP1000112”

226680_at

BF056303
0614
Transcribed locus
4.00E−07
−2.17
2.17
2.33

202157_s_at
CUGBP2
U69546
0989
“CUG triplet repeat, RNA
4.02E−07
−1.47
1.47
3.3

binding protein 2”

208988_at

BE675843
0589

4.05E−07
−1.46
1.46
2.28

222243_s_at
TOB2
AB051450
0094
“Transducer of ERBB2, 2”
4.21E−07
−1.35
1.35
2.03

217862_at

N24868
0746
Transcribed locus
4.42E−07
1.53
1.53
2.29

64486_at
CORO1B
AI341234
0185
“Coronin, actin binding
4.42E−07
1.38
1.38
2.35

protein, 1B”

230918_at

BE856598
0601

4.43E−07
−1.77
1.77
2.38

204978_at
SFRS16
NM_007056
0873
“Splicing factor,
4.48E−07
2.27
2.27
1.8

arginine/serine-rich 16”

232879_at
CRTC3
AK024981
0354
CREB regulated
4.61E−07
−2.01
2.01
1.96

transcription coactivator 3

235032_at
DNAJA5
BG112118
0672
DnaJ homology subfamily
4.73E−07
−1.89
1.89
2.4

A member 5

203591_s_at
CSF3R
NM_000760
0761
Colony stimulating factor 3
5.00E−07
2.01
2.01
2.16

receptor (granulocyte)

228098_s_at
MYLIP
AW292746
0497
Myosin regulatory light
5.00E−07
−1.57
1.57
3.02

chain interacting protein

234734_s_at
TNRC6A
AK025696
0358
Trinucleotide repeat
5.06E−07
1.67
1.67
2.26

containing 6A

244433_at

AI950023
0307

5.36E−07
−2.03
2.03
2.63

226641_at

AU157224
0438
“CDNA FLJ11570 fis,
5.42E−07
−1.56
1.56
2.93

clone HEMBA1003309”

222791_at
RSBN1
AK022166
0330
Round spermatid basic
5.54E−07
−2.12
2.12
3.08

protein 1

225706_at
GLCCI1
AI761989
0259
Glucocorticoid induced
5.60E−07
−1.86
1.86
3

transcript 1

243790_at
ZNF585A
AA203136
0015
Zinc finger protein 585A
5.73E−07
−2.21
2.21
2.19

244145_at

BG260337
0683

5.74E−07
−1.62
1.62
2.4

203751_x_at
JUND
AI762296
0260
Jun D proto-oncogene
5.89E−07
1.97
1.97
1.9

225216_at
CXorf39
AI590719
0220
Chromosome X open
5.91E−07
−1.37
1.37
2.62

reading frame 39

228853_at
“(LOC730432,
AI652546
0229
Serine/threonine/tyrosine
5.96E−07
−1.49
1.49
2.5

STYX)”

interacting protein

232909_s_at
“(BPTF,
AU146870
0426
“(Bromodomain PHD
6.00E−07
−1.58
1.58
2.89

LOC646043)”

finger transcription factor,

Similar to Enhancer of

bithorax CG32346-PB,

isoform B)”

36564_at
IBRDC3
W27419
0998
IBR domain containing 3
6.14E−07
1.89
1.89
2.03

200073_s_at
HNRPD
M94630
0742
“Heterogeneous nuclear
6.30E−07
−1.43
1.43
3.24

ribonucleoprotein D (AU-

rich element RNA binding

protein 1, 37 kDa)”

200808_s_at
ZYX
NM_003461
0804
Zyxin
6.30E−07
1.78
1.78
2.6

235125_x_at

AI078279
0167
Transcribed locus
6.45E−07
−2.67
2.67
2.17

226712_at

BF206389
0627
“CDNA: FLJ22100 fis,
6.45E−07
1.51
1.51
2.3

clone HEP17127”

208447_s_at
PRPS1
NM_002764
0795
Phosphoribosyl
6.64E−07
1.93
1.93
1.83

pyrophosphate synthetase 1

226426_at

BG149849
0674
Transcribed locus
6.67E−07
−1.5
1.5
2.66

239163_at
UBE2B
AW364833
0507
Ubiquitin-conjugating
6.80E−07
2.05
2.05
1.81

enzyme E2B (RAD6

homolog)

219426_at
EIF2C3
NM_024852
0949
“Eukaryotic translation
6.81E−07
1.65
1.65
1.64

initiation factor 2C, 3”

235341_at
LOC144871
AL119957
0387
Hypothetical protein
7.43E−07
1.78
1.78
2.3

LOC144871

242243_at
TMF1
AI767435
0264
TATA element modulatory
7.88E−07
−2.26
2.26
2.01

factor 1

201236_s_at
BTG2
NM_006763
0870
“BTG family, member 2”
8.07E−07
1.55
1.55
2.45

202577_s_at
DDX19A
BC005162
0553
DEAD (Asp-Glu-Ala-As)
8.20E−07
−1.44
1.44
2.07

box polypeptide 19A

227772_at

AV700849
0448

9.74E−07
−1.72
1.72
2.33

229897_at
ZNF641
BF195808
0626
Zinc finger protein 641
9.75E−07
1.86
1.86
2.15

218566_s_at
CHORDC1
NM_012124
0876
Cysteine and histidine-rich
9.81E−07
−1.61
1.61
2.33

domain (CHORD)-

containing 1

203839_s_at
TNK2
NM_005781
0845
“Tyrosine kinase, non-
9.95E−07
2.11
2.11
1.63

receptor, 2”

204361_s_at
SKAP2
AB014486
0085
Src kinase associated
1.02E−06
−1.79
1.79
2.09

phosphoprotein 2

224250_s_at
SECISBP2
BC001189
0541
SECIS binding protein 2
1.02E−06
1.74
1.74
2.57

225350_s_at
ZYG11B
AV701229
0449
Zyg-11 homolog B (C. elegans)
1.03E−06
−1.54
1.54
2.83

204516_at

BG390306
0692
Transcribed locus
1.05E−06
−2.17
2.17
2.56

225620_at
RAB35
AL534848
0412
“RAB35, member RAS
1.05E−06
1.56
1.56
2.27

oncogene family”

226965_at
FAM116A
BF438017
0636
“(Family with sequence
1.07E−06
−1.53
1.53
2.91

similarity 116, member A,

Transcribed locus)”

239808_at

AI084489
0169
Transcribed locus
1.08E−06
−1.87
1.87
2.47

227428_at
GABPA
BE876628
0605
“GA binding protein
1.20E−06
−1.53
1.53
2.52

transcription factor, alpha

subunit 60 kDa”

218595_s_at
“(HEATR1,
NM_018072
0921
“Lectin, galactoside-
1.20E−06
−1.43
1.43
2.3

LGALS8)”

binding, soluble, 8

(galectin 8)”

222266_at
C19orf2
BF796940
0661
Chromosome 19 open
1.23E−06
−1.72
1.72
2.17

reading frame 2

239597_at

AA993566
0080

1.23E−06
2.33
2.33
2.06

203415_at
PDCD6
NM_013232
0879
Programmed cell death 6
1.23E−06
1.36
1.36
2.2

208866_at

BF510713
0642
CDNA clone
1.23E−06
−1.59
1.59
2.2

IMAGE: 4044084

212575_at
C19orf6
BF966155
0665
Chromosome 19 open
1.27E−06
12.23
12.23
0.38

reading frame 6

225176_at

AA156754
0013
“CDNA FLJ42149 fis,
1.30E−06
−1.4
1.4
2.96

clone THYMU1000692”

227223_at
RBM39
BE466173
0575
RNA binding motif protein
1.32E−06
2.29
2.29
2.22

39

41386_i_at
JMJD3
AB002344
0082
Jumonji domain
1.33E−06
1.7
1.7
2.35

containing 3

225995_x_at
“(FAM39DP,
BG178695
0675
“(CXYorf1-related protein,
1.38E−06
1.64
1.64
2.45

FLJ00038,

Family with sequence

LOC376475,

similarity 39, member D

LOC727741)”

pseudogene)”

228328_at
KLHL28
AI982758
0311
Kelch-like 28 (Drosophila)
1.41E−06
−1.71
1.71
2.43

235409_at
MGA
AU149225
0429
MAX gene associated
1.41E−06
2.4
2.4
1.89

200649_at
NUCB1
BC002356
0544
Nucleobindin 1
1.42E−06
1.85
1.85
2.2

232615_at

AA632758
0034
Transcribed locus
1.43E−06
−2.01
2.01
3.06

205882_x_at
ADD3
AI818488
0278
Adducin 3 (gamma)
1.44E−06
−1.46
1.46
3.28

228496_s_at
CRIM1
AW243081
0489
Cysteine rich
1.44E−06
−2.14
2.14
2.18

transmembrane BMP

regulator 1 (chordin-like)

209189_at
FOS
BC004490
0549
V-fos FBJ murine
1.50E−06
3.42
3.42
2.61

osteosarcoma viral

oncogene homolog

239233_at
KIAA1212
AA744613
0053
KIAA1212
1.53E−06
−2.29
2.29
1.4

224308_s_at
INTS2
AL136800
0393
Integrator complex subunit 2
1.61E−06
−1.98
1.98
1.98

208705_s_at
EIF5
BG481972
0696
Eukaryotic translation
1.62E−06
1.3
1.3
2.56

initiation factor 5

218607_s_at
SDAD1
NM_018115
0922
SDA1 domain containing 1
1.63E−06
1.52
1.52
2.24

200041_s_at
BAT1
NM_004640
0826
HLA-B associated
1.71E−06
1.29
1.29
2.94

transcript 1

202850_at
ABCD3
NM_002858
0796
“ATP-binding cassette,
1.71E−06
−1.56
1.56
2.3

sub-family D (ALD),

member 3”

224562_at
“(LOC644739,
AK025566
0357
“(Similar to Wiskott-
1.73E−06
1.76
1.76
2.94

LOC647909,

Aldrich syndrome protein

WASF2)”

family member 4 (WASP-

family protein member 4),

WAS protein family,

member 2)”

222644_s_at
GLT25D1
AI924150
0296
Glycosyltransferase 25
1.80E−06
2.01
2.01
2.09

domain containing 1

212536_at
ATP11B
AB023173
0088
“ATPase, Class VI, type
1.81E−06
−1.52
1.52
2.17

11B”

215269_at
TMEM1
AI922538
0294
Transmembrane protein 1
1.82E−06
−1.96
1.96
2.01

243303_at

AA811657
0064

1.93E−06
−1.92
1.92
2.34

201991_s_at
KIF5B
BF223224
0630
Kinesin family member 5B
1.95E−06
−1.36
1.36
2.75

213327_s_at
USP12
AI820101
0280
Ubiquitin specific
1.97E−06
−1.58
1.58
1.97

peptidase 12

213882_at
TM2D1
AA012917
0001
TM2 domain containing 1
1.97E−06
−1.68
1.68
1.66

214715_x_at
ZNF160
AK024789
0348
Zinc finger protein 160
2.00E−06
−1.65
1.65
2.37

225845_at
ZBTB44
BG253884
0681
Zinc finger and BTB
2.01E−06
−1.68
1.68
2.81

domain containing 44

215529_x_at
DIP2A
AI590053
0219
DIP2 disco-interacting
2.01E−06
−1.99
1.99
1.89

protein 2 homolog A

(Drosophila)

242539_at
LOC730069
AW665509
0523
Similar to nuclear receptor
2.04E−06
−2.21
2.21
2.33

binding factor 2

203311_s_at
ARF6
M57763
0735
ADP-ribosylation factor 6
2.07E−06
1.9
1.9
2.23

205854_at
TULP3
AK024246
0342
Tubby like protein 3
2.08E−06
−1.57
1.57
1.79

212042_x_at
“(LOC653949,
BG389744
0691
Ribosomal protein L7
2.10E−06
−1.37
1.37
3.51

RPL7,

hCG_2015956,

hCG_31916)”

233369_at

AU146027
0424
“CDNA FLJ11835 fis,
2.23E−06
−1.78
1.78
2.42

clone HEMBA1006595”

212513_s_at
USP33
AB029020
0089
Ubiquitin specific
2.27E−06
−1.31
1.31
2.52

peptidase 33

218626_at
EIF4ENIF1
NM_019843
0930
Eukaryotic translation
2.30E−06
−1.33
1.33
2.1

initiation factor 4E nuclear

import factor 1

208246_x_at

NM_017618
0909

2.31E−06
−1.63
1.63
2.29

224559_at
MALAT1
AF001540
0104
Metastasis associated
2.36E−06
4.55
4.55
2.49

lung adenocarcinoma

transcript 1 (non-coding

RNA)

205312_at
SPI1
NM_003120
0798
Spleen focus forming virus
2.41E−06
2.77
2.77
1.91

(SFFV) proviral integration

oncogene spi1

213318_s_at
BAT3
BG028844
0669
HLA-B associated
2.45E−06
1.41
1.41
2.56

transcript 3

212099_at
RHOB
AI263909
0179
“Ras homolog gene
2.50E−06
2.36
2.36
2.32

family, member B”

223131_s_at
TRIM8
AI925572
0299
Tripartite motif-containing 8
2.51E−06
1.74
1.74
1.9

212487_at
GPATCH8
AI673812
0234
G patch domain
2.53E−06
2.33
2.33
1.57

containing 8

200011_s_at
ARF3
NM_001659
0775
ADP-ribosylation factor 3
2.55E−06
1.43
1.43
2.95

210543_s_at
“(LOC731751,
U34994
0981
“Protein kinase, DNA-
2.61E−06
−1.39
1.39
2.21

PRKDC)”

activated, catalytic

polypeptide”

217313_at

AC004692
0098

2.63E−06
−1.62
1.62
2.34

228106_at
C4orf30
AA031528
0004
Chromosome 4 open
2.66E−06
−1.57
1.57
2.42

reading frame 30

218043_s_at
AZI2
NM_022461
0940
5-azacytidine induced 2
2.67E−06
−2.08
2.08
1.89

203514_at
MAP3K3
BF971923
0666
Mitogen-activated protein
2.67E−06
−1.52
1.52
2.21

kinase kinase kinase 3

223295_s_at
LUC7L
BE049621
0566
LUC7-like (S. cerevisiae)
2.68E−06
−1.57
1.57
2.67

