(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)

(19) World Intellectual Property Organization International Bureau

(43) International Publication Date (10) International Publication Number 8 November 2007 (08.11.2007) PCT WO 2007/127458 A2

(51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/68 (2006.01) kind of national protection available): AE, AG, AL, AM, AT,AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, (21) International Application Number: CN, CO, CR, CU, CZ, DE, DK, DM, DZ, EC, EE, EG, ES, PCT/US2007/010392 FT, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, (22) International Filing Date: 30 April 2007 (30.04.2007) LS, LT, LU, LY,MA, MD, ME, MG, MK, MN, MW, MX, (25) Filing Language: English MY, MZ, NA, NG, NI, NO, NZ, OM, PG, PH, PL, PT, RO, RS, RU, SC, SD, SE, SG, SK, SL, SM, SV, SY, TJ, TM, (26) Publication Language: English TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW

(30) Priority Data: (84) Designated States (unless otherwise indicated, for every 60/796,260 28 April 2006 (28.04.2006) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, (71) Applicant (for all designated States except US): NSABP ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, TM), FOUNDATION, INC. [US/US]; Four Allegheny Center, European (AT,BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, Fifth Floor, Pittsburgh, PA 15212 (US). FR, GB, GR, HU, IE, IS, IT, LT,LU, LV,MC, MT, NL, PL, (72) Inventors; and PT, RO, SE, SI, SK, TR), OAPI (BF, BJ, CF, CG, CI, CM, (75) Inventors/Applicants (for US only): PAIK, Soonmyung GA, GN, GQ, GW, ML, MR, NE, SN, TD, TG). [US/US]; 539 Gettysburg St., Pittsburgh, PA 15206 (US). POGUE-GEILE, Katherine, Lea [US/US]; 421 Rich- Published: land Place, Pittsburgh, PA 15208 (US). KIM, Chungyeui — without international search report and to be republished [KR/US]; 414 Staghorn Dr., Wexford, PA 15090 (US). upon receipt of that report

(74) Agent: HIBLER, David, W.; Vinson & Elkins L.L.P., For two-letter codes and other abbreviations, refer to the "G uid First City Tower, 100 Fannin St., Suite 2500, Houston, TX ance Notes on Codes and Abbreviations" appearing at the beg in 77002 (US). ning of each regular issue of the PCT Gazette.

(54) Title: METHODS OF WHOLE GENOME OR MICROARRAY EXPRESSION PROFILING USING NUCLEIC ACIDS PREPARED FROM FORMALIN FIXED PARAFFIN EMBEDDED TISSUE

(57) Abstract: The present invention provides novel methods for analyzing gene expression levels from fresh or aged (more than one year old) formalin-fixed, paraffin-embedded tissue ("FFPET") samples that comprise pre-hybridizing a labeled nucleic acid sample prepared from the formalin-fixed, paraffin-embedded tissue sample with a first microarray, hybridizing the unbound labeled nucleic acid sample with a second microarray, and detecting the labeled nucleic acid sample bound to the second microarray. The pre- hybridization step results in an increase in the specific gene signals in subsequent hybridizations with high density gene expression arrays. The first microarray used for the pre-hybridization step can be either a new or used microarray. Importantly, from a cost- savings perspective, the inventors determined that when the first microarray used for the pre-hybridization step is a previously used microarray, the results of the subsequent hybridization on a second microarray are nearly identical to the results obtained when the pre-hybridization was carried out using a new or previously unused microarray. TITLE OF THE INVENTION

Methods Of Whole Genome Or Microarray Expression Profiling Using Nucleic Acids Prepared From Formalin Fixed Paraffin Embedded Tissue.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Patent Application Serial Number 60/796,260, filed April 28, 2006, which is incorporated herein by reference in its entirety.

TECHNICAL FIELD

The present disclosure relates to methods for analyzing gene expression levels from fresh or aged formalin-fixed, paraffin-embedded tissue samples.

BACKGROUND ART

The use of gene expression profiling is not only prevalent in various research applications, but is rapidly becoming part of many therapeutic regimes. For example, in cancer research and treatment, it is often advantageous to examine gene expression levels in samples that represent many stages of tumor advancement, and patients representing a wide variety of demographics, as well as multiple other variables. One potentially exceptional source for this type of information comes in the form of formalin-fixed, paraffin-embedded tissue ("FFPET") samples, which are routinely created from biopsy specimens taken from patients undergoing a variety of therapeutic regimens for a variety of different diseases, and are usually associated with the corresponding clinical records. For example, tumor biopsy FFPET samples are often linked with cancer stage classification, patient survival, and treatment regime, thereby providing a potential wealth of information that can be cross-referenced and correlated with gene expression patterns. However, the poor quality and quantity of nucleic acids isolated from FFPET samples has led to their underutilization in gene expression profiling studies.

It has long been known that RNA can be purified and analyzed from FFPET samples (Rupp and Locker, Biotechniques 6:56-60, 1988). Although RNA isolated from FFPET samples is moderately to highly degraded and fragmented, techniques were developed for isolating RNA from FFPET samples that was suitable for analysis by reverse transcription polymerase chain reaction ("RT-PCR"; Stanta and Schneider, Biotechniques 11:304-308, 1991, Finke et al, Biotechniques 14:448-453, 1993). In addition to being degraded and fragmented, chemical modification of RNA by formalin restricts the binding of oligo-dT primers to the polyadenylic acid tail and impedes the efficiency of reverse transcription. Heating in high-pH Tris buffer can partially reverse the modification and allow the reverse transcription to proceed. Therefore, for relatively fresh paraffin blocks with high molecular weight RNA preserved in the specimen, usual method of cDNA synthesis can be applied. Initial attempts to quantitatively analyze RNA isolated from FFPET samples involved techniques such as dot blot hybridization or capillary electrophoresis (Stanta and Bonin, Biotechniques 24:271-276, 1998), which are not amenable to the analysis of large numbers of samples.

More recently, techniques were developed to analyze gene expression information from FFPET samples using quantitative RT-PCR ("qRT-PCR"; Godfrey et al, J. MoI. Diagn. 2:84-91, 2000, Specht et al, Am. J. Pathol. 158:419-429, 2001, Abrahamsen et al, J. MoI Diagn. 5:34- 41, 2003). These real-time assays allow for interrogation of the expression level of one gene at a time, but with great accuracy and a wide dynamic range. However gene-specific priming is required for cDNA synthesis for each gene target because oligo-dT primed reverse transcription is not feasible with the fragmented and chemically modified RNA. This means that the assay for each gene has to be done in a separate reaction tube from the point of cDNA synthesis onward. Therefore, robotic assisted pipetting is usually used to ensure highly accurate quantitative pipetting in order to obtain reproducible assay results. For this reason, when more than a handful of genes are to be assayed, fairly sophisticated laboratory facilities are required. Furthermore, the number of genes that can be interrogated in a single qRT-PCR experiment is limited (typically around 70 genes/2 days/sample or 1 gene/2 days/70 samples). Even with extensive automation, perhaps 200 genes in a single sample could be interrogated using qRT-PCR in one experiment. Additionally, qRT-PCR requires a relatively large quantity of RNA, on the order of 30 genes/µg of RNA, and is quite labor and material intensive. In addition, at least one study has shown that the absolute signal decreases significantly if the paraffin blocks have been stored for a long time, resulting in 100-fold reduction in signal if the paraffin block is 10 years old compared with freshly produced block (Cronin et al, Am. J. Pathol. 164:35-42, 2004), but careful normalization based on genes with minimal variation of expression level among different tumor samples can largely compensate for these differences in absolute signal.

The development of microarray based analyses to interrogate gene expression profiles has allowed large numbers of genes to be analyzed with less labor and materials, and would appear to be ideally suited for the analysis of FFPET samples. Unfortunately, the use of microarray based assays to interrogate gene expression profiles in FFPET samples has been of limited usefulness. Recent studies using microarray analysis of FFPET samples concluded FFPET tissues did not yield reproducible gene expression data (Karsten et al, Nucleic Acids Res. 30:e4, 2002), and another study suggested that chemical modification and fragmentation of mRNA extracted from FFPET is a barrier to applying known methods of generating labeled probes that are suitable for whole genome expression profiling in microarray based assays (Paik, Clin. Cancer Res. 12: 10 19S-1023 S, 2006).

Recently, a method for obtaining gene expression information specifically developed for use with FFPET samples (Bibikova et al., Am. J. Pathol, 165:1799-1807, 2004) was developed by Illumina, Incorporated (San Diego, CA). This method is referred to as cDNA-mediated annealing, selection, extension, and ligation ("DASL"), and is based on a bead array platform. DASL is reportedly useful for analyzing FFPET samples that have been stored for up to 12 years (Illumina, Incorporated, and Bibikova, supra). The DASL assay monitors gene expression by targeting sequences in cDNAs with sets of query oligonucleotides composed of multiple parts. In addition to gene-specific sequences, the query oligonucleotides contain primer landing sites for PCR amplification and an address sequence for hybridization to the universal bead array. Because randomers are used in the cDNA synthesis, and the query oligonucleotides target cDNA sequences only 50 nucleotides in length, partially degraded RNAs can be used in the assay. The DASL assay design resembles RT-PCR with highly multiplexed templates, but with only three PCR primers. Because the oligonucleotides all share the same primers, and the amplicons are of a uniform size, the amplification step is expected to maintain an unbiased representation of transcript abundance. This methodology, however, only allows for the interrogation of hundreds of pre-selected genes in a single experiment (the DASL assay can monitor expression of up to 1,536 sequence targets (512 genes at 3 probes per gene) in 50 ng of total RNA derived from FFPET samples; Bibikova et al., supra).

Another protocol for analysis of gene expression profiling in FFPET samples has recently been developed at Arcturus Bioscience, Incorporated (Mountain View, CA), and involves isolation and amplification of FFPET RNA using the Paradise™ Reagent System, which is currently sold by Molecular Devices Corporation (Sunnyvale, CA). The Paradise™ Reagent System has been used to perform gene expression profiling of microdissected human breast cancer cells from FFPET samples (Erlander et al., Abstract No. 498, American Society of Clinical Oncology Annual Meeting, Chicago IL, May 31, 2003 through June 3, 2003), and gene expression profiling of microdissected colonic epithelial cells from FFPET samples (Coudry etal, J. MoI. Diagn. 9:70-79, 2007). The Paradise™ Reagent System is also reported to have an RNA extraction protocol that allows optimized microarray performance when used together with arrays, for example the GeneChip® X3P Array, from Affymetrix, Incorporated (Santa Clara, CA) or Agilent Technologies, Incorporated (Santa Clara, CA). However, the Paradise™ Reagent System appears to be best suited to relatively fresh paraffin blocks with high molecular weight RNA preserved in the specimen, as opposed to paraffin blocks that are more than a few years old.

Recently a method was described utilizing the TransPlex™ Whole Transcriptome Amplification ("WTA") kit from Rubicon Genomics, Incorporated (Ann Arbor, MI) for whole genome expression analysis of old FFPET samples using the GeneChip® U133-X3P Array (Affymetrix, Incorporated) was described (Paik, supra). The TransPlex™ WTA kit bypasses the need for an intact polyadenylic acid tail by using random primers for cDNA synthesis, and adaptor-based PCR for cDNA amplification. However, this method utilized direct end-labeling of cDNA product from the TransPlex™ WTA kit, and was not reproducible when the number of samples analyzed was expanded.

Therefore, the need remains for a method of analyzing gene expression profiles from FFPET samples that can address multiple genes and samples in one experiment from aged (greater than one year old) FFPET samples.

DISCLOSURE OF THE INVENTION

The methods of the present invention overcome the shortcomings present in the art by providing protocols that can be used to obtain biological relevant information using high density gene-expression arrays and probes obtained from FFPET nucleic acids. In one embodiment, the present invention provides a method for analyzing gene expression levels from a FFPET sample, comprising pre-hybridizing a labeled nucleic acid sample prepared from the FFPET sample with a first microarray, hybridizing the unbound labeled nucleic acid sample with a second microarray, and detecting the labeled nucleic acid sample bound to the second microarray. In certain aspects of the invention, the first microarray is a previously used microarray, while in other aspects of the present invention, the first microarray is a previously unused or new microarray.

The pre-hybridization can utilize any nucleic acid-based microarray, including, but not limited to, commercially available microarrays, for example microarrays available from Affymetrix, Incoφ orated, Agilent Technologies, Incorporated, Illumina, Incorporated (San Diego, CA), GE Healthcare (Piscataway, NJ), NimbleGen Systems, Incorporated (Madison, WI), Invitrogen Corporation (Carlsbad, CA), and the like. While in certain aspects of the present invention the first microarray and the second microarray are from the same manufacturer or source, or even the same type of microarray from the same manufacturer or source, in other aspects the first microarray and the second microarray are from different manufacturers or sources. Thus, in certain embodiments of the present invention, the first microarray is an Affymetrix GeneChip ®, for example a human X3P array, human genome U 133 Plus 2.0 array, human genome U 133A 2.0 array, or a human cancer GIlO array, and the second microarray is the same type of Affymetrix GeneChip® or a different type of Affymetrix GeneChip®.

In certain aspects of the present invention, the FFPET sample comes from a human. However, in other embodiments of the present invention, the FFPET sample can come from any source, including, but not limited to, a laboratory animal, a companion animal, or a livestock animal, for example a non-human primate, such as a chimpanzee, gorilla, orangutan, gibbon, monkey, macaque, baboon, mangabey, colobus, langur, marmoset, or lemur, a mouse, rat, rabbit, guinea pig, hamster, cat dog, ferret, fish, cow, pig, sheep, goat, horse, donkey, chicken, goose, duck, turkey, amphibian, or reptile.

While in certain aspects of the present invention, the FFPET sample is an aged FFPET sample, for example, a FFPET sample that is at least one year old, at least two years old, at least three years old, at least four years old, at least five years old, at least six years old, at least seven years old, at least eight years old, at least nine years old, at least ten years old, at least fifteen years old, at least twenty years old, or older, in other aspects of the present invention the FFPET sample is less than one year old, less than 9 months old, less than 6 months old, less than 3 months old, less than two months old, less than one month old, less than two weeks old, less than one week old, or a fresh FFPET sample.

In certain embodiments of the present invention, the labeled nucleic acid sample is prepared from nucleic acids that are isolated from the FFPET sample, for example, RNA or DNA that is isolated from the FFPET sample. In certain aspects of the present invention, the nucleic acids are isolated from the FFPET sample by dissecting, for example macrodissecting or microdissecting, tissue from the FFPET sample in order to create sections, or thin sections, of the FFPET sample. In certain aspects of the present invention the sections are less than 1 micron thick, about 1 micron thick, about 5 microns thick, about 10 microns thick, at least 1 micron thick, at least 5 microns thick, at least 10 microns thick, between about 1 and about 5 microns thick, between about 1 and about 10 microns thick, or between about 5 and about 10 microns thick.

In certain aspects of the present invention, the FFPET sample comprises an area of diseased tissue, for example a tumor or other cancerous tissue, while in other aspects of the present invention, the FFPET sample comprises normal, untreated, placebo-treated, or healthy tissue. In certain embodiments of the present invention, the diseased area or tissue, or an area of the tissue that contains a particular cellular or subcellular feature or structure, is identified in the FFPET sample, .or a section thereof, prior to the isolation of nucleic acids, while in other embodiments of the present invention the nucleic acids are isolated from the FFPET sample without identification of the diseased area or tissue, or cellular or subcellular feature or structure. In embodiments of the present invention where a diseased area or tissue, or particular cellular or subcellular feature or structure, is identified in the FFPET sample, or a section thereof, prior to the isolation of nucleic acids, such identification can be by any method known to those of skill in the art to identify a particular disease area, or cellular or subcellular feature or structure, in a tissue sample, or section thereof, including, but not limited to, visual identification, staining, for example hematoxylin and eosin staining, labeling, and the like.

In embodiments of the present invention where nucleic acids are isolated from the FFPET sample, such nucleic acids can be RNA, DNA, or both, and any technique known to those of skill in the art to isolate nucleic acids can be used, hi fact, numerous kits for either nucleic acid isolation are commercially available, and are suitable for use in these embodiments of the present invention. However, in certain embodiments of the present invention, kits specifically designed to isolate RNA from a FFPET sample are used.

In certain embodiments of the present invention, the nucleic acids, for example RNA, isolated from the FFPET sample are amplified. In such embodiments, any technique known to those of skill in the art can be used to amplify the nucleic acids. Once again, numerous kits for nucleic acid amplification are commercially available, and are suitable for use in these embodiments of the present invention. Thus, in certain aspects of the present invention, RNA isolated from the FFPET sample is converted into an amplified cDNA sample or an amplified RNA sample.

In certain aspects of the present invention, the amplified nucleic acid sample is labeled. In these aspects of the present invention, any technique known to those of skill in the art can be used to label the amplified nucleic acid sample. Once again, numerous kits for nucleic acid labeling are commercially available, and are suitable for use in these aspects of the present invention. Thus, in certain embodiments of the present invention, the amplified nucleic acid sample is labeled by 5' or 3' end labeling, or by direct chemical labeling. Any type of detectable label can be utilized in these aspects of the present invention, including, but not limited to, radioactive, fluorescent, phosphorescent, or visual labels or dyes, enzymatic labels, and chemical or biological labels that are recognized by a specific binding partner or antibody, or fragment thereof, such as biotin.

In certain aspects of the present invention, the labeled amplified cDNA sample is fragmented. In these aspects of the present invention, any technique known to those of skill in the art can be used to fragment the labeled amplified nucleic acid sample. In certain embodiments of the present invention, the labeled amplified nucleic acid sample is purified prior to and/or following fragmentation. In these embodiments of the present invention, any technique known to those of skill in the art can be used to purify the labeled amplified nucleic acid sample and/or the fragmented nucleic acid sample. As is the case above, numerous kits and reagents for nucleic acid purification are commercially available, and are suitable for use in these aspects of the present invention.

Following hybridization of the labeled nucleic acid probe to the second microarray, any bound labeled nucleic acid probe is detected. In certain aspects of the present invention, the second microarray is washed at least a first time following hybridization, using reagents and techniques that are commercially available or otherwise known to those of skill in the art. In certain embodiments of the present invention, the bound labeled nucleic acid is stained or otherwise treated to enable or enhance detection. The method of detection will usually depend upon the type of label used to label the nucleic acid sample, and will be commercially available or otherwise well-known to those of skill in the art.

Thus, certain embodiments of the present invention provide methods for analyzing gene expression levels from a FFPET sample, comprising identifying a disease area within the FFPET sample, dissecting the identified disease area to obtain at least a first section of the diseased area, isolaiing RNA from the at least a first section of the diseased area, converting the RNA into an amplified cDNA sample, labeling the amplified cDNA sample, purifying the labeled cDNA sample, fragmenting the purified and labeled cDNA sample, purifying the fragmented cDNA sample, pre-hybridizing the fragmented cDNA sample with a first microarray, hybridizing the unbound fragmented cDNA sample with a second microarray, and detecting the fragmented cDNA sample bound to the second microarray.

BRIEF DESCRIPTION OF THE DRAWINGS

Not applicable.

MODES FOR CARRYING OUT THE INVENTION

Formalin-fixed, paraffin-embedded tissue (FFPET) samples represent the most commonly collected and stored samples for use in the diagnosis and prognosis of disease, including cancer. Nevertheless, historically these samples have been underutilized for the purpose of gene expression profiling because of the poor quality and quantity of FFPET nucleic acids. The methods of the present invention overcome these and other problems and provide protocols that can be used to obtain biologically relevant, whole genome-expression information using high density gene-expression arrays and labeled probes obtained or created from nucleic acids isolated from new or aged (greater than one year old) FFPET tissues. Using the techniques of the present invention in a microarray based analysis, 60,000 genes can be interrogated in 32 samples in a single experiment, and completed in a 3 day period.

The present invention is thus applicable to basic research aimed at the discovery of gene expression profiles relevant to the diagnosis and prognosis of disease. However, the present invention is also applicable to other fields of research where the quality of nucleic acid is poor, such as forensics, archeology, medical history, and paleontology.

The present invention provides methods for analyzing gene expression levels from FFPET samples that comprise pre-hybridizing the labeled nucleic acid sample prepared from a FFPET sample with a first microarray, and then hybridizing the portion of the labeled nucleic acid sample that does not bind to the first microarray with a second microarray prior to detection of the labeled nucleic acid sample that binds to the second microarray. Although the first microarray can be a previously unused or new microarray, such microarrays are expensive. Importantly, from a cost-savings perspective, the inventors determined that when the first microarray used for the pre-hybridization step is a previously used microarray, the results of the subsequent hybridization on a second microarray are nearly identical to the results obtained when the pre-hybridization was carried out using a new or previously unused microarray. Without being limited to any particular theory of the invention, the fact that nucleic acids isolated from FFPET samples are moderately to heavily degraded, particularly as the FFPET samples age, generally precludes the use of an oligo-dT primer to amplify mRNA isolated from the FFPET sample, or produce and/or amplify cDNA produced from mRNA isolated from the FFPET sample. Therefore, random priming techniques are commonly used to produce a sufficient quantity of nucleic acid products from the FFPET sample for subsequent labeling. However, since random priming will also serve to amplify rRNA present in the isolated nucleic acids, labeled products from the amplified rRNA can mask or otherwise reduce the quality of the signal produced when hybridizing labeled nucleic acids from FFPET samples onto a microarray. Incorporating a "pre-hybridization" (or "first hybridization") of the labeled nucleic acid sample results in an increase in the specific gene signals in subsequent hybridizations with high density gene expression arrays.

Any nucleic acid-based microarray can be used with the methods of the present invention, for the pre-hybridization and any subsequent hybridizations, including, but not limited to, commercially available microarrays, for example microarrays available from Affymetrix, Incorporated, Agilent Technologies, Incorporated, Illumina, Incorporated (San Diego, CA), GE Healthcare (Piscataway, NJ), NimbleGen Systems, Incorporated (Madison, WI), Invitrogen Corporation (Carlsbad, CA), and the like. Using the methods of the present invention, the pre-hybridization and any subsequent hybridization can utilize microarrays from the same manufacturer or source, or even the same type of microarray from the same manufacturer or source, or microarrays from different manufacturers or sources. Thus, for example, the pre-hybridization could utilize a new, previously unused, or used Affymetrix GeneChip®, for example a human X3P array, human genome Ul 33 Plus 2.0 array, human genome U133A 2.0 array, or a human cancer GIlO array, and subsequent hybridizations could utilize the same type or a different type of Affymetrix GeneChip®, or a completely different type of nucleic acid-based microarray.

FFPET samples from any source can be used with the methods of the present invention, including, but not limited to, FFPET samples from human tissues, laboratory animal tissues, companion animal tissues, or livestock animal tissues. Thus, FFPET samples from, for example, a non-human primate, such as a. chimpanzee, gorilla, orangutan, gibbon, monkey, macaque, baboon, mangabey, colobus, langur, marmoset, or lemur, a mouse, rat, rabbit, guinea pig, hamster, cat dog, ferret, fish, cow, pig, sheep, goat, horse, donkey, chicken, goose, duck, turkey, amphibian, or reptile can be used in the methods of the present invention. In addition, FFPET samples of any age can be used with the methods of the present invention, including, but not limited to, FFPET samples that are fresh, less than one week old, less than two weeks old, less than one month old, less than two months old, less than three months old, less than six months old, less than 9 months old, less than one year old, at least one year old, at least two years old, at least three years old, at least four years old, at least five years old, at least six years old, at least seven years old, at least eight years old, at least nine years old, at least ten years old, at least fifteen years old, at least twenty years old, or older.

In the methods of the present invention, the labeled nucleic acid sample can be prepared directly or indirectly from nucleic acids, for example RNA, isolated from FFPET samples, or from sections that are prepared from FFPET samples. The sections can be of any desired thickness, depending on the volume of the desired area. Thus, the sections can be thin sections or thick sections, including, but not limited to, sections that are less than 1 micron thick, about 1 micron thick, about 2 microns thick, about 3 microns thick, about 4 microns thick, about 5 microns thick, about 6 microns thick, about 7 microns thick, about 8 microns thick, about 9 microns thick, or about 10 microns thick, depending upon the desired application. In applications where the exact thickness of the section is less important, the sections can be, for example, at least 1 micron thick, at least 2 microns thick, at least 3 microns thick, at least 4 microns thick, at least 5 microns thick, at least 6 microns thick, at least 7 microns thick, at least 8 microns thick, at least 9 microns thick, or at least 10 microns thick. In applications where a range of thicknesses can be utilized, the sections can be defined by a range of sizes, including, but not limited to, between about 1 and about 5 microns thick, between about 1 and about 10 microns thick, or between about 5 and about 10 microns thick.

In many cases, FFPET samples comprise an area of diseased tissue, for example a tumor or other cancerous tissue. While such FFPET samples find utility in the methods of the present invention, FFPET samples that do not comprise an area of diseased tissue, for example FFPET samples from normal, untreated, placebo-treated, or healthy tissues, also can be used in the methods of the present invention. In certain methods of the present invention, a desired diseased area or tissue, or an area containing a particular region, feature or structure within a particular tissue, is identified in a FFPET sample, or a section or sections thereof, prior to isolation of nucleic acids, in order to increase the percentage of nucleic acids obtained from the desired region. Such regions or areas can be identified using any method known to those of skill in the art, including, but not limited to, visual identification, staining, for example hematoxylin and eosin staining, labeling, and the like. In any event, the desired area of the FFPET sample, or sections thereof, can be dissected, either by macrodissection or microdissection, to obtain the starting material for the isolation of a nucleic acid sample.

Any technique known to those of skill in the art can be used to isolate nucleic acids from the FFPET samples. In fact, numerous reagents and/or kits for nucleic acid isolation are commercially available, and are suitable for use in the methods of the present invention. Examples of such kits include, but are not limited to, the PicoPure™ RNA Isolation Kit from Arcturus Bioscience. Incorporated, the High Pure RNA Paraffin Kit from Roche Diagnostics Corporation, Roche Applied Science, and RNA Isolation Kits from Ambion, Incorporated (Austin, TX). Certain commercially available kits are specifically designed to isolate nucleic acids, for example RNA, from FFPET samples, and such kits can also be used in certain of the present methods. One of ordinary skill in the art, will readily recognize that a wide variety of techniques, including other common laboratory techniques or other commercially available kits, are capable of isolating nucleic acids from FFPET samples, and can therefore be used in certain methods of the present invention.

In certain methods of the present invention, the isolated nucleic acids are amplified, creating an amplified nucleic acid sample. For example, RNA isolated from FFPET samples can be amplified directly using commercially available kits or reagents, including, but not limited to, the Paradise™ Reagent System (Arcturus Bioscience, Incorporated) and the SenseAMP or SenseAMP Plus Kits (Genisphere, Incorporated, Hatfϊeld, PA), each of which utilize T7 polymerase to amplify RNA, the RampUP or RampUP Plus Kits (Genisphere, Incorporated), which utilize both T7 and T3 promoters to amplify RNA, or any other methods known to those of skill in the art. In other methods of the present invention, RNA isolated from FFPET samples can be converted into cDNA and then amplified, using commercially available reagents or kits, including, but not limited to, the TransPlex™ Whole Transcriptome Amplification Kit (Rubicon Genomics, Incorporated), the WT-Ovation™ FFPE System or WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies, Incorporated, San Carlos, CA), the GeneChip ® WT cDNA Synthesis and Amplification Kit (Affymetrix, Incorporated), the MessageAmp™ II aRNA Amplification Kits (Ambion, Incorporated), or any other methods known to those of skill in the art. One of ordinary skill in the art will readily recognize that a wide variety of techniques, including other common laboratory techniques or other commercially available kits, are capable of amplifying RNA, cDNA, or DNA without depending on polyadenylated tail of mRNA, and can therefore be used in certain methods of the present invention. In certain embodiments of the present invention, the amplified nucleic acid sample can be labeled for identification or visualization within a microarray. Any of various common laboratory techniques for labeling DNA, RNA, or both, known to those of skill in the art can be used to label the amplified nucleic acid sample, including, but not limited to, 5' or 3' end labeling, direct chemical labeling, synthesis with labeled nucleotides or pseudo-nucleotides, biotin conjugate labeling, as well as random primer or specific primer labeling. Numerous techniques, reagents, and kits for nucleic acid labeling are commercially available, including, but not limited to, labeling the amplified nucleic acid sample with Biotin-ULS using ULS™ aRNA Biotin Labeling Kit (catalog number EA-OlO; Kreatech Biotechnology, Amsterdam, The Netherlands), the FL-Ovation™ cDNA Biotin Module V2 (NuGEN Technologies, Incorporated), or the GeneChip ® WT Terminal Labeling Kit (Affymetrix, Incorporated), and are suitable for use in certain methods of the present invention. Any type of detectable label can be utilized in these aspects of the present invention, including, but not limited to, radioactive, fluorescent, phosphorescent, or visual labels or dyes, enzymatic labels, and chemical or biological labels that are recognized by a specific binding partner or antibody, or fragment thereof. If desired, the labeled, amplified nucleic acid sample can be purified, using any of the numerous nucleic acid purification techniques known to those of skill in the art. As is the case above, numerous techniques, kits and reagents for nucleic acid purification are commercially available, including, but not limited to, KREApure™ columns (Kreatech Biotechnology), and GeneChip® Sample Cleanup Module (Affymetrix, Incorporated), and are generally used as recommended by the manufacturer.