235469_at
MGC40405
AV744101
0457
Hypothetical protein
2.73E−06
−2.48
2.48
1.95

MGC40405

209440_at
PRPS1
BC001605
0542
Phosphoribosyl
2.77E−06
1.42
1.42
2.22

pyrophosphate synthetase 1

227039_at
AKAP13
AI674926
0235
A kinase (PRKA) anchor
2.82E−06
1.92
1.92
2.46

protein 13

218499_at
RP6-213H19.1
NM_016542
0904
Serine/threonine protein
2.94E−06
−1.52
1.52
2.53

kinase MST4

232440_at
ZDHHC13
AU155198
0433
“Zinc finger, DHHC-type
2.95E−06
−1.75
1.75
2.26

containing 13”

209727_at
GM2A
M76477
0737
GM2 ganglioside activator
2.97E−06
5.7
5.7
1.01

241891_at

T92908
0972

2.97E−06
−1.82
1.82
2.64

227525_at
GLCCI1
AA058770
0006
Glucocorticoid induced
3.10E−06
−1.75
1.75
2.66

transcript 1

228088_at

AI092265
0170
“CDNA FLJ31513 fis,
3.17E−06
−1.49
1.49
2.11

clone NT2RI1000127”

242362_at

AI797788
0269

3.17E−06
−2.27
2.27
2.69

34478_at
RAB11B
X79780
1009
“RAB11B, member RAS
3.23E−06
2.63
2.63
1.27

oncogene family”

223135_s_at
BBX
AL136769
0392
Bobby sox homolog
3.25E−06
1.41
1.41
2.47

(Drosophila)

225780_at
RSC1A1
AL565415
0418
“Regulatory solute carrier
3.26E−06
−1.59
1.59
2.5

protein, family 1, member

1”

211791_s_at
KCNAB2
AF044253
0112
“Potassium voltage-gated
3.27E−06
4.73
4.73
1.31

channel, shaker-related

subfamily, beta member

2”

204252_at
CDK2
M68520
0736
Cyclin-dependent kinase 2
3.29E−06
−1.38
1.38
2.06

202420_s_at
DHX9
NM_001357
0771
DEAH (Asp-Glu-Ala-His)
3.31E−06
−1.29
1.29
2.35

box polypeptide 9

223138_s_at
DHX36
AI937206
0304
DEAH (Asp-Glu-Ala-His)
3.31E−06
1.69
1.69
2.21

box polypeptide 36

240452_at
GSPT1
AA580082
0030
G1 to S phase transition 1
3.38E−06
−2.24
2.24
2.5

202082_s_at
SEC14L1
AV748469
0458
SEC14-like 1 (S. cerevisiae)
3.38E−06
1.72
1.72
1.74

213038_at
IBRDC3
AL031602
0365
IBR domain containing 3
3.63E−06
1.55
1.55
1.95

232038_at
C6orf170
AI052103
0162
Chromosome 6 open
3.76E−06
−2
2
1.73

reading frame 170

229036_at
TNRC6B
AI681177
0238
“(Transcribed locus,
3.80E−06
1.83
1.83
2.32

Trinucleotide repeat

containing 6B)”

229235_at

AI983432
0312
Transcribed locus
3.81E−06
−1.53
1.53
2.59

226412_at
C6orf111
N66397
0752
Chromosome 6 open
3.84E−06
−1.63
1.63
2.76

reading frame 111

212637_s_at
WWP1
AU155187
0432
WW domain containing E3
3.95E−06
−1.64
1.64
1.62

ubiquitin protein ligase 1

220296_at

NM_024564
0947

3.99E−06
−1.96
1.96
2

240695_at

AA876138
0075

4.03E−06
1.68
1.68
1.78

224759_s_at
C12orf23
AK001731
0320
Chromosome 12 open
4.20E−06
−1.63
1.63
2.48

reading frame 23

222794_x_at
PAPD1
AK022188
0331
PAP associated domain
4.32E−06
−1.41
1.41
2.51

containing 1

224974_at
SUDS3
AK024460
0344
Suppressor of defective
4.36E−06
−1.94
1.94
2.27

silencing 3 homolog (S. cerevisiae)

242650_at

AW298590
0503
Transcribed locus
4.42E−06
−2.21
2.21
1.84

212921_at
SMYD2
AF070592
0121
SET and MYND domain
4.45E−06
−1.74
1.74
1.88

containing 2

217717_s_at
YWHAB
BF246499
0631
“Tyrosine 3-
4.47E−06
1.58
1.58
2.51

monooxygenase/tryptophan

5-monooxygenase

activation protein, beta

polypeptide”

221419_s_at

NM_013307
0880

4.56E−06
2.08
2.08
2.03

204809_at
CLPX
NM_006660
0866
ClpX caseinolytic
4.61E−06
−1.37
1.37
1.99

peptidase X homolog (E. coli)

201409_s_at
PPP1CB
NM_002709
0794
“Protein phosphatase 1,
4.64E−06
−1.38
1.38
2.43

catalytic subunit, beta

isoform”

209829_at
C6orf32
AB002384
0083
Chromosome 6 open
4.67E−06
−1.61
1.61
2.89

reading frame 32

225761_at
PAPD4
AI434509
0203
PAP associated domain
4.74E−06
−1.42
1.42
2.78

containing 4

228471_at
ANKRD44
AA744636
0054
Ankyrin repeat domain 44
4.84E−06
−1.71
1.71
2.75

201526_at
ARF5
NM_001662
0776
ADP-ribosylation factor 5
4.87E−06
1.49
1.49
2.21

241435_at

AA702930
0044

5.03E−06
−2.16
2.16
3.23

227567_at
AMZ2
AL524467
0407
Archaemetzincins-2
5.11E−06
−1.69
1.69
2.53

209563_x_at
CALM1
BC000454
0537
“Calmodulin 1
5.22E−06
1.68
1.68
2.84

(phosphorylase kinase,

delta)”

242518_at

AA748423
0056

5.26E−06
1.6
1.6
1.87

239049_at

BF514509
0644

5.31E−06
−1.85
1.85
2.38

209024_s_at
SYNCRIP
AI472757
0209
“Synaptotagmin binding,
5.50E−06
1.48
1.48
2.14

cytoplasmic RNA

interacting protein”

211948_x_at
BAT2D1
BG261071
0685
BAT2 domain containing 1
5.57E−06
2.77
2.77
2.01

228446_at
KIAA2026
BF062203
0616
KIAA2026
5.67E−06
−1.44
1.44
2.53

229541_at

BE669703
0583
“CDNA FLJ38918 fis,
5.86E−06
1.96
1.96
1.97

clone NT2NE2010633”

237330_at

AA603494
0033
Transcribed locus
5.89E−06
−2.48
2.48
1.96

217842_at
LUC7L2
NM_016019
0893
LUC7-like 2 (S. cerevisiae)
5.90E−06
−1.51
1.51
1.79

201828_x_at
FAM127A
NM_003928
0809
“Family with sequence
5.96E−06
1.27
1.27
2.33

similarity 127, member A”

229366_at

BG149765
0673
Transcribed locus
5.98E−06
−1.33
1.33
2.34

201986_at
THRAP1
AB011165
0084
Thyroid hormone receptor
6.02E−06
−1.46
1.46
2.51

associated protein 1

202373_s_at
RAB3GAP2
AF255648
0148
RAB3 GTPase activating
6.03E−06
−1.34
1.34
2.46

protein subunit 2 (non-

catalytic)

241906_at

BF001773
0612

6.07E−06
−2.1
2.1
2.45

201318_s_at
“(MRCL3,
NM_006471
0863
“(Myosin regulatory light
6.16E−06
−1.33
1.33
3.25

MRLC2)”

chain MRCL3, Myosin

regulatory light chain

MRLC2)”

207941_s_at
RBM39
NM_004902
0830
RNA binding motif protein
6.17E−06
−1.34
1.34
2.85

39

229586_at
CHD9
AW300405
0505
Chromodomain helicase
6.33E−06
1.64
1.64
2.01

DNA binding protein 9

217336_at

AL118510
0385

6.34E−06
−1.68
1.68
2.28

209648_x_at
SOCS5
AL136896
0394
Suppressor of cytokine
6.36E−06
−1.86
1.86
1.59

signaling 5

226664_at
TBC1D20
AL121747
0388
“TBC1 domain family,
6.40E−06
1.39
1.39
2.3

member 20”

225786_at
LOC284702
AI440495
0204
Hypothetical protein
6.49E−06
−1.6
1.6
2.45

LOC284702

208635_x_at
NACA
BF976260
0667
Nascent-polypeptide-
6.53E−06
−1.24
1.24
3.71

associated complex alpha

polypeptide

223444_at
SENP7
AL136599
0391
SUMO1/sentrin specific
6.56E−06
−1.88
1.88
2.36

peptidase 7

208975_s_at
KPNB1
L38951
0725
Karyopherin (importin)
6.58E−06
−1.54
1.54
2.17

beta 1

208935_s_at
LGALS8
L78132
0727
“Lectin, galactoside-
6.59E−06
−1.66
1.66
2.18

binding, soluble, 8

(galectin 8)”

200847_s_at
TMEM66
NM_016127
0895
Transmembrane protein
6.65E−06
−1.29
1.29
3.1

66

218247_s_at
RKHD2
NM_016626
0906
Ring finger and KH
6.67E−06
−1.93
1.93
2.32

domain containing 2

227121_at

BF476076
0640
MRNA; cDNA
6.71E−06
−1.51
1.51
2.61

DKFZp586K1922 (from

clone DKFZp586K1922)

235984_at

AL036662
0367
Transcribed locus
6.72E−06
1.85
1.85
2

212069_s_at
KIAA0515
AK026025
0360
KIAA0515
6.72E−06
1.73
1.73
1.89

243649_at

AI678692
0236

6.73E−06
−1.82
1.82
2.15

238549_at

AI420611
0201
Transcribed locus
6.84E−06
−1.43
1.43
2.5

233093_s_at
BIRC6
AK023788
0339
Baculoviral IAP repeat-
6.88E−06
−1.25
1.25
2.93

containing 6 (apollon)

221749_at
YTHDF3
AU157915
0439
“YTH domain family,
6.98E−06
−1.61
1.61
2.37

member 3”

242726_at

BF221850
0629
Transcribed locus
7.03E−06
−2
2
2.11

242195_x_at
NUMBL
BE350811
0573
Numb homolog
7.11E−06
−1.48
1.48
2.77

(Drosophila)-like

204020_at
PURA
BF739943
0658
Purine-rich element
7.23E−06
−1.4
1.4
2.5

binding protein A

208694_at
PRKDC
U47077
0984
“Protein kinase, DNA-
7.38E−06
−1.5
1.5
2.12

activated, catalytic

polypeptide”

200047_s_at
YY1
NM_003403
0802
YY1 transcription factor
7.42E−06
−1.29
1.29
2.83

228097_at
MYLIP
AW292746
0497
Myosin regulatory light
7.43E−06
−1.57
1.57
2.55

chain interacting protein

213605_s_at

AL049987
0376
MRNA; cDNA
7.49E−06
−2.47
2.47
2.16

DKFZp564F112 (from

clone DKFZp564F112)

218259_at
MKL2
NM_014048
0881
MKL/myocardin-like 2
7.81E−06
−1.57
1.57
2.02

240338_at
LRAP
AI807341
0272
Leukocyte-derived
7.89E−06
−2.06
2.06
1.76

arginine aminopeptidase

226366_at
SHPRH
AI828221
0285
SNF2 histone linker PHD
7.99E−06
−1.32
1.32
2.24

RING helicase

218237_s_at
SLC38A1
NM_030674
0955
“Solute carrier family 38,
8.02E−06
−1.91
1.91
2.93

member 1”

201473_at
JUNB
NM_002229
0783
Jun B proto-oncogene
8.04E−06
1.97
1.97
2.54

226786_at
RFX1
BF507952
0641
“Regulatory factor X, 1
8.06E−06
1.46
1.46
2.56

(influences HLA class II

expression)”

214948_s_at

AL050136
0377
MRNA; cDNA
8.09E−06
−1.4
1.4
2.26

DKFZp586L141 (from

clone DKFZp586L141)

225672_at
GOLGA2
AL514295
0405
“Golgi autoantigen, golgin
8.22E−06
1.32
1.32
2.53

subfamily a, 2”

229787_s_at
OGT
AI742039
0251
O-linked N-
8.27E−06
−2.15
2.15
2.41

acetylglucosamine

(GlcNAc) transferase

(UDP-N-

acetylglucosamine:polypeptide-

N-

acetylglucosaminyl

transferase)

202253_s_at
DNM2
NM_004945
0832
Dynamin 2
8.34E−06
1.63
1.63
1.93

225564_at
SPATA13
AW269397
0493
Spermatogenesis
8.50E−06
−1.7
1.7
2.97

associated 13

218967_s_at
PTER
NM_030664
0954
Phosphotriesterase
8.54E−06
−1.53
1.53
2.11

related

217007_s_at
ADAM15
AK000667
0316
ADAM metallopeptidase
8.61E−06
4.58
4.58
0.88

domain 15 (metargidin)

228250_at
FNIP1
AW263086
0491
Folliculin interacting
8.65E−06
2.39
2.39
1.78

protein 1

212291_at
HIPK1
AI393355
0199
Homeodomain interacting
8.65E−06
1.96
1.96
2.07

protein kinase 1

203203_s_at
KRR1
NM_007043
0872
“KRR1, small subunit
8.67E−06
−1.64
1.64
1.93

(SSU) processome

component, homolog

(yeast)”

229470_at
FAM105B
AW451634
0509
“Family with sequence
8.88E−06
−1.53
1.53
2.41

similarity 105, member B”

224698_at
FAM62B
AB033054
0090
Family with sequence
8.90E−06
−1.58
1.58
2.83

similarity 62 (C2 domain

containing) member B

244061_at

AI510829
0213

8.91E−06
−2.35
2.35
2.44

204075_s_at
KIAA0562
NM_014704
0887
KIAA0562
9.05E−06
−2.13
2.13
1.39

217019_at

AL137162
0395

9.06E−06
−2.35
2.35
1.82

218600_at
LIMD2
NM_030576
0953
LIM domain containing 2
9.07E−06
1.85
1.85
2.01

213606_s_at
ARHGDIA
AI571798
0218
Rho GDP dissociation
9.08E−06
2.93
2.93
1.41

inhibitor (GDI) alpha

201260_s_at
SYPL1
NM_006754
0869
Synaptophysin-like 1
9.26E−06
−1.5
1.5
2.48

234340_at

AK021431
0324
“CDNA FLJ11369 fis,
9.44E−06
−1.75
1.75
1.7

clone HEMBA1000338”

207686_s_at
CASP8
NM_001228
0770
“Caspase 8, apoptosis-
9.51E−06
2.19
2.19
1.79

related cysteine

peptidase”

201332_s_at
STAT6
NM_003153
0799
“Signal transducer and
9.57E−06
1.49
1.49
2.01

activator of transcription 6,

interleukin-4 induced”