If desired, in certain methods of the present invention the labeled nucleic acid sample can be fragmented prior to labeling. Such fragmentation can use any of a number of techniques known to those of skill in the art, including, but not limited to, chemical treatment, for example using an alkaline solution, enzyme treatment, or mechanical treatment, such as shearing or sonication, or use commercially available techniques, reagents, and/or kits, as exemplified by the GeneChip® WT Terminal Labeling Kit (Affymetrix, Incorporated). As described above, in certain methods of the present invention the fragmented and labeled nucleic acid sample can be purified, using any of the numerous nucleic acid purification techniques known to those of skill in the art. As detailed above, numerous techniques, kits and reagents for nucleic acid purification are commercially available, including, but not limited to, KREApure™ columns (Kreatech Biotechnology), and GeneChip® Sample Cleanup Module (Affymetrix, Incorporated). The labeled nucleic acid sample can then be used in a pre-hybridization with a new, previously unused, or used microarray. One of ordinary skill in the art will readily recognize that the pre-hybridization step may be performed using a variety of different buffers and under a variety of temperatures, times, and other conditions, which will generally depend on the particular microarray used in the pre-hybridization step. Optimization of such conditions is standard procedure in molecular biology laboratories. In certain embodiments, the microarray is pre-hybridized for 14 to 17 hours at 45°C at a rotation of 60 revolutions per minute. In certain embodiments, the pre-hybridization cocktail is the same as the hybridization cocktail recommended by Affymetrix, Incorporated (GeneChip® Hybridization, Wash, and Stain Kit), with the exception that the water is eliminated and replaced with an equal volume of KREAblock™ solution (Kreatech Biotechnology).

After pre-hybridization the pre-hybridization cocktail containing unbound labeled nucleic acid sample (the portion of the labeled nucleic acid sample that does not bind to the pre-hybridization microarray) is used to hybridize to a different microarray. One of ordinary skill in the art will readily recognize that the hybridization step may be performed using a variety of different buffers and under a variety of temperatures, times, and other conditions, which will generally depend on the particular microarray used in the hybridization step. Optimization of such conditions is standard procedure in molecular biology laboratories. In certain embodiments, the microarray is hybridized for 14 to 17 hours at 45°C at a rotation of 60 revolutions per minute.

After hybridization, the microarray chip is analyzed for positive probe binding, in certain cases after washing the microarray at least once. One of ordinary skill in the art will readily recognize that washing and detection of probe binding may be performed using a variety of different buffers and under a variety of temperatures, times, and other conditions, which will generally depend on the particular nucleic acid label and microarray used. Optimization of such conditions is standard procedure in molecular biology laboratories. In methods that utilize a commercially available microarray for the hybridization step, the particular washing (if required) and detection conditions are provided by the manufacturer of the particular microarray. In certain methods of the present invention that utilize a GeneChip® (Affymetrix, Incorporated) microarray for the hybridization step, the microarray can be washed, stained, and/or scanned using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, Incorporated). The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention. The present invention is not to be limited in scope by the specific embodiments described herein, which are intended as single illustrations of individual aspects of the invention, and functionally equivalent methods and components are within the scope of the invention. Indeed, various modifications of the invention, in addition to those shown and described herein, will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.

INDUSTRIAL APPLICABILITY

EXAMPLE l

The effect of a pre-hybridization step on detection of specific gene signals in a subsequent hybridization on a high density gene expression array was tested by comparing the percent present call (proportion of probes on a microarray that yield meaningful above background data within each experiment) for 25 FFPET samples from breast cancer patients using a GeneChip ® U133-X3P Array (Affymetrix, Incorporated) with and without pre-hybridization to a GeneChip® U 133 Plus 2.0 Array (Affymetrix, Incorporated).

The methodology used in this study is outlined below. Briefly, the tumor area was identified in each of the 25 FFPET samples by hematoxylin-eosin staining, and the tumor areas were macrodissected from thin sections ( 1 to 5 microns thick, depending on the tumor volume) generated from each of the FFPET samples. RNA was isolated from the macrodissected tumor areas using the High Pure RNA Paraffin Kit (Roche Diagnostics Corporation, Roche Applied Science), following the instructions provided by the manufacturer. The RNA isolated from each of the FFPET samples was then amplified using the TransPlex™ Whole Transcriptome Amplification Kit (Rubicon Genomics, Incorporated), following the instructions provided by the manufacturer, and the resulting cDNA samples were labeled with BIO-ULS using the ULS™ aRNA Biotin Labeling Kit (catalog number EA-OlO; Kreatech Biotechnology), following the instructions provided by the manufacturer. The labeled cDNA samples were purified using KREApure™ columns (Kreatech Biotechnology), as recommended by the manufacturer, and then fragmented and purified using the GeneChip® Sample Cleanup Module (Affymetrix, Incorporated), and then pre-hybridized on a new (fresh) GeneChip® U133 Plus 2.0 Arrays (Affymetrix, Incorporated) for 14 to 17 hours at 45°C at a rotation of 60 revolutions per minute. The pre-hybridization cocktail was identical to the hybridization cocktail recommended by Affymetrix, Incorporated, except that water was eliminated and replaced with the same volume of KREAblock™ solution (Kreatech Biotechnology). The pre-hybridization cocktail (containing the unbound portion of the labeled cDNA sample) from each sample was then used to hybridize to a new (fresh) GeneChip® U133-X3P Array (Affymetrix, Incorporated). The arrays were washed and stained using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, Incorporated), and then scanned using the conditions recommended by Affymetrix, Incorporated. The results are shown in Table 1.

Table 1 The results show a statistically significant (p=3.9E-9 by t-test) improvement of percent present call when a pre-hybridization step was included. When a subsequent hybridization was performed using the very same labeled cDNA sample/hybridization cocktail on a new (fresh) GeneChip® U133 Plus 2.0 Array (Affymetrix, Incorporated), the percent present call was higher than the percent present call without pre-hybridization, which also utilized a GeneChip® U133 Plus 2.0 Array (Affymetrix, Incorporated). The results are shown in Table 2.

Table 2 Removal of non-specific signals in the first hybridization (pre-hybridization) allows for greater detection of differentially expressed genes because during the pre-hybridization the elements responsible for many non-specific signals stuck to the chip and were removed from the sample so that subsequent hybridizations gave a better, more specific signal.

While pre-hybridization on chips covering whole genomes or arrays having substantially overlapping probes increases signal specificity, the use of a whole genome, or gene expression chip, for the purpose of removing non-specific hybridization signals is expensive. Therefore, a previously used gene expression chip was tested to determine if pre-hybridization on a previously used chip removed non-specific hybridization signals. In this experiment, a labeled sample was pre-hybridized on a new/unused chip or on a used chip. The sample that was pre- hybridized to the new chip had a percent present call (17.9) that was nearly identical to the sample that was pre-hybridized to the used chip (17.4). The use of a used gene expression chip for the purpose of filtering a sample represents a novel and cost effective feature of the present invention.

EXAMPLE 2

In order to compare the methodology described in Example I5 above, with the Paradise™ Reagent System on RNA extractable from paraffin blocks that are more than one year old, the methodology described in Example 1, above, and the Paradise™ Reagent System were tested on fourteen FFPET tumor samples that were between 1 and 10 years old. Significance Analysis of Microarray (SAM), a widely used method to identify genes that are differentially expressed between two phenotypes (Tusher al, Proc. Natl. Acad. ScL USA 98:51 16-5121, 2001), was used to see if the estrogen receptor (ER) gene ESRl, which is known to be differentially expressed between ER positive and ER negative tumors, could be identified as being a differentially expressed gene between ER positive and ER negative tumors in a dataset generated using the Paradise™ Reagent System, following the instructions provided by the manufacturer, and a dataset generated using the methodology described in Example 1, above. Of the fourteen FFPET tumor samples, three were known to be ER negative, ten were known to be ER positive, and one sample was undetermined as to the ER expression.

The results showed that a dataset generated using the Paradise™ Reagent System failed to identify any differentially expressed genes between the ER positive and ER negative samples, whereas the dataset generated using one of the methods of the present invention identified seven genes that were differentially expressed between the ER positive and ER negative samples (Table 3).

Table 3

In addition, the Paradise™ Reagent System was compared to an embodiment of the present invention with respect to the expression levels of key probe sets that describe estrogen receptor expression and HER2 expression in breast cancer (keratin 7 (KRT7), chemokine (C-X- C motif) ligand 1 (CXCL-I; GRO alpha), keratin 5 (KRT5), estrogen receptor 1 (ESRl), v-erb- b2 erythroblastic leukemia viral oncogene homolog 2 (ERBB2), GATA binding protein 3 (GATA3), and signal peptide, CUB domain, EGF-like 2 (SCUBE2)) using an Affymetrix Ul 33 X3P GeneChip. In unsupervised clustering of the fourteen FFPET samples described above, the gene expression data generated using the Paradise™ Reagent System failed to identify and cluster ER positive versus ER negative tumors, and failed to identify HER2 (ERBB2) positive tumors. In contrast, the embodiment of the current invention correctly identified and clustered the ER positive versus ER negative tumors, and identified a HER2 positive tumor, which also happened to be ER positive. These observations clearly demonstrate that the Paradise™ Reagent System method failed to produce biologically meaningful data from old FFPET samples, whereas the embodiment of the present invention produced biologically meaningful results.

EXAMPLE 3

To prove that methods of the present invention also work with oligonucleotide arrays from Agilent Technologies, Incorporated, 16 FFPET samples from breast cancer patients were prepared as described in Example 1, above, and analyzed using oligonucleotide arrays from Agilent Technologies, Incorporated.

Using Significance Analysis of Microarray (SAM), as described in Example 2, above, 35 genes were found to be differentially expressed between estrogen receptor positive versus negative cases with false discovery rate of zero. The genes included multiple probes for estrogen receptor gene (ESRl) as well as other known ER related genes such as GATA3, AREG, MAPT, and GSTM3. The results are shown in Table 4.

Table 4 When Prediction Analysis of Microarray (PAM) was applied to build a predictor for estrogen receptor status of these 16 cases, 16 probes were selected for the predictor (TFFl, ESRl, ESRl, ESRl, ESRl, ESRl, TFFl, ESRl, ESRl, ESRl, ESRl, GFRAl, ESRl, BCMPIl, KCNKl 5, and ENST00000343518), and on leave one out cross validation, prediction accuracy of 100% was achieved. The performance of PAM predictor in predicting ER status of samples (100% accuracy obtained) is shown in Table 5.

Table 5

Thus, methods of the present invention work on oligonucleotide arrays from Agilent Technologies, Incorporated, as well as those from Affymetrix, Incorporated.

EXAMPLE 4

In order to compare different techniques for labeling of cDNA samples, cDNA samples were produced from 8 FFPET samples from breast cancer patients, as described in Example 1, above, and labeled either with BIO-ULS using the ULS™ aRNA Biotin Labeling Kit (Kreatech Biotechnology), or end labeled using terminal deoxynucleotide transferase to incorporate biotin-tagged dUTP to the end of the cDNA samples. The labeled samples were then processed as described in Example 1, above, pre-hybridized to a new (fresh) GeneChip® U l 33 Plus 2.0 Arrays (Affymetrix, Incorporated), and hybridized to a new (fresh) GeneChip® U133-X3P Array (Affymetrix, Incorporated). The arrays were processed as described in Example 1, above, and the results are shown in Table 6. Table 6 The results show a statistically significant (p=0.0027 by t-test) improvement of percent present call by labeling with BIO-ULS using the ULS™ aRNA Biotin Labeling Kit (Kreatech Biotechnology) compared to end-labeling using terminal deoxynucleotide transferase to incorporate biotin-tagged dUTP to the end of the cDNA samples.

EXAMPLE 5

Gene expression information from 92 FFPET samples was analyzed using the methodology described in Example 1, above, using GeneChip® U133 Plus 2.0 and GeneChip® U133-X3P whole genome expression arrays (Affymetrix, Incorporated). The generated dataset was then used to identify over 900 differentially expressed genes between ER positive versus ER negative tumors using the SAM procedure, as described above. The list of differentially expressed genes included most known genes differentially expressed between ER positive versus ER negative tumors, such as ESRl, PR, GATA3, and SCUBE2. However, a number of previously unidentified differentially expressed genes were also identified. A complete listing of SAM positive genes identified using the GeneChip® U 133 Plus 2.0 Array is shown in Table 7 (see Appendix 1), and a complete listing of SAM positive genes identified using the GeneChip® U133-X3P Array is shown in Table 8 (see Appendix 1).

This dataset was also used to cluster the samples without supervision. This analysis found that the clustering is consistent with that previously published in the literature. For example, the gene expression data generated accurately clustered the breast cancer samples into ER positive and ER negative groups, and accurately clustered other gene expression groups previously published in the literature, including luminal, basal and HER2 positive groups.

All of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims. Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene 1552343_3p_s_at phosphodiesterase 7A PDE7A 8q13 5150 1552575_3p_a_at chromosome 6 open reading frame 141 C6orf141 6p12 3 135398 15531 14_3p_a_at PTK6 protein tyrosine kinase 6 PTK6 20q13 3 5753 1553706_3p_at 1555460_3p_a_at solute earner family 39 (zinc transporter), member 6 SLC39A6 18q12 2 25800 1557661_3p_at START domain containing 10 STARD10 11q13 10809 1558569_3p_at Mastermind-like 2 (Drosophila) MAML2 11q21 84441 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 1563253_3p_s_at (avian) ERBB3 12q13 2065 CO C 20001 1_s_at ADP-r ιbosyla1ιon factor 3 /// ADP-nbosylation factor 3 ARF3 12q13 377 co 20081 0_3p_s_at cold inducible RNA binding protein CIRBP 19p13 3 1153 CO 202917_3p_s_at S100 calcium binding protein A8 (calgranulin A) S100A8 1q21 6279 solute earner family 5 (sodium-dependent vitamin 204087_3p_s_at transporter), member 6 SLC5A6 2p23 8884 m 204846_3p_at ceruloplasmin (ferroxidase) CP 3q23-q25 1356 CO 206059_3p_at zinc finger protein 9 1 (HPF7, HTF10) ZNF91 19p13 1-p12 7644 m 208651_3p_x_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 m 208712_3p_at cyclin 0 1 CCND1 11q13 595 208865_3p_at casein kinase 1, alpha 1 CSNK1A1 5q32 1452 c 209771_3p_x_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 m 210926_3p_at actin-like protein FKSG30 2q21 1 440915 IO Immunoglobulin kappa light chain (IGKV) mRNA variable 2 11645_3p_x_at region, joining region, and constant region 2 11959_3p_at insulin-like growth factor binding protein 5 IGFBP5 2q33-q36 3488 212196_3p_at lnterleukin 6 signal transducer (gp130, oncostatin M receptor) IL6ST 5q1 1 3572 212593_3p_S_at programmed cell death 4 (neoplastic transformation inhibitor) PDCD4 10q24 27250 213605_3p_s_at 213627_3p_at melanoma antigen family D, 2 MAGED2 Xp1 1 2 10916 214164_3p_x_at carbonic anhydrase XII CA12 15q22 771 214669_3p_x_at Immunoglobulin kappa variable 1-5 IGKC 2p12 3514 immunoglobulin heavy constant alpha 1// immunoglobulin heavy constant deltaffimmunoglobulm heavy constant gamma IGHA1//IGHD// 3493// 3495// 1 (G1 m marker)// immunoglobulin heavy constant mu//sιmιlar IGHG1//IGHM// 3500// 3507// 214916_3p_x_at to Ig heavy chain V-IlI region VH26 precursor LOC390714 14q32 33//16p11 2 390714 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene 215043_3p_s_at SMA3//SMA5 SMA3//SMA5 5q13 10571// 11042 215135_3p_at aspartyl aminopeptidase DNPEP 2q35 23549 Immunoglobulin kappa light chain variable region (IGKV 215176_3p_x_at gene), clone 25 — 216510_3p_x_at 217138_3p_x_at 217598_3p_at 217894_3p_at potassium channel tetramerisatio π domain containing 3 KCTD3 1q41 5 1133 22061 3_3p_s_at synaptotagmin-like 2 SYTL2 11q14 54843 CO C 223103_3p_at START domain containing 10 STARD1 0 11q13 10809 00 metastasis associated lung adenocarcinoma transcript 1 CO 224558_3p_s_at (non-coding RNA) MALAT1 11q13.1 378938 224795_3p_x_at immunoglobulin kappa constant//immunoglobuli π kappa variable 1-5 IGKC//IGKV1-5 2p12 28299// 351 4 m K) 230742_3p_at CO 231211_3p_s_at Hypothetical LOC541469 protein C19orf33 19q13.2 64073 m Ig lambda mRNA V-region (V-J) heterohybridoma// m Immunoglobulin lambda joining 3// Immunoglobulin lambda 234764_3p_x_at constant 1 (Meg marker) IGLC2 22q1 1.2 3538 73 235281_3p_x_at AHNAK nucleoprotein (desmoyokin) AHNAK 11q12.2 79026 c 235791_3p_x_at chromodomain helicase DNA binding protein 1 CHD1 5q15-q21 1105 m 238021_3p_s_at IO sema domain, immunoglobulin domain (Ig), short basic 35666_3p_at domain, secreted, (semaphorin) 3F SEMA3F 3p21 .3 6405 4847541 C_3p_s_at Ras association (RalGDS/AF-6) domain family 4 RASSF4 10q1 1.21 83937 cadherin, EGF LAG seven-pass G-type receptor 1 (flamingo 4862730_3p_s_at homolog, Drosophila) CELSR1 22q13.3 9620 sema domain, immunoglobulin domain (Ig), short basic 4871689C_3p_s_at domain, secreted, (semaphorin) 3F SEMA3F 3p21.3 6405 49452_3p_at acetyl-Coenzyme A carboxylase beta ACACB 12q24.1 1 32 63825_3p_at abhydrolase domain containing 2 ABHD2 15q26.1 11057 g10181099_3p_s_at neural proliferation, differentiation and control, 1 NPDC1 9q34.3 56654 g1019071 1_3p_at S100 calcium binding protein A14 S100A14 1q21.3 57402 g10197627_3p_a_at transmembrane BAX inhibitor motif containing 4 TMBIM4 12q14.1-q15 51643 g 106441 21_3p_a_at trichorhinophalangeal syndrome I TRPS1 8q24.12 7227 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene g10834586_3p_a_at fer-1-like 3, myoferlin (C. elegaπs) FER1L3 10q24 26509 g 10835020_3p_s_at insulin-like growth factor binding protein 4 IGFBP4 17q12-q21.1 3487 g10835134_3p_at C-reactive protein, pentraxin-related CRP 1q21-q23 1401 g10835237_3p_s_at interferon induced transmembrane protein 2 (1-8D) IFITM2 11p15.5 10581 g10863894_3p_a_at thymosin, beta 10 TMSB10 2p1 1.2 9168 g10864030_3p_at ovo-like 2 (Drosophila) OVOL2 20pter-q1 1.23 58495 g10934058_3p_a_at methylcrotonoyl-Coenzyme A carboxylase 2 (beta) MCCC2 5q12-q13 64087 g 1093801 3_3p_a_at juπ D proto-oncogene JUND 19p13.2 3727 CO g10947028_3p_at secretoglobin, family 1D, member 2 SCGB1D2 11q13 10647 C 1p22-p21 5825 co g 109471 25_3p_at ATP-binding cassette, sub-family D (ALD), member 3 ABCD3 CO g 1 1037056_3p_a_at myosin X MYO10 5p15.1-p14.3 4651 g11055593_3p_a_at paraneoplastic antigen MA2 PNMA2 8p21.2 10687 g11321602_3p_at TNF receptor-associated factor 5 TRAF5 1q32 7188 m t g11497037_3p_at ADAM metallopeptidase domain 20 ADAM20 14q24.1 8748 CO g 11545842_3p_a_at PERP, TP53 apoptosis effector PERP 6q24 64065 m g 11545860_3p_at calsyntenin 2 CLSTN2 3q23-q24 64084 m g 11559249_3p_s_at membrane-spanning 4-domains, subfamily A, member 7 MS4A7 11q12 58475 g 11611735_3p_at GREB1 protein GREB1 2p25.1 9687 c protein phosphatase 2 (formerly 2A), regulatory subunit B (PR g 11643584_3p_a_at 52), gamma isoform PPP2R2C 4p1 6.1 5522 m g 11907834_3p_a_at estrogen receptor 1 ESR1 6q25.1 2099 IO g11967980_3p_s_at RAB17, member RAS oncogene family RAB17 2q37.3 64284 g12003430_3p_a_at g12005903_3p_at hypothetical protein DKFZp434L142 DKFZp434L142 4q32.1 51313 endoplasmic reticulum-golgi intermediate compartment 32 g12006036_3p_a_at kDa protein KIAA1181 5q35.1 57222 g12006345_3p_a_at inositol 1,3,4-triphosphate 5/6 kinase ITPK1 14q31 3705 ELOVL family member 5, elongation of long chain fatty acids g12053372_3p_at (FEN1/Elo2, SUR4/Elo3-like, yeast) ELOVL5 6p21.1-p12.1 60481 g12053382_3p_at solute carrier family 40 (iron-regulated transporter), member 1 SLC40A1 2q32 30061 g12056469_3p_at retinoic acid induced 2 RAI2 Xp22 10742 g12056470_3p_at G protein-coupled receptor, family C, group 5, member A GPRC5A 12p13-p12.3 9052 g12232424_3p_at chromosome 1 open reading frame 149 C1orf149 1p35.3-p33 64769 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Eπtrez Gene g12232472_3p_at DEP domain containing 6 DEPDC6 8q24 12 64798 g12407398_3p_S_at tripartite motif-containing 8 TRIM8 10q24 3 81603 g12408251_3p_at actin like protein FKSG30 2q21 1 440915 g12408251_3p_x_at actin like protein FKSG30 2q21 1 440915 g12652656_3p_s_at cycliπ D 1 CCND1 11q13 595 g12652708_3p_at NCK adaptor protein 2 NCK2 2q12 8440 g12652786_3p_at H 1 histone family, member O H 1F0 22q13 1 3005 g12652946_3p_a_at chromosome 5 open reading frame 18 C5orf18 5q22-q23 7905 CO g12653028_3p_a_at carbonic anhydrase XII CA12 15q22 771 C reticulon 1 RTN1 14q23 1 6252 co g12653096_3p_a_at CO g12653334_3p_at endosulfine alpha ENSA 1q21 2 2029 g 12653600 3p at Quiπoid dihydropte πdine reductase QDPR 4p1 5 31 5860 g12653744_3p_S_at stanniocalcin 2 STC2 5q35 1 8614 m g126541 28_3p_a_at kyπureπinase (L-kynurenine hydrolase) KYNU 2q22 3 8942 CO g12654362_3p_a_at protein kinase C binding protein 1 PRKCBP1 20q13 12 23613 m g12654376_3p_s_at carbonic anhydrase XII CA12 1Sq22 771 m g12654878_3p_a_at nuclear factor I/B NFIB 9p24 1 4781 g12655880_3p_at protein kinase (cAMP-dependent, catalytic) inhibitor beta PKIB 6q22 3 1 5570 73 c g12669906_3p_at acyl-CoA synthetase long-chain family member 1 ACSL1 4q34-q35 2180 m g12751474_3p_a_at solute earner family 39 (zinc transporter), member 6 SLC39A6 18q12 2 25800 D 1 EFHD1 2q37 1 80303 IO g12803268_3p_at EF-hand domain family, member g12803342_3p_s_at CXXC finger 5 CXXC5 5q31 2 51523 g12803638_3p_at tubulin, beta 6 TUBB6 18p1 1 2 1 84617 g12803670_3p_a_at dual specificity phosphatase 4 DUSP4 8p12-p1 1 1846 g12803726_3p_x_at keratin 7 KRT7 12q12-q13 3855 g12803756_3p_a_at hypothetical protein FLJ22679 RP13-360B22 2 Xq22 3 84187 g12803794_3p_a_at vesicle-associated membrane protein 2 (syπaptobreviπ 2) VAMP2 17p13 1 6844 g12803794_3p_x_at vesicle-associated membrane protein 2 (synaptobrevi π 2) VAMP2 17p13 1 6844 g12804520_3p_a_at HD domain containing 2 HDDC2 6q13-q24 3 51020 g 130971 67_3p_x_at laminin, alpha 5 LAMA5 20q13 2-q13 3 391 1 g13097617_3p_a_at MYC associated factor X MAX 14q23 4149 g 1309781 8_3p_a_at LIM domain only 4 LMO4 1p22 3 8543 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Eπtrez Gene g131 11765_3p_a_at GATA binding protein 3 GATA3 10p15 2625 g13111980_3p_a_at solute earner family 43, member 3 SLC43A3 11q1 1 29015 g1311 1980_3p_s_at solute earner family 43, member 3 SLC43A3 11q1 1 29015 g13111982_3p_a_at leukocyte receptor cluster (LRC) member 4 LENG4 19q13 4 79143 g131291 07_3p_a_at melanophiliπ MLPH 2q37 3 79083 g13177655_3p_a_at death-associated protein kinase 1 DAPK1 9q34 1 1612 g13236503_3p_s_at SLC2A4 regulator SLC2A4RG 20q13 33 56731 g13276638_3p_a_at chromosome 9 open reading frame 58 C9orf58 9q34 13-q34 3 83543 π CO ret proto-oncogene (multiple endoc ne neoplasia and C g13279040_3p_s_at medullary thyroid carcinoma 1, Hirschsprung disease) RET 10q11 2 5979 co g13324676_3p_s_at ectonucleotide pyrophosphatase/phosphodiesterase 1 ENPP1 6q22-q23 5167 CO cadheπn, EGF LAG seven-pass G-type receptor 2 (flamingo g13325063_3p_s_at homolog, Drosophila) CELSR2 1p21 1952 g133251 63_3p_a_at chromosome 1 open reading frame 34 C1orf34 1p32 3 22996 m g13325399_3p_s_at calcium channel, voltage-dependent, gamma subunit 4 CACNG4 17q24 27092 CO family with sequence similanty 77, member C 1p35 2 79570 t g13375663_3p_at FAM77C m g 1337571 2_3p_S_at hypothetical protein FLJ21127 FU21 127 12q24 11 79600 m g13375714_3p_at adiponectin receptor 2 ADIPOR2 12p13 3 1 79602 g13375745_3p_at chromosome 6 open reading frame 2 11 C6orf21 1 6q25 1 79624 c pleckstnn homology domain containing, family F (with FYVE m g13375826_3p_a_at domain) member 2 PLEKHF2 8q22 1 79666 g13376090_3p_a_at multimerin 2 MMRN2 10q23 2 79812 IO g13376209_3p_a_at hypothetical protein FU13710 FU13710 15q23 79875 g13376256_3p_a_at cytochrome b reductase 1 CYBRD1 2q31 1 79901 g13376293_3p_at transcπption elongation factor A (Sll)-l ιke 4 TCEAL4 Xq22 2 79921 g13376407_3p_at KIAA1772 KIAA1772 18q1 1 1-q1 1 2 80000 g13376651_3p_at hypothetical protein FLJ22635 FU22635 11p15 5 80162 g13386479_3p_a_at Nedd4 family interacting protein 1 NDFIP1 5q31 3 80762 g13436094_3p_at hypothetical protein FLJ14525 FLJ14525 1q42 13-q43 84886 fascin homolog 1, actin-bundling protein (Strongylocentrotus g 13436196_3p_s_at purpuratus) FSCNI 7p22 6624 g13436316_3p_s_at tubulin alpha 6 TUBA6 12q12-q14 84790 g 1344301 9_3p_x_at zinc finger protein 552 ZNF552 19q13 43 79818 g13469728_3p_at ankyrin repeat domain 3OA ANKRD30A 10p11 21 91074 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene carcinoembryonic antigen-related cell adhesion molecule 6 g 134771 06_3p_s_at (non-specific cross reacting antigen) CEACAM6 19q13.2 4680 g13517963_3p_at G protein-coupled receptor 8 1 GPR81 12q24.31 27198 g13518030_3p_at dynein, axonemal, light intermediate polypeptide 1 DNALI1 1p35.1 7802 g13518227_3p_at methylcrotonoyl-Coenzyme A carboxylase 1 (alpha) MCCC1 3q27 56922 g13528881_3p_a_at FXYD domain containing ion transport regulator 3 FXYD3 19q13.1 1-q13.12 5349 cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits g 1353569_3p_a_at CDK4) CDKN2A 9p21 1029 g13537354_3p_s_at leucine-rich repeats and immunoglobulin-like domains 1 LRIG 1 3p14 26018 CO g1354061 9_3p_s_at phospholipase A2, group XIIA PLA2G12A 4q25 81579 C co g13543331_3p_at annexin A9 ANXA9 1q21 8416 CO g1356991 8_3p_s_at C1q and tumor necrosis factor related protein 3 C1QTNF3 ... 114899 ST6 (alpha-N-acetyl-neuraminyl^.S-beta-galactosyl-i ,3)-N- g13569937_3p_s_at acetylgalactosaminide alpha-2,6-sialyltransferase 5 ST6GALNAC5 1p31.1 81849 g13623528_3p_s_at steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 m alpha-steroid delta 4-dehydrogenase alpha 1) SRD5A1 5p15 6715 to CO g13625796_3p_s_at asporin (LRR class 1) ASPN 9q22 54829 m cytochrome P450, family 2, subfamily B, polypeptide 7 m g 1369981 4_3p_s_at pseudogene 1 CYP2B7P1 19q13.2 1556 g13775195_3p_s_at tetraspanin 9 TSPAN9 12p13.33-p13.32 10867 c g1673574_3p_x_at keratin 8 KRT8 12q13 3856 m g1710215_3p_at fatso FTO 16q12.2 79068 IO g1777756_3p_a_at protein tyrosine phosphatase type IVA, member 2 PTP4A2 1p35 8073 androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy g178655_3p_at disease) AR Xq1 1.2-q12 367 g178696_3p_at annexin A3 ANXA3 4q13-q22 306 g179364_3p_x_at cyclin D1 CCND1 11q13 595 g180167_3p_s_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 cytochrome P450, family 2, subfamily B, polypeptide 7 g181293_3p_at pseudogene 1 CYP2B7P1 19q13.2 1556 diazepam binding inhibitor (GABA receptor modulator, acyl- g181960_3p_s_at Coenzyme A binding protein) DBI 2q12-q21 1622 immunoglobulin kappa constant// immunoglobulin kappa g184847_3p_a_at variable 1-5 1GKC//1GKV1-5 2p12 28299// 351 4 g185361_3p_s_at immunoglobulin heavy locus//immunoglobu!in heavy constant IGH@//IGHG1// 14q32.33 3492// 3500// Table7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene gamma 1 (G1m marker)//immunoglobul ιn heavy constant IGHG2//IGHG3// 3501// 3502// gamma 2 (G2m marker)// immunoglobulin heavy constant IGHG4//IGHM 3503// 3507 gamma 3 (G3m marker)//immunoglobul ιn heavy constant gamma 4 (G4m marker)//immu πoglobuhn heavy constant mu g189501_3p_at lymphocyte cytosolic protein 1 (L-plastm) LCP1 13q14 3 3936 g 1899219_3p_at iroquois homeobox protein 5 IRX5 16q11 2-q13 10265 g2055308_3p_at bone morphogenetic protein receptor, type IB BMPR1B 4q22-q24 658 g220150_3p_x_at alpha-2-glycoprote ιn 1, zinc AZGP1 7q22 1 563 g2306763_3p_a_at phosphodiesterase 7A PDE7A 8q13 5150 CO g2415416_3p_a_at secreted frizzled-related protein 1 SFRP1 8p12-p1 1 1 6422 C g2673967_3p_at seven in absentia homolog 2 (Drosophila) SIAH2 3q25 6478 CO g307297_3p_at glucosaminyl (N-acetyl) transferase 2, l-branching enzyme GCNT2 6p24 2651 BUB3 budding uninhibited by benzimidazoles 3 homolog g3378103_3p_a_at (yeast) BUB3 10q26 9184 m g338684_3p_a_at microtubule-associated protein tau MAPT 17q21 1 4137 CO g340300_3p_a_at vascular endothelial growth factor VEGF 6p12 7422 U m O g34891 1_3p_at chitinase 3-lιke 1 (cartilage glycoprotein 39) CHI3L1 1q32 1 1116 m g348911_3p_x_at chitinase 3-lιke 1 (cartilage glycoprotein-39) CHI3L1 1q32 1 1116 g349450_3p_a_at filamin B, beta (actin binding protein 278) FLNB 3p14 3 2317 73 {pseudogene} Ig V lambda IJ psi C lambda 6=lg lambda chain c surface Ig receptor VJC region {truncated light chain constant m region} [human, B lymphoma cell line OCI LY8, mRNA IO Partial, 623 πt]// (clone 9F2L) Ig rearranged L-chain mRNA V- region, 5' end//Clone ds1-1 immunoglobulin lambda chain VJ g398493_3p_s_at region, (IGL)//lmmunoglobul ιn lambda joining 3 IGLC2 22q1 1 2 3538 g405736_3p_s_at protein kinase D3 PRKD3 2p21 23683 inhibitor of kappa light polypeptide gene enhancer in B-cells, g418S274_3p_a_at kinase beta IKBKB Sp1 1 2 3551 g4204879_3p_a_at heat shock 7OkDa protein 2 HSPA2 14q24 1 3306 g4416405_3p_a_at vav 3 oncogene VAV3 1p13 3 10451 aldo-keto reductase family 7, member A2 (aflatoxin aldehyde g4502020_3p_a_at reductase) AKR7A2 1p35 1-p36 23 8574 g4502198_3p_at amphiregulin (schwannoma-denved growth factor) AREG 4q13-q21 374 g4502202_3p_a_at ADP-nbosylation factor 3 ARF3 12q13 377 g4502396_3p_at B-factor, properdin BF 6p21 3 629 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene g4502722_3p_at cadherin 3, type 1, P-cadherin (placental) CDH3 16q22.1 1001 g4502846_3p_at cold inducible RNA binding protein CIRBP 19p13.3 1153 g4502846_3p_s_at cold inducible RNA binding protein CIRBP 19p13.3 1153 g4502966_3p_a_at collagen, type IX, alpha 3 COL9A3 20q13.3 1299 g4503002_3p_at carboxypeptidase B 1 (tissue) CPB1 3q24 1360 g4503008_3p_a_at carboxypeptidase E CPE 4q32.3 1363 g4503046_3p_at cysteine-rich protein 1 (intestinal) CRIP1 14q32.33 1396 g4503132_3p_at CTP synthase CTPS 1p34.1 1503

CO g4503172_3p_at coxsackie virus and adenovirus receptor CXADR 21q21.1 1525 C co g4503298_3p_a_at basic helix-loop-helix domain containing, class B, 2 BHLHB2 3p26 8553 CO g4503570_3p_s_at enolase 1, (alpha) EN01 1p36.3-p36.2 2023 g4503570_3p_x_at enolase 1, (alpha) EN01 1p36.3-p36.2 2023 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 m g4503596_3p_a_at (avian) ERBB3 12q13 2065 g4503602_3p_at estrogen receptor 1 ESR1 6q25.1 2099 CO acyl-CoA synthetase long-chain family member 1 ACSL1 4q34-q35 2180 m g4503650_3p_s_at m farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, g4503684_3p_at geranyltranstransferase) FDPS 1q22 2224 c famesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, m g4503684. 3p_x_at geranyltranstransferase) FDPS 1q22 2224 IO g4503728. 3p_a_at FK506 binding protein 4, 59kDa FKBP4 12p13.33 2288 g4504026..3p_a_at glutamate-ammonia ligase (glutami πe synthetase) GLUL 1q31 2752 g4504276..3p_s_at histone 2, H2be HIST2H2BE 1q21-q23 8349 g4504432 . 3p_x_at high mobility group AT-hook 1 HMGA1 6p21 3159 g4504464. 3p_at homeo box B2 HOXB2 17q21-q22 3212 g4504772. 3p_a_at integrin, beta S ITGB5 3q21.2 3693 g4504914_.3p_at keratin 15 KRT15 17q21.2 3866 g4504960. 3p_at lamiπ B receptor LBR 1q42.1 3930 g4505042. 3p_a_at lactotransferrin LTF 3q21-q23 4057 g4505168. 3p_at secretoglobin, family 2A, member 2 SCGB2A2 11q13 4250 g4505170. 3p_at secretoglobin, family 2A, member 1 SCGB2A1 11q13 4246 g4505282..3p_s_at mucin 1, transmembrane MUC1 1q21 4582 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene g4505444_3p_s_at neuropeptide Y receptor Y1 NPY1 R 4q31 .3-q32 4886 g4505622_3p_at pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 g4505766_3p_at progesterone receptor PGR 11q22-q23 5241 g4505860_3p_a_al plasminogen activator, tissue PLAT 8p12 5327 g4505870_3p_at phospholipase C, gamma 2 (phosphatidylinositol-specific) PLCG2 16q24.1 5336 g4506106_3p_at prolactin receptor PRLR 5p14-p13 5618 prion protein (p27-30) (Creutzfeld-Jakob disease, Gerεtmann- g4506112_3p_a_at Strausler-Scheinker syndrome, fatal familial insomnia) PRNP 20pter-p12 5621 g4506430_3p_at RAS p21 protein activator (GTPase activating protein) 1 RASA1 5q13.3 5921 CO C g 4506440_3p_a_a1 retinoblastoma binding protein 8 RBBP8 18q1 1.2 5932 co S100 calcium binding protein A10 (annexin Il ligand, calpactin CO g4506760_3p_s_at I, light polypeptide (p1 1)) S100A10 1q21 6281 special AT-rich sequence binding protein 1 (binds to nuclear g4506790_3p_a_at matrix/scaffold-associating DNA's) SATB1 3p23 6304 m g4506814_3p_at sodium channel, nonvoltage-gated 1 alpha SCNN1A 12p13 6337 CO g4506924_3p_a_at SH3 domain binding glutamic acid-rich protein like SH3BGRL Xq13.3 6451 m g4507004_3p_x_at solute carrier family 22 (organic cation transporter), member 5 SLC22A5 5q31 6584 m solute carrier family 4, sodium bicarbonate cotransporter, g4507028_3p_a_at member 7 SLC4A7 3p22 9497 to solute carrier family 7 (cationic amino acid transporter, y+ c g4507048_3p_a_at system), member 2 SLC7A2 8p22-p21.3 6542 m g4507064_3p_at secretory leukocyte peptidase inhibitor SLPI 20q12 6590 IO g4507432_3p_at testis enhanced gene transcript (BAX inhibitor 1) TEGT 12q12-q13 7009 trefoil factor 1 (breast cancer, estrogen-inducible sequence g4507450_3p_at expressed in) TFF1 21q22.3 7031 g4507452_3p_at trefoil factor 3 (intestinal) TFF3 21q22.3 7033 g4507488_3p_at thrombospondin 4 THBS4 5q13 7060 g4507810_3p_at UDP-glucose ceramide glucosyltra πsferase UGCG 9q31 7357 g4507812_3p_at UDP-glucose dehydrogenase UGDH 4p15.1 7358 g4507836_3p_at unc-5 homolog C (C. elegans) UNC5C 4q21-q23 8633 g4557031_3p_x_at lactate dehydrogenase B LDHB 12p12.2-p12.1 3945 amylo-1 , 6-glucosidase, 4-alpha-glucanotra πsferase (glycogen debranching enzyme, glycogen storage disease g4557282_3p_a_at type III) AGL 1p21 178 g4557336_3p_a_at argininosuccinate synthetase ASS 9q34.1 445 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene g4557354_3p_at B-cell CLL/lymphoma 2 BCL2 18q21 .33|18q21.3 596 g4557384_3p_at complement component 3 C3 19p13.3-p13.2 718 g4557580_3p_a_at fatty acid binding protein 5 (psoriasis-associated) FABP5 8q21.13 2171 g4557584_3p_al fatty acid binding protein 7, brain FABP7 6q22-q23 2173 g4557800_3p_a_at nucleoside phosphorylase NP 14q13.1 4860 keratin 18//similarto Keratin, type I cytoskeletal 18 (Cytokeratin 18) (K18) (CK 18)//similar to Keratin, type I KRT18//L0C1 32391 132391//3875// g4557887_3p_at cytoskeletal 18 (Cytokeratin 18) (K18) (CK 18) //LOC391827 12q13//4q26//5q23.2 391827 g4557887_3p_x_at keratin 18 KRT18 12q13 3875 CO keratin 5 (epidermolysis bullosa simplex, Dowling- C KRT5 12q12-q13 3852 co g4557889_3p_at Meara/Kobner/Weber-Cockayne types) CO ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, g4586929_3p_a_at yeast) UBE2E3 2q32.1 10477 g4755136_3p_at gap junction protein, alpha 1, 43kDa (connexin 43) GJA1 6q21-q23.2 2697 597 m g4757839_3p_at BCL2-related protein A 1 BCL2A1 15q24.3 g4757985_3p_a_at carbohydrate (chondroitin 6) sulfotra πsferase 3 CHST3 10q22.1 9469 CO m g4758039_3p_at cytochrome c oxidase subunit VIc COX6C 8q22-q23 1345 m g4758187_3p_at CDK2-associated protein 1 CDK2AP1 12q24.31 8099 g4758477_3p_s_at growth factor receptor-bound protein 14 GRB14 2q22-q24 2888 c g4758533_3p_at forkhead box A 1 F0XA1 14q12-q13 3169 g4758553_3p_a_at homeo box C6 H0XC6 12q13.3 3223 m g475881 1_3p_a_at interleukin 32 IL32 16p13.3 9235 IO g4758813_3p_at N-myc (and STAT) interactor NMI 2p24.3-q21 .3 9 111 solute carrier family 16 (monocarboxylic acid transporters), g4759117_3p_at member 6 SLC16A6 17q24.2 9120 solute carrier family 9 (sodium/hydrogen exchanger), member g4759139_3p_at 3 regulator 1 SLC9A3R1 17q25.1 9368 g4827037_3p_a_at tumor protein D52 TPD52 8q21 7163 g4827057_3p_s_at X-box binding protein 1 XBP1 22q12.1|22q12 7494 g4885060_3p_a_at v-akt murine thymoma viral oncogene homolog 1 AKT1 14q32.32|14q32.32 207 g4885094_3p_at polycomb group ring finger 4 PCGF4 10p1 1.23 648 g4885094_3p_x_at polycomb group ring finger 4 PCGF4 10p1 1.23 648 g4885132_3p_a_at centromere protein F, 350/400ka (mitosin) CENPF 1q32-q41 1063 g4885228_3p_at FAT tumor suppressor homolog 1 (Orosophila) FAT 4q35 2195 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene g4885268_3p_at GONF family receptor alpha 1 GFRA1 10q26 2674 g4885268_3p_a_at GDNF family receptor alpha 1 GFRA1 10q26 2674 g4885268_3p_x_at GDNF family receptor alpha 1 GFRA1 10q26 2674 g4885280_3p_a_at glutamate dehydrogenase 1 GLUD1 10q23.3 2746 g4885496_3p_at v-myb myeloblastosis viral oncogene homolog (avian) MYB 6q22-q23 4602 g4886476_3p_a_at ral guanine nucleotide dissociation stimulator-like 2 RGL2 6p21.3 5863 g4929572_3p_at START domain containing 10 STARD10 11q13 10809 g496077_3p_at sorbitol dehydrogenase SORD 15q15.3 6652 CO g4996892_3p_x_at heat shock 27kDa protein 1 HSPB1 7q1 1.23 3315 C co g5031976_3p_a_at pre-B-cell colony enhancing factor 1 PBEF1 7q22.3 10135 CO protein phosphatase 3 (formerly 2B), catalytic subunit, g5031988_3p_s_at gamma isoform (calcineurin A gamma) PPP3CC 8p21.3 5533 g5059165_3p_at chemokine (C-X-C motif) ligand 14 CXCL14 5q31 9547 m g5174386_3p_a_at prominin 1 PR0M1 4p15.32 8842 amyloid beta (A4) precursor protein-binding, family B, CO g5174436_3p_s_at member 3 APBB3 5q31 10307 m g5174628_3p_a_at 10401 m protein inhibitor of activated STAT, 3 PIAS3 1q21 OJ g5174656_3p_s_at N-myc downstream regulated gene 1 NDRG1 8q24.3 10397 g5174744_3p_a_at ubiquinol-cytochrome c reductase hinge protein UQCRH 1p34.1 7388 c g5453325_3p_at solute carrier family 19 (thiamine transporter), member 2 SLC19A2 1q23.3 10560 m g5453709_3p_at LIM and SH3 protein 1 LASP1 17q11-q21.3 3927 IO g5453757_3p_a_at nebulette NEBL 10p12 10529 g5453855_3p_a_at pericentriolar material 1 PCM1 8p22-p21.3 5108 ST6 (alpha-N-acetyl-neuraminy!-2,3-beta-galactosyl-1 ,3)-N- g5454091_3p_at acetylgalactosaminide alpha-2,6-sialyltransferase 2 ST6GALNAC2 17q25.1 10610 g5454143_3p_a_at ubiquitin D UBD 6p21 .3 10537 g5454183_3p_a_at mitogen-activated protein kinase kinase kinase 12 MAP3K12 12q13 7786 complement component 4A//complement component 432395//720// g5579450_3p_s_at 4B//complement component 4B, telomeric C4A//C4B 6p21.3 721 g5730086_3p_at t-complex-a εsociated-testis-expressed 1-like TCTE1L Xp21 6990 g5802975_3p_at chromosome 10 open reading frame 116 C10orf1 16 10q23.2 10974 g5802987_3p_a_at BTG family, member 2 BTG2 1q32 7832 g5803124_3p_x_at pim-2 oncogene PIM2 Xp11 .23 11040 g5817105_3p_s_at TSC22 domain family, member 3 TSC22D3 Xq22.3 1831 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene g5901 560_3p_a_at vascular endothelial growth factor VEGF 6p12 7422 g5901560_3p_s_at vascular endothelial growth factor VEGF 6p12 7422 g5901977_3p_at abhydralase domain containing 2 ABHD2 15q26 1 11057 solute earner family 7 (cationic amino acid transporter, y+ g5926731. .3p_a_at system), member 5 SLC7A5 16q24 3 8140 g6002658. .3p_a_at myelin protein zero-like 1 MPZL1 1q24 2 9019 g6005881_ 3p_at protease, seπne, 23 PRSS23 11q14 1 11098 g6005991_.3p_a_at calume πm CALU 7q32 813 g6006030. 3p_a_at S-phase kinase-associated protein 1A (p19A) SKP1A 5q31 6500 CO C g6382069. 3p_at cellular retiπoic acid binding protein 2 CRABP2 1q21 3 1382 co g65271 11. .3p_a_at SRY (sex determining region Y)-box 11 6664 CO S0X1 1 2p25 g6552334. .3p_s_at glutathione S-transferase pi GSTP1 11q13 2950 g6552334_.3p_x_at glutathione S-transferase pi GSTP1 11q13 2950 m g6642755. .3p_a_at PRO1 073 protein PRO1073 11cen-q12 3 29005 g665281 1 3p_at anterior gradient 2 homolog (Xenopus laevis) AGR2 7p21 3 10551 CO g6653225_ 3p_at m m g6912263_3p_s_at beta-site APP-cleaving enzyme 2 BACE2 21q22 3 25825 U J g6912277_3p_at COMM domain containing 3 COMMD3 10pter-q22 1 23412 g6912529_3p_at tetraspanin 15 TSPAN15 10q22.1 23555 c protein tyrosine phosphatase, non-receptor type 22 m g6912613_3p_a_at (lymphoid) PTPN22 1p13 3-p13 1 26191 IO solute earner family 7 (cationic ammo acid transporter, y+ g6912669_3p_a_at system), member 8 SLC7A8 14q11 2 23428 g7019542_3p_at seππe threonine kinase 39 (STE20/SPS1 homolog, yeast) STK39 2q24 3 27347 g7106795_3p_at chromosome 14 open reading frame 112 C14orf1 12 14q24 2 51241 g7262390_3p_at vav 3 oncogene VAV3 1p13 3 10451 g7305052_3p_a_at fer-1-lιke 3, myoferlin (C. elegans) FER1L3 10q24 26509 g7582287_3p_a_at protein tyrosine phosphatase type IVA, member 2 PTP4A2 1p35 8073 g7656921_3p_a_at chromatin modifying protein 2A CHMP2A 19q 27243 g7657105_3p_at gamma-aminobuty πc acid (GABA) A receptor, pi GABRP 5q33-q34 2568 g7657235_3p_at ιnosιtol(myo)-1(or 4)-monophosphatase 2 IMPA2 18p1 1 2 3613 g7657258_3p_a_at KIAA0040 KIAA0040 1q24-25 9674 g7657336_3p_at mutL homolog 3 (E coll) MLH3 14q24 3 27030 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene g7657372_3p_at tetraspanin 13 TSPAN 13 7p21 1 27075 g7657448_3p_at programmed cell death 4 (neoplastic transformation inhibitor) PDCD4 10q24 27250 g7657448_3p_s_at programmed cell death 4 (neoplastic transformation inhibitor) PDCD4 10q24 27250 g7657658_3p_a_at tπchorhiπophalangeal syndrome I TRPS1 8q24 12 7227 22q13 2-q13 31// g7661545_3p_a_at CGI 96 proteιn//simιlarto CGI-96 CG(-96// dJ222E13 2 22q13 2 27341//91 695 g7661607_3p_a_at putative ankyπn-repeat containing protein DKF2P564D166 17q23 3 261 15 g7662049_3p_s_at aryl-hydrocarbon receptor nuclear translocator 2 ARNT2 15q24 9915 g7662329_3p_s_at actin binding LIM protein family, member 3 ABLIM3 5q32 22885 CO C g7662395_3p_a_at pleckst πn and Sec7 domain containing 3 PSD3 8pter-p23 3 23362 CO g7705756_3p_s_at SID1 transmembrane family, member 2 S1DT2 11q23 3 51092 CO g7706187_3p_at mitochondrial ribosomal protein S30 MRPS30 5q1 1 10884 g7706434_3p_at headcase homolog (Drosophila) HECA 6q23-q24 51696 51704 m g7706450_3p_a_at G protein-coupled receptor, family C, group 5, member B GPRC5B 16p12 g7706520_3p_s_at nebulette NEBL 10p12 10529 CO g7706662_3p_a_at COMM domain containing 10 COMMD10 5q23 1 51397 m m g7706686_3p_s_at Enah/Vasp-like EVL 14q32 2 51466 g7706694_3p_s_at stathmin-like 3 STMN3 20q13 3 50861 T g7706728_3p_s_at T-box 3 (ulnar mammary syndrome) TBX3 12q24 1 6926 ι- g7770168_RC_3p_at m g7770258_RC_3p_a_at casein kinase 1, alpha 1 CSNK1A1 5q32 1452 IO g7959862_3p_at chromosome 6 open reading frame 115 C6orf115 6q24 1 58527