203388_at
ARRB2
NM_004313
0819
“Arrestin, beta 2”
9.59E−06
1.54
1.54
2.66

204275_at
SOLH
AI796687
0268
Small optic lobes homolog
9.61E−06
1.51
1.51
1.72

(Drosophila)

238057_at
USP45
AW195800
0487
Ubiquitin specific
9.61E−06
−2.28
2.28
1.91

peptidase 45

242352_at
NIPBL
AW272262
0494
Nipped-B homolog
9.63E−06
2.68
2.68
1.78

(Drosophila)

212846_at
RRP1B
AA811192
0063
KIAA0179
9.81E−06
−1.28
1.28
2.51

212090_at
GRINA
AL571424
0420
“Glutamate receptor,
9.90E−06
1.94
1.94
1.99

ionotropic, N-methyl D-

asparate-associated

protein 1 (glutamate

binding)”

227636_at
THAP5
BG500677
0698
THAP domain containing 5
9.92E−06
−1.73
1.73
2.29

209379_s_at
KIAA1128
AF241785
0147
KIAA1128
9.94E−06
−1.5
1.5
2.33

230180_at

AA521056
0025

9.99E−06
2.56
2.56
1.96

217489_s_at
IL6R
S72848
0968
Interleukin 6 receptor
1.01E−05
2.12
2.12
1.44

200014_s_at
“(HNRPC,
NM_004500
0824
Heterogeneous nuclear
1.03E−05
−1.21
1.21
2.71

hCG_1641229)”

ribonucleoprotein C

(C1/C2)

221628_s_at
N-PAC
AF326966
0155
Cytokine-like nuclear
1.03E−05
2.06
2.06
1.63

factor n-pac

214594_x_at
ATP8B1
BG252666
0680
“ATPase, Class I, type 8B,
1.05E−05
−2.44
2.44
2.17

member 1”

218528_s_at
RNF38
NM_022781
0941
Ring finger protein 38
1.05E−05
−1.27
1.27
2.49

223494_at
MGEA5
AF307332
0152
Meningioma expressed
1.08E−05
−1.49
1.49
3.22

antigen 5 (hyaluronidase)

234260_at

AL122039
0390
MRNA; cDNA
1.09E−05
−2.06
2.06
1.99

DKFZp434E0572 (from

clone DKFZp434E0572)

203104_at
CSF1R
NM_005211
0838
“Colony stimulating factor
1.09E−05
1.96
1.96
2.55

1 receptor, formerly

McDonough feline

sarcoma viral (v-fms)

oncogene homolog”

221755_at
EHBP1L1
BG334196
0688
EH domain binding protein
1.10E−05
1.88
1.88
1.68

1-like 1

200976_s_at
TAX1BP1
NM_006024
0850
Tax1 (human T-cell
1.11E−05
−1.26
1.26
2.84

leukemia virus type I)

binding protein 1

212297_at
ATP13A3
BF218804
0628
ATPase type 13A3
1.12E−05
−1.73
1.73
2

208841_s_at
G3BP2
AB014560
0086
GTPase activating protein
1.12E−05
−1.37
1.37
2.55

(SH3 domain) binding

protein 2

200632_s_at
NDRG1
NM_006096
0853
N-myc downstream
1.13E−05
1.38
1.38
2.35

regulated gene 1

215383_x_at
SPG21
AL137312
0397
“Spastic paraplegia 21,
1.13E−05
−1.61
1.61
2.29

maspardin (autosomal

recessive, Mast

syndrome)”

235493_at

AI927329
0300
Transcribed locus
1.15E−05
−1.86
1.86
2.33

236614_at
LOC729683
AW006288
0463
Hypothetical protein
1.15E−05
1.36
1.36
2.25

LOC729683

209273_s_at
ISCA1
BG387555
0690
Iron-sulfur cluster
1.16E−05
−1.44
1.44
2.16

assembly 1 homolog (S. cerevisiae)

227621_at
WTAP
BE464729
0574
Wilms tumor 1 associated
1.18E−05
−1.37
1.37
3.2

protein

225431_x_at
ACY1L2
BE779764
0596
Aminoacylase 1-like 2
1.18E−05
−2.17
2.17
2.43

235879_at

AI697540
0245
Transcribed locus
1.20E−05
−2.13
2.13
2.94

226825_s_at
TMEM165
AW665624
0524
Transmembrane protein
1.22E−05
1.67
1.67
2.76

165

218143_s_at
SCAMP2
NM_005697
0843
Secretory carrier
1.22E−05
1.46
1.46
2.38

membrane protein 2

203890_s_at
DAPK3
BF686824
0655
Death-associated protein
1.24E−05
1.7
1.7
1.41

kinase 3

208313_s_at
SF1
NM_004630
0825
Splicing factor 1
1.27E−05
1.4
1.4
2.67

211352_s_at
NCOA3
U80737
0991
Nuclear receptor
1.28E−05
1.88
1.88
1.74

coactivator 3

224579_at
SLC38A1
BF247552
0632
“Solute carrier family 38,
1.28E−05
−1.46
1.46
3.14

member 1”

201752_s_at
ADD3
AI763123
0262
Adducin 3 (gamma)
1.28E−05
−1.44
1.44
3.26

231747_at
CYSLTR1
NM_006639
0864
Cysteinyl leukotriene
1.30E−05
1.73
1.73
2.57

receptor 1

208319_s_at
RBM3
NM_006743
0868
“RNA binding motif
1.30E−05
−1.66
1.66
2.61

(RNP1, RRM) protein 3”

227159_at
GHDC
AI827015
0284
GH3 domain containing
1.33E−05
1.45
1.45
2.3

230387_at

AL038450
0371
Transcribed locus
1.33E−05
−1.75
1.75
2.34

TABLE 2B

Known
Genbank
SEQ

Mean Signal
Log10
Mean
Top 42

Fragment
Genes: Gene
Accession
ID
Sequence Clusters:
Control
Mean (MS
Signal MS
(FC

Name
Symbol
No.
NO.
Cluster Title
Samples
Samples)
Samples
Filtered)

214847_s_at
GPSM3
BG111168
0671
“G-protein signalling
158.4893192
2.46
288.4031503

modulator 3 (AGS3-like,

C. elegans)”

227510_x_at

AL037917
0369
Transcribed locus
194.98446
3.09
1230.268771
1

223578_x_at
MALAT1
AF113016
0131
Metastasis associated
67.60829754
2.36
229.0867653
2

lung adenocarcinoma

transcript 1 (non-coding

RNA)

232431_at

AI934556
0302
“Glucocorticoid receptor
331.1311215
2.08
120.2264435
3

alpha mRNA, variant 3′

UTR”

219878_s_at
KLF13
NM_015995
0892
Kruppel-like factor 13
2.511886432
1.53
33.88441561
4

214352_s_at
KRAS
BF673699
0652
V-Ki-ras2 Kirsten rat
114.8153621
2.41
257.0395783
5

sarcoma viral oncogene

homolog

228582_x_at
MALAT1
AI475544
0211
Metastasis associated
245.4708916
3.37
2344.228815
6

lung adenocarcinoma

transcript 1 (non-coding

RNA)

243981_at

AI763206
0263
Transcribed locus
316.227766
2.12
131.8256739
7

201753_s_at
ADD3
NM_019903
0931
Adducin 3 (gamma)
1445.439771
2.89
776.2471166

211074_at
FOLR1
AF000381
0102
Folate receptor 1 (adult)
144.5439771
2.54
346.7368505
8

225956_at
LOC153222
AL565238
0417
Adult retina protein
741.3102413
2.7
501.1872336

223161_at
KIAA1147
AA029331
0003
KIAA1147
186.2087137
2.63
426.5795188
9

218389_s_at
APH1A
NM_016022
0894
Anterior pharynx defective
181.9700859
2.44
275.4228703

1 homolog A (C. elegans)

236924_at
GLMN
AA814383
0065
“Glomulin, FKBP
112.2018454
1.66
45.70881896
10

associated protein”

226148_at
ZBTB44
AU144305
0422
Zinc finger and BTB
912.0108394
2.71
512.861384

domain containing 44

219696_at
FLJ20054
NM_019049
0927
Hypothetical protein
151.3561248
2.02
104.7128548

FLJ20054

223940_x_at

AF132202
0134

281.8382931
2.92
831.7637711
11

225889_at
AEBP2
BF475280
0639
AE binding protein 2
489.7788194
2.41
257.0395783

214697_s_at
ROD1
AW190873
0485
ROD1 regulator of
79.43282347
2.26
181.9700859
12

differentiation 1 (S. pombe)

208610_s_at
SRRM2
AI655799
0233
Serine/arginine repetitive
52.48074602
2.22
165.9586907
13

matrix 2

241751_at
OFD1
AW292752
0498
Oral-facial-digital
147.9108388
1.79
61.65950019
14

syndrome 1

204049_s_at
PHACTR2
NM_014721
0889
Phosphatase and actin
213.796209
2.1
125.8925412

regulator 2

225377_at
C9orf86
BE783949
0597
Chromosome 9 open
186.2087137
2.55
354.8133892

reading frame 86

225139_at
RBM35B
AW070424
0473
RNA binding motif protein
1000
2.8
630.9573445

35B

216177_at
LOC391132
AW582267
0519
Similar to 60S ribosomal
154.8816619
1.92
83.17637711

protein L29 (P23)

242232_at

AI652864
0232

50.11872336
2.03
107.1519305
15

200734_s_at
ARF3
BG341906
0689
ADP-ribosylation factor 3
177.827941
2.5
316.227766

211716_x_at
ARHGDIA
BC005851
0554
Rho GDP dissociation
416.8693835
2.84
691.8309709

inhibitor (GDI) alpha

215460_x_at
BRD1
AL080149
0380
Bromodomain containing 1
177.827941
2.11
128.8249552

222576_s_at
EIF2C1
AW071829
0475
“Eukaryotic translation
138.0384265
2.42
263.0267992

initiation factor 2C, 1”

230141_at
ARID4A
AI640594
0226
AT rich interactive domain
154.8816619
1.92
83.17637711

4A (RBP1-like)

227740_at
UHMK1
AW173222
0481
U2AF homology motif
234.4228815
2.76
575.4399373
16

(UHM) kinase 1

204805_s_at
H1FX
NM_006026
0851
“H1 histone family,
181.9700859
2.63
426.5795188
17

member X”

208624_s_at
EIF4G1
BE966878
0610
“Eukaryotic translation
75.8577575
2.03
107.1519305

initiation factor 4 gamma,

1”

243612_at
NSD1
AL526448
0408
Nuclear receptor binding
154.8816619
1.77
58.88436554
18

SET domain protein 1

201167_x_at
ARHGDIA
D13989
0704
Rho GDP dissociation
52.48074602
2.11
128.8249552
19

inhibitor (GDI) alpha

241786_at

AI380514
0198
Transcribed locus
407.3802778
2.25
177.827941
20

238430_x_at
SLFN5
AI923675
0295
Schlafen family member 5
371.5352291
3
1000
21

202102_s_at
BRD4
BF718610
0657
Bromodomain containing 4
208.9296131
2.51
323.5936569

201737_s_at
MARCH6
NM_005885
0847
Membrane-associated
338.8441561
2.28
190.5460718

ring finger (C3HC4) 6

229926_at

AI633738
0225
Transcribed locus
109.6478196
1.83
67.60829754

230961_at

BE856980
0603

117.4897555
1.76
57.54399373
22

201996_s_at
SPEN
AL524033
0406
“Spen homolog,
35.48133892
1.96
91.20108394
23

transcriptional regulator

(Drosophila)”

231858_x_at
DKFZp761E198
BC004895
0552
DKFZp761E198 protein
104.7128548
2.28
190.5460718

200608_s_at
RAD21
NM_006265
0855
RAD21 homolog (S. pombe)
407.3802778
2.45
281.8382931

201168_x_at
ARHGDIA
NM_004309
0818
Rho GDP dissociation
234.4228815
2.63
426.5795188

inhibitor (GDI) alpha

224631_at
ZFP91
AA758013
0058
Zinc finger protein 91
104.7128548
2.31
204.1737945

homolog (mouse)

225563_at
PAN3
AI970788
0309
PAN3 polyA specific
1071.519305
2.82
660.693448

ribonuclease subunit

homolog (S. cerevisiae)

222133_s_at
PHF20L1
AK022280
0332
PHD finger protein 20-like 1
131.8256739
1.91
81.28305162

237768_x_at

AA825925
0066

371.5352291
2.21
162.1810097
24

208677_s_at
BSG
AL550657
0415
Basigin (Ok blood group)
83.17637711
2.27
186.2087137
25

224572_s_at
IRF2BP2
BG485163
0697
Interferon regulatory factor
426.5795188
3
1000
26

2 binding protein 2

221899_at
PFAAP5
AI809961
0274
Phosphonoformate
316.227766
2.22
165.9586907

immuno-associated

protein 5

224969_at
ATXN7L3
AL390158
0401
Ataxin 7-like 3
208.9296131
2.54
346.7368505

229389_at
ATG16L2
AA741058
0050
ATG16 autophagy related
208.9296131
2.8
630.9573445
27

16-like 2 (S. cerevisiae)

242134_at

AI733194
0247
Transcribed locus
52.48074602
2.06
114.8153621
28

224676_at
TMED4
AI472339
0208
Transmembrane emp24
281.8382931
2.77
588.8436554
29

protein transport domain

containing 4

224568_x_at
MALAT1
AW005982
0462
Metastasis associated
190.5460718
2.78
602.5595861
30

lung adenocarcinoma

transcript 1 (non-coding

RNA)

218659_at
ASXL2
NM_018263
0923
Additional sex combs like
758.577575
2.72
524.8074602

2 (Drosophila)

203497_at
PPARBP
NM_004774
0829
PPAR binding protein
251.1886432
2.21
162.1810097

204285_s_at
PMAIP1
AI857639
0289
Phorbol-12-myristate-13-
66.0693448
2.23
169.8243652
31

acetate-induced protein 1

213015_at

BF448315
0638
“ARTC1 mRNA, complete
89.12509381
2.35
223.8721139
32

sequence”

224567_x_at
MALAT1
BG534952
0699
Metastasis associated
295.1209227
2.91
812.8305162
33

lung adenocarcinoma

transcript 1 (non-coding

RNA)

222790_s_at
RSBN1
AK022166
0330
Round spermatid basic
741.3102413
2.53
338.8441561
34

protein 1

207057_at
SLC16A7
NM_004731
0828
“Solute carrier family 16,
25.70395783
2.01
102.3292992
35

member 7

(monocarboxylic acid

transporter 2)”