g804748_3p_at major histocompatibility complex, class I1B HLA-B 6p21 3 3106 g804748_3p_x_at major histocompatibility complex, class I1 B HLA-B 6p21 3 3106 g8922146_3p_a_at zinc finger protein 395 ZNF395 8p21 1 55893 g8922156_3p_at DKFZp564J157 protein DKF2p564J157 12q12 54458 g8922180_3p_at hypothetical protein DKFZp762E1312 DKF2p762E1312 2q37 1 55355 g8922236_3p_at dilute suppressor DSU 2q35 55686 g8922319_3p_at transmembrane protein 16A TMEM16A 11q13 3 55107 g8922902_3p_a_at hypothetical protein FLJ1 1155 FLJ1 1155 4q32 1 55314 g8922967_3p_a_at solute carrier family 39 {zinc transporter), member 9 SLC39A9 14q24 1 55334 g8923340_3p_at hypothetical protein FLJ20366 FU20366 8q23 2 55638 g8923408_3p_s_at nucleoredoxin NXN 17p13 3 64359 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene g8923568_3p_a_at hypoxia-inducible factor 1, alpha subunit inhibitor HIF1AN 10q24 55662 g8923685_3p_x_at zinc finger protein 587 ZNF587 19q13.43 84914 g8923782_3p_a_at chromosome 20 open reading frame 35 C20orf35 20q13.12 55861 g8924051_3p_at calcium/calmoduli π-dependent protein kinase Il inhibitor 1 CAMK2N1 1p36.12 55450 g928081 5_3p_a_at myosin Vl MYO6 6q13 4646 g9502012_3p_a_at choline phosphotransferase 1 CHPT1 12q 56994 g9506660_3p_a_at hypothetical protein FLJ20152 FU20152 5p15.1 54463 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, g9665246_3p_at antitrypsin), member 3 SERPINA3 14q32.1 12 CO C g9801844_3p_at RNA binding motif protein 5 RBM5 3p21.3 10181 CO g9951924_3p_at carbonic anhydrase XII CA1 2 15q22 771 CO sema domain, transmembrane domain (TM), and cytoplasmic g9963852_3p_at domain, (semaphorin) 6A SEMA6A 5q23.1 57556 Hs.100000.1.A1_3p_at S100 calcium binding protein A8 (calgra πulin A) S100A8 1q21 6279 m Hs.100686.0.A1_3p_at breast cancer membrane protein 11 BCMP1 1 7p21.1 155465 CO Hs.102406.0.A1_3p_at Melanophilin MLPH 2q37.3 79083 > m Hs.10247.0.S3_3p_at activated leukocyte cell adhesion molecule ALCAM 3q13.1 214 m Hs.102793.0.A1_3p_at chromosome 4 open reading frame 7 C4oπ7 4q13|4q13 260436 Hs.103189.1 .A1_3p_at chromosome 14 open reading frame 43 C14orf43 14q24.3 91748 T Hs.103391.0.A2_3p_at insulin-like growth factor binding protein 5 IGFBP5 2q33-q36 3488 ι- m Hs.1 03391 .0.A2_3p_s_at insulin-like growth factor binding protein 5 IGFBP5 2q33-q36 3488 IO Hs.10432.0.A1_3p_at Rho-related BTB domain containing 3 RHOBTB3 5q15 22836 Hs.1 04696.0.S1 _3p_a_at KIAA1324 KIAA1324 1p13.3 57535 Hs.1 04696.0.S2_3p_at KIAA1324 KIAA1324 1p13.3 57535 Hs.105445.2.A1_3p_at GDNF family receptor alpha 1 GFRA1 10q26 2674 Hs.10587.0.S1_3p_at desmuslin DMN 15q26.3 23336 Hs.106283.2.A1_3p_at retinol dehydrogenase 10 (all-trans) RDH10 8q21.1 1 157506 Hs.1 07001 .0.S1_3p_a_at RNA binding motif protein 17 RBM17 10p15.1 84991 Hs.1 07767. 1.A1_3p_at calcium/calmodulin-dependent protein kinase Il inhibitor 1 CAMK2N1 1p36.12 55450 Hs.107767.1 .A1_3p_x_at calcium/calmodulin-dependent protein kinase Il inhibitor 1 CAMK2N1 1p36.12 55450 Hs.108327.1 .A2_3p_at forkhead box P 1 FOXP1 3p14.1 27086 Hs.108957.0.A1_3p_a_at Hs.1 10080.0.S 1_3p_s_at ovostatin 2 OVOS2 12p1 1.21 144203 Table7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez ( microtubule associated serine/threonine kinase family Hs.1 10341.0.A2_3p_at member 4 MAST4 5q12.3 23227 Hs.1 104.0.S2_3p_at bone morphogenetic protein 5 BMP5 6p12.1 653 Hs.1 1050.2.A2_3p_s_at fatty acid synthase FASN 17q25 2194 Hs.1 1090.0.S2_3p_at membrane-spanning 4-domains, subfamily A , member 7 MS4A7 11q12 58475 Hs.1 11334.2.S1_3p_at epithelial membrane protein 2 EMP2 16p13.2 2013 Hs.1 11334.3.A1_3p_at Chromosome 9 open reading frame 132 EEIG1 — 399665 Hs.1 12034.1.S1_3p_a_at oxysterol binding protein-like 5 0SBPL5 11p15.4 114879 Hs.1 12165.0.A1_3p_at hypothetical LOC401052 LOC401 052 3p25.3 401052 CO C Hs.115127.0.S1_3p_at Insulin-like growth factor 1 receptor IGF1R 15q26.3 3480 CO Hs.116038.0.A1_3p_at spermatogenesis associated 18 homolog (rat) SPATA18 4q11 132671 CO Hs.116369.0.S1_3p_at Transcribed locus Hs.1 1637.0.A1_3p_at AF4/FMR2 family, member 4 AFF4 5q31 27125 Hs.1 17176.1.S1_3p_at poly(A) binding protein, nuclear 1 PABPN1 14q1 1.2-q13 8106 m Hs.1 1951.0.S2_3p_at ectonucleotide pyrophosphatase/phosphodiesterase 1 ENPP1 6q22-q23 5167 CO Hs.1 19598.1.A1_3p_at hypothetical protein MGC13024 MGC13024 16p1 1.2 93129 m m CD59 antigen p18-20 (antigen identified by monoclonal OO Hs.1 19663.0.S1_3p_a_at antibodies 16.3A5, EJ16, EJ30, EL32 and G344) CD59 11p13 966 Hs.119769.0.A1_3p_at KIAA0907 KIAA0907 1q22 22889 T Hs.121706.0.A1_3p_a_at Leucine-rich repeats and immunoglobulin-like domains 1 LRIG1 3p14 26018 ι- m Hs.122489.0.S1_3p_at hypothetical protein LOC201895 LOC201895 4p14 201895 IO Hs.122489.0.S2_3p_at Hypothetical protein LOC201895 LOC201895 4p14 201895 Hs.12365.0.S2_3p_at synaptotagmin XIII SYT13 11p12-p11 57586 Hs.124427.0.A1_3p_at RAD9 homolog A (S. pombe) RAD9A 11q13.1-q13.2 5883 Hs.124427.0.A1_3p_x_at RAD9 homolog A (S. pombe) RAD9A 11q13.1-q13.2 5883 Hs.124740.0.A1_3p_at MARVEL domain containing 2 MARVELD2 5q13.2 153562 Hs.125019.0.A1_3p_at AF4/FMR2 family, member 3 AFF3 2q1 1.2-q12 3899 Hs.1 2532.0.A2_3p_s_at chromosome 1 open reading frame 2 1 C1orf21 1q25 81563 Hs.127264.0.A1_3p_at Hs.127756.0.A1_3p_at RAS-like, estrogen-regulated, growth inhibitor RERG 12p12.3 85004 Hs.127842.0.S2_3p_at hepatoma-derived growth factor, related protein 3 HDGFRP3 15q1 1.2 50810 Hs.1 27842.1 .A1_3p_a_at Hepatoma-derived growth factor, related protein 3 HDGFRP3 15q1 1.2 50810 Hs.128280.0.A1_3p_at Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.128685.0.A1_3p_at chloride intracellular channel 6 CLIC6 21q22.12 54102 Hs.12921.0.A1_3p_at transmembrane protein 25 TMEM25 11q23.3 84866 Hs.129943.0.S1_3p_at signal-induced proliferation-associated 1 like 3 SIPA1L3 19q13.13 23094 Hs. 129943.0.S1_3p_s_at signal-induced proliferation-associated 1 like 3 SIPA1L3 19q13.13 23094 Potassium voltage-gated channel, Isk-related family, member Hs.130315.0.A1_3p_at 4 KCNE4 2q36.3 23704 Hs.133107.0.A1_3p_at Pvt1 oncogene homolog, MYC activator (mouse) PVT1 8q24 5820 Hs.133107.0.S1_3p_at Pvt1 oncogene homolog, MYC activator (mouse) PVT1 8q24 5820 Hs.133300.0. A1_3p_x_at CO C Hs.133342.0.S1_3p_at Glypican 1 GPC1 2q35-q37 2817 co Hs.133342.0.S1_3p_x_at Glypican 1 GPC1 2q35-q37 2817 CO Solute carrier family 40 (iron-regulated transporter), member Hs.133525.0.A1_3p_at 1 SLC40A1 2q32 30061 Hs.13472.2.A1_3p_at Echinoderm microtubule associated protein like 4 EML4 2p22-p21 27436 m Hs. 136525.0.A1_3p_at hypothetical protein MGC33214 MGC33214 5q14.3 153396 CO Hs.143563.0.A1_3p_at Hypothetical protein MGC33365 MGC33365 3q24 205428 m VO Hs.14368.0.S1_3p_a_at SH3 domain binding glutamic acid-rich protein like SH3BGRL Xq13.3 6451 m Hs.144151.0.A1_3p_at Transcribed locus ... Hs.1 44477.0.S2_3p_x_at casein kinase 1, alpha 1 CSNK1A1 5q32 1452 73 c Hs.144477.0.S3_3p_at Casein kinase 1, alpha 1 CSNK1A1 5q32 1452 m Hs.144477.0.S3_3p_x_at Casein kinase 1, alpha 1 CSNK1A1 5q32 1452 IO Hs.14449.0.S1_3p_s_at KIAA1609 protein KIAA1609 16q24.1 57707 Hs.145362.3.A1_3p_a_at hypothetical LOC541469 protein LOC541469 19q13.2 541469 Hs.1466.3.S1_3p_a_at glycerol kinase GK Xp21.3 2710 quiπolinate phosphoribosyltransferase (πicotinate- πucleotide Hs.148324.0.S1_3p_x_at pyrophosphorylase (carboxylating)) QPRT 16p1 1.2 23475 Hs.148661 .0.A1_3p_a_at Immunoglobulin kappa variable 1-5 IGKC 2p12 3514 Hs.148661 .0.A1_3p_x_at Immunoglobulin kappa variable 1-5 IGKC 2p12 3514 Hs.149006.0.A1_3p_at Enah/Vasp-like EVL 14q32.2 51466 Hs.149846.1.A1_3p_at Integrin, beta 5 ITGB5 3q21.2 3693 Hs.149846.1.S1_3p_a_at integrin, beta 5 ITGB5 3q21.2 3693 Hs.150395.2.A1_3p_at Hs.150551.0.S1_3p_at ADP-ribosylatio π factor-like 6 interacting protein 2 ARL6IP2 2p22.2-p2Z1 64225 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.152167.0.A1_3p_at CDNA FU42561 fis, clone BRACE3006463 Hs.152738.2.A1_3p_s_at Mof4 family associated protein 1 MRFAP1 4p16.1 93621 Hs.15299.0.S1_3p_s_at hexamethylene bis-acetamide inducible 1 HEXIM1 17q21.31 10614 Hs.153205.0.S1_3p_at LIM homeobox transcription factor 1, beta LMX1B 9q34 4010 Solute carrier family 7 (cationic amino acid transporter, y+ Hs.153985.1.A1_3p_at system), member 2 SLC7A2 8p22-p21 .3 6542 Hs.154654.0.S2_3p_a_at cytochrome P450, family 1, subfamily B, polypeptide 1 CYP1B1 2p21 1545 Hs.15501 7.0.S1_3p_a_at nuclear receptor interacting protein 1 NRIP1 21q1 1.2 8204 8614 CO Hs.155223.0.S4_3p_at stanniocalcin 2 STC2 5q35.1 C Hs.155489.1.S1_3p_a_at synaptotagmin binding, cytoplasmic RNA interacting protein SYNCRIP 6q14-q15 10492 co CO Hs.155956.0.S1_3p_at N-acetyltransferase 1 (arylamine N-acetyltransferase) NAT1 8p23.1-p21 .3 9 immunoglobulin kappa constant /// immunoglobulin kappa Hs.1561 10.2.A1_3p_a_at variable 1-5 IGKC /// IGKV1-5 2p12 28299/3514 Hs.156456.0.A1_3p_at Hypothetical protein MGC2477 MGC2477 11q12.3 79081 m Hs.157494.0.A1_3p_at CO o Hs.16064.0.A1_3p_at CNKSR family member 3 CNKSR3 6q25.2 154043 m 202 m Hs.161002.0.S1_3p_at absent in melanoma 1 AIM1 6q21 Hs.161712.0.S1_3p_at Bone morphogenetic protein receptor, type IB BMPR1B 4q22-q24 658 Hs.163533.0.A1_3p_at c V-erb-a erythroblastic leukemia viral oncogene homolog 4 m Hs.163533.0.S1_3p_at (avian) ERBB4 2q33.3-q34 2066 Hs.164226.0.A1_3p_at IO Hs.164568.1.Ai_3p_at Transcribed locus Hs.1 65728.0.A1 _3p_x_at Polymerase (RNA) Il (DNA directed) polypeptide E, 25kDa P0LR2E 19p13.3 5434 Hs.1 66361 .0.S1_3p_x_at Glucuronidase, beta-like 1 ... 5q13.2 402223 Hs.1 67531 .0.S2_3p_at methylcrotonoyl-Coenzyme A carboxylase 2 (beta) MCCC2 5q12-q13 64087 Hs.167791.1.A1_3p_x_at CDNA FLJ45662fis, clone CTONG2027150 Hs.1 6931 3.0.S1 _3p_s_at phosphoglycerate kinase 1 PGK1 Xq13 5230 Hs.169946.0.S3_3p_at GATA binding protein 3 GATA3 10p15 2625 Hs.170171.1.A1_3p_a_at glutamate-ammonia ligase (glutamine synthetase) GLUL 1q31 2752 Hs.170290.0.A2_3p_at discs, large homolog 5 (Drosophila) DLG5 10q23 9231 Hs.170290.2.A1_3p_at Discs, large homolog 5 (Drosophila) DLG5 10q23 9231 Hs.170345.0.S2_3p_at hypothetical protein FLJ13710 FLJ13710 15q23 79875 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.170610.0.A1_3p_at mitogen-activated protein kinase kinase kinase 1 MAP3K1 5q1 1.2 4214 Hs.170917.7.S2_3p_at Hs.171395.0.S1_3p_at B-cell CLL/lymphoma 2 BCL2 18q21 .33 596 Hs.171626.0.S1_3p_a_at S-phase kiπase-associated protein 1A (p19A) SKP1A 5q31 6500 Hs.171626.0.S3_3p_at S-phase kinase-associated protein 1A (p19A) SKP 1A 5q31 6500 Transcribed locus, moderately similar to NP_689672.2 Hs.171952.1.S1_3p_at hypothetical protein MGC45438 [Homo sapiens] microtubule associated monoxygenase, calponin and LIM Hs.172035.0.S1_3p_at domain containing 3//chromosome 16 open reading frame 34 MICAL3//C16orf34 22q11.21//16p13.3 57553//90861 CO π C Hs.172932.0.S1_3p_at bromodomai and WD repeat domain containing 1 8RWD1 21q22.2 54014 CO¬ Hs.173108.0.A1_3p_at Sprouty-related, EVH1 domain containing 2 SPRED2 2p14 200734 CO Hs.173802.0.S2_3p_at TBC1 domain family, member 4 TBC1D4 13q22.2 9882 Hs.177781.0.S1_3p_s_at hypothetical protein MGC5618 MGC5618 ... 79099 Hs.178137.1.A1_3p_at transducer of ERBB2, 1 TOB1 17q21 10140 m Hs.17962.0.A1_3p_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 CO Hs.180059.0.S1_3p_at cyclin-dependent kinase 6 CDK6 7q21-q22 1021 m endoplasmic reticulum-golgi intermediate compartment 32 m Hs.180428. 1.S2_3p_a_at kDa protein KIAA1 181 5q35.1 57222 Hs.180908.0.S1_3p_at FLJ45983 protein FU45983 10p14 399717 c Hs.1 80952.0.A2_3p_a_at dynactin 4 (p62) DCTN4 5q31-q32 51 164 Hs.18106.0.A1_3p_at Polycomb group ring finger 3 PCGF3 4p16.3 10336 m immunoglobulin lambda locus//immunog[obulin lambda IO constant 1 (Meg marker)//immunoglobulin lambda constant 2 (Kern-Oz- marker)// immunoglobulin lambda variable 3-25// IGL@//IGLC1// 28793// 2881 5// immunoglobulin lambda variable 2-14// immunoglobulin IGLC2//IGLV3-25 22q1 1.1-q1 1.2// 28831//3535// Hs.181125.2.A1_3p_x_at lambda joining 3 //IGLV2-14//IGLJ3 22q11.2 3537//3538 Hs.181693.0.A1_3p_s_at WD repeat and P rVE domain containing 3 WDFY3 4q21.23 23001 Hs.1 82429.2.S1 _3p_a_at protein disulfide isomerase family A, member 6 PDIA6 2p25.1 10130 heterogeneous nuclear ribonucleoprotein C (C1/C2) /// similar to Heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNP HNRPC /// Hs.1 82447.3.A1 _3p_a_at C 1 / hnRNP C2) LOC390615 14q1 1.2 /// 15q25.1 3 183 /// 390615 Hs.182723.0.S1_3p_at Hypothetical gene supported by AB002449 5q22.3 441 104 Hs.183803.0.A1_3p_at deoxyribonuclease I DNASE1 16p13.3 1773 Hs.183803.0.A1_3p_x_at deoxyribonuclease I DNASE1 16p13.3 1773 Hs.1 84325.1 .A 1_3p_a_at Ubiquitiπ-conjugating enzyme E2, J 1 (UBC6 homolog, yeast) UBE2J1 6q15 51465 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.188006.0.S1_3p_s_at Rho-related BTB domain containing 3 RH0BTB3 5q15 22836 Hs.18821 1.0.A1_3p_at AF4/FMR2 family, member 3 AFF3 2q1 1.2-q12 3899 Hs.18948.0.A1_3p_at abhydrolase domain containing 2 ABHD2 15q26.1 11057 Hs.1906.2.S1_3p_s_at prolactin receptor PRLR 5p14-p13 5618 Hs.1 92905.0.A1_3p__s_at Mortality factor 4 like 2 M0RF4L2 Xq22 9643 Hs.194359.0.A1_3p_at hypothetical protein FLJ32130 FLJ32130 16p1 1.2 146540 Hs.195729.0.A1_3p_at jumonji domain containing 2B JMJD2B 19p13.3 23030 Hs.197653.0.A1_3p_at Mitochondrial ribosomal protein S30 MRPS30 5q11 10884

CO Hs.199754.0.S1_3p_at KIAA1324 KIAA1324 1p13.3 57535 C co Hs.2006.0.S1_3p_a_at glutathione S-transferase M3 (brain) GSTM3 1p13.3 2947 CO Hs.201925.0.S1_3p_at CDNA FLJ13446 fis, clone PLACE1002968 Hs.20196.0.S2_3p_at adenylate cyclase 9 ADCY9 16p13.3 115 Hs.2021.0.S1_3p_s_at Sp1 transcription factor SP1 12q13.1 6667 m Hs.20341 8.0.A1_3p_s_at Hypothetical protein LOC440253 LOC339005 15q1 1.2 339005 CO Hs.204354.0.S2_3p_at ras hotnolog gene family, member B RHOB 2p24 388 m Hs.205660.0.A1_3p_at Inositol 1,4,5-triphosphate receptor, type 1 ITPR 1 3p26-p25 3708 m Hs.205660. 1.A1_3p_a_at Inositol 1,4,5-triphosphate receptor, type 1 ITPR1 3p26-p25 3708 HS.206868.0.S1_3p_at B-cell CLL/lymphoma 2 BCL2 18q21.33 596 c Calcium channel, voltage-dependent, L type, alpha 1D Hs.208647.0.A1_3p_at subunlt CACNA1D 3p14.3 776 m Hs.209065.0.S2_3p_at KIAA0319-like KIAA0319L 1p34.2 79932 IO UDP-N-acetyl-alpha-D-galactosaminerpolypeptide N Hs.21035.0.S1_3p_a_at acetylgalactosaminyltransferase-like 1 GALNTL1 14q24.1 57452 Hs.210761 .0.S1_3p_a1 Hs.21 1535.0.A1_3p_at Guanylate binding protein 5 GBP5 1p22.2 115362 Hs.21 1601.1.S1_3p_al Poly(rC) binding protein 2 PCBP2 12q13.12-q13.13 5094 MRNA; cDNA DKFZp686N1345 (from clone Hs.21380.0.S1_3p_at DKFZp686N1345) — Hs.21851.0.S1_3p_al Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 Hs.21851.0.S2_3p_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 Hs.21948.0.A1_3p_at Zinc finger protein 533 ZNF533 2q31.2-q31.3 151 126 Hs.222399.0.S1_3p_a_at signal peptide, CUB domain, EGF-like 2 SCUBE2 11p15.3 57758 Hs.223025.0.S2_3p_a_at RAB31, member RAS oncogene family RAB31 18p1 1.3 11031 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.22483.0.S1_3p_at MRNA; cDNA DKFZp762M127 (from clone DKFZp762M127) inhibitor of kappa light polypeptide gene enhancer in B-cells, Hs.226573.0.S3_3p_a_at kinase beta IKBKB 8p1 1.2 3551 inhibitor of kappa light polypeptide gene enhancer in B-celts, Hs.226573.0.S3_3p_x_at kinase beta IKBKB 8p1 1.2 3551 Hs.227513.0.A1_3p_at DπaJ (Hsp40) homolog, subfamily C, member 1 DNAJC1 10p12.31 64215 Hs.22862.0.A1_3p_at SRY (sex determining region Y)-box 9 (campomelic Hs.2316.0.S1_3p_a_at dysplasia, autosomal sex-reversal) SOX9 17q24.3-q25.1 6662

CO Hs.234489.1.A1_3p_a_at lactate dehydrogenase B LDHB 12p12.2-p12.1 3945 C Hs.235857.0.A1_3p_at CDNA FU32401 fis, clone SKMUS2000339 CO CO Hs.23703.0.A2_3p_at UDP-glucose ceramide glucosyltransferase UGCG 9q31 7357 Hs.237396.1 .A1_3p_a_at hypothetical gene supported by AF275804 LOC388279 16q12.2 388279 Hs.237868.1 .S1_3p_at lnterleukin 7 receptor IL7R 5p13 3575 m Hs.23838.1.A2_3p_at calcium channel, voltage-dependent, L type, alpha 1D subunit CACNA1D 3p14.3 776 Hs.2384.0.S1_3p_a_at tumor protein D52 TPD52 8q21 7163 CO 4-. m Hs.2384.0.S3_3p_a_at tumor protein D52 TPD52 8q21 7163 m Hs.23881.1.A1_3p_at Keratin 7 KRT7 12q12-q13 3855 Hs.239138.0.S2_3p_at pre-B-cell colony enhancing factor 1 PBEF1 7q22.3 10135 T Hs.239176.0.S3_3p_at insulin-like growth factor 1 receptor IGF1 R 15q26.3 3480 ι- Hs.239727.0.S1 _3p_a_at desmocolliπ 2 DSC2 18q12.1 1824 m Hs.239870.1 .S2_3p_a_at chromosome 2 open reading frame 12 C2orf12 2q24.3 192137 IO Hs.24131.0.S1_3p_at serum/glucocorticoid regulated kinase family, member 3 SGK3 8q12.3-8q13.1 23678 Hs.241471 .1.A1_3p_at Eπah/Vasp-like EVL 14q32.2 51466 Hs.24192.0.S2_3p_at Synaptopodin 2 SYNP02 4q26 171024 Hs.242322.0.A1_3p_at RNA (guanine-9-) methyltransferase domain containing 3 RG9MTD3 9p13.2 158234 Hs.24341.0.A2_3p_at WW domain containing transcription regulator 1 WWTR1 3q23-q24 25937 ATP synthase, H+ transporting, mitochondrial FO complex, HS.247790.0.S1_3p_s_at subunit c (subunit 9), isoform 2 ATP5G2 12q13.13 517 Hs.247898.0.A1_3p_s_at Hs.247898.0.S1_3p_x_at immunoglobulin lambda variable 2-14 IGLV2-14 22q1 1.2 28815 Hs.24791 1.0.A1_3p_at Hs.247954.0.S1_3p_at Thrombospondin 1 THBS1 15q15 7057 HS.247976.0.S1 _3p_s_at estrogen receptor 1 ESR1 6q25.1 2099 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.247984.0.S1_3p_s_at glutamate-ammo πia ligase (glutami πe synthetase) GLUL 1q31 2752 Hs.250535.1.A2_3p_at rabaptin, RAB GTPase binding effector protein 1 RABEP1 17p13.2 9135 Hs.252514.0.A1_3p_at CDNA FLJ43403 fis, clone OCBBF2016612 ... — ... Hs.25252.0.S1_3p_at Prolactin receptor PRLR 5p14-p13 561 8 Hs.252639.0.A1_3p_at hypothetical protein FLJ21439 FLJ21439 15q14 80208 Hs.25318.0.S1_3p_at Clone 25194 mRNA sequence ... — Hs.25338.0.A1_3p_at protease, serine, 23 PRSS23 11q14.1 11098 Hs.253594.0.A1_3p_at Trichorhinophalangeal syndrome I TRPS1 8q24.12 7227

CO Hs.2541 05.1 ,A1 _3p_a_at enolase 1, (alpha) EN01 1p36.3-p36.2 2023 C Hs.2541 05.1 .A1 _3p_x_at enolase 1, (alpha) ENO1 1p36.3-p36.2 2023 CO CO Hs.2541 05.1 .S1_3p_s_at Hs.2554.0.A2_3p_at ST6 beta-galactosamide alpha-2,6-sialyltranferase 1 ST6GAL1 3q27-q28 6480 Hs.2554.1.A1_3p_x_at m Hs.256703.0.A1_3p_at likely ortholog of mouse schlafen 5 MGC19764 17q12 162394 CO Hs.257786.0.A1_3p_at _ m Hs.258822.0.A1_3p_at Transcribed locus m Hs.25925.0.S1_3p_at hypothetical gene supported by AF038182; BC009203 LOC90355 5q21.1 90355 Hs.259768.0.A1_3p_at T proline/arginine-rich end leucine-rich repeat protein /// ι- Hs.26102.0.A1_3p_a_at trichorhinophalangeal syndrome I PRELP /// TRPS1 1q32 /// 8q24.12 5549/ 7227 m Hs.26102.2.S1_3p_a_at trichorhinophaiangeal syndrome I TRPS1 8q24.12 7227 IO Hs.26395.0.A1_3p_at Erythrocyte membrane protein band 4.1-like 1 EPB41L1 20q1 1.2-q12 2036 Hs.26395.0.S1_3p_s_at erythrocyte membrane protein band 4.1-like 1 EPB41L1 20q1 1.2-q12 2036 Hs.2641 0.0.A1_3p_s_at hypothetical protein FLJ34443 FU34443 4p16.3 285464 Transcribed locus, weakly similar to XP_510104.1 PREDICTED: similar to hypothetical protein FLJ25224 [Pan Hs.264622.0.S1_3p_at troglodytes] — — — Transcribed locus, weakly similar to XP_510104.1 PREDICTED: similar to hypothetical protein FU25224 [Pan Hs.264622.0.S1_3p_x_at troglodytes] — — — Hs.265829.2.S1_3p_at KlAA1 856 protein KIAA1856 7p22.1 84629 Hs.2671 82.0.S2_3p_at T-box 3 (ulnar mammary syndrome) TBX3 12q24.1 6926 Hs.267182.1.A1_3p_at T-box 3 (ulnar mammary syndrome) TBX3 12q24.1 6926 Hs.2671 82.1.A1_3p_s_at T-box 3 (ulnar mammary syndrome) TBX3 12q24.1 6926 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.2671 82.1 .S1_3p_s_at T-box 3 (ulnar mammary syndrome) TBX3 12q24.1 6926 Hs.267963.0.S2_3p_at Hs.270016.0.S1_3p_at Hypothetical protein LOC92312 LOC92312 1q22 92312 Ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, Hs.270124.0.S1_3p_at yeast) UBE2E3 2q32.1 10477 HsJ271536.0.S1_3p_at X (inactive)-specific transcript XIST Xq13.2 7503 Hs.272288.0.S1_3p_at estrogen receptor 1 ESR1 6q25.1 2099 monogenic, audiogenic seizure susceptibility 1 homolog Hs.272306.0.S1_3p_at (mouse) MASS1 5q13 84059 CO 2813 C Hs.274454.0.S1_3p_at glycoprotein 2 (zymogen granule membrane) GP2 16p12 CO Hs.27495.0.S1_3p_al synaptotagmin VII SYT7 11q12-q13.1 9066 CO Hs.278004.0.S1_3p_at Trichorhinophatangeal syndrome I TRPS1 8q24.12 7227 Hs.278244.0.A1_3p_at HS.278422.0.S1_3p_a_at zinc finger protein 385 2NF385 12q13.13 25946 m Hs.2785.1.S1_3p_a_at keratin 17 KRT17 17q12-q21 3872 CO Hs.278528.1 .A1_3p_x_at myeloid-associated differentiation marker MYADM 19q13.42 91663 m Hs.278628.0.S1_3p_at shroom SHRM 4q21.1 57619 m Phosphatase and tensin homolog (mutated in multiple Hs.27865.0.S1_3p_at advanced cancers 1) PTEN 10q23.3 5728 T macrophage stimulating 1 (hepatocyte growth factor- ι- Hs.278657.1 .S1_3p_a_at like)//macrophage stimulating, pseudogene 9 MST1//MSTP9 3p21//1p36.13 11223//4485 m Hs.278850.1 .S1_3p_at KIAA1772 KIAA1772 18q11.1-q1 1.2 80000 IO metastasis associated iung adenocarcinoma transcript 1 Hs.279789.6.S1_3p_a_at (non-coding RNA) MALAT1 11q13.1 378938 metastasis associated lung adenocarcinoma transcript 1 HS.279789.6.S1_3p_x_at (non-coding RNA) MALAT1 11q13.1 378938 metastasis associated lung adenocarcinoma transcript 1 Hs.279789.6.S2_3p_s_at (non-coding RNA) MALAT1 11q13.1 378938 Hs.281022.0.A1_3p_at KIAA1 456 protein KIAA1456 8p22 57604 Hs.282908.0.A1_3p_at AF4/FMR2 family, member 4 AFF4 5q31 27125 Hs.283330.1 .S1_3p_s_at eukaryotic translation initiation factor 4B EIF4B 12q13.13 1975 Hs.283738.1.A1_3p_at Casein kinase 1, alpha 1 CSNK1A1 5q32 1452 Hs.283742.0.S1_3p_at hypothetical protein L0C1 53561 L0C1 53561 5q13.2 153561 Hs.284394.1.A2_3p_at collagen, type XXVII, alpha 1 COL27A1 9q32 85301 Hs.284394.1.A3_3p_at Collagen, type XXVII, alpha 1 COL27A1 9q32 85301 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Eπtrez Gene Hs 285753 OS2_3p_at stathmin-like 3 STMN3 20q13 3 50861 Hs 285803 0 S1_3p_at LOC440156 ... 14q11 1 440156 Hs 285976 2 S1_3p_a_at LAG1 longevity assurance homolog 2 (S cerevisiae) LASS2 1q21 2 29956 solute earner family 1 (glutamate/neutral amino acid Hs 286049 2 S1_3p_s_at transporter), member 4 SLC1A4 2p15-p13 6509 Hs 286124 OA2_3p_S_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 Hs 286124 1 A1_3p_s_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 Hs 28777 3 A1_3p_a_at histone 1, H2ac HIST1H2AC 6p21 3 8334 Hs 287791 0 A1_3p_at RAS-like, estrogen-regulated, growth inhibitor RERG 12p12 3 85004 CO C Hs 287791 0 S1_3p_at RAS-like, estrogen-regulated, growth inhibitor RERG 12p12 3 85004 CO Hs 288042 OA2_3p_at zinc finger protein 703 ZNF703 8p12 80139 CO Hs 288512 0 S1_3p_at chromosome X open reading frame 10 CXorflO Xq26 93949 Hs 288549 0 S1_3p_at Zinc finger protein 587 ZNF587 19q13 43 84914 Hs 288660 0 A1_3p_at G protein-coupled receptor, family C, group 5, member A GPCR5A 12p13-p12 3 9052 m Hs 288684 0 S1_3p_at RAS p21 protein activator (GTPase activating protein) 1 RASA1 5q13 3 5921 CO -P- Hs 288973 1 S1_3p_a_at selenium binding protein 1 SELENBP1 1q21-q22 8991 m m Hs 289103 0 A1_3p_at SMA4 SMA4 5q13 11039 Hs 290217 0 A1_3p_at CDNA FU43851 fis, clone TESTI4006728 T hypothetical gene supported by AY338954// hypothetical LOC400880// 400880// gene supported by AY338954// hypothetical gene supported LOC440155// 22q1 1 1//14q11 Vl 440155// ι- m Hs 290347 0 A1_3p_at by AY338954 LOC440161 14q11 2 440161 Transcribed locus, weakly similar to NP_060190 1 sigπal- IO transducing adaptor proteιn-2, brk kinase substrate [Homo Hs 292396 0 S1_3p_at sapiens] Hs 293702 0 S1_3p_at X (inactive) specific transcript XIST Xq13 2 7503 Hs 296162 0 A1_3p_at Ras association (RalGDS/AF-6) domain family 4 RASSF4 10q1 1 2 1 83937 Hs 296638 1 A1_3p_a_at Hs 29716 0 S1_3p_at hypothetical protein FU10980 FU10980 15q21 2-q21 3 56204 pleckstnn homology domain containing, family F (with FYVE Hs 29724 0 S1_3p_a_at domain) member 2 PLEKHF2 8q22 1 79666 Hs 30101 1 0 S1_3p_a_at jumonji domain containing 2B JMJ D2B 19p13 3 23030 Hs 30101 1 0 S2_3p_at jumonji domain containing 2B JMJD2B 19p13 3 23030 Hs 30101 1 1 A1_3p_a_at Jumonji domain containing 2B JMJD2B 19p13 3 23030 Hs 301365 0 S1_3p_s_at immunoglobulin heavy constant mu IGHM 14q32 33 3507 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene HS.301417.0.A1. 3p_at AHNAK nucleoprotein (desmoyokin) AHNAK 11q12.2 79026 HS.301746.1.S1..3p_at RAP2A, member of RAS oncogene family RAP2A 13q34 5911 HS.301760.0.S2. 3p_s_at frequeπin homolog (Drosophila) FREQ 9q34 23413 Hs.301997.LS1. 3p_s_at chromosome 1 open reading frame 22 C1orf22 1q24-q25 80267 Hs.302073-0.S1. 3p_s_at calumeπiπ CALU 7q32 813 Hs.303090.0-S2. 3p_at protein phosphatase 1, regulatory (inhibitor) subunit 3C PPP1R3C 10q23-q24 5507 Hs.303125-0.S2. 3p_at PERP, TP53 apoptosis effector PERP 6q24 64065 HS.303125.0.S2. 3p_x_at PERP, TP53 apoptosis effector PERP 6q24 64065