212852_s_at
TROVE2
AL538601
0414
“TROVE domain family,
407.3802778
2.46
288.4031503

member 2”

238761_at

BE645241
0581

724.4359601
2.46
288.4031503
36

214198_s_at
DGCR2
AU150824
0430
DiGeorge syndrome
177.827941
2.03
107.1519305

critical region gene 2

202809_s_at
INTS3
NM_023015
0943
Integrator complex subunit 3
154.8816619
2.09
123.0268771

236072_at

N64578
0751
Transcribed locus
81.28305162
1.54
34.67368505
37

225827_at
EIF2C2
AI832074
0288
“Eukaryotic translation
138.0384265
2.54
346.7368505
38

initiation factor 2C, 2”

241775_at

AW298119
0502
“CDNA FLJ26437 fis,
316.227766
2.16
144.5439771
39

clone KDN02067”

215706_x_at
ZYX
BC002323
0543
Zyxin
398.1071706
2.83
676.0829754

201730_s_at
TPR
BF110993
0619
Translocated promoter
194.98446
2.54
346.7368505

region (to activated MET

oncogene)

226447_at
ASH1L
BG290742
0687
“Ash1 (absent, small, or
398.1071706
2.42
263.0267992

homeotic)-like

(Drosophila)”

200623_s_at
CALM3
NM_005184
0836
“Calmodulin 3
213.796209
2.6
398.1071706

(phosphorylase kinase,

delta)”

215990_s_at
BCL6
S67779
0966
B-cell CLL/lymphoma 6
63.09573445
2.1
125.8925412

(zinc finger protein 51)

212007_at
UBXD2
AI927512
0301
UBX domain containing 2
112.2018454
2.23
169.8243652

225885_at
EEA1
AI336848
0183
Early endosome antigen 1
316.227766
2.29
194.98446

212629_s_at
PKN2
AI633689
0224
Protein kinase N2
67.60829754
2.06
114.8153621

216971_s_at
PLEC1
Z54367
1015
“Plectin 1, intermediate
35.48133892
2.07
117.4897555
40

filament binding protein

500 kDa”

225289_at
STAT3
AI139252
0174
Signal transducer and
416.8693835
2.82
660.693448

activator of transcription 3

(acute-phase response

factor)

217713_x_at

AA126763
0008

165.9586907
2.01
102.3292992

225361_x_at
FAM122B
AI348001
0187
Family with sequence
630.9573445
2.64
436.5158322

similarity 122B

242920_at

AW590838
0520

331.1311215
2.1
125.8925412
41

227754_at

AV700815
0447
“CDNA FLJ10417 fis,
173.7800829
1.93
85.11380382
42

clone NT2RP1000112”

226680_at

BF056303
0614
Transcribed locus
213.796209
1.99
97.7237221

202157_s_at
CUGBP2
U69546
0989
“CUG triplet repeat, RNA
1995.262315
3.14
1380.384265

binding protein 2”

208988_at

BE675843
0589

190.5460718
2.11
128.8249552

222243_s_at
TOB2
AB051450
0094
“Transducer of ERBB2, 2”
107.1519305
1.9
79.43282347

217862_at

N24868
0746
Transcribed locus
194.98446
2.47
295.1209227

64486_at
CORO1B
AI341234
0185
“Coronin, actin binding
223.8721139
2.49
309.0295433

protein, 1B”

230918_at

BE856598
0601

239.8832919
2.14
138.0384265

204978_at
SFRS16
NM_007056
0873
“Splicing factor,
63.09573445
2.15
141.2537545

arginine/serine-rich 16”

232879_at
CRTC3
AK024981
0354
CREB regulated
91.20108394
1.65
44.66835922

transcription coactivator 3

235032_at
DNAJA5
BG112118
0672
DnaJ homology subfamily
251.1886432
2.13
134.8962883

A member 5

203591_s_at
CSF3R
NM_000760
0761
Colony stimulating factor 3
144.5439771
2.47
295.1209227

receptor (granulocyte)

228098_s_at
MYLIP
AW292746
0497
Myosin regulatory light
1047.128548
2.83
676.0829754

chain interacting protein

234734_s_at
TNRC6A
AK025696
0358
Trinucleotide repeat
181.9700859
2.48
301.995172

containing 6A

244433_at

AI950023
0307

426.5795188
2.32
208.9296131

226641_at

AU157224
0438
“CDNA FLJ11570 fis,
851.1380382
2.73
537.0317964

clone HEMBA1003309”

222791_at
RSBN1
AK022166
0330
Round spermatid basic
1202.264435
2.75
562.3413252

protein 1

225706_at
GLCCI1
AI761989
0259
Glucocorticoid induced
1000
2.73
537.0317964

transcript 1

243790_at
ZNF585A
AA203136
0015
Zinc finger protein 585A
154.8816619
1.85
70.79457844

244145_at

BG260337
0683

251.1886432
2.19
154.8816619

203751_x_at
JUND
AI762296
0260
Jun D proto-oncogene
79.43282347
2.19
154.8816619

225216_at
CXorf39
AI590719
0220
Chromosome X open
416.8693835
2.48
301.995172

reading frame 39

228853_at
“(LOC730432,
AI652546
0229
Serine/threonine/tyrosine
316.227766
2.33
213.796209

STYX)”

interacting protein

232909_s_at
“(BPTF,
AU146870
0426
“(Bromodomain PHD
776.2471166
2.69
489.7788194

LOC646043)”

finger transcription factor,

Similar to Enhancer of

bithorax CG32346-PB,

isoform B)”

36564_at
IBRDC3
W27419
0998
IBR domain containing 3
107.1519305
2.31
204.1737945

200073_s_at
HNRPD
M94630
0742
“Heterogeneous nuclear
1737.800829
3.08
1202.264435

ribonucleoprotein D (AU-

rich element RNA binding

protein 1, 37 kDa)”

200808_s_at
ZYX
NM_003461
0804
Zyxin
398.1071706
2.85
707.9457844

235125_x_at

AI078279
0167
Transcribed locus
147.9108388
1.75
56.23413252

226712_at

BF206389
0627
“CDNA: FLJ22100 fis,
199.5262315
2.48
301.995172

clone HEP17127”

208447_s_at
PRPS1
NM_002764
0795
Phosphoribosyl
67.60829754
2.12
131.8256739

pyrophosphate synthetase 1

226426_at

BG149849
0674
Transcribed locus
457.0881896
2.49
309.0295433

239163_at
UBE2B
AW364833
0507
Ubiquitin-conjugating
64.5654229
2.13
134.8962883

enzyme E2B (RAD6

homolog)

219426_at
EIF2C3
NM_024852
0949
“Eukaryotic translation
43.65158322
1.86
72.44359601

initiation factor 2C, 3”

235341_at
LOC144871
AL119957
0387
Hypothetical protein
199.5262315
2.55
354.8133892

LOC144871

242243_at
TMF1
AI767435
0264
TATA element modulatory
102.3292992
1.66
45.70881896

factor 1

201236_s_at
BTG2
NM_006763
0870
“BTG family, member 2”
281.8382931
2.63
426.5795188

202577_s_at
DDX19A
BC005162
0553
DEAD (Asp-Glu-Ala-As)
117.4897555
1.91
81.28305162

box polypeptide 19A

227772_at

AV700849
0448

213.796209
2.09
123.0268771

229897_at
ZNF641
BF195808
0626
Zinc finger protein 641
141.2537545
2.42
263.0267992

218566_s_at
CHORDC1
NM_012124
0876
Cysteine and histidine-rich
213.796209
2.12
131.8256739

domain (CHORD)-

containing 1

203839_s_at
TNK2
NM_005781
0845
“Tyrosine kinase, non-
42.65795188
1.96
91.20108394

receptor, 2”

204361_s_at
SKAP2
AB014486
0085
Src kinase associated
123.0268771
1.84
69.18309709

phosphoprotein 2

224250_s_at
SECISBP2
BC001189
0541
SECIS binding protein 2
371.5352291
2.81
645.654229

225350_s_at
ZYG11B
AV701229
0449
Zyg-11 homolog B (C. elegans)
676.0829754
2.64
436.5158322

204516_at

BG390306
0692
Transcribed locus
363.0780548
2.22
165.9586907

225620_at
RAB35
AL534848
0412
“RAB35, member RAS
186.2087137
2.47
295.1209227

oncogene family”

226965_at
FAM116A
BF438017
0636
“(Family with sequence
812.8305162
2.72
524.8074602

similarity 116, member A,

Transcribed locus)”

239808_at

AI084489
0169
Transcribed locus
295.1209227
2.2
158.4893192

227428_at
GABPA
BE876628
0605
“GA binding protein
331.1311215
2.33
213.796209

transcription factor, alpha

subunit 60 kDa”

218595_s_at
“(HEATR1,
NM_018072
0921
“Lectin, galactoside-
199.5262315
2.15
141.2537545

LGALS8)”

binding, soluble, 8

(galectin 8)”

222266_at
C19orf2
BF796940
0661
Chromosome 19 open
147.9108388
1.93
85.11380382

reading frame 2

239597_at

AA993566
0080

114.8153621
2.43
269.1534804

203415_at
PDCD6
NM_013232
0879
Programmed cell death 6
158.4893192
2.33
213.796209

208866_at

BF510713
0642
CDNA clone
158.4893192
2
100

IMAGE: 4044084

212575_at
C19orf6
BF966155
0665
Chromosome 19 open
2.398832919
1.47
29.51209227

reading frame 6

225176_at

AA156754
0013
“CDNA FLJ42149 fis,
912.0108394
2.81
645.654229

clone THYMU1000692”

227223_at
RBM39
BE466173
0575
RNA binding motif protein
165.9586907
2.58
380.1893963

39

41386_i_at
JMJD3
AB002344
0082
Jumonji domain
223.8721139
2.58
380.1893963

containing 3

225995_x_at
“(FAM39DP,
BG178695
0675
“(CXYorf1-related protein,
281.8382931
2.67
467.7351413

FLJ00038,

Family with sequence

LOC376475,

similarity 39, member D

LOC727741)”

pseudogene)”

228328_at
KLHL28
AI982758
0311
Kelch-like 28 (Drosophila)
269.1534804
2.2
158.4893192

235409_at
MGA
AU149225
0429
MAX gene associated
77.62471166
2.27
186.2087137

200649_at
NUCB1
BC002356
0544
Nucleobindin 1
158.4893192
2.46
288.4031503

232615_at

AA632758
0034
Transcribed locus
1148.153621
2.75
562.3413252

205882_x_at
ADD3
AI818488
0278
Adducin 3 (gamma)
1905.460718
3.11
1288.249552

228496_s_at
CRIM1
AW243081
0489
Cysteine rich
151.3561248
1.85
70.79457844

transmembrane BMP

regulator 1 (chordin-like)

209189_at
FOS
BC004490
0549
V-fos FBJ murine
407.3802778
3.14
1380.384265

osteosarcoma viral

oncogene homolog

239233_at
KIAA1212
AA744613
0053
KIAA1212
25.11886432
1.04
10.96478196

224308_s_at
INTS2
AL136800
0393
Integrator complex subunit 2
95.4992586
1.68
47.86300923

208705_s_at
EIF5
BG481972
0696
Eukaryotic translation
363.0780548
2.67
467.7351413

initiation factor 5

218607_s_at
SDAD1
NM_018115
0922
SDA1 domain containing 1
173.7800829
2.42
263.0267992

200041_s_at
BAT1
NM_004640
0826
HLA-B associated
870.96359
3.06
1148.153621

transcript 1

202850_at
ABCD3
NM_002858
0796
“ATP-binding cassette,
199.5262315
2.11
128.8249552

sub-family D (ALD),

member 3”

224562_at
“(LOC644739,
AK025566
0357
“(Similar to Wiskott-
870.96359
3.19
1548.816619

LOC647909,

Aldrich syndrome protein

WASF2)”

family member 4 (WASP-

family protein member 4),

WAS protein family,

member 2)”

222644_s_at
GLT25D1
AI924150
0296
Glycosyltransferase 25
123.0268771
2.39
245.4708916

domain containing 1

212536_at
ATP11B
AB023173
0088
“ATPase, Class VI, type
147.9108388
1.99
97.7237221

11B”

215269_at
TMEM1
AI922538
0294
Transmembrane protein 1
102.3292992
1.72
52.48074602

243303_at

AA811657
0064

218.7761624
2.06
114.8153621

201991_s_at
KIF5B
BF223224
0630
Kinesin family member 5B
562.3413252
2.62
416.8693835

213327_s_at
USP12
AI820101
0280
Ubiquitin specific
93.32543008
1.77
58.88436554

peptidase 12

213882_at
TM2D1
AA012917
0001
TM2 domain containing 1
45.70881896
1.43
26.91534804

214715_x_at
ZNF160
AK024789
0348
Zinc finger protein 160
234.4228815
2.15
141.2537545

225845_at
ZBTB44
BG253884
0681
Zinc finger and BTB
645.654229
2.58
380.1893963

domain containing 44

215529_x_at
DIP2A
AI590053
0219
DIP2 disco-interacting
77.62471166
1.59
38.9045145

protein 2 homolog A

(Drosophila)

242539_at
LOC730069
AW665509
0523
Similar to nuclear receptor
213.796209
1.99
97.7237221

binding factor 2

203311_s_at
ARF6
M57763
0735
ADP-ribosylation factor 6
169.8243652
2.51
323.5936569

205854_at
TULP3
AK024246
0342
Tubby like protein 3
61.65950019
1.59
38.9045145

212042_x_at
“(LOC653949,
BG389744
0691
Ribosomal protein L7
3235.936569
3.37
2344.228815

RPL7,

hCG_2015956,

hCG_31916)”

233369_at

AU146027
0424
“CDNA FLJ11835 fis,
263.0267992
2.17
147.9108388

clone HEMBA1006595”

212513_s_at
USP33
AB029020
0089
Ubiquitin specific
331.1311215
2.4
251.1886432

peptidase 33

218626_at
EIF4ENIF1
NM_019843
0930
Eukaryotic translation
125.8925412
1.98
95.4992586

initiation factor 4E nuclear

import factor 1

208246_x_at

NM_017618
0909

194.98446
2.08
120.2264435

224559_at
MALAT1
AF001540
0104
Metastasis associated
309.0295433
3.15
1412.537545

lung adenocarcinoma

transcript 1 (non-coding

RNA)

205312_at
SPI1
NM_003120
0798
Spleen focus forming virus
81.28305162
2.35
223.8721139