CO HS.303632.0.A1. .3p_at hypothetical protein LOC1 53561 LOC1 53561 5q13.2 153561 C Hs.304918-0.S1. 3p_at par-6 partitioning defective 6 homolog beta (C. elegans) PARD6B 20q13.13 84612 CO¬ CO 4q31 .3-q33|4q31.1- Hs.306079.1.A1_3p_s_at guanylate cyclase 1, soluble, alpha 3 GUCY1A3 q31.2 2982 Hs.306201 .0.S1 _3p_s_at SLIT and NTRK-like family, member 6 SLITRK6 13q31.1 84189 Hs.306314.0.S1_3p_at m Estrogen receptor 1 ESR1 6q25.1 2099 Hs.306344.0.S1_3p_at hypothetical gene supported by AL1 17475 LOC439948 10p15.1 439948 CO -P- m Hs.306357.0.A1_3p_at m Hs.30671 6.0.S1 _3p_x_at CDNA: FLJ21228 fis, clone COL00739 Hs.306741.0.S1_3p_at CDNA: FLJ21346 fis, clone COL02705 Hs.309950.0.A1_3p_at eukaryotic translation initiation factor 4E member 3 EIF4E3 3p14 317649 c Hs.31218.1.S1_3p_at secretory carrier membrane protein 1 SCAMPI 5q13.3-q14.1 9522 m Hs.31236.0.S2_3p_at ADP-ribosylation factor-like 6 interacting protein 2 ARL6IP2 2p22.2-p22.1 64225 IO Hs.31293.0.A1_3p_at Hs.31 3760.0.A1 _3p_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 Hs.31412.0.A1_3p_at εynaptopodin 2 SYNPO2 4q26 171024 Hs.317589.0.S1_3p_s_at WD repeat domain 32 WDR32 9p13.2 79269 Hs.318885.1.S1_3p_a_at superoxide dismutase 2, mitochondrial SOD2 6q25.3 6648 Hs.31 8885.2.S1_3p_a_at superoxide dismutase 2, mitochondrial SOD2 6q25.3 6648 hypothetical protein DJ328E19.C1 .1//hypothetical protein DJ328E19.C1.1// 1q12-1q21 .2// 25832// Hs.323463.0.S1_3p_at FLJ20719//AG1 protein FLJ20719//AG1 1p36.13//1q21.1 440673// 55672 hypothetical protein DJ328E19.C1.1//hypothetical protein DJ328E19.C1 .1// 1q12-1q21 .2// 25832// Hs.323463.0.S1_3p_x_at FU20719//AG1 protein FLJ20719//AG1 1p36.13//1q21 .1 440673// 55672 Hs.323512.0.S1_3p_at putative nuclear protein ORF1-FL49 ORF1-FL49 5q31.2 84418 Hs.323936.0.S1_3p_at immunoglobulin kappa variable 1-5 IGKV1-5 2p12 28299 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Eπtrez Gene Hs.323936.0.S1_3p_x_at immunoglobulin kappa variable 1-5 IGKV1-5 2p12 28299 MRNA; cDNA DKFZp586G0321 (from clone Hs.32405.0.S1_3p_at DKFZp586G0321) amyloid beta (A4) precursor protein-binding, family B, Hs.3241 25.0.S1_3p_s_at member 2 (Fe65-like) APBB2 4p14 323 Hs.324275.0.S1_3p_S_a1 WW domain containing E3 ubiquitin protein ligase 1 WWP1 8q21 11059 Hs.324275.0.S2_3p_a_at WW domain containing E3 ubiquitin protein ligase 1 WWP1 8q21 11059 Hs.324728.0.S1_3p_at hypothetical protein LOC1 53561 LOC1 53561 5q13.2 153561 Hs.324728.0.S1_3p_x_at hypothetical protein LOC1 53561 LOC 153561 5q13.2 153561 CO Hs.324747.0.S1_3p_x_at C CO Hs.326248.0.A1_3p_at hypothetical protein LOC92482 LOC92482 10q25.2 92482 CO Hs.326248.1 .A1_3p_at programmed cell death 4 (neoplastic transformation inhibitor) PDCD4 10q24 27250 Hs.326248.2.S1_3p_at hypothetical protein LOC92482 LOC92482 10q25.2 92482 Hs.326248.2.S2_3p_at hypothetical protein LOC92482 LOC92482 10q25.2 92482 m Hs.326416.0.A1_3p_at Nuclear factor I/B NFIB 9p24.1 4781 CO Hs.326416.0.A2_3p_at Nuclear factor I/B NFIB 9p24.1 4781 m Hs.326416.1.A1_3p_at Nuclear factor I/B NFIB 9p24.1 4781 m Hs.328704.0.A1_3p_at Hs.32964.0.S2_3p_a_at SRY (sex determining region Y)-box 11 S0X1 1 2p25 6664 T Hs.3314.1.A1_3p_at Selenoprotein P, plasma, 1 SEPP1 5q31 6414 ι- m Hs.33287.1 .S2_3p_at Nuclear factor I/B NFIB 9p24.1 4781 IO Hs.33455.0.S2_3p_at peptidyl arginine deiminase, type Il PADI2 1p35.2-p35.1 11240 Hs.34114.0.S1_3p_x_at ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide ATP1A2 1q21-q23 477 Hs.34744.0.S1_3p_at ATP-binding cassette, sub-family C (CFTR/MRP), member 5 ABCC5 3q27 10057 Hs.3542.0.S2_3p_a_at hypothetical protein FLJ1 1273 FLJ1 1273 7p21.3 54664 Hs.35861.0.A1_3p_at Ras-induced senescence 1 RIS1 3p21.3 25907 Hs.39122.0.S1_3p_at transcription elongation factor A (Sll)-like 3 TCEAL3 Xq22.2 85012 Hs.40268.0.A1_3p_at Complexin 1 CPLX1 4p16.3 10815 BUB3 budding uninhibited by benzimidazoles 3 homolog Hs.40323.0.S2_3p_a_at (yeast) BUB3 10q26 9184 Hs.4084.0.S1_3p_at thyroid hormone receptor associated protein 2 THRAP2 12q24.21 23389 Hs.4084.0.S3_3p_x_at thyroid hormone receptor associated protein 2 THRAP2 12q24.21 23389 Hs.41380.0.A1_3p_at Zinc finger protein 587 ZNF587 19q13.43 84914 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.41380.0.A1_3p_x_at Zinc finger protein 587 ZNF587 19q13.43 84914 Hs.42179.0.A1_3p_at musashi homolog 2 (Drosophila) MSI2 17q23.2 124540 Hs.42179. 0.A2_3p_a_at musashi homolog 2 (Drosophila) MSI2 17q23.2 124540 Hs.42294.0.A1_3p_at metastasis associated lung adenocarcinoma transcript 1 Hs.42346-3.A1_3p_s_at (non-coding RNA) MALAT1 11q13.1 378938 Hs.42409.0.S1_3p_a_at Hs.42699.0.A1_3p_at Thrombospondi π 1 THBS1 15q15 7057 Hs.44017.3.A1_3p_a_at Mitochondrial ribosomal protein L41 MRPL41 9q34.3 64975 CO C Hs.44829.0.A1_3p_at Hypothetical protein LOC201895 LOC201895 4p14 201895 co Hs.44865.1.A1_3p_a_at lymphoid enhancer-binding factor 1 LEF1 4q23-q25 51176 CO Hs.44898.1.A1_3p_at Clone TCCCTA001 5 1 mRNA sequence Hs.44898.2.A1_3p_at CDNA FLJ40901 fis, Clone UTERU2003704 IGF1 R 15q26.3 3480 m Hs.47023.0.A1_3p_at Insulin-like growth factor 1 receptor Hs.4746.0.S2_3p_at pyridoxal (pyridoxine, vitamin B6) kinase PDXK 21q22.3 8566 CO DKC1 Xq28 1736 m Hs.4747.1 .S1_3p_a_at dyskeratosis congenita 1, dyskerin m Hs.4749.0.S1_3p_at CDNA FLJ31660 fis, clone NT2RI2004410 Hs.5025.0.A2_3p_at nebulette NEBL 10p12 10529 Hs.5025.1 .A1_3p_s_at nebulette NEBL 10p12 10529 c Hs.50895.0.S2_3p_at hypothetical gene supported by AK022887; AK056417 FU 12825 12q13.13 440101 m Hs.50915.1.S1_3p_a_at kallikrein 5 KLK5 19q13.3-q13.4 25818 IO Hs.5344.1.A1_3p_s_at carbonic anhydrase XII CA12 15q22 771 Hs.55468.0.A1_3p_at Histone 2, H4 HIST2H4 1q21 8370 Transcribed locus, weakly similar to NP_004563.1 plakophilin Hs.60802.0.A1_3p_at 2 [Homo sapiens] Hs.6131 1.0.A1_3p_at Calpain 8 (nCL-2) CAPN8 2 10754 Hs.61638.1.S1_3p_a_at myosin X MYO10 5p15.1-p14.3 4651 Hs.6189.0.A1_3p_at KIAA1467 protein KIAA1467 12p13.1 57613 Hs.62264.0.S1_3p_at deltex 4 homolog (Drosophila) DTX4 11q12.1 23220 Hs.6612.0.A1_3p_at CDNA FLJ34896 fis, clone NT2NE2018180 Hs.6630.0.A1_3p_at F-box protein 32 FBXO32 8q24.13 114907 Hs.6630.1.A1_3p_at Hs.6763.0.S1_3p_a_at pleckstrin and Sec7 domain containing 3 PSD3 8pter-p23.3 23362 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.67776.0.A1_3p_at FLJ46072 protein FLJ46072 8q24.3 286077 Hs.6975.0.A1_3p_a_at PRO1073 protein PRO1073 11cen-q12.3 29005 metastasis associated lung adenocarcinoma transcript 1 Hs.6975.2.A2_3p_at (non-coding RNA) MALAT1 11q13.1 378938 metastasis associated lung adenocarcinoma transcript 1 Hs.6975.2.A2_3p_S_at (non-coding RNA) MALAT1 11q13.1 378938 Metastasis associated lung adenocarcinoma transcript 1 Hs.6975.3.A1_3p_at (non-coding RNA) MALAT1 11q13.1 378938 Meisi, myeloid ecotropic viral integration site 1 homolog 4 Hs.71968.0.A1_3p_S_at (mouse) MEIS4 17p12 4213 CO C Hs.71968.0.A2_3p_at lnterleukin 6 signal transducer (gp130, oncostatin M receptor) IL6ST 5q1 1 3572 CO Hs.72402.0.A1_3p_at hypothetical protein AY099107 LOC152185 3q13.2 152185 CO Hs.72472.0.A1_3p_at Bone morphogenetic protein receptor, type IB BMPR1B 4q22-q24 658 Hs.72S6.1.A1_3p_at Protein phosphatase 6, catalytic subunit PPP6C 9q33.3 5537 Hs.7358.0.S1_3p_a_at chromosome 2 open reading frame 23 C2orf23 2p1 1.2 65055 m Hs.7413.0.A1_3p_at Transcribed locus CO Hs.74313.0.S1_3p_x_at Transcribed locus, strongly similar to XP_523650.1 m PREDICTED: similar to keratin 17 [Pan troglodytes] m Hs.74376.0.S1_3p_at olfactomedi π 1 OLFM1 9q34.3 10439 O Hs.74497.1.S1_3p_a_at Y box binding protein 1 YBX1 1p34 4904 T prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmaππ- ι- Hs.74621.2.S1_3p_a_at Strausler-Scheinker syndrome, fatal familial insomnia) PRNP 20pter-ρ12 5621 m Hs.74861 .0.A2_3p_a_at SUB1 homolog (S. cerevisiae) SUB1 5p13.3 10923 IO Hs.75318.0.S1_3p_at tubulin, alpha 1 (testis specific) TUBA1 2q35 7277 Hs.75318.0.S1_3p_x_at tubulin, alpha 1 (testis specific) TUBA1 2q35 7277 Hs.75544.1.S1_3p_at chromosome 9 open reading frame 19 C9orf19 9p13-p12 152007 Hs.7581 1.3.S1_3p_a_at N-acylsphingosine amidohydrolase (acid ceramidase) 1 ASAH1 8p22-p21.3 427 Hs.76084.1.S1_3p_s_at lamin B2 LMNB2 19p13.3 84823 Immunoglobulin J polypeptide, linker protein for Hs.76325.1.A1_3p_at immunoglobulin alpha and mu polypeptides IGJ 4q21 3512 Immunoglobulin J polypeptide, linker protein for Hs.76325.1.A1_3p_x_at immunoglobulin alpha and mu polypeptides IGJ 4q21 3512 Hs.76704.0.A1_3p_at Transcribed locus, strongly similar to XP_496055.1 Hs.76704.0.A2_3p_at PREDICTED: similar to p40 [Homo sapiens] Hs.77515.1 .A1_3p_at Transcribed locus Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez V-erb-a erythroblastic leukemia viral oncogene homolog 4 Hs.7888.0.S1_3p_at (avian) ERBB4 2q33.3-q34 2066 Hs.79019.0.S1_3p_a_at baculoviral IAP repeat-containing 1 BIRC1 5q13.1 4671 Hs.791 1.1 .S1_3p_s_at chromosome 14 open reading frame 124 C14orf124 14q1 1.2 56948 Hs.79136.0.S2_3p_at solute earner family 39 (zinc transporter), member 6 SLC39A6 18q12.2 25800 Hs.79414.1.A1_3p_a_at SAM pointed domain containing ets transcription factor SPDEF 6p21.3 25803 Hs.79414.1.A1_3p_s_at SAM pointed domain containing ets transcription factor SPDEF 6p21.3 25803 Hs.79414.1.A1_3p_x_at SAM pointed domain containing ets transcription factor SPDEF 6p21.3 25803 Hs.79414.2.A1_3p_a_at SAM pointed domain containing ets transcription factor SPDEF 6p21.3 25803 CO C Hs.7941 4.2.A1_3p_S_at SAM pointed domain containing ets transcription factor SPDEF 6p21.3 25803 CO Hs.7941 4.2.A1_3p_x_at SAM pointed domain containing ets transcription factor SPDEF 6p21.3 25803 CO Hs.7946.0.S2_3p_a_at mitochondrial tumor suppressor 1 MTUS1 8p22 57509 Hs.80976. 1-S1_3p_a_at antigen identified by monoclonal antibody Ki-67 MKI67 10q25-qter 4288 Hs.82065.0.A1_3p_a_at interleukin 6 signal transducer (gp130, oncostatin M receptor) IL6ST 5q1 1 3572 m phosphoribosylglycinamide formyltransferase, CO phosphoribosylglycinamide synthetase, m Hs.82285.1.S2_3p_at phosphoribosylaminoimidazole synthetase GART 21q22.1 |21q22.11 2618 m Hs.8236.0.A1_3p_at πephronectin NPNT 4q24 255743 Hs.82432.0.S1_3p_a1 glycerol-3-phosphate dehydrogenase 1-like GPD1L 3p24.1 23171 T Hs.8291 1.0.S2_3p_a_at protein tyrosine phosphatase type IVA, member 2 PTP4A2 1p35 8073 ι- m Hs.8291 1.1.S1_3p_a_at protein tyrosine phosphatase type IVA, member 2 PTP4A2 1p35 8073 Hs.83623.2.S4_3p_a_at X (inactive)-specific transcript XIST Xq13.2 7503 IO Hs.8372.2.S1_3p_at Poliovirus receptor-related 2 (herpesvirus entry mediator B) PVRL2 19q13.2-q13.4 5819 Hs.84152.2.S1_3p_s_at cystathioni πe-beta-synthase CBS 21q22.3 875 signal transducer and activator of transcription 3 interacting Hs.8739.0.S1_3p_a_at protein 1 STATIP1 18q12.2 55250 Hs.87409.0.A2_3p_a_at thrombospondin 1 THBS1 15q15 7057 Hs.87409.1 .S1_3p_s_at Zinc finger protein 552 ZNF552 19q13.43 79818 Hs.87409.1.S1_3p_x_at Hs.88155.0.S1_3p_at hypothetical protein FLJ20719 FLJ20719 1p36.13 55672 Hs.88252.0.A1_3p_at ATPase, Class Vl, type 11C ATP1 1C Xq27.1 286410 Hs.88253.1.A1_3p_a_at Hs.89414.1.S1_3p_at chemokine (C-X-C motif) receptor 4 CXCR4 2q21 7852 Hs.89548.1.S1_3p_at Erythropoietin receptor EPOR 19p13.3-p13.2 2057 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs.89603.6.A1_3p_a_at mucin 1, transmembrane MUC1 1q21 4582 Hs.9006.1 .S1_3p_at Abhydrolase domain containing 2 ABHD2 15q26.1 11057 Hs.90419.0.S2_3p_at KIAA0882 protein KIAA0882 4q31.21 23158 Hs.90790.0.S1_3p_at hypothetical protein LOC284018 LOC28401 8 17q24.2 284018 solute carrier family 1 (neuronal/epithelial high affinity Hs.91 139.1.A1_3p_at glutamate transporter, system Xag), member 1 SLC1A1 9p24 6505 Hs.92254.1.S1_3p_a_at synaptotagmin-like 2 SYTL2 11q14 54843 Hs.9299.0.S1_3p_at CDNA FLJ12425 fis, clone MAMMA1003104 solute carrier family 7 (cationic amino acid transporter, y+ CO Hs.93961.0.A1_3p_at system), member 2 SLC7A2 8p22-p21.3 6542 C CO Hs.94694.0.S1_3p_at hypothetical protein L0C1 43381 LOC143381 10q26.1 1 143381 CO Hs.94952.0.A1_3p_at transcription elongation factor A (SII), 3 TCEA3 1p36.12 6920 Hs.95110.0.S1_3p_s_at phospholipase C, delta 3 PLCD3 17q21.31 113026 Hs.95549.0.A1_3p_a_at RNA-binding protein FLJ20273 4p13-p12 54502 m Hs.96125.0.S1_3p_at RAB1 1 family interacting protein 1 (class I) RAB1 1RP1 8p1 1.22 80223 CO Hs.96844.0.A1_3p_at sarcalume πin SRL 16p13.3 6345 m Phosphatase and tensin homolog (mutated in multiple m Hs.98267.0.A1_3p_at advanced cancers 1) PTEN 10q23.3 5728 N Hs.98614.0.S1_3p_at T Hs.98614.2.A1_3p_a_at Ribosome binding protein 1 homolog 18OkDa (dog) RRBP1 20p12 6238 ι- Hs.99029.0.S2_3p_at CCAAT/enhancer binding protein (C/EBP), beta CEBPB 20q13.1 1051 m Hs2.102784.1 .S1_3p_at PAP associated domain containing 4 PAPD4 5q14.1 167153 IO Hs2.1 12083.1.S1_3p_s_at Zic family member 4 ZIC4 3q24 84107 Hs2.1 18722.3.S1_3p_s_at fucosyltransferase 8 (alpha (1,6) fucosyltransferase) FUT8 14q24.3 2530 HS2.129598.1 .S1_3p_s_at fibrous sheath interacting protein 1 FSIP1 15q14 161835 Hs2.1 3640.1 ,S1_3p_x_at Roundabout, axon guidance receptor, homolog 1 (Drosophila) ROBO1 3p12 6091 Hs2.1 44530. 1.S1_3p_at Trichorhinophalangeal syndrome I TRPS1 8q24.12 7227 HS2.144530.1 .S1_3p_s_at Trichorhinophalangeal syndrome I TRPS1 8q24.12 7227 Hs2.1 45582. 1.S1_3p_s_at prominin 2 PROM2 2q1 1.1 150696 Hs2.150833.1.S1_3p_at Transcribed locus Hs2.1 57862. 1.A1_3p_at Jumonji domain containing 2B JMJD2B 19p13.3 23030 Hs2.166817.2.S1_3p_at Hs2.1 6681 7.2.S1_3p_x_at Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs2.1 8063.2.S1_3p_s_at v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) ETS1 1 1q23.3 2 1 13 Hs2.21016.2.S1_3p_at coagulation factor C homolog, cochlin (Limulus polyphemus) COCH 14q12-q13 1690 Hs2.234734.3.S1_3p_s_at lysozyme (renal amyloidosis) LYZ 12q15 4069 Hs2.239138.2.S1_3p_s_at pre-B-cell colony enhancing factor 1 PBEF1 7q22.3 10135 Hs2.248522. 1 .S1_3p_x_at START domain containing 10 STARD10 1 1q13 10809 Hs2.249303. 1-S1_3p_x_at ADP-ribosylation factor-like LOC51326 17q21.31 51326 Hs2.250158.1.S1_3p_s_at Hs2.271473.1.S1_3p_S_at PDZK1 interacting protein 1 PDZK1IP1 1p33 10158

CO HS2.271478.1 .A1_3p_s_at Sushi, nidogen and EGF-like domains 1 SNED1 2q37.3 25992 C Hs2.290347. 1 .S1_3p_at Similar to mKIAA0767 protein — 2q21 .1 391444 CO CO Hs2.293659.2.S1_3p_at similar to RIKEN cDNA A430101B06 gene MGC13017 5q31.1 91368 Hs2.33074.1.S1_3p_at Homo sapiens, clone IMAGE:360651 9 Hs2.343765.1 .S1_3p_s_at cytochrome c oxidase subunit VIb polypeptide 2 (testis) COX6B2 19q13.42 125965 m Hs2.344235.1 .A1_3p_at Hs2.348522.1.S1_3p_at potassium voltage-gated channel, Isk-related family, member CO 4 KCNE4 2q36.3 23704 m m Hs2.349084.1.S1_3p_at dynein, axonemal, heavy polypeptide 1 1 DNAH11 77pp2211 88770011 HS2.351292.1 .A1_3p_x_at FLJ34306 protein LOC474170 1177 447744117700

T HS2.351 442.2.S1_3p_at RAS and EF-hand domain containing RASEF 99qq2211..3322 115588115588 ι- Hs2.352401.1.A1_3p_s_at CXYorfi -related protein FU00038 99pp2244..33 337755669900 m integral membrane glycoprotei π-like//similar to bA110H4.2 LOC1 66994// 116666999944//// IO (similar to membrane protein)//similar to P0M121 membrane LOC340089// 334400008899//// glycoprotein-like 1//similarto bA110H4.2 (similar to LOC401485// 440011448855//// membrane protein)//similar to bA1 1 0H4.2 (similar to LOC441 079// 444411 007799//// membrane protein)//similar to P0M121 membrane LOC441081// 444411008811//// glycoprotein-like 1//similar to POM121 membrane LOC441082// 444411008822//// glycoprotein-like 1//similarto P0M121 membrane LOC441083// 444411008833//// glycoprotein-like 1//similarto bA110H4.2 (similar to LOC441 084// 444411008844//// membrane protein)//similar to bA1 10H4.2 (similar t o LOC441 098// 66pp2222..11////55qq1133..22//// 444411009988////

Hs2.355978.1.S1_3p_at membrane protein) LOC441 100 55qq2211..11 444411 110000 hypothetical protein LOC339005//hypothetical protein LOC339005// 333399000055////

Hs2.362800.1.S1_3p_at LOC440253 LOC440253 1155q11α 11..22////1155q1133..11α 444400225533 HS2.362932.1 .A1_3p_s_at CDNA FLJ25030 fis, clone CBL02631 Hs2.363342. 1.A1_3p_at CDNA FU37989 fis, clone CTONG201 1676 Hs2.367975.1.S1_3p_at Zinc finger protein 586 ZNF586 19q13.43 54807 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene Hs2.3761 09.1.S1_3p_at FLJ39531 protein FLJ39531 15q14 400360 Hs2.376819.1.A1_3p_at Hs2.376832.1.S1_3p_at Activated leukocyte cell adhesion molecule ALCAM 3q13.1 214 ELOVL family member 5, elongation of long chain fatty acids Hs2.376929.1.S1. 3p_at (FEN1/EI02, SUR4/Elo3-like, yeast) ELOVL5 6p21.1-p12.1 60481 Hs2.379185.1-S1. 3p_x_ai potassium channel tetramerisation domain containing 18 KCTD18 2q33.1 130535 Hs2.379904.1.S1. .3p_at AT rich interactive domain 2 (ARID, RFX-like) ARID2 12q12 196528 Hs2.380094.1 .S1. _3p_s_at phospholipase C, delta 3 PLCD3 17q21.31 113026 Hs2.380494.2.A1. 3p_at Zinc finger protein 587 ZNF587 19q13.43 84914 CO C Hs2.380494.3.S1. .3p_a_at zinc finger protein 587 ZNF587 19q13.43 84914 CO¬ HS2.381240.1.A1. .3p_x_at CO HS2.381 909.1.S1. .3p_at Thyroid hormone receptor associated protein 2 THRAP2 12q24.21 23389 ρ -S-. Hs2.382194.1.S1. 3 _s_at ANKRD30A// ankyrin repeat domain 30A//ankyrin repeat ANKRD30B// 10p1 1.21// 374860// m domain 30B//similar to PRED4 LOC400858 18p1 1.21//21q1 1.2 400858// 9 1074 CO Hs2.382631.1.A1_3p_at CDNA clone IMAGE-.4753178, containing frame-shift errors π m immunoglobulin lambda locus// ϊmmu oglobulin lambda m constant 1 (Meg marker)//immunoglobulin lambda constant 2 (Kern-Oz- marker)// immunoglobulin lambda variable 3-25// IGL@//IGLC1// 28793// 28815// immunoglobulin lambda variable 2-14// immunoglobulin IGLC2//IGLV3-25// 22q11.1-q11.2// 28831//3535// c Hs2.383932. 1.S1_3p_x_at lambda joining 3 IGLV2-14//IGU3 22q11.2 3537//3538 m Hs2.384938.1.A1_3p_at ELOVL family member 5, elongation of long chain fatty acids IO Hs2.384938. 1.S1_3p_s_at (FEN1/EI02, SUR4/Elo3-like, yeast) EL0VL5 6p21.1-p12.1 60481 Hs2.384944.1.A1_3p_at Transcribed locus Hs2.396848.1.S1_3p_at EF-hand domain family, member D 1 EFHD1 2q37.1 80303 Hs2.399943.1 .S1_3p_s_at solute carrier family 39 (zinc transporter), member 6 SLC39A6 18q12.2 25800 Calcium channel, voltage-dependent, L type, alpha 1D Hs2.399966.1.A1_3p_at subunit CACNA1D 3p14.3 776 HS2.401 226. 1.A1_3p_at Trichorhinophalangeal syndrome I TRPS1 8q24.12 7227 LOC389295// 389295// hypothetical LOC389295//hypothetical LOC401 178 LOC401 178// 401 178// HS2.404066. 1.S1_3p_s_at //LOC441080 LOC441 080 5q13.2//5p13.3 441080 HS2.406064. 1.A2_3p_s_at ras homolog gene family, member B RHOB 2p24 388 HS2.406064. 1.A2_3p_x_at ras homolog gene family, member B RHOB 2p24 388 Table 7 Chromosomal Probe Set ID Gene Title Gene Symbol Location Entrez Gene AF4/FMR2 family, member 3//myeloid/lymphoid or mixed- Hs2.406233.4.S1_3p_s_at lineage leukemia (trithorax homolog, Drosophila) AFF3//MLL 2q1 1.2-q12//1 1q23 3899//4297 Hs2.407179.1 .A1_3p_at cysteine sulfiπic acid decarboxylase CSAD 12q13.1 1-q14.3 51380 Hs2.407347.1 .S1_3p_s_at Methylcrotonoyl-Coenzyme A carboxylase 2 (beta) MCCC2 5q12-q13 64087 Hs2.407588.1.S1_3p_at Vacuolar protein sorting 13A (yeast) VPS13A 9q21 23230 CDNA FLJ42669 fis, clone BRAMY2022168, highly similar to !DURONATE 2-SULFATASE PRECURSOR (EC Hs2.41 8490. 1.A1 _3p_S_at 3.1 .6.13)//CDNA FU44451 fis, clone UTERU2023039 Hs2.422339. 1.S1_3p_s_at WW domain containing E3 ubiquitin protein ligase 2 WWP2 16q22.1 11060