(SFFV) proviral integration

oncogene spi1

213318_s_at
BAT3
BG028844
0669
HLA-B associated
363.0780548
2.71
512.861384

transcript 3

212099_at
RHOB
AI263909
0179
“Ras homolog gene
208.9296131
2.7
501.1872336

family, member B”

223131_s_at
TRIM8
AI925572
0299
Tripartite motif-containing 8
79.43282347
2.15
141.2537545

212487_at
GPATCH8
AI673812
0234
G patch domain
37.15352291
1.94
87.096359

containing 8

200011_s_at
ARF3
NM_001659
0775
ADP-ribosylation factor 3
891.2509381
3.1
1258.925412

210543_s_at
“(LOC731751,
U34994
0981
“Protein kinase, DNA-
162.1810097
2.07
117.4897555

PRKDC)”

activated, catalytic

polypeptide”

217313_at

AC004692
0098

218.7761624
2.13
134.8962883

228106_at
C4orf30
AA031528
0004
Chromosome 4 open
263.0267992
2.22
165.9586907

reading frame 30

218043_s_at
AZI2
NM_022461
0940
5-azacytidine induced 2
77.62471166
1.57
37.15352291

203514_at
MAP3K3
BF971923
0666
Mitogen-activated protein
162.1810097
2.02
104.7128548

kinase kinase kinase 3

223295_s_at
LUC7L
BE049621
0566
LUC7-like (S. cerevisiae)
467.7351413
2.47
295.1209227

235469_at
MGC40405
AV744101
0457
Hypothetical protein
89.12509381
1.56
36.30780548

MGC40405

209440_at
PRPS1
BC001605
0542
Phosphoribosyl
165.9586907
2.37
234.4228815

pyrophosphate synthetase 1

227039_at
AKAP13
AI674926
0235
A kinase (PRKA) anchor
288.4031503
2.74
549.5408739

protein 13

218499_at
RP6-213H19.1
NM_016542
0904
Serine/threonine protein
338.8441561
2.34
218.7761624

kinase MST4

232440_at
ZDHHC13
AU155198
0433
“Zinc finger, DHHC-type
181.9700859
2.02
104.7128548

containing 13”

209727_at
GM2A
M76477
0737
GM2 ganglioside activator
10.23292992
1.77
58.88436554

241891_at

T92908
0972

436.5158322
2.38
239.8832919

227525_at
GLCCI1
AA058770
0006
Glucocorticoid induced
457.0881896
2.41
257.0395783

transcript 1

228088_at

AI092265
0170
“CDNA FLJ31513 fis,
128.8249552
1.94
87.096359

clone NT2RI1000127”

242362_at

AI797788
0269

489.7788194
2.33
213.796209

34478_at
RAB11B
X79780
1009
“RAB11B, member RAS
18.62087137
1.69
48.97788194

oncogene family”

223135_s_at
BBX
AL136769
0392
Bobby sox homolog
295.1209227
2.62
416.8693835

(Drosophila)

225780_at
RSC1A1
AL565415
0418
“Regulatory solute carrier
316.227766
2.3
199.5262315

protein, family 1, member

1”

211791_s_at
KCNAB2
AF044253
0112
“Potassium voltage-gated
20.41737945
1.98
95.4992586

channel, shaker-related

subfamily, beta member

2”

204252_at
CDK2
M68520
0736
Cyclin-dependent kinase 2
114.8153621
1.92
83.17637711

202420_s_at
DHX9
NM_001357
0771
DEAH (Asp-Glu-Ala-His)
223.8721139
2.24
173.7800829

box polypeptide 9

223138_s_at
DHX36
AI937206
0304
DEAH (Asp-Glu-Ala-His)
162.1810097
2.44
275.4228703

box polypeptide 36

240452_at
GSPT1
AA580082
0030
G1 to S phase transition 1
316.227766
2.15
141.2537545

202082_s_at
SEC14L1
AV748469
0458
SEC14-like 1 (S. cerevisiae)
54.95408739
1.98
95.4992586

213038_at
IBRDC3
AL031602
0365
IBR domain containing 3
89.12509381
2.14
138.0384265

232038_at
C6orf170
AI052103
0162
Chromosome 6 open
53.70317964
1.43
26.91534804

reading frame 170

229036_at
TNRC6B
AI681177
0238
“(Transcribed locus,
208.9296131
2.58
380.1893963

Trinucleotide repeat

containing 6B)”

229235_at

AI983432
0312
Transcribed locus
389.045145
2.41
257.0395783

226412_at
C6orf111
N66397
0752
Chromosome 6 open
575.4399373
2.54
346.7368505

reading frame 111

212637_s_at
WWP1
AU155187
0432
WW domain containing E3
41.68693835
1.4
25.11886432

ubiquitin protein ligase 1

220296_at

NM_024564
0947

100
1.71
51.2861384

240695_at

AA876138
0075

60.25595861
2.01
102.3292992

224759_s_at
C12orf23
AK001731
0320
Chromosome 12 open
301.995172
2.26
181.9700859

reading frame 23

222794_x_at
PAPD1
AK022188
0331
PAP associated domain
323.5936569
2.36
229.0867653

containing 1

224974_at
SUDS3
AK024460
0344
Suppressor of defective
186.2087137
1.98
95.4992586

silencing 3 homolog

(S. cerevisiae)

242650_at

AW298590
0503
Transcribed locus
69.18309709
1.5
31.6227766

212921_at
SMYD2
AF070592
0121
SET and MYND domain
75.8577575
1.64
43.65158322

containing 2

217717_s_at
YWHAB
BF246499
0631
“Tyrosine 3-
323.5936569
2.71
512.861384

monooxygenase/tryptophan

5-monooxygenase

activation protein, beta

polypeptide”

221419_s_at

NM_013307
0880

107.1519305
2.35
223.8721139

204809_at
CLPX
NM_006660
0866
ClpX caseinolytic
97.7237221
1.85
70.79457844

peptidase X homolog (E. coli)

201409_s_at
PPP1CB
NM_002709
0794
“Protein phosphatase 1,
269.1534804
2.29
194.98446

catalytic subunit, beta

isoform”

209829_at
C6orf32
AB002384
0083
Chromosome 6 open
776.2471166
2.68
478.6300923

reading frame 32

225761_at
PAPD4
AI434509
0203
PAP associated domain
602.5595861
2.63
426.5795188

containing 4

228471_at
ANKRD44
AA744636
0054
Ankyrin repeat domain 44
562.3413252
2.51
323.5936569

201526_at
ARF5
NM_001662
0776
ADP-ribosylation factor 5
162.1810097
2.39
245.4708916

241435_at

AA702930
0044

1698.243652
2.9
794.3282347

227567_at
AMZ2
AL524467
0407
Archaemetzincins-2
338.8441561
2.3
199.5262315

209563_x_at
CALM1
BC000454
0537
“Calmodulin 1
691.8309709
3.07
1174.897555

(phosphorylase kinase,

delta)”

242518_at

AA748423
0056

74.13102413
2.07
117.4897555

239049_at

BF514509
0644

239.8832919
2.12
131.8256739

209024_s_at
SYNCRIP
AI472757
0209
“Synaptotagmin binding,
138.0384265
2.31
204.1737945

cytoplasmic RNA

interacting protein”

211948_x_at
BAT2D1
BG261071
0685
BAT2 domain containing 1
102.3292992
2.45
281.8382931

228446_at
KIAA2026
BF062203
0616
KIAA2026
338.8441561
2.38
239.8832919

229541_at

BE669703
0583
“CDNA FLJ38918 fis,
93.32543008
2.27
186.2087137

clone NT2NE2010633”

237330_at

AA603494
0033
Transcribed locus
91.20108394
1.56
36.30780548

217842_at
LUC7L2
NM_016019
0893
LUC7-like 2 (S. cerevisiae)
61.65950019
1.61
40.73802778

201828_x_at
FAM127A
NM_003928
0809
“Family with sequence
213.796209
2.43
269.1534804

similarity 127, member A”

229366_at

BG149765
0673
Transcribed locus
218.7761624
2.22
165.9586907

201986_at
THRAP1
AB011165
0084
Thyroid hormone receptor
323.5936569
2.35
223.8721139

associated protein 1

202373_s_at
RAB3GAP2
AF255648
0148
RAB3 GTPase activating
288.4031503
2.33
213.796209

protein subunit 2 (non-

catalytic)

241906_at

BF001773
0612

281.8382931
2.13
134.8962883

201318_s_at
“(MRCL3,
NM_006471
0863
“(Myosin regulatory light
1778.27941
3.13
1348.962883

MRLC2)”

chain MRCL3, Myosin

regulatory light chain

MRLC2)”

207941_s_at
RBM39
NM_004902
0830
RNA binding motif protein
707.9457844
2.72
524.8074602

39

229586_at
CHD9
AW300405
0505
Chromodomain helicase
102.3292992
2.23
169.8243652

DNA binding protein 9

217336_at

AL118510
0385

190.5460718
2.06
114.8153621

209648_x_at
SOCS5
AL136896
0394
Suppressor of cytokine
38.9045145
1.32
20.89296131

signaling 5

226664_at
TBC1D20
AL121747
0388
“TBC1 domain family,
199.5262315
2.44
275.4228703

member 20”

225786_at
LOC284702
AI440495
0204
Hypothetical protein
281.8382931
2.25
177.827941

LOC284702

208635_x_at
NACA
BF976260
0667
Nascent-polypeptide-
5128.61384
3.62
4168.693835

associated complex alpha

polypeptide

223444_at
SENP7
AL136599
0391
SUMO1/sentrin specific
229.0867653
2.09
123.0268771

peptidase 7

208975_s_at
KPNB1
L38951
0725
Karyopherin (importin)
147.9108388
1.98
95.4992586

beta 1

208935_s_at
LGALS8
L78132
0727
“Lectin, galactoside-
151.3561248
1.96
91.20108394

binding, soluble, 8

(galectin 8)”

200847_s_at
TMEM66
NM_016127
0895
Transmembrane protein
1258.925412
2.99
977.237221

66

218247_s_at
RKHD2
NM_016626
0906
Ring finger and KH
208.9296131
2.04
109.6478196

domain containing 2

227121_at

BF476076
0640
MRNA; cDNA
407.3802778
2.43
269.1534804

DKFZp586K1922 (from

clone DKFZp586K1922)

235984_at

AL036662
0367
Transcribed locus
100
2.27
186.2087137

212069_s_at
KIAA0515
AK026025
0360
KIAA0515
77.62471166
2.13
134.8962883

243649_at

AI678692
0236

141.2537545
1.88
75.8577575

238549_at

AI420611
0201
Transcribed locus
316.227766
2.35
223.8721139

233093_s_at
BIRC6
AK023788
0339
Baculoviral IAP repeat-
851.1380382
2.83
676.0829754

containing 6 (apollon)

221749_at
YTHDF3
AU157915
0439
“YTH domain family,
234.4228815
2.16
144.5439771

member 3”

242726_at

BF221850
0629
Transcribed locus
128.8249552
1.81
64.5654229

242195_x_at
NUMBL
BE350811
0573
Numb homolog
588.8436554
2.6
398.1071706

(Drosophila)-like

204020_at
PURA
BF739943
0658
Purine-rich element
316.227766
2.36
229.0867653

binding protein A

208694_at
PRKDC
U47077
0984
“Protein kinase, DNA-
131.8256739
1.94
87.096359

activated, catalytic

polypeptide”

200047_s_at
YY1
NM_003403
0802
YY1 transcription factor
676.0829754
2.72
524.8074602

228097_at
MYLIP
AW292746
0497
Myosin regulatory light
354.8133892
2.35
223.8721139

chain interacting protein

213605_s_at

AL049987
0376
MRNA; cDNA
144.5439771
1.76
57.54399373

DKFZp564F112 (from

clone DKFZp564F112)

218259_at
MKL2
NM_014048
0881
MKL/myocardin-like 2
104.7128548
1.83
67.60829754

240338_at
LRAP
AI807341
0272
Leukocyte-derived
57.54399373
1.45
28.18382931

arginine aminopeptidase

226366_at
SHPRH
AI828221
0285
SNF2 histone linker PHD
173.7800829
2.12
131.8256739

RING helicase

218237_s_at
SLC38A1
NM_030674
0955
“Solute carrier family 38,
851.1380382
2.65
446.6835922

member 1”

201473_at
JUNB
NM_002229
0783
Jun B proto-oncogene
346.7368505
2.83
676.0829754

226786_at
RFX1
BF507952
0641
“Regulatory factor X, 1
363.0780548
2.72
524.8074602

(influences HLA class II

expression)”

214948_s_at

AL050136
0377
MRNA; cDNA
181.9700859
2.11
128.8249552

DKFZp586L141 (from

clone DKFZp586L141)

225672_at
GOLGA2
AL514295
0405
“Golgi autoantigen, golgin
338.8441561
2.65
446.6835922

subfamily a, 2”

229787_s_at
OGT
AI742039
0251
O-linked N-
257.0395783
2.08
120.2264435

acetylglucosamine

(GlcNAc) transferase

(UDP-N-

acetylglucosamine:polypeptide-

N-

acetylglucosaminyl

transferase)

202253_s_at
DNM2
NM_004945
0832
Dynamin 2
85.11380382
2.15
141.2537545

225564_at
SPATA13
AW269397
0493
Spermatogenesis
933.2543008
2.74
549.5408739

associated 13

218967_s_at
PTER
NM_030664
0954
Phosphotriesterase
128.8249552
1.93
85.11380382

related

217007_s_at
ADAM15
AK000667
0316
ADAM metallopeptidase
7.58577575
1.54
34.67368505

domain 15 (metargidin)

228250_at
FNIP1
AW263086
0491
Folliculin interacting
60.25595861
2.16
144.5439771

protein 1

212291_at
HIPK1
AI393355
0199
Homeodomain interacting
117.4897555
2.36
229.0867653

protein kinase 1

203203_s_at
KRR1
NM_007043
0872
“KRR1, small subunit
85.11380382
1.71
51.2861384

(SSU) processome

component, homolog

(yeast)”

229470_at
FAM105B
AW451634
0509
“Family with sequence
257.0395783
2.22
165.9586907

similarity 105, member B”

224698_at
FAM62B
AB033054
0090
Family with sequence
676.0829754
2.63
426.5795188

similarity 62 (C2 domain

containing) member B

244061_at

AI510829
0213

275.4228703
2.07
117.4897555

204075_s_at
KIAA0562
NM_014704
0887
KIAA0562
24.54708916
1.07
11.74897555

217019_at

AL137162
0395

66.0693448
1.45
28.18382931

218600_at
LIMD2
NM_030576
0953
LIM domain containing 2
102.3292992
2.28
190.5460718