CO v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 C HS2.430933.1.S1_3p_S_at (avian) ERBB3 12q13 2065 CO HS2.438760. 1.A2_3p_s_at Casein kinase 1, alpha 1 CSNK1A1 5q32 1452 CO Hs2.57787.1.S1_3p_s_at membrane targeting (tandem) C2 domain containing 1 MTAC2D1 14q32.12 123036 Hs2.58006.2.S1_3p_s_at BCL2/adenovirus E1B 19kD interacting protein like BNIPL 1q21.2 149428 151 126 m Hs2.6295.2.S1_3p_at zinc finger protein 533 ZNF533 2q31.2-q31.3 HS2.7581 1.3.S1_3p_S_at N-acylsphingosine amidohydrolase (acid ceramidase) 1 ASAH1 8p22-p21.3 427 CO Hs2.791 36.2.S1_3p_s_at solute carrier family 39 (zinc transporter), member 6 SLC39A6 18q12.2 25800 m m Hs2.98573.1.S1_3p_s_at chromosome 6 open reading frame 141 C6orf141 6p12.3 135398 Hs2.98573.1 .S1_3p_x_at chromosome 6 open reading frame 141 C6orf141 6p12.3 135398 T Hs2Affx.1.27.S1_3p_at Kenae KENAE 5q13.2 202243 ι- L33930_3p_s_at CD24 antigen (small ceil lung carcinoma cluster 4 antigen) CD24 6q21 934 m IO Table 8 Probe Set ID Gene Title Gene Symbol Chromosomal Entrez Gene Location 1552264_a_at mitogen-activated protein kinase 1 MAPK1 22q1 1.2|22q1 1.21 5594 1552343_s_at phosphodiesterase 7A PDE7A 8q13 5 150 1552364_s_at musashi homolog 2 (Drosophila) MSI2 17q23.2 124540 155241 1_at defensin, beta 106A DEFB1 06A 8p23-p22 245909 1552507_at potassium voltage-gated channel, Isk-related family, member 4 KCN E4 2q36.3 23704 1552575_a_at chromosome 6 open reading frame 141 C6orf141 6p12.3 135398 1552639_at kelch domain containing 7B KLHDC7B 22q1 3.33 113730 1552703_s_at caspase 1, apoptosis-related cysteine peptidase (interleukin 1, CASP1//C0P1 11q23 114769//834 beta, convertase)//caspase-1 dominant-negative inhibitor CO C pseudo-ICE CO 1552797_s_at prominin 2 PR0M2 2q11 .1 150696 CO 1552839_at chromosome 14 open reading frame 54 C14orf54 14q23.3 16 1142 1552862_at chromosome 1 open reading frame 104 C1orf104 1q22 28461 8 1553530_a_at integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen ITGB1 10p1 1.2 3688 m CD29 includes MDF2, MSK12) CO 1553542_at Kenae KENAE 5q13.2 202243 m 1553589_a_at PDZK1 interacting protein 1 PDZK1 IP1 1p33 10 158 m 1553706_at 1553906_s_at FYVE, RhoGEF and PH domain containing 2 FGD2 6p21 .2 221 472 T 1553986_at RAS and EF-hand domain containing RASEF 9q21 .32 1581 58 ι- m 1554014_at chromodomain helicase DNA binding protein 2 CHD2 15q26 1106 IO 15541 13_a_at solute carrier family 4, sodium bicarbonate cotransporter, SLC4A8 12q1 3 9498 member 8 1554351_a_at TIP41 , TOR signalling pathway regulator-like (S. cerevisiae) TIPRL 1q23.2 261726 1554385_a_at peptidyl arginine deiminase, type Il PADI2 1p35.2-p35.1 11240 1554390_s_at ARP2 actin-related protein 2 homolog (yeast) ACTR2 2p14 10097 1554665_at Zinc finger protein 586 ZNF586 19q1 3.43 54807 1554686_at staufen, RNA binding protein, homolog 2 (Drosophila) STAU2 8q13-q21 .1 27067 155471 2_a_at glycine-N-acyltransferase-like 2 GLYATL2 11q1 2.1 2 19970 1554830_a_at STEΞAP family member 3 STEAP3 2q14.2 55240 1554906_a_at M-phase phosphoprotein 6 MPH0SPH6 16q23.3 10200 1555037_a_at isocitrate dehydrogenase 1 (NADP+), soluble IDH1 2q33.3 3417 1555203_s_at solute carrier family 44, member 4 SLC44A4 6p21 .3 80736 1555229_a_at complement component 1, s subcomponent C 1S 12p1 3 716 Table 8 1555326_a_a1 ADAM metallopeptidase domain 9 (meltrin gamma) ADAM9 8p1 1.23 8754 1555358_a_at ectonucleoside triphosphate diphosphohydrolase 4 ENTPD4 8p21 .3 9583 1555407_s_at FYVE, RhoGEF and PH domain containing 3 FGD3 — 89846 1555460_a_at solute carrier family 39 (zinc transporter), member 6 SLC39A6 18q12.2 25800 1555543_a_at chloride channel CLIC-like 1 CLCC1 1p13.3 231 55 1555565_s_at TAP binding protein (tapasin) TAPBP 6p21 .3 6892 1555594_a_at muscleblind-like (Drosophila) MBNL1 3q25 4 154 155561 3_a_at zeta-chain (TCR) associated protein kinase 7OkDa ZAP70 2q12 7535 1555730_a_at cofilin 1 (non-muscle) CFL1 11q13 1072 1555745_a_at lysozyme (renal amyloidosis) LYZ 12q1 5 4069 CO 1555797_a_at actin related protein 2/3 complex, subunit 5, 16kDa ARPC5 1q25.3 10092 C co 1555832_s_at Kruppel-like factor 6 KLF6 10p15 1316 CO 1555844_s_at heterogeneous nuclear ribonucleoprotei π M HNRPM 19p13.3-p13.2 4670 1555944_at chromosome 9 open reading frame 10 C9orf10 9q22.31 231 96 1556007_s_at Casein kinase 1, alpha 1 CSNK1A1 5q32 1452 m 1556345_s_at Methylcroto πoyl-Coenzyme A carboxylase 2 (beta) MCCC2 5q12-q13 64087 CO 1556551 _s_at solute carrier family 39 (zinc transporter), member 6 SLC39A6 18q1 2.2 25800 m 1556658_a_at Muscieblind-like (Drosophila) MBNL1 3q25 4154 m 1556663_s_at Ras homolog gene family, member Q RHOQ 2p21 23433 1556665_at tetratricopeptide repeat domain 6 TTC6 14q21.1 115669 1556721 _at hypothetical protein FLJ33706 FLJ33706 20q1 1.21 284805 c 1556921_at CDNA clone IMAGE:4826441 m 1556956_at ATPase, H+ transporting, lysosomal 14kDa, V 1 subunit F ATP6V1 F 7q32 9296 IO 1557078_at likely ortholog of mouse schlafen 5 MGC19764 17q12 162394 15571 55_a_at Zic family member 4 ZIC4 3q24 841 07 1557236_at 1557248_at Zinc finger protein 587 ZNF587 19q13.43 8491 4 1557374_at ATP-binding cassette, sub-family C (CFTR/MRP), member 9 ABCC9 12p12.1 10060 1557701 _s_at polymerase (DNA directed), eta POLH 6p21 . 1 5429 155781 3_at Single-stranded DNA binding protein 2 SSBP2 5q14.1 23635 1557905_s_at CD44 antigen (homing function and Indian blood group system) CD44 11p13 960 1557910_at heat shock 9OkDa protein 1, beta HSPCB 6p12 3326 155791 5_s_at glutathione S-transferase omega 1 GSTO1 10q25.1 9446 155801 1_at integral membrane g!ycoprotein-like//similar to bA1 10H4.2 (similar L0C1 66994// 6p22.1/5q1 3.2/ 166994// to membrane protein)//similar to POM121 membrane glycoprotein- LOC340089// 5q21 .1 340089// Table 8 like 1//similar to bA1 10H4.2 (similar to membrane protein)//similar LOC401485// 401485// to bA1 10H4.2 (similar to membrane proteiπ)//similar to P0M1 2 1 LOC441079// 441079// membrane glycoprotein-like 1//similar to P0M121 membrane LOC441081// 441081// glycoprotein-Iike 1//similar to P0M121 membrane glycoprotein-like LOC441082// 441082// 1//similar to bA1 10H4.2 (similar to membrane protein)//similar to LOC441083// 441083// bA1 10H4.2 (similar to membrane protein) LOC441084// 441084// LOC441098// 441098// LOC441 100 441 100 155801 5_s_at ARP2 actin-related protein 2 homolog (yeast) ACTR2 2p14 10097 1558034_s_at ceruloplasmin (ferroxidase) CP 3q23-q25 1356 15581 11_at Muscleblind-like (Drosophila) MBNL1 3q25 4 154 CO 1558164_s_at Peroxisome biogenesis factor 13 PEX13 2p14-p16 5194 co 1558251_a_at zinc finger protein 587 ZNF587 19q13.43 84914 CO 1558253_x_at zinc finger protein 587 ZNF587 19q13.43 8491 4 H 1558569_at Mastermind-like 2 (Drosophila) MAML2 11q21 84441 C 1558641_at hypothetical protein LOC202051 LOC202051 5q31 .2 202051 _ | m 1558747_at structural maintenance of chromosomes flexible hinge domain SMCHD1 18p1 1.32 23347 CO OO containing 1 m 155881 5_at sorbin and SH3 domain containing 2 SORBS2 4q35.1 8470 m 1558937_s_at Hypothetical protein L0C1 53561 L0C1 53561 5q13.2 153561 —I 1559036_at Transcribed locus 1559073_at Jumonji domain containing 2B JMJD2B 19p1 3.3 23030 CI ι- 1559078_at B-cell CLL/lymphoma 11A (zinc finger protein) BCL1 1A 2p16.1 53335 m 1559224_at late cornified envelope 1E LCE1 E 1q21 .3 3531 35 σ> 1559226_x_at late cornified envelope 1E LCE1 E 1q21 .3 3531 35 1559949_at Trichorhinophalangeal syndrome I TRPS1 8q24.12 7227 1560034_a_at MRNA; cDNA DKFZp31 3E1515 (from clone DKFZp31 3E1 5 15) 1560102_at Rho GTPase activating protein 26 ARHGAP26 5q31 23092 1560397_s_at kelch-like 6 (Drosoph ϋa) KLHL6 — 89857 1560579_s_at CDNA clone IMAGE:5930892//CDNA clone IMAGE:4620359 1562235_s_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 1562294_x_at ankyrin repeat domain 3OB ANKRD30B 18p1 1.21 374860 1562628_at type I hair keratin KA36 KA36 17q21 .2 1251 15 1562899_at T-cell immunomodulatory protein CDA08 16q1 2.1 81533 1563253_s_at v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) ERBB3 12q13 2065 1564064_a_at ATPase, Class Vl, type 11B ATP1 1B 3q27 23200 Table 8 1564281 _at hypothetical protein LOC285708 LOC285708 5q21 .2 285708 1564494 S at procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4- P4HB 17q25 5034 hydroxylase), beta polypeptide (protein disulfide isomerase- associated 1) 1565034_s_at AF4/FMR2 family, member 3//myeloid/lymphoid or mixed-lineage AFF3//MLL 2q1 1.2-q12//1 1q23 3899//4297 leukemia (trithorax homolog, Drosophila) 1565254_s_at myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, MLL//ELL 11q23//1 9p13.1 4297//8178 Drosophila)//elongation factor RNA polymerase Il 1565537_at HPX-1 53 homeobox NKX1-1 4p1 6.3 54729 1565752_at P rVE, RhoGEF and PH domain containing 2 FGD2 6p21 .2 221472 1566084_at Homo sapiens, clone 1MAGE:36O6519 CO 1566342_at C Transcribed locus CO 1566879_at AF4/FMR2 family, member 3 LAF4 2q1 1.2-q12 3899 CO 1566923_at CDNA: FU20971 fis, clone ADSU01 565 1567105_at 1567107_s_at tropomyosin 3//tropomyosin 4 TPM3//TPM4 1q21 .2//19p13.1 7170//7171 m 156721 9_at ELOVL family member 5, elongation of long chain fatty acids EL0VL5 6p21 .1-p12.1 60481 CO (FEN1/EIO2, SUR4/Elo3-like, yeast) m 1567628_at CD74 antigen (invariant polypeptide of major histocompatibility CD74 5q32 972 m complex, class II antigen-associated) 1567997_x_at T 1568126_at annexin A2 ANXA2 15q21 -q22 302 ι- 1568365_at Kinesin-associated protein 3 KIFAP3 1q24.2 22920 m 1568609_s_at family with sequence similarity 9 1, member A2//FLJ39739 protein FAM91A2// 1q21 .1 388685// IO FU39739 57234 156861 8_a_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- GALNT1 18q12.1 2589 acetylgalactosaminyltransferase 1 (GaINAc-TI ) 1568620_at cysteine sulfinic acid decarboxylase CSAD 12q13.1 1-q14.3 51380 1568879_a_at laminin, alpha 3 LAMA3 18q1 1.2 3909 1569568_at 1569867_at Essential meiotic endonuclease 1 homolog 2 (S. pombe) EME2 16p13.3 197342 1569935_at CDNA clone IMAGE:4819052 1570090_at EF-ha πd domain family, member D 1 EFHD1 2q37.1 80303 1570295_at Vacuolar protein sorting 13A (yeast) VPS1 3A 9q21 23230 1570623_at 200008 s at GDP dissociation inhibitor 2 GDI2 10p1 5 2665 Table 8 200009_at GDP dissociation inhibitor 2 GDI2 10p1 5 2665 20001 7_at ribosomal protein S27a RPS27A 2p16 6233 200052_s_at interJeukin enhancer binding factor 2 , 45kDa ILF2 1q21 .3 3608 200064_at heat shock 9OkDa protein 1, beta HSPCB 6p12 3326 200079_S_at lysyl-tRNA synthetase KARS 16q23-q24 3735 200086_S_at cytochrome c oxidase subunit IV isoform 1 COX4I1 16q22-qter 1327 200095_x_at ribosomal protein S10 /// ribosomal protein S10 RPS10 6p21 .31 6204 200598_s_at tumor rejection antigen (gρ96) 1 TRA1 12q24.2-q24.3 7184 200599_s_at tumor rejection antigen (gp96) 1 TRA1 12q24.2-q24.3 7184 200602_at amyloid beta (A4) precursor protein (peptidase nexin-ll, Alzheimer APP 2 1q21 .2|21q21 .3 351

CO disease) C 200628_s_at tryptophanyl-tRNA synthetase WARS 14q32.31 7453 co CO 200629_at tryptophanyl-tRNA synthetase WARS 14q32.31 7453 200632_s_at N-myc downstream regulated gene 1 NDRG1 8q24.3 10397 200634_at profilin 1 PFN1 17p1 3.3 5216 m 200635_s_at protein tyrosine phosphatase, receptor type, F PTPRF 1p34 5792 200638_s_at tyrosine 3-monooxygenase/tryptophan 5-monooxygenase YWHAZ 8q23.1 7534 CO activation protein, zeta polypeptide m m 200640_at tyrosine 3-monooxygenase/tryptophan 5-monooxygenase YWHAZ 8q23.1 7534 O activation protein, zeta polypeptide 200641_s_at tyrosine 3-monooxygenase/tryptophan 5-monooxygenase YWHAZ 8q23.1 7534 c activation protein, zeta polypeptide m 200642_at superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 SOD1 21q22.1 |21q22.1 1 6647 IO (adult)) 200648_s_at glutamate-ammonia ligase (glutamine synthetase) GLUL 1q31 2752 200653_s_at calmodulin 1 (phosphorylase kinase, delta) CALM1 14q24-q31 801 200657_at solute carrier family 25 (mitochondrial carrier; adenine nucleotide SLC25A5 Xq24-q26 292 translocator), member 5 200660_at S100 calcium binding protein A 11 (calgizzarin) S100A1 1 1q21 6282 200670_at X-box binding protein 1 XBP1 22q1 2.1 |22q1 2 7494 200677_at pituitary tumor-transforming 1 interacting protein PTTG1 IP 2 1q22.3 754 200683_s_at ubiquitin-conjugating enzyme EΞ2L 3 UBE2L3 22q1 1.21 7332 200693_at tyrosine 3-monooxygenase/tryptophan 5-monooxygenase YWHAQ//MIB1 2p25.1//18q1 1.2 10971 //57534 activation protein, theta polypeptide/ Λnindbomb homolog 1 (Drosophila) 200698 at KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention KDELR2 7p22.1 11014 Table 8 receptor 2 200700_s_at KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention KDELR2 7p22.1 110 14 receptor 2 200705_s_at eukaryotic translation elongation factor 1 beta 2 EEF1 B2 2q33-q34 1933 20071 8_s_at S-phase kinase-associated protein 1A (p1 9A) SKP1A 5q31 6500 200727_s_at ARP2 actin-related protein 2 homolog (yeast) ACTR2 2p14 10097 200728_at ARP2 actin-related protein 2 homolog (yeast) ACTR2 2p14 10097 200738_s_at phosphoglycerate kinase 1 PGK1 Xq13 5230 200755_s_at calumenin CALU 7q32 813 200756_x_at calumenin CALU 7q32 813

CO 200757_s_at calumenin CALU 7q32 813 C 200782_at annexin A5 ANXA5 4q26-q28|4q28-q32 308 CO CO 200790_at ornithine decarboxylase 1 ODC1 2p25 4953 200796_s_at myeloid cell leukemia sequence 1 (BCL2-related) MCL1 1q21 4170 200800_s_at heat shock 7OkDa protein 1A//heat shock 7OkDa protein 1B HSPA1A// 6p21 .3 3303//3304 HSPA1 B m 200806_s_at heat shock 6OkDa protein 1 (chaperonin) HSPD1 2q33.1 3329 CO 20081 0_s_at cold inducible RNA binding protein CIRBP 19p1 3.3 1153 m m 20081 1_at cold inducible RNA binding protein ClRBP 19p1 3.3 1153 O N 20081 2_at chaperonin containing TCP1 , subunit 7 (eta) CCT7 2p13.2 10574 T 200824_at glutathione S-transf erase pi GSTP1 11q13 2950 200838_at cathepsin B CTSB 8p22 1508 ι- m 200839_s_at cathepsin B CTSB 8p22 1508 IO 200841_s_at glutamyl-prolyl-tRNA synthetase EPRS 1q41 -q42 2058 200842_s_at glutamyl-prolyl-tRNA synthetase EPRS 1q41 -q42 2058 200868_s_at zinc finger protein 313 ZNF31 3 20q13.1 3 55905 200872_at S100 calcium binding protein A10 (annexin Il ligand, calpactin I, S 100A1 0 1q21 6281 light polypeptide (p1 1)) 200873_S_at chaperonin containing TCP1 , subunit 8 (theta) CCT8 21q22.1 1 10694 200877_at chaperonin containing TCP1 , subunit 4 (delta) CCT4 2p15 10575 200878_at endothelial PAS domain protein 1 EPAS1 2p21-p1 6 2034 200889_s_at signal sequence receptor, alpha (translocon-associated protein SSR1 6p24.3 6745 alpha) 200890_s_at signal sequence receptor, alpha (translocon-associated protein SSR1 6p24.3 6745 alpha) 200891 s at signal sequence receptor, alpha (translocon-associated protein SSR1 6p24.3 6745 Table 8 alpha) 200895_s_at FK506 binding protein 4, 59kDa FKBP4 12p1 3.33 2288 200904_at major histocompatibility complex, class I, E HLA-E 6p21 .3 3133 200905_x_at major histocompatibility complex, class I, E HLA-E 6p21 .3 3 133 200916_at transgelin 2 TAGLN2 1q21 -q25 8407 200920_s_at B-cell translocation gene 1, anti-proliferative BTG 1 12q22 694 200935_at calreticulin CALR 19p13.3-p13.2 8 11 200937_s_at ribosomal protein L5 RPL5 1p22.1 6125 200949_x_at ribosomal protein S20 RPS20 8q12 6224 200958_s_at syndecan binding protein (syntenin) SDCBP 8q12 6386

CO 200967_at peptidylprolyl isomerase B (cyclophilin B) PPIB 15q21-q22 5479 C 200968_s_at peptidylprolyl isomerase B (cyclophilin B) PPIB 15q21-q22 5479 CO CO 200983_x_at CD59 antigen p 18-20 (antigen identified by monoclonal antibodies CD59 11p13 966 16.3A5, EJ1 6, EJ30, EL32 and G344) 200984_s_at CD59 antigen p 18-20 (antigen identified by monoclonal antibodies CD59 11p 13 966 16.3A5, EJ16, EJ30, EL32 and G344) m 200985_s_at CD59 antigen p 18-20 (antigen identified by monoclonal antibodies CD59 11p 13 966 CO 16.3A5, EJ16, EJ30, EL32 and G344) m 200989_at hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix HIF1A 14q21-q24 3091 m transcription factor) 200996_at ARP3 actin-related protein 3 homolog (yeast) ACTR3 2q14.1 10096 T 200999_s_at cytoskeleton-associated protein 4 CKAP4 12q23.3 10970 ι- m 201012_at annexin A 1 ANXA1 9q12-q21 .2|9q12- 301 q21 .2 IO 201068_s_at proteasome (prosome, macropain) 26S subunit, ATPase, 2 PSMC2 7q22.1 -q22.3 5701 201077_s_at NHP2 non-histo πe chromosome protein 2-like 1 (S. cerevisiae) NHP2L1 22q1 3.2-q13.31 4809 201086_x_at SON DNA binding protein SON 2 1q22.1-q22.2 6651 |21q22.1 1 201088_at karyopherin alpha 2 (RAG cohort 1, importin alpha 1) KPNA2 17q23.1 -q23.3 3838 201098_at coatomer protein complex, subunit beta 2 (beta prime) C0PB2 3q23 9276 201 105_at lectin, galactoside-binding, soluble, 1 (galectin 1) LGALS1 22q13.1 3956 201 114_x_at proteasome (prosome, macropain) subunit, alpha type, 7 PSMA7 20q13.33 5688 201 116_s_at carboxypeptidase E CPE 4q32.3 1363 201 123_s_at eukaryotic translation initiation factor 5A EIF5A 17p13-p12 1984 201 138_s_at Sjogren syndrome antigen B (autoantigen La) SSB 2q31 .1 6741 201 14 1 at glycoprotein (transmembrane) nmb GPNMB 7p15 10457 Table 8 201 160_s_at cold shock domain protein A CSDA 12p13.1 8531 201 169_s_at basic helix-loop-helix domain containing, class B, 2 BHLHB2 3p26 8553 201 170_s_at basic helix-loop-helix domain containing, class B, 2 BHLHB2 3p26 8553 201193_at isocitrate dehydrogenase 1 (NADP+), soluble IDH1 2q33.3 341 7 201 195_s_at solute carrier family 7 (cationic amino acid transporter, y+ system), SLC7A5 16q24.3 8140 member 5 201 196_s_at adenosylmethionine decarboxylase 1 AMD1 6q21 -q22 262 201197_at adenosylmethioni πe decarboxylase 1 AMD1 6q21 -q22 262 201201_at cystatin B (stefin B) CSTB 2 1q22.3 1476 201205_at ribosome binding protein 1 homolog 18OkDa (dog) RRBP1 20p12 6238

CO 201206_s_at ribosome binding protein 1 homolog 18OkDa (dog) RRBP1 20p12 6238 C 201231_s_at enolase 1, (alpha) ENO1 1p36.3-p36.2 2023 co CO 201239_s_at signal peptidase complex subunit 2 homolog (S. cerevisiae) SPCS2 11q 13.4 9789 201244_s_at v-raf-1 murine leukemia viral oncogene homolog 1 RAF1 3p25 5894 201266_at thioredoxin reductase 1 TXNRD1 12q23-q24.1 7296 m 201286_at syndecan 1 SDC1 2p24.1 6382 201287_s_at syndecan 1 SDC1 2p24.1 6382 CO 201291_s_at topoisomerase (DNA) Il alpha 17OkDa TOP2A 17q21-q22 7153 m m 201300_s_at prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann- PRNP 20pter-p12 5621 Strausler-Scheinker syndrome, fatal familial insomnia) 20131 1_s_at SH3 domain binding glutamic acid-rich protein like SH3BGRL Xq13.3 6451 c 201312_s_at SH3 domain binding glutamic acid-rich protein like SH3BGRL Xq1 3.3 6451 m 201318_s_at myosin regulatory light chain MRCL3//myosin regulatory light chain MRCL3// 18p1 1.31 10391 0//10627 IO MRLC2 MRLC2 201351_s_at YME1 -like 1 (S. cerevisiae) YME1 L 1 10p14 10730 201392_s_at insulin-like growth factor 2 receptor IGF2R 6q26 3482 201393_s_at insulin-like growth factor 2 receptor IGF2R 6q26 3482 201398_s_at translocation associated membrane protein 1 TRAM1 8q13.3 23471 201399_s_at translocation associated membrane protein 1 TRAM1 8q13.3 23471 201416_at SRY (sex determining region Y)-box 4 SOX4 6p22.3 6659 201425_at aldehyde dehydrogenase 2 family (mitochondrial) ALDH2 12q24.2 2 17 201426_s_at vimentin VIM 10p13 7431 201433_s_at phosphatidylserine synthase 1 PTDSS1 8q22 9791 201453_x_at Ras homolog enriched in brain RHEB 7q36 6009 201465_s_at v-jun sarcoma virus 17 oncogene homolog (avian) JUN 1p32-p31 3725 Table 8 201487_at cathepsin C CTSC 11q14.1-q14.3 1075 201506_at transforming growth factor, beta-induced, 68kDa TGFBI 5q31 7045 201508_at insulin-like growth factor binding protein 4 IGFBP4 17q12-q21 .1 3487 201533_at catenin (cadherin-associated protein), beta 1, 88kDa CTNNB1 3p21 1499 201 551_s_at lysosomal-associated membrane protein 1 LAMP1 13q34 391 6 201552_at lysosomal-associated membrane protein 1 LAMP1 13q34 3916 201563_at sorbitol dehydrogenase SORD 15q1 5.3 6652 201569_s_at sorting and assembly machinery component 50 homolog SAMM50 22q1 3.31 2581 3 (S. cerevisiae) 201579_at FAT tumor suppressor homolog 1 (Drosophila) FAT 4q35 2 195 201596_x_at keratin 18 KRT18 12q13 3875 CO C 20161 5_x_at caldesmon 1 CALD1 7q33 800 CO 20161 6_s_at caldesmon 1 CALD1 CO 7q33 800 201623_s_at aspartyl-tRNA synthetase DARS 2q21 .3 16 15 201 645_at tenascin C (hexabrachion) TNC 9q33 3371 m 201663_s_at SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SMC4L1 3q26.1 10051 201664_at SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SMC4L1 3q26.1 10051 CO 201 667_at gap junction protein, alpha 1, 43kDa (connexin 43) GJA1 6q21-q23.2 2697 m m 201668_x_at myristoylated alanine-rich protein kinase C substrate MARCKS 6q22.2 4082 201670_s_at myristoylated alanine-rich protein kinase C substrate MARCKS 6q22.2 4082 T 201674_s_at A kinase (PRKA) anchor protein 1 AKAP1 17q21 -q23 8 165 ι- 201681_s_at discs, large homolog 5 (Drosophila) DLG5 10q23 9231 m 201720_s_at lysosomal associated muitispanning membrane protein 5 LAPTM5 1p34 7805 IO 201721_s_at lysosomal associated muitispanning membrane protein 5 LAPTM5 1p34 7805 201754_at cytochrome c oxidase subunit VIc C0X6C 8q22-q23 1345 201757_at NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa (NADH- NDUFS5 1p34.2-p33 4725 coenzyme Q reductase) 201785_at riboπuclease, RNase A family, 1 (pancreatic) RNASE1 14q1 1.2 6035 201798_s_at fer-1-like 3, myoferlin (C. elegans) FER1 L3 10q24 26509 201820_at keratin 5 (epidermolysis bullosa simplex, Dowling- KRT5 12q12-q13 3852 Meara/Kobner/Weber-Cockayne types) 201825_s_at saccharopine dehydrogenase (putative) SCCPDH 1q44 5 1097 201826_s_at saccharopine dehydrogenase (putative) SCCPDH 1q44 5 1097 201839_s_at tumor-associated calcium signal transducer 1 TACSTD1 2p21 4072 201853_s_at cell division cycle 25B CDC25B 20p1 3 994 Table 8 201858_s_at proteoglycan 1, secretory granule PRG1 10q22.1 5552 201860_s_at plasminogen activator, tissue PLAT 8p12 5327 201874_at myelin protein zero-like 1 MPZL1 1q24.2 901 9 201885_s_at cytochrome b5 reductase 3 CYB5R3 22q13.31-qter 1727 |22q1 3.2-q1 3.31 201891_s_at beta-2-microglobulin B2M 15q21 -q22.2 567 201900_s_at aldo-keto reductase family 1, member A 1 (aldehyde reductase) AKR1A1 1p33-p32 10327 201914_s_at SEC63-like (S. cerevisiae) SEC63 6q21 11231 201923_at peroxiredoxin 4 PRDX4 Xp22.1 1 10549 201931 at electron-transfer-flavoprotein, alpha polypeptide (glutaric aciduria ETFA 15q23-q25 2 108 H) CO C 201938. at CDK2-associated protein 1 CDK2AP1 12q24.31 8099 CO 201960. s_at MYC binding protein 2 MYCBP2 13q22 23077 CO 201963. at acyl-CoA synthetase long-chain family member 1 ACSL1 4q34-q35 2180 201971. .s_at ATPase, H+ transporting, lysosomal 7OkDa, V 1 subuπit A ATP6V1A 3q13.2-q1 3.31 523 201998. at ST6 beta-galactosamide aipha-2,6-sialyltranferase 1 ST6GAL1 3q27-q28 6480 m 202012. .s_at exostoses (multiple) 2 EXT2 11pi 2-p1 1 2 132 CO 202018. U l s_at lactotransferrin LTF 3q21 -q23 4057 m 202036. .s_at secreted frizzled-related protein 1 SFRP1 8p12-p1 1.1 6422 m 202037. s_at secreted frizzled-related protein 1 SFRP1 8p12-p1 1.1 6422 202085. at tight junction protein 2 (zona occlude πs 2) TJP2 9q13-q21 9414 T 202086 at myxovirus (influenza virus) resistance 1, interferon-inducible protein MX1 2 1q22.3 4599 ι- m p78 (mouse) 202088_at solute carrier family 39 (zinc transporter), member 6 SLC39A6 18q12.2 25800 IO 202089_s_at solute carrier family 39 (zinc transporter), member 6 SLC39A6 18q12.2 25800 2021 10_at cytochrome c oxidase subunit VIIb COX7B Xq21 .1 1349 2021 69_s_at aminoadipate-sem ϊaldehyde dehydrogenase-phosphopantetheinyl AASDHPPT 11q22 60496 transferase 202223_at integral membrane protein 1 ITM1 11q23.3 3703 202233_s_at ubiquinol-cytochrome c reductase hinge protein UQCRH 1p34.1 7388 202237_at nicotinamide N-methyltransferase NNMT 11q23.1 4837 202243_s_at proteasome (prosome, macropain) subunit, beta type, 4 PSMB4 1q21 5692 202244_at proteasome (prosome, macropain) subunit, beta type, 4 PSMB4 1q21 5692 202265_at polycomb group ring finger 4 PCGF4 10p1 1.23 648 202269_x_at guanylate binding protein 1, interferon-inducible, 67kDa GBP1 1p22.2 2633 202283 at serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment SERPINF1 17p1 3.1 5176 Table 8 epithelium derived factor), member 1 202298_at NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1, 7.5kDa NDUFA1 Xq24 4694 202336_s_at peptidylglycine alpha-amidating monooxygenase PAM 5q14-q21 5066 202345_s_at fatty acid binding protein 5 (psoriasis-associated) FABP5 8q21 .13 2171 202371_at transcription elongation factor A (Sll)-like 4 TCEAL4 Xq22.2 79921 202376_at serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, SERPINA3 14q32.1 12 antitrypsin), member 3 202397_at nuclear transport factor 2 NUTF2 16q22.1 10204 202409_at putative insulin-like growth factor Il associated protein LOC492304 11p 15.5 492304 202428_x_at diazepam binding inhibitor (GABA receptor modulator, acyl- DBi 2q12-q21 1622 Coenzyme A binding protein) CO C 202431_s_at v-myc myelocytomatosis viral oncogene homolog (avian) MYC 8q24.1 2-q24.13 4609 CO 202435_s_at cytochrome P450, family 1, subfamily B, polypeptide 1 CYP 1B 1 2p21 1545 CO 202436_s_at cytochrome P450, family 1, subfamily B, polypeptide 1 CYP 1B 1 2p21 1545 202454_s_at v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) ERBB3 12q1 3 2065 202458_at protease, serine, 23 PRSS23 11q14.1 11098 m 202475_at seven transmembrane domain protein NIFIE1 4 19q1 3.1 10430 CO 202489_s_at FXYD domain containing ion transport regulator 3 FXYD3 19q1 3.1 1-q1 3.12 5349 m 202522_at phosphatidylinositol transfer protein, beta PITPNB 22q12.1 23760 m CΛ 202554_s_at glutathione S-transferase M3 (brain) GSTM3 1p13.3 2947 202599_s_at nuclear receptor interacting protein 1 NRIP1 2 1q 11.2 8204 T 202605_at glucuronidase, beta GUSB 7q21 .1 1 2990 ι- m 20261 3_at CTP synthase CTPS 1p34.1 1503 IO 202643_s_at tumor necrosis factor, alpha-induced protein 3 TNFAIP3 6q23 7 128 202648_at ribosomal protein S 19 RPS19 19q1 3.2 6223 202649_x_at ribosomal protein S19 RPS19 19q13.2 6223 202671_s_at pyridoxal (pyridoxine, vitamin B6) kinase PDXK 21q22.3 8566 202708_s_at histone 2, H2be HIST2H2BE 1q21-q23 8349 20271 2_s_at creatine kinase, mitochondrial 1B//creatine kinase, mitochondrial CKMT1 Bl/ 15q15 1159//548596 1A CKMT1 A 202729_s_at latent transforming growth factor beta binding protein 1 LTBP1 2p22-p21 4052 202752_x_at solute carrier family 7 (cationic amino acid transporter, y+ system), SLC7A8 14q1 1.2 23428 member 8 202759_s_at PALM2-AKAP2 protein PALM2-AKAP2 9q31-q33 44581 5 202806_at drebrin 1 DBN1 5q35.3 1627 202887 s at DNA-damage-inducible transcript 4 DDIT4 10pter-q26.1 2 54541 Table 8 202899_s_at splicing factor, arginine/serine-rich 3 SFRS3 6p21 6428 202908_at Wolfram syndrome 1 (wolframin) WFS1 4p16 7466 20291 7_s_at S100 calcium binding protein A8 (calgranulin A) S100A8 1q21 6279 202935_s_at SRY (sex determining region Y)-box 9 (campomelic dysplasia; SOX9 17q24.3-q25.1 6662 autosomal sex-reversal) 202961_s_at ATP synthase, H+ transporting, mitochondrial FO complex, subunit ATP5J2 7q22.1 9551 f, isoform 2 203021_at secretory leukocyte peptidase inhibitor SLPI 20q1 2 6590 203038_at protein tyrosine phosphatase, receptor type, K PTPRK 6q22.2-23.1 5796 203062_s_at mediator of DNA damage checkpoint 1 MDC1 6pter-p21 .31 9656

CO 203064_s_at forkhead box K2 FOXK2 17q25 3607 C 203108_at G protein-coupled receptor, family C, group 5, member A GPRC5A 12p1 3-p1 2.3 9052 co CO 203131_at platelet-derived growth factor receptor, alpha polypeptide PDGFRA 4q1 1-q13 5 156 203157_s_at glutaminase GLS 2q32-q34 2744 203159_at glutaminase GLS 2q32-q34 2744 203167_at TIMP metallopeptidase inhibitor 2 TIMP2 17q25 7077 m 203207_s_at mitochondrial fission regulator 1 MTFR1 8q13.1 9650 CO O N 203254_s_at talin 1 TLN 1 9p13 7094 m m 203255_at F-box protein 11 FBXO1 1 2p1 6.3 80204 203256_at cadher ϊn 3, type 1, P-cadherin (placental) CDH3 16q22.1 1001 203304_at BMP and activin membrane-bound inhibitor homolog (X. laevis) BAMBI 10p12.3-p1 1.2 25805 c 20331 5_at NCK adaptor protein 2 NCK2 2q12 8440 m 203343_at UDP-glucose dehydrogenase UGDH 4p1 5.1 7358 IO 203354_s_at pleckstrin and Sec7 domain containing 3 PSD3 8pter-p23.3 23362 203355_s_at pleckstrin and Sec7 domain containing 3 PSD3 8pter-p23.3 23362 203396_at proteasome (prosome, macropain) subunit, alpha type, 4 PSMA4 15q25.1 5685 203408_s_at special AT-rich sequence binding protein 1 (binds to nuclear SATB1 3p23 6304 matrix/scaffold-associati πg DNA's) 20341 6_at CD53 antigen CD53 1p13 963 203426_s_at insulin-like growth factor binding protein 5 IGFBP5 2q33-q36 3488 203430_at heme binding protein 2 HEBP2 6q24 23593 203439_s_at stanniocalcin 2 STC2 5q35.1 8614 203453_at sodium channel, nonvoltage-gated 1 alpha SCNN1 A 12p13 6337 203455_s_at spermidine/spermine N1-acetyltransferase SAT Xp22.1 6303 203476 at trophoblast glycoprotein TPBG 6q14-q15 7162 Table 8 203528_at sema domain, immunoglobulin domain (Ig), transmembrane SEMA4D 9q22-q31 10507 domain (TM) and short cytoplasmic domain, (semaphorin) 4D 203567_s_at tripartite motif-containing 38 TRIM38 6p21 .3 10475 203628_at insulin-like growth factor 1 receptor IGF1 R 15q26.3 3480 203632_s_at G protein-coupled receptor, family C, group 5, member B GPRC5B 16p1 2 51704 203675_at nucleobindin 2 NUCB2 11p15.1 -p14 4925 203685_at B-cell CLL/lymphoma 2 BCL2 18q21 .33[1 8q21 .3 596 203708_at phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 PDE4B 1p31 5142 dunce homolog, Drosophila) 203752_s_at jun D proto-oncogene JUND 19p1 3.2 3727 203757_s_at carcinoembryonic antigen-related cell adhesion molecule 6 (non¬ CEACAM6 19q13.2 4680 CO C specific cross reacting antigen) CO 203827_at WD40 repeat protein Interacting with phospholnositides of 49kDa WIPI49 17q24.2 55062 CO 20391 5_at chemokine (C-X-C motif) ligand 9 CXCL9 4q21 4283 203922_s_at cytochrome b-245, beta polypeptide (chronic granulomatous CYBB Xp21 .1 1536 disease) m 203923_s_at cytochrome b-245, beta polypeptide (chronic granulomatous CYBB Xp21 .1 1536 CO oo disease) m 203936_s_at matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa MMP9 20q1 1.2-q1 3.1 4318 m type IV collagenase) 203956_at MORC family CW-type zinc finger 2 M0RC2 22q12.2 22880 T 203961_at nebulette NEBL 10p12 10529 ι- 203962_s_at nebulette NEBL 10p12 10529 m 203963_at carbonic anhydrase XII CA1 2 15q22 771 IO 204006_s_at Fc fragment of IgG, low affinity Ilia, receptor (CD1 6a)//Fc fragment FCGR3A// 1q23 2214//2215 of IgG, low affinity HIb, receptor (CD1 6b) FCGR3B 204014_at dual specificity phosphatase 4 DUSP4 8p12-p1 1 1846 20401 5_s_at dual specificity phosphatase 4 DUSP4 8p12-p1 1 1846 204050_s_at ciathrin, light polypeptide (Lea) CLTA 9p13 121 1 204083_s_at tropomyosin 2 (beta) TPM2 9p13.2-p1 3.1 7169 204087_s_at solute carrier family 5 (sodium-dependent vitamin transporter), SLC5A6 2p23 8884 member 6 204131_s_at forkhead box 03A F0X03A 6q21 2309 204222_s_at GLI pathogenesis-related 1 (glioma) GLIPR1 12q21 .1 11010 204241_at acyl-Coenzyme A oxidase 3 , pristanoyl AC0X3 4p15.3 8310 204259 at matrix metallopeptidase 7 (matrilysin, uterine) MMP7 11q21-q22 4316 Table 8 204279_at proteasome (prosome, macropain) subunit, beta type, 9 (large PSMB9 6p21 .3 5698 multifunctional peptidase 2) 204284_at protein phosphatase 1, regulatory (inhibitor) subunit 3C PPP1 R3C 10q23-q24 5507 204304_s_at prominin 1 PR0M1 4p15.32 8842 204364_s_at chromosome 2 open reading frame 23 C2orf23 2p1 1.2 65055 204400_at embryonal Fyn-associated substrate EFS 14q1 1.2-q12 10278 204489_s_at CD44 antigen (homing function and Indian blood group system) CD44 11p13 960 204490_s_at CD44 antigen (homing function and Indian blood group system) CD44 11p13 960 204508_s_at carbonic anhydrase XII CA1 2 15q22 771 204533_at chemokine (C-X-C motif) ligand 10 CXCL1 0 4q21 3627 204560_at FK506 binding protein 5 FKBP5 6p21 .3-21 .2 2289 CO C 204597_x_at stanniocalcin 1 STC1 8p21 -p1 1.2 6781 co 20461 3_at phospholipase C, gamma 2 (phosphatidyli πositol-specific) PLCG2 16q24.1 5336 CO 204622_x_at nuclear receptor subfamily 4, group A, member 2 NR4A2 2q22-q23 4929 204623_at trefoil factor 3 (intestinal) TFF3 21q22.3 7033 204670_x_at major histocompatibility complex, class II, DR beta 1 HLA-DRB1 6p21 .3 3123 m 204750_s_at desmocollin 2 DSC2 18q1 2.1 1824 CO 204798_at v-myb myeloblastosis viral oncogene homolog (avian) MYB 6q22-q23 4602 m m 204806_x_at major histocompatibility complex, class I, F HLA-F 6p21 .3 3134 204820_s_at butyrophili π, subfamily 3, member A3//butyrophilin, subfamily 3, BTN3A3// 6p21 .3//6p22.1 10384//1 1118 member A2 BTN3A2 c 204821_at butyrophilin, subfamily 3, member A3 BTN3A3 6p21 .3 10384 m 204846_at ceruloplasmin (ferroxidase) CP 3q23-q25 1356 IO 204863_s_at interleukin 6 signal transducer (gp1 30, oncostatin M receptor) IL6ST 5q1 1 3572 204864_s_at interleukin 6 signal transducer (gp1 30, oncostatin M receptor) IL6ST 5q11 3572 204875_s_at GDP-mannose 4,6-dehydratase GMDS 6p25 2762 204881 _s_at UDP-glucose ceramide glucosyltransferase UGCG 9q31 7357 204949_at intercellular adhesion molecule 3 ICAM3 19p1 3.3-p1 3.2 3385 204967_at apical protein-like (Xenopus laevis) APXL Xp22.3 357 205009_at trefoil factor 1 (breast cancer, estrogen-inducibl β sequence TFF1 2 1q22.3 7031 expressed in) 205030_at fatty acid binding protein 7, brain FABP7 6q22-q23 2173 205066_s_at ectonucleotide pyrophosphatase/phosphodiesterase 1 ENPP1 6q22-q23 5167 205074_at solute carrier family 22 (organic cation transporter), member 5 SLC22A5 5q31 6584 205081 at cysteine-rich protein 1 (intestinal) CRIP1 14q32.33 1396 Table 8 205098_at chemokine (C-C motif) receptor 1 CCR1 3p21 1230 2051 57_s_at keratin 17 KRT1 7 17q1 2-q21 3872 205225_at estrogen receptor 1 ESR1 6q25.1 2099 205249_at early growth response 2 (Krox-20 homolog, Drosophila) EGR2 10q21 .1 1959 205253_at pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 205267_at POU domain, class 2, associating factor 1 P0U2AF1 11q23.1 5450 205270_s_at lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte LCP2 5q33.1 -qter 3937 protein of 76kDa) 205358_at glutamate receptor, ionotropic, AMPA 2 GRIA2 4q32-q33 2891 205566_at abhydrolase domain containing 2 ABHD2 15q26.1 11057 205644_s_at small nuclear ribonucleoprotein polypeptide G CO SNRPG 2p13.3 6637 C 205735_s_at AF4/FMR2 family, member 3 AFF3 2q1 1.2-q12 3899 CO 205763_s_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 2q14.1 CO DDX1 8 8886 205822_s_at 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) HMGCS1 5p14-p13 3 157 205849_s_at ubiquinol-cytochrome c reductase binding protein UQCRB 8q22 7381 205868_s_at protein tyrosine phosphatase, non-receptor type 11 (Noonan PTPN 11 12q24 5781 m syndrome 1) CO 205890_s_at ubiquitin D UBD 6p21 .3 10537 m 205907_s_at osteomodulin OMD 9q22.31 4958 m o 205923_at reelin RELN 7q22 5649 205948_at protein tyrosine phosphatase, receptor type, T PTPRT 20q12-q13 11122 T 205967_at histone 1, H4c HIST1 H4C 6p21 .3 8364 ι- m 206059_at zinc finger protein 9 1 (HPF7, HTF1 0) ZNF91 19p13.1-p12 7644 IO 206074_s_at high mobility group AT-hook 1 HMGA1 6p21 3159 2061 16_s_at tropomyosin 1 (alpha) TPM1 15q22.1 7 168 2061 89_at unc-5 homolog C (C. elegans) UNC5C 4q21 -q23 8633 206245_s_at influenza virus NS1A binding protein IVNS1ABP 1q25.1-q31 .1 10625 206346_at prolactin receptor PRLR 5p14-p13 5618 206378_at secretoglobi π, family 2A, member 2 SCGB2A2 11q 13 4250 206391_at retinoic acid receptor responder (tazarote πe induced) 1 RARRES1 3q25.32 591 8 206509_at prolactin-induced protein PIP 7q34 5304 206754_s_at cytochrome P450, family 2, subfamily B, polypeptide 7 pseudogene CYP2B7P1 19q1 3.2 1556 1 206799_at secretoglobin, family 1D, member 2 SCGB1 D2 11q 13 10647 206858_s at homeo box C6 H0XC6 12q1 3.3 3223 Table 8 206951_at histone 1, H4e HIST1 H4E 6p21 .3 8367 207039_at cyclin-dependent kinase inhibitor 2A (melanoma, p 16, inhibits CDKN2A 9p21 1029 CDK4) 207040_s_at suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 ST13 22q13.2 6767 interacting protein) 207046_at histone 2, H4 HIST2H4 1q21 8370 207076_s_at argininosuccinate synthetase ASS 9q34.1 445 2071 98_s_at LIM and senescent cell antigen-like domains 1 LIMS1 2q12.3-q13 3987 207238_s_at protein tyrosine phosphatase, receptor type, C PTPRC 1q31 -q32 5788 207275_s_at acyl-CoA synthetase long-chain family member 1 ACSL1 4q34-q35 2180 207279_s_at nebulette NEBL 10p12 10529 CO C 207332_s_at transferrin receptor (p90, CD71) TFRC 3q29 7037 CO 207508_at ATP synthase, H+ transporting, mitochondrial FO complex, subunit ATP5G3 2q31 . 1 518 CO c (subunit 9) isoform 3 207580_at melanoma antigen family B, 4 MAGEB4 Xp21 .3 4 115 207604_s_at solute carrier family 4, sodium bicarbonate cotransporter, member SLC4A7 3p22 9497 m 7 CO 207626_s_at solute carrier family 7 (cationic amino acid transporter, y+ system), SLC7A2 8p22-p21 .3 6542 m member 2 m 20771 4_s_at serpin peptidase inhibitor, clade H (heat shock protein 47), member SERPINH1 11q13.5 871 1, (collagen binding protein 1) T 207791 _s_at RAB1 A, member RAS oncogene family RAB1A 2p14 5861 ι- 207828_s_at centromere protein F, 350/400ka (mitosin) CENPF 1q32-q41 1063 m 207847_s_at mucin 1, transmembrane MUC1 1q21 4582 IO 207929_at gastrin-releasing peptide receptor GRPR Xp22.2-p22.1 3 2925 207966_s_at golgi apparatus protein 1 GLG1 16q22-q23 2734 208029_s_at lysosomal associated protein transmembrane 4 beta LAPTM4B 8q22.1 55353 208083_s_at integrin, beta 6 ITGB6 2q24.2 3694 208084_at integrin, beta 6 ITGB6 2q24.2 3694 2081 13_x_at poly(A) binding protein, cytoplasmic 3 PABPC3 13q12-q13 5042 208305_at progesterone receptor PGR 11q22-q23 5241 208308_s_at glucose phosphate isomerase GPI 19q1 3.1 2821 208451 _s_at complement component 4A//complement component 4B// C4A//C4B 6p21 .3 432395//720// complement component 4B, telomeric 721 208460_at gap junction protein, alpha 7, 45kDa (connexin 45) GJA7 17q21 .31 10052 208490 x at histone 1, H2bf HIST1 H2BF 6p21 .3 8343 Table 8 208523_x_at histone 1 H2bi HIST1 H2BI 6p21 .3 8346 208527_x_at histone 1 H2be HIST1 H2BE 6p21 .3 8344 208546_x_at histone 1 H2bh HIST1 H2BH 6p21 .3 8345 208576_s_at histone 1 H3b HIST1 H3B 6p21 .3 8358 208579_x_at H2B histone family, member S H2BFS 2 1q22.3 54145 20861 2_at protein disulfide isomerase family A, member 3 PDIA3 15q1 5 2923 20861 5_s_at protein tyrosine phosphatase type IVA, member 2 PTP4A2 1p35 8073 20861 6_s_at protein tyrosine phosphatase type IVA, member 2 PTP4A2 1p35 8073 20861 7_s_at protein tyrosine phosphatase type IVA, member 2 PTP4A2 1p35 8073 208624_s_at eukaryotic translation initiation factor 4 gamma, 1 EIF4G1 3q27-qter 1981

CO 208627_s_at Y box binding protein 1 YBX1 1p34 4904 C 208628_s_at Y box binding protein 1 YBX1 1p34 4904 CO CO 208637_x_at actinin, alpha 1 ACTN 1 14q24.1 -q24.2 87 |14q24|14q22-q24 208641_s_at ras-related C3 botulinum toxin substrate 1 (rho family, small GTP RAC1 7p22 5879 binding protein Rad) m 208649_s_at valosin-containing protein VCP 9p13.3 741 5 CO 208650_s_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 m 208651_x_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 m o 208675_s_at dolichyl-diphosphooligosaccharide-protein glycosyltransf erase DDOST 1p36.1 1650 actin related protein 2/3 complex, subunit 2, 34kDa ARPC2 2q36.1 10109 73 208679_s_at c 208680_at peroxiredoxin 1 PRDX1 1p34.1 5052 m 208683_at calpain 2, (m/ll) large subunit CAPN2 1q41-q42 824 IO 208687_x_at heat shock 7OkDa protein 8 HSPA8 11q24.1 3312 208691_at transferrin receptor (p90, CD71 ) TFRC 3q29 7037 208693_s_at glycyl-tRNA synthetase GARS 7p15 2617 208695_s_at ribosomal protein L39 RPL39 Xq22-q24 6170 208696_at chaperonin containing TCP1, subunit 5 (epsilon) CCT5 5p15.2 22948 208697_s_at eukaryotic translation initiation factor 3, subunit 6 48kDa EIF3S6 8q22-q23 3646 208699_x_at transketolase (Wernicke-Korsakoff syndrome) TKT 3p14.3 7086 208701_at Amyloid beta (A4) precursor-like protein 2 APLP2 11q23-q25 334 20871 1_s_at cyclin D 1 CCND1 11q 13 595 20871 2_at cyclin D 1 CCND1 11q 13 595

208729_x_at major histocompatibility complex, class I1 B HLA-B 6p21 .3 3106 208739 x at SMT3 suppressor of mif two 3 homolog 2 (yeast) SUMO2 17q25.1 6613 Table 8 208746_x_at ATP synthase, H+ transporting, mitochondrial FO complex, subuπit ATP5L 11q23.3 10632 9 208747_s_at complement component 1, s subcomponent C 1S 12p1 3 716 208750_s_at ADP-ribosylation factor 1 ARF1 1q42 375 208767_s_at lysosomal associated protein transmembrane 4 beta LAPTM4B 8q22,1 55353 208778_s_at t-complex 1 TCP1 6q25.3-q26 6950 208788_at ELOVL family member 5, elongation of long chain fatty acids ELOVL5 6p21 . 1-p12.1 60481 (FEN1/Elo2, SUR4/Elo3-like, yeast) 208798_x_at golgi autoantigen, golgin subfamily a, 8A GOLGA8A 15q1 1.2 2301 5 20881 2_x_at major histocompatibility complex, class I, C HLA-C 6p21 .3 3107 208836_at ATPase, Na+/K+ transporting, beta 3 polypeptide ATP1 B3 3q23 483 CO C 208864_s_at thioredoxin TXN 9q31 7295 CO 208865_at casein kinase 1, alpha 1 CSNK1 A 1 5q32 1452 CO 208873_s_at chromosome 5 open reading frame 18 C5orf1 8 5q22-q23 7905 208885_at lymphocyte cytosolic protein 1 (L-plastin) LCP1 13q14.3 3936 208894_at major histocompatibility complex, class II, DR alpha HLA-DRA 6p21 .3 3122 m 208895_s_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 DDX18 2q14.1 8886 CO 208905_at cytochrome c, somatic CYCS 7p15.3 54205 m 208909_at ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 UQCRFS1 19q12-q13.1 7386 m 20891 2_s_at 2',3'-cyclic nucleotide 31phosphodiesterase CNP 17q21 1267 ) U 20891 8_s_at NAD kinase NADK 1p36.33-p36.21 65220 T 208952_s_at La ribonucleoprotein domain family, member 5 LARP5 10p15.3 23185 ι- m 20901 6_s_at keratin 7 KRT7 12q1 2-q13 3855 IO 209024_s_at synaptotagmin binding, cytoplasmic RNA interacting protein SYNCRiP 6q14-q1 5 10492 209026_x_at tubulin, beta polypeptide TUBB 6p21 .33 203068 209036_s_at malate dehydrogenase 2, NAD (mitochondrial) MDH2 7p1 2.3-q1 1.2 4191 209041 _s_at ubiquitin-conjugati πg enzyme E2G 2 (UBC7 homolog, yeast) UBE2G2 21q22.3 7327 209056_s_at CDC5 cell division cycle 5-like (S. pombe) CDC5L 6p21 988 209066_x_at ubiquinol-cytochrome c reductase binding protein UQCRB 8q22 7381 209070_s_at regulator of G-protein signalling 5 RGS5 1q23.1 8490 209076_s_at WDR45-like WDR45L 17q25.3 56270 209123_at quinoid dihydropteridine reductase QDPR 4p15.31 5860 209134_s_at ribosomal protein S6 RPS6 9p21 6194 2091 38_x_at Immunoglobulin lambda joining 3 IGLC2 22q1 1.2 3538 209140_x_at major histocompatibility complex, class I, B HLA-B 6p21 .3 3106 Table 8 2091 54_at Taxi (human T-cell leukemia virus type I) binding protein 3 TAX1 BP3 17p13 30851 2091 73_at anterior gradient 2 homolog (Xeπopus laevis) AGR2 7p21 .3 10551 2091 91_at tubulin, beta 6 TUBB6 18p1 1.21 8461 7 209201_x_at chemokine (C-X-C motif) receptor 4 CXCR4 2q21 7852 209205_s_at LIM domain only 4 LM04 1p22.3 8543 209251_x_at tubulin alpha 6 TUBA6 12q12-q14 84790 209257_s_at chondroitin sulfate proteoglycan 6 (bamacan) CSPG6 10q25 9126 209258_s_at chondroitin sulfate proteoglycan 6 (bamacan) CSPG6 10q25 9 126 209289_at Nuclear factor I/B NFIB 9p24.1 4781 209290_s_at nuclear factor I/B NFIB 9p24.1 4781

CO 20931 2_x_at major histocompatibility complex, class II, DR beta 1 HLA-DRB1 6p21 .3 3 123 C 209316_s_at HBS1 -like (S. cerevisiae) HBS1 L 6q23-q24 10767 co CO 209341 _s_at inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase IKBKB 8p1 1.2 3551 beta 209343_at EF-hand domain family, member D 1 EFHD1 2q37.1 80303 m 209369_at annexϊn A3 ANXA3 4q13-q22 306 209377_s_at high mobility group nucleosomal binding domain 3 HMG N3 6q14.1 9324 CO 209386_at transmembrane 4 L six family member 1 TM4SF1 3q21-q25 4071 m m 209387_s_at transmembrane 4 L six family member 1 TM4SF1 3q21-q25 4071 209389_x_at diazepam binding inhibitor (GABA receptor modulator, acyl- DBI 2q12-q21 1622 Coenzyme A binding protein) c 209395_at chitinase 3-like 1 (cartilage glycoprotein-39) CHI3L1 1q32.1 1116 m 209396_s_at chitinase 3-like 1 (cartilage glycoprotein-39) CHI3L1 1q32.1 1116 IO 20941 1_s_at golgi associated, gamma adaptin ear containing, ARF binding GGA3 17q25.1 23163 protein 3 209436_at spondin 1, extracellular matrix protein SP0N1 11p 15.2 1041 8 209457_at dual specificity phosphatase 5 DUSP5 10q25 1847 209460_at 4-aminobutyrate aminotransferase ABAT 16p13.2 18 209524_at hepatoma-derived growth factor, related protein 3 HDGFRP3 15q1 1.2 50810 209537_at exostoses (multiple)-like 2 EXTL2 1p21 2 135 209574_s_at chromosome 18 open reading frame 1 C18orf1 18p1 1.2 753 209602_s_at GATA binding protein 3 GATA3 10p15 2625 209603_at GATA binding protein 3 GATA3 10p15 2625 209604_s_at GATA binding protein 3 GATA3 10p15 2625 209610 s at solute carrier family 1 (glutamate/neutral amino acid transporter), SLC1A4 2p15-p1 3 6509 member 4 Table 8 209624_s_at methylcrotonoyl-Coenzyme A carboxylase 2 (beta) MCCC2 5q12-q13 64087 209626_s_at oxysterol binding protein-like 3 0SBPL3 7p1 5 26031 209681_at solute carrier family 19 (thiamine transporter), member 2 SLC19A2 1q23.3 10560 209688_s_at hypothetical protein FLJ10996 FLJ1 0996 2q14.1 54520 209694_at 6-pyruvoyltetrahydropterin synthase PTS 11q22.3-q23.3 5805 209699_x_at aldo-keto reductase family 1, member C2 (dihydrodiol AKR 1C2 10p15-p1 4 1646 dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III) 209728_at major histocompatibility complex, class II, DR beta 4 HLA-DRB4 6p21 .3 3126 209771 _x_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 209772_s_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 CO C 209773_s_at ribonucleotide reductase M2 polypeptide RRM2 2p25-p24 6241 CO peptidyl arginine deiminase, type Ii PADI2 1p35.2-p35.1 11240 CO 209791 _at 209835_x_at CD44 antigen (homing function and Indian blood group system) CD44 11p 13 960 209846_s_at butyrophilin, subfamily 3, member A2 BTN3A2 6p22.1 11118 adrenergic, a!pha-2A-, receptor ADRA2A 10q24-q26 150 m 209869_at 209896_s_at protein tyrosine phosphatase, non-receptor type 11 (Noonan PTPN 11 12q24 5781 CO syndrome 1) m - j m 209916_at dehydrogenase E 1 and transketolase domain containing 1 DHTKD1 10p14 55526 209969_s_at signal transducer and activator of transcription 1, 9 1kDa STAT1 2q32.2 6772 20q13 . 1522 T 210042_s_at cathepsin Z CTSZ 210046_s_at isocitrate dehydrogenase 2 (NADP+), mitochondrial IDH2 15q26.1 3418 ι- m 210052_s_at TPX2, microtubule-associated, homolog (Xenopus laevis) TPX2 20q1 1.2 22974 IO 210087_s_at myelin protein zero-like 1 MPZL1 1q24.2 901 9 210092_at mago-nashi homolog, proliferation-associated (Drosophila) MAGOH 1p34-p33 4 116 210108_at calcium channel, voltage-dependent, L type, alpha 1D subuπit CACNA1 D 3p14.3 776 210154_at malic enzyme 2, NAD(+)-depe πdent, mitochondrial ME2 6p25-p24|1 8q21 4200 2 10222_s_at reticulon 1 RTN1 14q23.1 6252 210272_at cytochrome P450, family 2, subfamily B, polypeptide 7 pseudogene CYP2B7P1 19q13.2 1556 1 210338_s_at heat shock 7OkDa protein 8 HSPA8 11q24.1 3312 210476_s_at prolactin receptor PRLR 5p14-p13 5618 210512_s_at vascular endothelial growth factor VEGF 6p12 7422 210513_s_at vascular endothelial growth factor VEGF 6p12 7422 210523_at bone morphogenetic protein receptor, type IB BMPR1 B 4q22-q24 658 210563_x at CASP8 and FADD-like apoptosis regulator CFLAR 2q33-q34 8837 Table 8 210592_s_at spermidine/spermine N 1-acetyltransferase SAT Xp22.1 6303 210648_x_at sorting nexin 3 SNX3 6q21 8724 210735_s_at carbonic anhydrase XII CA12 15q22 771 210764_s_at cysteine-rich, angiogenic inducer, 6 1 CYR61 1p31-p22 3491 210843_s_at microfibrillar-associated protein 3-like MFAP3L 4q32.3 9848 210916_s_at CD44 antigen (homing function and Indian blood group system) CD44 1 1 p 13 960 210926_at actin-like protein FKSG30 2q21 .1 44091 5 210933_s_at fascin homolog 1, actin-bundling protein (Strongylocentrotus FSCN 1 7p22 6624 purpuratus) 210982_s_at major histocompatibility complex, class II, D R alpha HLA-DRA 6p21 .3 3122 interleukin 6 signal transducer (gp1 30, o πcostatin M receptor) IL6ST 5q1 1 3572 CO 211000_s_at C 211017_s_at neurofibroma 2 (bilateral acoustic neuroma) NF2 22q12.2 4771 CO glucosaminyl (N-acetyl) transferase 2 , l-branching enzyme GCNT2 6p24 2651 CO 211020_at 211070 x at diazepam binding inhibitor (GABA receptor modulator, acyl- DBI 2q12-q21 1622 Coenzyme A binding protein) /// diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein) m 211075 s at CD47 antigen (Rh-related antigen, integrin-associated signal CD47 3q13.1 -q13.2 961 CO transducer) /// CD47 antigen (Rh-related antigen, integrin- m associated signal transducer) m 211090—s at PRP4 pre-mRNA processing factor 4 homolog B (yeast) /// PRP4 PRPF4B 6p25.2 8899 pre-mRNA processing factor 4 homolog B (yeast) T 2 1 11 10_s_at androgen receptor (dihydrotestosterone receptor; testicular A R Xq1 1 .2-q1 2 367 ι- feminization; spinal and bulbar muscular atrophy; Kennedy m disease) IO 2 1 1139. s_at NGFI-A binding protein 1 (EGR1 binding protein 1) NAB1 2q32.3-q33 4664 2 1 1214. s_at death-associated protein kinase 1 DAPK1 9q34.1 1612 2 1 1233. x_at estrogen receptor 1 ESR1 6q25.1 2099 2 11234. x_at estrogen receptor 1 ESR1 6q25.1 2099 2 1 1235. s_at estrogen receptor 1 ESR1 6q25.1 2099 2 1 1323. .s_at inositol 1,4,5-triphosphate receptor, type 1 ITPR1 3p26-p25 3708 2 1 1345. _x_at eukaryotic translation elongation factor 1 gamma EEF1G 11q12.3 1937 2 11363. .s_at methylthioadenosine phosphorylase MTAP 9p21 4507 2 11388. s_at 2 11430 s at immunoglobulin heavy locus /// immunoglobulin heavy constant IGH @ /// 14q32.33 3492 /// 3500

gamma 1 (G1 m marker) /// immunoglobulin heavy constant gamma IIGGHHGG11 ////// /// 3501 /// 2 (G2m marker) /// immunoglobulin heavy constant gamma 3 (G3m IIGGHHGG22 ////// 3502 /// 3507 Table 8 marker) /// immunoglobulin heavy constant mu IGHG3 /// IGHM 2 11467_s_at nuclear factor I/B NFIB 9p24.1 4781