213606_s_at
ARHGDIA
AI571798
0218
Rho GDP dissociation
25.70395783
1.88
75.8577575

inhibitor (GDI) alpha

201260_s_at
SYPL1
NM_006754
0869
Synaptophysin-like 1
301.995172
2.3
199.5262315

234340_at

AK021431
0324
“CDNA FLJ11369 fis,
50.11872336
1.45
28.18382931

clone HEMBA1000338”

207686_s_at
CASP8
NM_001228
0770
“Caspase 8, apoptosis-
61.65950019
2.13
134.8962883

related cysteine

peptidase”

201332_s_at
STAT6
NM_003153
0799
“Signal transducer and
102.3292992
2.18
151.3561248

activator of transcription 6,

interleukin-4 induced”

203388_at
ARRB2
NM_004313
0819
“Arrestin, beta 2”
457.0881896
2.85
707.9457844

204275_at
SOLH
AI796687
0268
Small optic lobes homolog
52.48074602
1.9
79.43282347

(Drosophila)

238057_at
USP45
AW195800
0487
Ubiquitin specific
81.28305162
1.55
35.48133892

peptidase 45

242352_at
NIPBL
AW272262
0494
Nipped-B homolog
60.25595861
2.21
162.1810097

(Drosophila)

212846_at
RRP1B
AA811192
0063
KIAA0179
323.5936569
2.41
257.0395783

212090_at
GRINA
AL571424
0420
“Glutamate receptor,
97.7237221
2.27
186.2087137

ionotropic, N-methyl D-

asparate-associated

protein 1 (glutamate

binding)”

227636_at
THAP5
BG500677
0698
THAP domain containing 5
194.98446
2.05
112.2018454

209379_s_at
KIAA1128
AF241785
0147
KIAA1128
213.796209
2.16
144.5439771

230180_at

AA521056
0025

91.20108394
2.37
234.4228815

217489_s_at
IL6R
S72848
0968
Interleukin 6 receptor
27.54228703
1.77
58.88436554

200014_s_at
“(HNRPC,
NM_004500
0824
Heterogeneous nuclear
512.861384
2.63
426.5795188

hCG_1641229)”

ribonucleoprotein C

(C1/C2)

221628_s_at
N-PAC
AF326966
0155
Cytokine-like nuclear
42.65795188
1.95
89.12509381

factor n-pac

214594_x_at
ATP8B1
BG252666
0680
“ATPase, Class I, type 8B,
147.9108388
1.79
61.65950019

member 1”

218528_s_at
RNF38
NM_022781
0941
Ring finger protein 38
309.0295433
2.38
239.8832919

223494_at
MGEA5
AF307332
0152
Meningioma expressed
1659.586907
3.05
1122.018454

antigen 5 (hyaluronidase)

234260_at

AL122039
0390
MRNA; cDNA
97.7237221
1.68
47.86300923

DKFZp434E0572 (from

clone DKFZp434E0572)

203104_at
CSF1R
NM_005211
0838
“Colony stimulating factor
354.8133892
2.84
691.8309709

1 receptor, formerly

McDonough feline

sarcoma viral (v-fms)

oncogene homolog”

221755_at
EHBP1L1
BG334196
0688
EH domain binding protein
47.86300923
1.95
89.12509381

1-like 1

200976_s_at
TAX1BP1
NM_006024
0850
Tax1 (human T-cell
691.8309709
2.74
549.5408739

leukemia virus type I)

binding protein 1

212297_at
ATP13A3
BF218804
0628
ATPase type 13A3
100
1.77
58.88436554

208841_s_at
G3BP2
AB014560
0086
GTPase activating protein
354.8133892
2.41
257.0395783

(SH3 domain) binding

protein 2

200632_s_at
NDRG1
NM_006096
0853
N-myc downstream
223.8721139
2.49
309.0295433

regulated gene 1

215383_x_at
SPG21
AL137312
0397
“Spastic paraplegia 21,
194.98446
2.08
120.2264435

maspardin (autosomal

recessive, Mast

syndrome)”

235493_at

AI927329
0300
Transcribed locus
213.796209
2.05
112.2018454

236614_at
LOC729683
AW006288
0463
Hypothetical protein
177.827941
2.38
239.8832919

LOC729683

209273_s_at
ISCA1
BG387555
0690
Iron-sulfur cluster
144.5439771
2
100

assembly 1 homolog

(S. cerevisiae)

227621_at
WTAP
BE464729
0574
Wilms tumor 1 associated
1584.893192
3.07
1174.897555

protein

225431_x_at
ACY1L2
BE779764
0596
Aminoacylase 1-like 2
269.1534804
2.09
123.0268771

235879_at

AI697540
0245
Transcribed locus
870.96359
2.61
407.3802778

226825_s_at
TMEM165
AW665624
0524
Transmembrane protein
575.4399373
2.98
954.992586

165

218143_s_at
SCAMP2
NM_005697
0843
Secretory carrier
239.8832919
2.54
346.7368505

membrane protein 2

203890_s_at
DAPK3
BF686824
0655
Death-associated protein
25.70395783
1.64
43.65158322

kinase 3

208313_s_at
SF1
NM_004630
0825
Splicing factor 1
467.7351413
2.82
660.693448

211352_s_at
NCOA3
U80737
0991
Nuclear receptor
54.95408739
2.02
104.7128548

coactivator 3

224579_at
SLC38A1
BF247552
0632
“Solute carrier family 38,
1380.384265
2.98
954.992586

member 1”

201752_s_at
ADD3
AI763123
0262
Adducin 3 (gamma)
1819.700859
3.1
1258.925412

231747_at
CYSLTR1
NM_006639
0864
Cysteinyl leukotriene
371.5352291
2.81
645.654229

receptor 1

208319_s_at
RBM3
NM_006743
0868
“RNA binding motif
407.3802778
2.39
245.4708916

(RNP1, RRM) protein 3”

227159_at
GHDC
AI827015
0284
GH3 domain containing
199.5262315
2.47
295.1209227

230387_at

AL038450
0371
Transcribed locus
218.7761624
2.1
125.8925412

TABLE 3

Fragment

Id
Name
SEQ ID NO.
Accession
Symbol
Gene Name

235101
204439_at
0871
NM_006820
IFI44L
interferon-induced protein 44-like

273089
242625_at
0483
AW189843
RSAD2
radical S-adenosyl methionine domain containing 2

244312
213797_at
0184
AI337069
RSAD2
radical S-adenosyl methionine domain containing 2

244967
214453_s_at
0860
NM_006417
IFI44
interferon-induced protein 44

272333
241869_at
0469
AW026509
APOL6
apolipoprotein L, 6

232750
202086_at
0786
NM_002462
MX1
myxovirus (influenza virus) resistance 1, interferon-inducible

protein p78 (mouse)

243517
212999_x_at
0496
AW276186
LOC650557
similar to HLA class II histocompatibility antigen, DQ(W1.1) beta

chain precursor (DQB1*0501)

259919
229450_at
0166
AI075407
IFIT3
interferon-induced protein with tetratricopeptide repeats 3

232809
202145_at
0785
NM_002346
LY6E
lymphocyte antigen 6 complex, locus E

236145
205483_s_at
0835
NM_005101
ISG15
ISG15 ubiquitin-like modifier

262204
231735_s_at
0882
NM_014086

243866
213350_at
0654
BF680255
RPS11
ribosomal protein S11

261953
231484_at
0202
AI424825

245632
215123_at
0375
AL049250

236794
206133_at
0908
NM_017523
XAF1
XIAP associated factor-1

257172
226702_at
0252
AI742057
LOC129607
hypothetical protein LOC129607

244573
214059_at
0565
BE049439
IFI44
interferon-induced protein 44

241463
210873_x_at
0973
U03891
APOBEC3A
apolipoprotein B mRNA editing enzyme, catalytic

polypeptide-like 3A

250106
219607_s_at
0945
NM_024021
MS4A4A
membrane-spanning 4-domains, subfamily A, member 4

257227
226757_at
0009
AA131041
IFIT2
interferon-induced protein with tetratricopeptide repeats 2

269075
238611_at
0292
AI906424

235409
204747_at
0772
NM_001549
IFIT3
interferon-induced protein with tetratricopeptide repeats 3

268477
238013_at
0634
BF347859

265621
235157_at
0501
AW297731

247363
216858_x_at
0379
AL080112

235077
204415_at
0942
NM_022873
IFI6
interferon, alpha-inducible protein 6

235634
204972_at
0907
NM_016817
OAS2
2′-5′-oligoadenylate synthetase 2, 69/71 kDa

263006
232537_x_at
0440
AU159474
MARK3
MAP/microtubule affinity-regulating kinase 3

272288
241824_at
0002
AA019641

264429
233964_at
0381
AL110135

268332
237868_x_at
0267
AI791828

247318
216813_at
0402
AL512728

245901
215392_at
0428
AU148154

272081
241617_x_at
0607
BE961949

245771
215262_at
0115
AF052160

118805
44673_at
0748
N53555
SIGLEC1
sialic acid binding Ig-like lectin 1, sialoadhesin

249851
219352_at
0915
NM_017912
HERC6
hect domain and RLD 6

245223
214712_at
0340
AK023827
RUNDC2B
RUN domain containing 2B

238391
207735_at
0913
NM_017831
RNF125
ring finger protein 125

236214
205552_s_at
0787
NM_002534
OAS1
2′,5′-oligoadenylate synthetase 1, 40/46 kDa

267022
236558_at
0043
AA699809

255042
224568_x_at
0462
AW005982
MALAT1
metastasis associated lung adenocarcinoma transcript 1 (non-

coding RNA)

273157
242693_at
0522
AW664859

233351
202687_s_at
0987
U57059
TNFSF10
tumor necrosis factor (ligand) superfamily, member 10

259086
228617_at
0011
AA142842
XAF1
XIAP associated factor-1

254068
223577_x_at
0068
AA827878
MALAT1
metastasis associated lung adenocarcinoma transcript 1 (non-

coding RNA)

268806
238342_at
0653
BF677084

273735
243271_at
0164
AI064690

258078
227609_at
0035
AA633203
EPSTI1
epithelial stromal interaction 1 (breast)

274457
243993_at
0020
AA436887

250190
219691_at
0911
NM_017654
SAMD9
sterile alpha motif domain containing 9

231959
201295_s_at
0620
BF111821
WSB1
WD repeat and SOCS box-containing 1

235195
204533_at
0774
NM_001565
CXCL10
chemokine (C—X—C motif) ligand 10

247438
216933_x_at
0967
S67788
APC
adenomatosis polyposis coli

244919
214405_at
1014
Z39557

249708
219209_at
0938
NM_022168
IFIH1
interferon induced with helicase C domain 1

258895
228426_at
0492
AW268886
CLEC2D
C-type lectin domain family 2, member D

255711
225239_at
0188
AI355441

241858
211300_s_at
0718
K03199
TP53
tumor protein p53 (Li-Fraumeni syndrome)

248900
218400_at
0854
NM_006187
OAS3
2′-5′-oligoadenylate synthetase 3, 100 kDa

260469
230000_at
0214
AI523817
RNF213
ring finger protein 213

254430
223940_x_at
0134
AF132202

250362
219863_at
0899
NM_016323
HERC5
hect domain and RLD 5

274878
244414_at
0175
AI148006

267794
237330_at
0033
AA603494

274252
243788_at
0060
AA789293

246704
216197_at
0328
AK021569
ATF7IP
activating transcription factor 7 interacting protein

263872
233406_at
0329
AK022100

241392
210797_s_at
0117
AF063612
OASL
2′-5′-oligoadenylate synthetase-like

239530
208900_s_at
0468
AW025108
TOP1
topoisomerase (DNA) I

266011
235547_at
0701
BG548427

270025
239561_at
0059
AA780679

263432
232964_at
0396
AL137266
LOC441257
hypothetical LOC441257

LOC442609
similar to Williams Beuren syndrome chromosome region 19

WBSCR19
Williams Beuren syndrome chromosome region 19

252807
222313_at
0528
AW972359

258499
228030_at
0161
AI041522
RBM6
RNA binding motif protein 6

252260
221765_at
0196
AI378044
UGCG
UDP-glucose ceramide glucosyltransferase

254110
223619_x_at
0133
AF119841
PECR
peroxisomal trans-2-enoyl-CoA reductase

265453
234989_at
0445
AV699657
TncRNA
trophoblast-derived noncoding RNA

252824
222330_at
0530
AW974995

242071
211530_x_at
0740
M90686
HLA-G
HLA-G histocompatibility antigen, class I, G

241567
210985_s_at
0116
AF056322
SP100
SP100 nuclear antigen

246107
215599_at
1012
X83300
GUSBP1
glucuronidase, beta pseudogene 1

LOC730390
similar to SMA4

SMA4
SMA4

275143
244679_at
0160
AI032730

244135
213620_s_at
0007
AA126728
ICAM2
intercellular adhesion molecule 2

274272
243808_at
0486
AW193531

234059
203397_s_at
0618
BF063271
GALNT3
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-

acetylgalactosaminyltransferase 3

(GalNAc-T3)

272396
241932_at
0165
AI073803

251201
220702_at
0925
NM_018616

246681
216174_at
0356
AK025343
HCRP1
hepatocellular carcinoma-related HCRP1

247070
216565_x_at
0389
AL121994

239595
208965_s_at
0682
BG256677
IFI16
interferon, gamma-inducible protein 16

246029
215521_at
0335
AK023029
PHC3
polyhomeotic homolog 3 (Drosophila)

272488
242024_at
0971
T90999

274112
243648_at
0017
AA280627
ZC3H11A
zinc finger CCCH-type containing 11A

264725
234260_at
0390
AL122039

271008
240544_at
0745
N23033

261578
231109_at
0962
R44974

244828
214314_s_at
0567
BE138647
EIF5B
eukaryotic translation initiation factor 5B

238481
207827_x_at
0724
L36675
SNCA
synuclein, alpha (non A4 component of amyloid precursor)

235128
204466_s_at
0684
BG260394
SNCA
synuclein, alpha (non A4 component of amyloid precursor)

265641
235177_at
0221
AI625022
FAM119A
family with sequence similarity 119, member A

233540
202876_s_at
0789
NM_002586
PBX2
pre-B-cell leukemia homeobox 2

263328
232860_x_at
0337
AK023732
RBM41
RNA binding motif protein 41

242745
212224_at
0759
NM_000689
ALDH1A1
aldehyde dehydrogenase 1 family, member A1

252300
221805_at
0413
AL537457
NEFL
neurofilament, light polypeptide 68 kDa

256137
225665_at
0173
AI129320
ZAK
sterile alpha motif and leucine zipper containing kinase AZK

252427
221932_s_at
0010
AA133341
GLRX5
glutaredoxin 5 homolog (S. cerevisiae)

258398
227929_at
0431
AU151342

257281
226811_at
0372
AL046017
FAM46C
family with sequence similarity 46, member C

239330
208700_s_at
0720
L12711
TKT
transketolase (Wernicke-Korsakoff syndrome)

257126
226656_at
0467
AW024741
CRTAP
cartilage associated protein

TABLE 4

Fragment Id
Name
SEQ ID NO.
Accession
Symbol
Gene Name

255042
224568_x_at
0462
AW005982
MALAT1
metastasis associated lung adenocarcinoma transcript 1 (non-coding

RNA)

254430
223940_x_at
0134
AF132202

269238
238774_at
0526
AW960454

272333
241869_at
0469
AW026509
APOL6
apolipoprotein L, 6

255041
224567_x_at
0699
BG534952
MALAT1
metastasis associated lung adenocarcinoma transcript 1 (non-coding

RNA)

257145
226675_s_at
1002
W80468
MALAT1
metastasis associated lung adenocarcinoma transcript 1 (non-coding

RNA)

238469
207815_at
0792
NM_002620
PF4V1
platelet factor 4 variant 1

247363
216858_x_at
0379
AL080112

272488
242024_at
0971
T90999

245632
215123_at
0375
AL049250

238391
207735_at
0913
NM_017831
RNF125
ring finger protein 125

239530
208900_s_at
0468
AW025108
TOP1
topoisomerase (DNA) I

265492
235028_at
0686
BG288330

235672
205010_at
0929
NM_019067
GNL3L
guanine nucleotide binding protein-like 3 (nucleolar)-like

268477
238013_at
0634
BF347859

240326
209703_x_at
0550
BC004492
METTL7A
methyltransferase like 7A

247318
216813_at
0402
AL512728

255711
225239_at
0188
AI355441

262881
232412_at
0347
AK024690

273238
242774_at
0242
AI684761
SYNE2
spectrin repeat containing, nuclear envelope 2

257532
227062_at
0434
AU155361
TncRNA
trophoblast-derived noncoding RNA

247055
216550_x_at
1010
X80821
ANKRD12
ankyrin repeat domain 12

241039
210426_x_at
0974
U04897
RORA
RAR-related orphan receptor A

263432
232964_at
0396
AL137266
LOC441257
hypothetical LOC441257

LOC442609
similar to Williams Beuren syndrome chromosome region 19

WBSCR19
Williams Beuren syndrome chromosome region 19

265852
235388_at
0700
BG538482
CHD9
chromodomain helicase DNA binding protein 9

268332
237868_x_at
0267
AI791828

264429
233964_at
0381
AL110135

137612
60815_at
0031
AA601208
LOC441257
hypothetical LOC441257

249611
219112_at
0900
NM_016340
RAPGEF6
Rap guanine nucleotide exchange factor (GEF) 6

272343
241879_at
0513
AW511222

245894
215385_at
0334
AK022473

251439
220940_at
0952
NM_025190
KIAA1641
KIAA1641

248290
217790_s_at
0874
NM_007107
SSR3
signal sequence receptor, gamma (translocon-associated protein

gamma)

232068
201404_x_at
0536
BC000268
PSMB2
proteasome (prosome, macropain) subunit, beta type, 2

246382
215874_at
0361
AK026820

247438
216933_x_at
0967
S67788
APC
adenomatosis polyposis coli

246107
215599_at
1012
X83300
GUSBP1
glucuronidase, beta pseudogene 1

LOC730390
similar to SMA4

SMA4
SMA4

270035
239571_at
0172
AI123399

260649
230180_at
0025
AA521056

273380
242916_at
0037
AA642477
CEP110
centrosomal protein 110 kDa

272196
241732_at
0643
BF513820

274821
244357_at
0970
T90760

244165
213650_at
0464
AW006438
GOLGA8A
golgi autoantigen, golgin subfamily a, 8A

245771
215262_at
0115
AF052160

252807
222313_at
0528
AW972359

274112
243648_at
0017
AA280627
ZC3H11A
zinc finger CCCH-type containing 11A

248204
217704_x_at
0281
AI820796
SUZ12P
suppressor of zeste 12 homolog pseudogene

241090
210479_s_at
0722
L14611
RORA
RAR-related orphan receptor A

245901
215392_at
0428
AU148154

241969
211424_x_at
0130
AF113007
METTL7A
methyltransferase like 7A

251085
220586_at
0951
NM_025134
CHD9
chromodomain helicase DNA binding protein 9

257461
226991_at
0023
AA489681
NFATC2
nuclear factor of activated T-cells, cytoplasmic, calcineurin-

dependent 2

268805
238341_at
0653
BF677084

255023
224549_x_at
0142
AF194537

243107
212587_s_at
0273
AI809341
PTPRC
protein tyrosine phosphatase, receptor type, C

270156
239692_at
0168
AI083578

262855
232386_at
0450
AV703288
VPS13C
vacuolar protein sorting 13 homolog C (S. cerevisiae)

262458
231989_s_at
0095
AC003007
SMG1
PI-3-kinase-related kinase SMG-1

252481
221986_s_at
0465
AW006750
KLHL24
kelch-like 24 (Drosophila)

238601
207953_at
0106
AF010144
AD7C-NTP
neuronal thread protein AD7c-NTP

269722
239258_at
0578
BE551407

274495
244031_at
0072
AA868193

273155
242691_at
0070
AA829017

241975
211430_s_at
0739
M87789
IGHG1
immunoglobulin heavy constant gamma 1 (G1m marker)

265453
234989_at
0445
AV699657
TncRNA
trophoblast-derived noncoding RNA

269566
239102_s_at
0500
AW293296

236769
206108_s_at
0856
NM_006275
SFRS6
splicing factor, arginine/serine-rich 6

274342
243878_at
0177
AI248610

242548
212027_at
0298
AI925305
RBM25
RNA binding motif protein 25

274316
243852_at
0308
AI963460

252824
222330_at
0530
AW974995

271008
240544_at
0745
N23033

272689
242225_at
0216
AI569482

245204
214693_x_at
0593
BE732345
LOC727908
hypothetical protein LOC727908

LOC728936
similar to CG10522-PA

LOC728980
hypothetical protein LOC728980

NBPF1
neuroblastoma breakpoint family, member 1

NBPF11
neuroblastoma breakpoint family, member 11

NBPF14
neuroblastoma breakpoint family, member 14

NBPF15
neuroblastoma breakpoint family, member 15

259656
229187_at
0159
AI026708
LOC283788
hypothetical protein LOC283788

246029
215521_at
0335
AK023029
PHC3
polyhomeotic homolog 3 (Drosophila)

272833
242369_x_at
0215
AI561070

239243
208610_s_at
0233
AI655799
SRRM2
serine/arginine repetitive matrix 2

243962
213446_s_at
0237
AI679073
IQGAP1
IQ motif containing GTPase activating protein 1

264616
234151_at
0346
AK024629

231152
AFFX-r2-
0729
M10098

Hs18SrRNA-

M_x_at

261953
231484_at
0202
AI424825

274272
243808_at
0486
AW193531

264020
233554_at
0157
AF339764

245521
215012_at
0423
AU144775

247997
217497_at
0521
AW613387

273343
242879_x_at
0305
AI939442

265524
235060_at
0373
AL047052
DKFZp547E087
hypothetical gene LOC283846

251975
221477_s_at
0647
BF575213
SOD2
superoxide dismutase 2, mitochondrial

248110
217610_at
0374
AL047879

244919
214405_at
1014
Z39557

252260
221765_at
0196
AI378044
UGCG
UDP-glucose ceramide glucosyltransferase

245538
215029_at
0383
AL117451

268267
237803_x_at
0021
AA455236

265068
234604_at
0350
AK024881

239886
209257_s_at
0660
BF795297
SMC3
structural maintenance of chromosomes 3

239489
208859_s_at
0227
AI650257
ATRX
alpha thalassemia/mental retardation syndrome X-linked (RAD54

LOC728849
homolog, S. cerevisiae)

similar to transcriptional regulator ATRX isoform 1

236256
205594_at
0890
NM_014897
ZNF652
zinc finger protein 652

242515
211993_at
0266
AI768512
WNK1
WNK lysine deficient protein kinase 1

268806
238342_at
0653
BF677084

254110
223619_x_at
0133
AF119841
PECR
peroxisomal trans-2-enoyl-CoA reductase

261578
231109_at
0962
R44974

263939
233473_x_at
0437
AU156202

266109
235645_at
0512
AW501507
ESCO1
establishment of cohesion 1 homolog 1 (S. cerevisiae)

266011
235547_at
0701
BG548427

246096
215588_x_at
0352
AK024958
RIOK3
RIO kinase 3 (yeast)

270605
240141_at
0617
BF062399

270275
239811_at
0664
BF954306

242529
212007_at
0301
AI927512
UBXD2
UBX domain containing 2

264725
234260_at
0390
AL122039

237626
206965_at
0898
NM_016285
KLF12
Kruppel-like factor 12

233810
203147_s_at
0608
BE962483
TRIM14
tripartite motif-containing 14

274340
243876_at
0062
AA806845

246372
215864_at
0355
AK025077

262735
232266_x_at
0343
AK024379
CDC2L5
cell division cycle 2-like 5 (cholinesterase-related cell division

controller)

267016
236552_at
0261
AI762475

265187
234723_x_at
0350
AK024881

239295
208663_s_at
0230
AI652848
TTC3
tetratricopeptide repeat domain 3

269628
239164_at
0586
BE674896

244440
213926_s_at
0254
AI742626
HRB
HIV-1 Rev binding protein

274283
243819_at
0425
AU146329

264641
234176_at
0349
AK024877

259455
228986_at
0531
AW978375
OSBPL8
oxysterol binding protein-like 8

239465
208835_s_at
0478
AW089673
CROP
cisplatin resistance-associated overexpressed protein

247068
216563_at
1010
X80821
ANKRD12
ankyrin repeat domain 12

246736
216229_x_at
1011
X81001
HCG2P7
HLA complex group 2 pseudogene 7

267786
237322_at
0293
AI914323
MIAT
myocardial infarction associated transcript (non-protein coding)

231366
200702_s_at
0693
BG421209
DDX24
DEAD (Asp-Glu-Ala-Asp) box polypeptide 24

262879
232410_at
0694
BG428861

243866
213350_at
0654
BF680255
RPS11
ribosomal protein S11

272288
241824_at
0002
AA019641

241872
211317_s_at
0111
AF041461
CFLAR
CASP8 and FADD-like apoptosis regulator

253530
223036_at
0708
D84430
FARSB
phenylalanyl-tRNA synthetase, beta subunit

240136
209508_x_at
0105
AF005774
CFLAR
CASP8 and FADD-like apoptosis regulator

251203
220704_at
0924
NM_018563

267085
236621_at
0444
AV683684

242600
212079_s_at
0046
AA715041
MLL
myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,

Drosophila)

238023
207365_x_at
0888
NM_014709
USP34
ubiquitin specific peptidase 34

238386
207730_x_at
0916
NM_017932

243314
212794_s_at
0319
AK001728
KIAA1033
KIAA1033

266926
236462_at
0051
AA742310

265631
235167_at
0611
BE972419

266723
236259_at
0635
BF433725
STK4
serine/threonine kinase 4

240866
210251_s_at
0129
AF112221
RUFY3
RUN and FYVE domain containing 3

245168
214657_s_at
0421
AU134977
TncRNA
trophoblast-derived noncoding RNA

269022
238558_at
0205
AI445833

273291
242827_x_at
0061
AA806368

264284
233819_s_at
0336
AK023499
ZNF294
zinc finger protein 294

246694
216187_x_at
0146
AF222691

236717
206056_x_at
1007
X52075
SPN
sialophorin (leukosialin, CD43)

52
AFFX-
0729
M10098

HUMRGE/

M10098_3_at

243544
213026_at
0609
BE965998
ATG12
ATG12 autophagy related 12 homolog (S. cerevisiae)

269715
239251_at
0527
AW963634

246037
215529_x_at
0219
AI590053
DIP2A
DIP2 disco-interacting protein 2 homolog A (Drosophila)

239887
209258_s_at
0193
AI373676
SMC3
structural maintenance of chromosomes 3

250837
220338_at
0920
NM_018037
RALGPS2
Ral GEF with PH domain and SH3 binding motif 2

244471
213957_s_at
0036
AA635523
CEP350
centrosomal protein 350 kDa

234292
203630_s_at
0859
NM_006348
COG5
component of oligomeric golgi complex 5

252480
221985_at
0465
AW006750
KLHL24
kelch-like 24 (Drosophila)

237212
206551_x_at
0910
NM_017644
KLHL24
kelch-like 24 (Drosophila)

247346
216841_s_at
1006
X15132
SOD2
superoxide dismutase 2, mitochondrial

232118
201454_s_at
0471
AW055008
NPEPPS
aminopeptidase puromycin sensitive

246112
215604_x_at
0338
AK023783

268974
238510_at
0055
AA744964
ZNF720
zinc finger protein 720

250731
220232_at
0950
NM_024906
SCD5
stearoyl-CoA desaturase 5

262594
232125_at
0427
AU147419

233043
202379_s_at
0190
AI361805
NKTR
natural killer-tumor recognition sequence

269738
239274_at
0454
AV729557

238885
208246_x_at
0909
NM_017618

271687
241223_x_at
0282
AI821721

231749
201085_s_at
0040
AA664291
SON
SON DNA binding protein

245712
215203_at
0508
AW438464

105867
39313_at
0081
AB002342
WNK1
WNK lysine deficient protein kinase 1

241338
210742_at
0118
AF064103
CDC14A
CDC14 cell division cycle 14 homolog A (S. cerevisiae)

248079
217579_x_at
0506
AW301806

258784
228315_at
0223
AI632728

262204
231735_s_at
0882
NM_014086

267022
236558_at
0043
AA699809

270061
239597_at
0080
AA993566

273495
243031_at
0753
N90377

266718
236254_at
0564
BE048857
VPS13B
vacuolar protein sorting 13 homolog B (yeast)

264495
234030_at
0125
AF090925

274975
244511_at
0446
AV700591

239717
209088_s_at
0969
T70262
UBN1
ubinuclein 1

236173
205511_at
0918
NM_017976

260682
230213_at
0569
BE220399
C19orf43
chromosome 19 open reading frame 43

253127
222633_at
0149
AF268193
TBL1XR1
transducin (beta)-like 1X-linked receptor 1

242364
211833_s_at
0977
U19599
BAX
BCL2-associated X protein

264377
233912_x_at
0327
AK021525

261710
231241_at
0511
AW469714
LOC645744
similar to PCAF associated factor 65 beta isoform b

272801
242337_at
0186
AI347128

248179
217679_x_at
0240
AI683552

260844
230375_at
0303
AI936531
C6orf111
chromosome 6 open reading frame 111

271706
241242_at
0577
BE503118

272920
242456_at
0079
AA931565
MRE11A
MRE11 meiotic recombination 11 homolog A (S. cerevisiae)

268417
237953_at
0171
AI092511

271732
241268_x_at
0306
AI939447

262856
232387_at
0359
AK025700
AP1GBP1
AP1 gamma subunit binding protein 1

248249
217749_at
0896
NM_016128
COPG
coatomer protein complex, subunit gamma

269075
238611_at
0292
AI906424

273157
242693_at
0522
AW664859

246444
215936_s_at
0318
AK001657
KIAA1033
KIAA1033

274291
243827_at
0370
AL038125

237453
206792_x_at
0763
NM_000923
PDE4C
phosphodiesterase 4C, cAMP-specific (phosphodiesterase E1 dunce

homolog, Drosophila)

269728
239264_at
0529
AW973078

275230
244766_at
0676
BG180003
LOC440354
PI-3-kinase-related kinase SMG-1 pseudogene

253746
223254_s_at
0077
AA887053
KIAA1333
KIAA1333

274016
243552_at
0466
AW008914

273410
242946_at
0499
AW293276
CD53
CD53 molecule

260055
229586_at
0504
AW300405
CHD9
chromodomain helicase DNA binding protein 9

239076
208442_s_at
0754
NM_000051
ATM||LOC651610

ataxia telangiectasia mutated (includes complementation groups A, C

and D)

similar to Serine-protein kinase ATM (Ataxia telangiectasia mutated)

(A-T, mutated)

275010
244546_at
0257
AI760495
CYCS
cytochrome c, somatic

260997
230528_s_at
0228
AI651726
MGC2752
hypothetical protein MGC2752

273598
243134_at
0484
AW190862
CHD2
chromodomain helicase DNA binding protein 2

265990
235526_at
0595
BE748802
C11orf58
chromosome 11 open reading frame 58

256821
226350_at
0435
AU155565
CHML
choroideremia-like (Rab escort protein 2)

240298
209675_s_at
0548
BC004242
HNRPUL1
heterogeneous nuclear ribonucleoprotein U-like 1

253682
223189_x_at
0476
AW082219
MLL5
myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog,

Drosophila)

262364
231895_at
0024
AA501453
SASS6
spindle assembly 6 homolog (C. elegans)

273868
243404_at
0029
AA553477

255450
224977_at
0386
AL119182
C6orf89
chromosome 6 open reading frame 89

254234
223743_s_at
0539
BC000756
MRPL4
mitochondrial ribosomal protein L4

232220
201556_s_at
0546
BC002737
VAMP2
vesicle-associated membrane protein 2 (synaptobrevin 2)

255483
225010_at
0351
AK024913
CCDC6
coiled-coil domain containing 6

261662
231193_s_at
0571
BE326569

263781
233314_at
0326
AK021487
PTEN
phosphatase and tensin homolog (mutated in multiple advanced

cancers 1)

233906
203243_s_at
0861
NM_006457
PDLIM5
PDZ and LIM domain 5

268932
238468_at
0016
AA214704
TNRC6B
trinucleotide repeat containing 6B

261248
230779_at
0649
BF594371
TNRC6B
trinucleotide repeat containing 6B

TABLE 5

Fragment Id
Name
SEQ ID NO.
Accession
Symbol
Gene Name

238391
207735_at
0913
NM_017831
RNF125
ring finger protein 125

239530
208900_s_at
0468
AW025108
TOP1
topoisomerase (DNA) I

243866
213350_at
0654
BF680255
RPS11
ribosomal protein S11

244919
214405_at
1014
Z39557

245632
215123_at
0375
AL049250

245771
215262_at
0115
AF052160

245901
215392_at
0428
AU148154

246029
215521_at
0335
AK023029
PHC3
polyhomeotic homolog 3 (Drosophila)

246107
215599_at
1012
X83300
GUSBP1
glucuronidase, beta pseudogene 1

LOC730390
similar to SMA4

SMA4
SMA4

247318
216813_at
0402
AL512728

247363
216858_x_at
0379
AL080112

247438
216933_x_at
0967
S67788
APC
adenomatosis polyposis coli

252260
221765_at
0196
AI378044
UGCG
UDP-glucose ceramide glucosyltransferase

252807
222313_at
0528
AW972359

252824
222330_at
0530
AW974995

254110
223619_x_at
0133
AF119841
PECR
peroxisomal trans-2-enoyl-CoA reductase

255042
224568_x_at
0462
AW005982
MALAT1
metastasis associated lung adenocarcinoma transcript 1 (non-

coding RNA)

255711
225239_at
0188
AI355441

261578
231109_at
0962
R44974

261953
231484_at
0202
AI424825

262204
231735_s_at
0882
NM_014086

264429
233964_at
0381
AL110135

264725
234260_at
0390
AL122039

265453
234989_at
0445
AV699657
TncRNA
trophoblast-derived noncoding RNA

266011
235547_at
0701
BG548427

267022
236558_at
0043
AA699809

268332
237868_x_at
0267
AI791828

268477
238013_at
0634
BF347859

268806
238342_at
0653
BF677084

269075
238611_at
0292
AI906424

271008
240544_at
0745
N23033

272288
241824_at
0002
AA019641

272333
241869_at
0469
AW026509
APOL6
apolipoprotein L, 6

273157
242693_at
0522
AW664859

274112
243648_at
0017
AA280627
ZC3H11A
zinc finger CCCH-type containing 11A

274272
243808_at
0486
AW193531

TABLE 6

SEQ ID NO
Accession No.

0001
AA012917.1

0002
AA019641.1

0003
AA029331.1

0004
AA031528.1

0005
AA045257.1

0006
AA058770.1

0007
AA126728.1

0008
AA126763.1

0009
AA131041.1

0010
AA133341.1

0011
AA142842.1

0012
AA149545.1

0013
AA156754.1

0014
AA194149.1

0015
AA203136.1

0016
AA214704.1

0017
AA280627.1

0018
AA359612.1

0019
AA416756.1

0020
AA436887.1

0021
AA455236.1

0022
AA468591.1

0023
AA489681.1

0024
AA501453.1

0025
AA521056.1

0026
AA521056.1

0027
AA530892.1

0028
AA530892.1

0030
AA580082.1

0031
AA601208.1

0032
AA602532.1

0033
AA603494.1

0034
AA632758.1

0035
AA633203.1

0036
AA635523.1

0037
AA642477.1

0038
AA650558.1

0039
AA664258.1

0040
AA664291.1

0041
AA679988.1

0042
AA699443.1

0043
AA699809.1

0044
AA702930.1

0045
AA703523.1

0046
AA715041.1

0047
AA721230.1

0048
AA732581.1

0049
AA732581.1

0050
AA741058.1

0051
AA742310.1

0052
AA743390.1

0053
AA744613.1

0054
AA744636.1

0055
AA744964.1

0056
AA748423.1

0057
AA749101.1

0058
AA758013.1

0059
AA780679.1

0060
AA789293.1

0061
AA806368.1

0062
AA806845.1

0063
AA811192.1

0064
AA811657.1

0065
AA814383.1

0066
AA825925.1

0067
AA827805.1

0068
AA827878.1

0069
AA828049.1

0070
AA829017.1

0071
AA843122.1

0072
AA868193.1

0073
AA872593.1

0074
AA873350.1

0075
AA876138.1

0076
AA877910.1

0077
AA887053.1

0078
AA916568.1

0079
AA931565.1

0080
AA993566.1

0081
AB002342.2

0084
AB011165.2

0085
AB014486.1

0086
AB014560.1

0087
AB019490.1

0088
AB023173.1

0090
AB033054.2

0091
AB035482.1

0092
AB043821.1

0093
AB044805.1

0094
AB051450.1

0095
AC003007.1

0096
AC003030.1

0097
AC004528.1

0098
AC004692.2

0099
AC004832.3

0102
AF000381.2

0103
AF000381.2

0104
AF001540.1

0106
AF010144.1

0107
AF021834.1

0108
AF022991.1

0109
AF037194.1

0110
AF041261.1

0111
AF041461.1

0112
AF044253.1

0113
AF044253.1

0114
AF047002.1

0116
AF056322.1

0117
AF063612.1

0118
AF064103.1

0119
AF065389.1

0121
AF070592.1

0122
AF070620.1

0123
AF078866.1

0124
AF086041.1

0126
AF092128.1

0129
AF112221.1

0130
AF113007.1

0131
AF113016.1

0132
AF116273.1

0133
AF119841.1

0134
AF132202.1

0135
AF132202.1

0136
AF141304.1

0137
AF143684.1

0138
AF159567.1

0139
AF165187.1

0140
AF172449.1

0141
AF176039.1

0142
AF194537.1

0143
AF194973.1

0144
AF212842.1

0146
AF222691.1

0147
AF241785.1

0148
AF255648.1

0149
AF268193.1

0150
AF274954.1

0151
AF302786.1

0152
AF307332.1

0153
AF315633.1

0154
AF317392.1

0155
AF326966.1

0156
AF327066.1

0157
AF339764.1

0159
AI026708.1

0161
AI041522.1

0162
AI052103.1

0163
AI057333.1

0164
AI064690.1

0165
AI073803.1

0166
AI075407.1

0167
AI078279.1

0168
AI083578.1

0169
AI084489.1

0170
AI092265.1

0171
AI092511.1

0172
AI123399.1

0173
AI129320.1

0174
AI139252.1

0175
AI148006.1

0176
AI241945.1

0177
AI248610.1

0178
AI249980.1

0179
AI263909.1

0181
AI283051.1

0182
AI332638.1

0183
AI336848.1

0184
AI337069.1

0185
AI341234.1

0186
AI347128.1

0187
AI348001.1

0188
AI355441.1

0190
AI361805.1

0191
AI363213.1

0192
AI369073.1

0193
AI373676.1

0194
AI377324.1

0195
AI378026.1

0196
AI378044.1

0197
AI379691.1

0198
AI380514.1

0199
AI393355.1

0200
AI418892.1

0201
AI420611.1

0202
AI424825.1

0203
AI434509.1

0204
AI440495.1

0205
AI445833.1

0206
AI458949.1

0207
AI459274.1

0208
AI472339.1

0209
AI472757.1

0210
AI473796.1

0211
AI475544.1

0212
AI492388.1

0213
AI510829.1

0214
AI523817.1

0215
AI561070.1

0216
AI569482.1

0217
AI571419.1

0218
AI571798.1

0219
AI590053.1

0220
AI590719.1

0221
AI625022.1

0222
AI632224.1

0223
AI632728.1

0225
AI633738.1

0228
AI651726.1

0229
AI652546.1

0230
AI652848.1

0231
AI652861.1

0232
AI652864.1

0233
AI655799.1

0234
AI673812.1

0235
AI674926.1

0236
AI678692.1

0238
AI681177.1

0239
AI681868.1

0240
AI683552.1

0241
AI683805.1

0242
AI684761.1

0243
AI688640.1

0244
AI689052.1

0245
AI697540.1

0246
AI732802.1

0247
AI733194.1

0248
AI738675.1

0249
AI738965.1

0250
AI741056.1

0251
AI742039.1

0252
AI742057.1

0253
AI742378.1

0254
AI742626.1

0255
AI753747.1

0256
AI754928.1

0257
AI760495.1

0259
AI761989.1

0260
AI762296.1

0261
AI762475.1

0262
AI763123.1

0263
AI763206.1

0264
AI767435.1

0265
AI767751.1

0266
AI768512.1

0267
AI791828.1

0268
AI796687.1

0269
AI797788.1

0270
AI805266.1

0271
AI806984.1

0272
AI807341.1

0274
AI809961.1

0275
AI810244.1

0276
AI814329.1

0277
AI814527.1

0278
AI818488.1

0279
AI819630.1

0281
AI820796.1

0282
AI821721.1

0284
AI827015.1

0285
AI828221.1

0286
AI829170.1

0287
AI829875.1

0288
AI832074.1

0289
AI857639.1

0290
AI860647.1

0291
AI871160.1

0292
AI906424.1

0293
AI914323.1

0295
AI923675.1

0296
AI924150.1

0297
AI924660.1

0298
AI925305.1

0299
AI925572.1

0300
AI927329.1

0301
AI927512.1

0302
AI934556.1

0303
AI936531.1

0304
AI937206.1

0305
AI939442.1

0306
AI939447.1

0307
AI950023.1

0308
AI963460.1

0309
AI970788.1

0310
AI979301.1

0311
AI982758.1

0312
AI983432.1

0313
AJ239383.1

0314
AJ275469.1

0315
AJ292969.1

0316
AK000667.1

0317
AK000677.1

0318
AK001657.1

0319
AK001728.1

0320
AK001731.1

0321
AK001734.1

0322
AK001816.1

0323
AK001822.1

0324
AK021431.1

0325
AK021457.1

0326
AK021487.1

0327
AK021525.1

0328
AK021569.1

0329
AK022100.1

0330
AK022166.1

0331
AK022188.1

0332
AK022280.1

0333
AK022303.1

0334
AK022473.1

0335
AK023029.1

0336
AK023499.1

0337
AK023732.1

0338
AK023783.1

0339
AK023788.1

0340
AK023827.1

0341
AK024072.1

0342
AK024246.1

0343
AK024379.1

0344
AK024460.1

0345
AK024482.1

0346
AK024629.1

0347
AK024690.1

0348
AK024789.1

0349
AK024877.1

0350
AK024881.1

0351
AK024913.1

0352
AK024958.1

0353
AK024960.1

0354
AK024981.1

0355
AK025077.1

0356
AK025343.1

0357
AK025566.1

0358
AK025696.1

0359
AK025700.1

0360
AK026025.1

0361
AK026820.1

0362
AK075503.1

0364
AK098125.1

0366
AL035687.13

0367
AL036662.1

0368
AL037339.1

0369
AL037917.2

0370
AL038125.1

0371
AL038450.1

0372
AL046017.1

0373
AL047052.1

0377
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METHODS, SYSTEMS, AND KITS FOR EVALUATING MULTIPLE SCLEROSIS

Information

Publication Number

Date Filed

Date Published

Inventors

Original Assignees

CPC

US Classifications

International Classifications

Abstract

Description

Claims

PRIORITY

PCT Information

Provisional Applications (1)