2 11529_x_at HLA-G histocompatibility antigen, class I1 G HLA-G 6p21 .3 3135 2 11538_s_at heat shock 7OkDa protein 2 HSPA2 14q24.1 3306 2 11637_x_at IgH chain VDJ region /// IgH chain VDJ region 2 11639 x at Ig rearranged H-chain (V4-D-J4) mRNA encoding cold agglutinin FS-2 /// Ig rearranged H-chain (V4-D-J4) mRNA encoding cold agglutinin FS-2 2 11644_x_at immunoglobulin kappa constant /// immunoglobulin kappa constant IGKC 2p12 351 4 2 11645_x_at Immunoglobulin kappa light chain (IGKV) mRNA variable region, CO joining region, and constant region /// Immunoglobulin kappa light C CO chain (IGKV) mRNA variable region, joining region, and constant CO region 2 11650_x_at IgG heavy chain variable region (Vh26) /// IgG heavy chain variable region (Vh26) m 2 11695_x_at mucin 1, transmembrane /// mucin 1, transmembrane MUC1 1q21 4582 CO 2 11712_s_at annexin A9 /// annexin A9 ANXA9 1q21 8416 m 2 11714_X_at tubulin, beta polypeptide /// tubulin, beta polypeptide TUBB 6p21 .33 203068 m 211726_S_at flavin containing monooxygenase 2 /// flavin containing FMO2 1q23-q25 2327 monooxygenase 2 T 2 11750_x_at tubulin alpha 6 /// tubulin alpha 6 TUBA6 12q12-q14 84790 ι- 2 11755 s at ATP synthase, H+ transporting, mitochondrial FO complex, subunit ATP5F1 1p13.2 515 m b, isoform 1 /// ATP synthase, H+ transporting, mitochondrial FO IO complex, subunit b, isoform 1 2 11798_x_at immunoglobulin lambda joining 3 IGU3 22q1 1.1 -q1 1.2 28831 2 11799_x_at major histocompatibility complex, class I, C HLA-C 6p21 .3 3 107 2 11862_x_at CASP8 and FADD-like apoptosis regulator CFLAR 2q33-q34 8837 2 11864_s_at fer-1 -like 3, myoferlin (C. elegans) FER1 L3 10q24 26509 2 11907_s_at par-6 partitioning defective 6 homolog beta (C. elegans) /// par-6 PARD6B 20q1 3.1 3 8461 2 partitioning defective 6 homolog beta (C. elegans) 2 1191 1_x_at major histocompatibility complex, class I1 B /// major HLA-B 6p21 .3 3106 histocompatibility complex, class I, B 2 11919_s_at chemokine (C-X-C motif) receptor 4 /// chemokine (C-X-C motif) CXCR4 2q21 7852 receptor 4 2 11921_x_at prothymosin, alpha (gene sequence 28) /// prothymosin, alpha PTMA 2q35-q36 5757 (gene sequence 28) Table 8 211926_s_at myosin, heavy polypeptide 9, non-muscle MYH9 22q1 3.1 4627 211927_x_at eiikaryotic translation elongation factor 1 gamma EEF1 G 11q12.3 1937 211945_s_at integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen ITGB1 10p1 1.2 3688 CD29 includes MDF2, MSK12) 211963_s_at actin related protein 2/3 complex, subunit 5, 16kDa ARPC5 1q25.3 10092 211966_at collagen, type IV, alpha 2 COL4A2 13q34 1284 2 11968_s_at heat shock 9OkDa protein 1, alpha HSPCA 14q32.33 3320 2 11969_at heat shock 9OkDa protein 1, alpha HSPCA 14q32.33 3320 2 11981_at collagen, type IV, alpha 1 C0L4A1 13q34 1282 2 11986_at AHNAK nucleoprotein (desmoyokin) AHNAK 11q 12.2 79026 212012_at peroxidasin homolog (Drosophila) PXDN 2p25 7837 CO C 212013_at peroxidasin homolog (Drosophila) PXDN 2p25 7837 CO 212014_x_at CD44 antigen {homing function and Indian blood group system) CD44 11p1 3 960 CO 212055_at chromosome 18 open reading frame 10 C 18orf1 0 18q1 2.2 25941 212067_s_at complement component 1, r subcomponent C1R 12p1 3 7 15 212077_at caldesmon 1 CALD1 7q33 800 m 212099_at ras homolog gene family, member B RHOB 2p24 388 CO 212100_s_at polymerase (DNA-directed), delta interacting protein 3 POLDIP3 22q1 3.2 84271 m 8q11 .2 m 212142_at MCM4 minichromosome maintenance deficient 4 (S. cerevisiae) MCM4 4173 212148_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 212151_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 T o 212160_at exportin, tRNA (nuclear export receptor for tRNAs) XPOT 12q14.2 11260 ι- m 212178 s at P0M121 membrane glycoprotein (rat) /// nuclear envelope pore P0M121 /// 7q1 1.23 340318 /// IO membrane LOC34031 8 /// nuclear envelope pore membrane LOC34031 8 /// 441253 /// LOC441253 LOC441253 9883 212195_at lnterleukin 6 signal transducer (gp130, oncostatin M receptor) IL6ST 5q1 1 3572 212196_at lnterleukin 6 signal transducer (gp130, oncostatin M receptor) IL6ST 5q1 1 3572 212218_s_at fatty acid synthase FASN 17q25 2 194 212219_at proteasome (prosome, macropain) activator subunit 4 PSME4 2p16.3 23198 212220_at proteasome (prosome, macropain) activator subunit 4 PSME4 2p16.3 23198 212240_s_at phosphoinositide-3-kinase, regulatory subunit 1 (p85 alpha) PIK3R1 5q13.1 5295 212250_at metadherin MTDH 8q22.1 92140 212251_at metadherin MTDH 8q22.1 92140 212320_at tubulin, beta polypeptide TUBB 6p21 .33 203068 212417 at secretory carrier membrane protein 1 SCAMP1 5q1 3.3-q14.1 9522 Table 8 212442_S_at LAG1 longevity assurance homolog 6 (S. cerevisiae) LASS6 2q24.3 253782 212444_at G protein-coupled receptor, family C, group 5, member A GPCR5A 12p13-p1 2.3 9052 212463_at CD59 antigen p 18-20 {antigen identified by monoclonal antibodies CD59 11p13 966 16.3A5, EJ16, EJ30, EL32 and G344) 2 12492_s_at jumonji domain containing 2B JMJD2B 19p13.3 23030 2 12496_s_at jumonji domain containing 2B JMJD2B 19p13.3 23030 2 12501_at CCAAT/enhancer binding protein (C/EBP), beta CEBPB 20q13.1 1051 212581_x_at glyceraldehyde-3-phosphate dehydrogenase GAPDH 12p13 2597 212587_s_at protein tyrosine phosphatase, receptor type, C PTPRC 1q31-q32 5788 212591_at RNA binding motif protein 34 RBM34 1q42.3 23029 212592_at Immunoglobulin J polypeptide, linker protein for immunoglobulin IGJ 4q21 3512 CO C alpha and mu polypeptides CO 212593_s_at programmed cell death 4 (neoplastic transformation inhibitor) PDCD4 10q24 27250 CO 212613_at butyrophilin, subfamily 3, member A2 BTN3A2 6p22.1 11118 212631_at Syntaxin 7 STX7 6q23.1 8417 212637_s_at WW domain containing E3 ubiquitin protein ligase 1 WWP1 8q21 11059 m 212638_s_at WW domain containing E3 ubiquitin protein ligase 1 WWP1 8q21 11059 CO 212671_s_at major histocompatibility complex, class II, DQ alpha 1 /// major HLA-DQA1 /// 6p21.3 3117 /// 3 118 m histocompatibility complex, class II, DQ alpha 2 HLA-DQA2 m 212788_x_at ferritin, light polypeptide FTL 19q13.3-q13.4 2512 212810_s_at solute carrier family 1 (glutamate/neutral amino acid transporter), SLC1 A4 2p15-p13 6509 T member 4 ι- 212827_at immunoglobulin heavy constant mu /// immunoglobulin heavy IGHM 14q32.33 3507 m constant mu IO 212859_x_at metallothionein 1E (functional) MT1 E 16q13 4493 212883_at Apolipoprotein E APOE 19q13.2 348 212956_at KIAA0882 protein KIAA0882 4q31 .21 231 58 212971_at cysteinyl-tRNA synthetase CARS 11p15.5 833 212998_x_at major histocompatibility complex, class II, DQ beta 1 /// major HLA-DQB1 6p21 .3 3 119 histocompatibility complex, class II, DQ beta 1 213002_at Myristoylated alanine-rich protein kinase C substrate MARCKS 6q22.2 4082 213007_at hypothetical protein FLJ1 071 9 FLJ1071 9 15q25-q26 5521 5 213029_at Nuclear factor I/B NFIB 9p24.1 4781 213032_at Nuclear factor I/B NFIB 9p24.1 4781 213080_x_at ribosomal protein L5 RPL5 1p22.1 6125 213089_at hypothetical protein L0C1 53561 L0C1 53561 5q13.2 153561 Table 8 2 13 101_s_at ARP3 actin-related protein 3 homolog (yeast) ACTR3 2q14.1 10096 2 13122_at TSPY-like 5 TSPYL5 8q22.1 85453 2 13 164_at solute carrier family 5 (inositol transporters), member 3 SLC5A3 21q22.12 6526 2131 70_at glutathione peroxidase 7 GPX7 1p32 2882 213187_x_at ferritin, light polypeptide FTL 19q1 3.3-q13.4 2512 2 131S3_x_at T cell receptor beta variable 19 /// T cell receptor beta variable 19 TRBV19 /// 7q34 28568 /// /// T cell receptor beta constant 1 /// T cell receptor beta constant 1 TRBC1 28639 213232_at KIAA1467 protein KIAA1467 12p1 3.1 5761 3 2 13234_at KIAA1467 protein KIAA1467 12p1 3.1 5761 3 213274_s_at cathepsin B CTSB 8p22 1508

CO 213338_at Ras-induced senescence 1 RIS1 3p21 .3 25907 C 213377_x_at ribosomal protein S12 RPS12 6q23.2 6206 CO CO 213385_at Chimerin (chimaerin) 2 CHN2 7p15.3 1124 2 13392_at hypothetical protein MGC35048 MGC35048 16p12.3 1241 52 2 13399_x_at ribophorin Il RPN2 20q1 2-q13.1 6185 m 2 13409_S_at Ras homolog enriched in brain RHEB 7q36 6009 2 13453_x_at glyceraldehyde-3-phosphate dehydrogenase GAPDH 12p1 3 2597 CO 2 13491_x_at ribophorin Il RPN2 20q12-q13.1 6185 m o m 2 13495_s_at Ribosome binding protein 1 homolog 18OkDa (dog) RRBP1 20p12 6238 213502_x_at similar to bK246H3.1 (immunoglobulin lambda-like polypeptide 1, LOC91 3 16 22q1 1.23 9131 6 T pre-B-cell specific) 2 13503_x_at annexin A2 ANXA2 15q21-q22 302 ι- m 2 13564_x_at lactate dehydrogenase B LDHB 12p12.2-p12.1 3945 IO 2 13605_s_at Glucuronidase, beta-like 1 /// Glucuronidase, beta-like 2 C6orf216 5q13.2 /// 6 37551 3 /// 402223 2 13627_at melanoma antigen family D, 2 MAGED2 Xp1 1.2 1091 6 213693_s_at mucin 1, transmembrane MUC1 1q21 4582 2 13697_at Homeodomain interacting protein kinase 3 HIPK3 11p 13 10 114 2 13699 s at tyrosine 3-monooxygenase/tryptophan 5-monooxygenase YWHAQ /// 2p25.1 /// 18q1 1.2 10971 /// activation protein, theta polypeptide /// mindbomb homolog 1 MIB1 57534 (Drosophila) 213702_x_at N-acylsphingosine amidohydrolase (acid ceramidase) 1 ASAH1 8p22-p21 .3 427 213746_s_at filamin A, alpha (actin binding protein 280) FLNA Xq28 231 6 213798_s_at CAP, adenylate cyclase-associated protein 1 (yeast) CAP1 1p34.2 10487 2 13813_x_at Ferritin, light polypeptide FTL 19q1 3.3-q1 3.4 2512 213843_x_at solute carrier family 6 (neurotransmitter transporter, creatine), SLC6A8 Xq28 6535 Table 8 member 8 213857_S_at CD47 antigen (Rh-related antigen, integrin-associated signal CD47 3q1 3.1 -q1 3.2 961 transducer) 213863_s_at Ornithine decarboxylase antizyme 3 OAZ3 1q21 .3 51686 21391 1_s_at H2A histone family, member Z H2AFZ 4q24 301 5 213923_at RAP2B, member of RAS oncogene family RAP2B 3q25.2 5912 213932_x_at Major histocompatibility complex, class I, A HLA-A 6p21 .3 3105 213941_x_at ribosomal protein S7 RPS7 2p25 6201 213962_s_at KIAA0692 protein KIAA0692 12q24.33 23141 213975_s_at lysozyme (renal amyloidosis) /// leukocyte immunoglobu ϋn-like LYZ /// LILRB1 12q1 5 /// 19q1 3.4 10859 /// 4069 receptor, subfamily B (with TM and ITIM domains), member 1 CO C 213988_s_at spermidine/spermine N 1-acetyltransferase SAT Xp22.1 6303 CO 214031_s_at Keratin 7 KRT7 12q12-q1 3 3855 CO 214038_at chemokine (C-C motif) ligand 8 CCL8 17q1 1.2 6355 214039_s_at lysosomal associated protein transmembrane 4 beta LAPTM4B 8q22.1 55353 214052_x_at BAT2 domain containing 1 XTP2 1q23.3 2321 5 m 214053_at V-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) ERBB4 2q33.3-q34 2066 CO 214096_s_at serine hydroxymethyltransferase 2 (mitochondrial) SHMT2 12q12-q14 6472 m m 2141 19_s_at FK506 binding protein 1A, 12kDa FKBP1A 20p13 2280 2141 64_x_at carbonic anhydrase XII CA12 15q22 771 hypothetical protein FLJ22269 T 214269_at FU22269 4p16.3 84179 214288_s_at proteasome (prosome, macropain) subunit, beta type, 1 PSMB1 6q27 5689 ι- m 21431 3_s_at Eukaryotic translation initiation factor 5B EIF5B 2p1 1.1 -q1 1. 1 9669 IO 214315_x_at calreticulin CALR 19p13.3-p13.2 8 11 214324_at glycoprotein 2 (zymogen granule membrane) GP2 16p12 2813 214349_at Hypothetical LOC388388 — 17p1 3.3 388388 214370_at S 1OO calcium binding protein A8 (calgranu ϋn A) S100A8 1q21 6279 214428_x_at complement component 4A /// complement component 4B /// C4A /// C4B 6p21 .3 432395 /// 720 complement component 4B, telomeric /// 721 214431_at guanine monphosphate synthetase GMPS 3q24 8833 214440_at N-acetyltransferase 1 (arylamine N-acetyltransferase) NAT1 8p23.1-p21 .3 9 214453_s_at interferon-induced protein 44 IFI44 1p31 .1 10561 214459_x_at major histocompatibility complex, class I, C HLA-C 6p21 .3 3107 214464_at CDC42 binding protein kinase alpha (DMPK-like) CDC42BPA 1q42.1 1 8476 214469 at histone 1, H2ae HIST1 H2AE 6p22.2-p21 .1 3012 Table 8 214486_x_at CASP8 and FADD-likβ apoptosis regulator CFLAR 2q33-q34 8837 214487_s_at RAP2A, member of RAS oncogene family /// RAP2B, member of RAP2A /// 13q34 /// 3q25.2 591 1 /// 5912 RAS oncogene family RAP2B 214560_at formyl peptide receptor-like 2 FPRL2 19q1 3.3-q1 3.4 2359 214669_x_at Immunoglobulin kappa variable 1-5 IGKC 2p12 3514 214673_s_at HECT, UBA and WWE domain containing 1 HUWE1 Xp1 1.22 10075 214677_x_at immunoglobulin lambda locus /// immunoglobulin lambda constant IGL@ /// 22q1 1.1 -q1 1.2 /// 28793 /// 1 (Meg marker) /// immunoglobulin lambda constant 2 (Kern-Oz- IGLC1 /// 22q1 1.2 2881 5 /// marker) /// immunoglobulin lambda variable 3-25 /// immunoglobulin IGLC2 /// 28831 /// 3535 lambda variable 2-1 4 /// immunoglobulin lambda joining 3 IGLV3-25 /// /// 3537 /// IGLV2-14 /// 3538 CO C IGLJ3 CO 214701_s_at fibronectin 1 FN1 2q34 2335 CO 214730_s_at golgi apparatus protein 1 GLG1 16q22-q23 2734 214768_x_at immunoglobulin kappa variable 1-5 IGKV1 -5 2p12 28299 214777_at Ig rearranged kappa-chain mRNA V-J1-region, hybridoma AE6-5, m to 5 " end CO 214827_at par-6 partitioning defective 6 homolog beta (C. elegans) PARD6B 20q13.13 84612 m 214836 x at Immunoglobulin kappa light chain VJ region (ID POM010) /// m Immunoglobulin kappa light chain VJ region (ID POM022) /// (clone TR1 .6VL) anti-thyroid peroxidase monoclonal autoantibody IgK T chain, V region ι- 214838_at SFT2 domain containing 2 SFT2D2 1q24.2 375035 m 214845_s_at calumenin CALU 7q32 813 IO 214916 x at immunoglobulin heavy locus /// immunoglobulin heavy constant IGH @ /// 14q32.33 /// 283650 /// alpha 1 /// immunoglobulin heavy constant alpha 2 (A2m marker) /// IGHA1 /// 16p1 1.2 3492 /// 3493 immunoglobulin heavy constant delta /// immunoglobulin heavy IGHA2 /// IGHD /// 3494 /// constant gamma 1 (G1 m marker) /// immunoglobulin heavy /// IGHG1 /// 3495 /// 3500 constant gamma 2 (G2m marker) /// immunoglobulin heavy IGHG2 /// /// 3501 /// constant gamma 3 (G3m marker) /// immunoglobulin heavy IGHG3 /// 3502 /// 3507 constant mu /// hypothetical protein MGC27165 /// similar to Ig IGHM /// /// 390714 heavy chain V-III region VH26 precursor MGC271 65 /// LOC39071 4 214953_s_at amyloid beta (A4) precursor protein (peptidase nexin-ll, Alzheimer APP 2 1q21 .2|21q21 .3 351 disease) 214973_x_at immunoglobulin heavy constant delta IGHD 14q32.33 3495 215001_s_at glutamate-ammonia ligase (glutamine synthetase) GLUL 1q31 2752 Table 8 215034_s_at transmembrane 4 L six family member 1 TM4SF1 3q21 -q25 4071 215043_s_at SMA3 /// SMA5 SMA3 /// SMA5 5q13 10571 /// 11042 2 15071_s_at histone 1, H2ac HIST1 H2AC 6p21 .3 8334 215099_s_at retinoid X receptor, beta RXRB 6p21 .3 6257 2151 18_s_at Translocation associated fusion protein IRTA1/IGA1 (IRTA1/IGHA1) 215121_x_at immunoglobulin lambda locus /// immunoglobulin lambda constant IGL@ /// 22q1 1.1-q1 1.2 /// 28793 /// 1 (Meg marker) /// immunoglobulin lambda constant 2 (Kern-Oz- IGLC1 /// 22q1 1.2 2881 5 /// 3535 marker) /// immunoglobulin lambda variable 3-25 /// immunoglobulin IGLC2 /// /// 3537 /// lambda variable 2-14 IGLV3-25 /// 3538 CO IGLV2-14 C 2 15127_s_at RNA binding motif, single stranded interacting protein 1 RBMS1 2q24.2 5937 CO CO 2151 35_at aspartyl aminopeptidase DNPEP 2q35 23549 2151 57_x_at poly(A) binding protein, cytoplasmic 1 PABPC1 8q22.2-q23 26986 215176_x_at Immunoglobulin kappa light chain variable region (IGKV gene), m clone 25 integrin, alpha 6 ITGA6 2q31 .1 3655 CO 215177_s_at HLA-DRB1 6p21 .3 3123 m 2151 93_x_at major histocompatibility complex, class II, DR beta 1 m 2 15207 x_at YDD19 protein /// chromosome 6 open reading frame 68 /// similar YDD19 /// 13q1 2 /// 6q22.1 /// 11049 /// U ) to hypothetical protein, MGC:71 99 /// similar to hypothetical protein, C6orf68 /// Xp1 1.3 /// 13q1 2.12 1161 50 /// MGC:71 99 LOC389850 /// 389850 /// ι- LOC440128 440128 m 215217_at IO 2 15223_s_at superoxide dismutase 2, mitochondrial S0D2 6q25.3 6648 2 15236_s_at phosphatidylinositol binding clathrin assembly protein PICALM 11q14 8301 2 15304_at Clone 23948 mRNA sequence 2 15313_x_at major histocompatibility complex, class I, A HLA-A 6p21 .3 3105 2 15379_x_at immunoglobulin lambda locus /// immunoglobulin lambda constant IGL@ /// 22q1 1.1-q1 1.2 /// 28793 /// 1 (Meg marker) /// immunoglobulin lambda constant 2 (Kern-Oz- IGLC1 /// 22q1 1.2 2881 5 /// marker) /// immunoglobulin lambda variable 3-25 /// immunoglobulin IGLC2 /// 28831 /// 3535 lambda variable 2-14 /// immunoglobulin lambda joining 3 IGLV3-25 /// III 3531 III IGLV2-14 /// 3538 IGLJ3 215380_s_at chromosome 7 open reading frame 24 C7orf24 7p15-p14 7901 7 215552_s_at estrogen receptor 1 ESR1 6q25.1 2099 2 15561 s_at interleukin 1 receptor, type I IL1 R 1 2q12 3554 Table 8 215707_S_at prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann- PRNP 20pter-p12 5621 Strausler-Scheinker syndrome, fatal familial insomnia) 215708_s_at primase, polypeptide 2A, 58kDa PRIM2A 6p12-p1 1. 1 5558 2 1571 1_s_at WEE1 homolog (S. pombe) WEE1 11p 15.3-p15.1 7465 2 15779_s_at histone 1, H2bg HIST1 H2BG 6p21 .3 8339 2 15823_x_at poly(A) binding protein, cytoplasmic 3 /// poly(A) binding protein, PABPC3 /// 13q12-q1 3 /// 26986 /// cytoplasmic 1 /// similar to Polyadenylate-binding protein 1 PABPC1 /// 8q22.2-q23 /// 341315 /// (Poly(A)-binding protein 1) (PABP 1} LOC341 3 15 12q14.2 5042 215867_x_at carbonic anhydrase XII CA12 15q22 771 215891_s_at GM2 ganglioside activator GM2A 5q31 .3-q33.1 2760 2 15946_x_at similar to omega protein LOC91353 22q1 1.23 91353 CO C 215959_at PTPRF interacting protein, binding protein 2 (liprin beta 2) PPFIBP2 11p 15.4 8495 CO 216088_s_at proteasome (prosome, macropain) subuπit, alpha type, 7 PSMA7 20q13.33 5688 CO 216092_s_at solute carrier family 7 (cationic amino acid transporter, y+ system), SLC7A8 14q1 1.2 23428 member 8 oo 2 16207_x_at immunoglobulin kappa variable 1D-13 IGKV1 D-13 2p12 28902 m 2 16231_s_at beta-2-microglobulin B2M 15q21-q22.2 567 CO 2 16246_at m 2 16366_x_at m 2 16379_x_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 2 16438_s_at thymosin, beta 4, X-linked /// thymosin-like 3 TMSB4X /// Xq21 .3-q22 /// 7 114 /// 7 1 17 T TMSL3 4q22.1 ι- m 2 16450_x_at tumor rejection antigen (gp96) 1 TRA1 12q24.2-q24.3 7184 2 16491_x_at immunoglobulin heavy constant mu IGHM 14q32.33 3507 IO 2 16503_s_at myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, MLLT10 10p12 8028 Drosophila); translocated to, 10 2 16510_x_at immunoglobulin heavy constant alpha 1 /// immunoglobulin heavy IGHA1 /// IGHD 14q32.33 /// 3493 /// 3495 constant delta /// immunoglobulin heavy constant gamma 1 (G1 m /// IGHG1 /// 16p1 1.2 /// 3500 /// marker) /// immunoglobulin heavy constant mu /// similar to Ig IGHM /// 3507 /// heavy chain V-III region VH26 precursor LOC39071 4 390714 21651 1_s_at transcription factor 7-like 2 (T-cell specific, HMG-box) TCF7L2 10q25.3 6934 216526_x_at major histocompatibility complex, class I, C HLA-C 6p21 .3 3107 216542_x_at immunoglobulin heavy constant gamma 1 (G1 m marker) /// IGHG1 /// 14q32.33 283650 /// hypothetical protein MGC27165 MGC271 65 3500 216554_s_at enolase 1, (alpha) EN01 1p36.3-p36.2 2023 216557_x_at immunoglobulin heavy constant alpha 1 /// immunoglobulin heavy IGHA1 /// 14q32.33 /// 3493 /// 3500 Table 8 constant gamma 1 (G1 m marker) /// immunoglobulin heavy IGHG1 /// 16p1 1.2 /// 3502 /// constant gamma 3 (G3m marker) /// similar to Ig heavy chain V-III IGHG3/// 390714 region VH26 precursor LOC390714 216576_x_at IG light chain V-region, VK gene 216604_s_at Solute carrier family 7 (cationic amino acid transporter, y+ system), SLC7A8 14q1 1.2 23428 member 8 216609_at Thioredoxin TXN 9q31 7295 216708_x_at Immunoglobulin lambda joining 3 IGLC2 22q1 1.2 3538 216841_s_at superoxide dismutase 2, mitochondrial S0D2 6q25.3 6648 216915_s_at protein tyrosine phosphatase, non-receptor type 12 PTPN12 7q1 1.23 5782 216942_s_at CD58 antigen, (lymphocyte function-associated antigen 3) CD58 1p13 965 CO C 216984_x_at Immunoglobulin lambda joining 3 IGLC2 22q1 1.2 3538 CO 2 16988_s_at protein tyrosine phosphatase type IVA, member 2 PTP4A2 1p35 8073 CO 217022 s at immunoglobulin heavy constant alpha 1 /// immunoglobulin heavy IGHA1 /// 14q32.33 283650 /// constant alpha 2 (A2m marker) /// hypothetical protein MGC271 65 IGHA2 /// 3493 /// 3494 MGC27165 m OO 217028_at chemokine (C-X-C motif) receptor 4 CXCR4 2q21 7852 CO 2171 33_x_at cytochrome P450, family 2, subfamily B, polypeptide 6 CYP2B6 19q1 3.2 1555 m 2171 38_x_at Immunoglobulin lambda joining 3 IGLC2 22q1 1.2 3538 m 217148_x_at immunoglobulin lambda variable 2-1 4 IGLV2-14 22q1 1.2 2881 5 217157_x_at IGK mRNA for immunoglobulin kappa light chain VLJ region, partial T cds, clone: K 142 ι- 217179_x_at (clone 9F2L) Ig rearranged L-chain mRNA V-region, 5' end m 2171 90_x_at estrogen receptor 1 ESR1 6q25.1 2099 IO 217208_s_at discs, large homolog 1 (Drosophila) DLG 1 3q29 1739 217222_at Similar to Ig heavy chain V-I region HG3 precursor V-set and 15q1 1.2 388078 immunoglobuli n domain containing 6 217239_x_at Similar to immunoglobulin M chain /// (fetal) Ig rearranged H-chain — 16p1 1.2 440361 VDJ-region mRNA, clone 60P2 /// Immunoglobulin heavy chain

variable region (VH 111 family) from IgM rheumatoid factor 217260_x_at Polyreactive Ig rearranged mu-chain, V-D21/1 0-JH4 /// IGHM 14q32.33 3507 Immunoglobulin heavy constant mu 2 17276_x_at serine hydrolase-like 2 SERHL2 22q13 253190 217281 x at Isolate Rice94 immunoglobulin heavy chain variable region (IGVH) Table 8 217284_x_at serine hydrolase-like SERHL 22q13.2-q13.31 94009 217294_s_at eπolase 1, (alpha) EN01 1p36.3-p36.2 2023 217356_s_at phosphoglycerate kinase 1 PGK1 Xq1 3 5230 217378_x_at similar to Ig kappa chain precursor V region (orphon V108) - human LOC391 427 2q13 391427 (fragment) 217383_at Phosphoglycerate kinase 1 PGK1 Xq13 5230 217398_x_at glyceraIdehyde-3-phosphate dehydrogenase GAPDH 12p13 2597 217431_x_at cytochrome b-245, beta polypeptide (chronic granulomatous CYBB Xp21 .1 1536 disease) 217449_at MRNA; cDNA DKFZp434D151 6 (from clone DKFZp434D1 516) 217456_x_at major histocompatibility complex, class I, E HLA-E 6p21 .3 3133 CO C 2 17480_x_at similar to Ig kappa chain LOC339562 2p1 1.1 339562 CO 217617_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 CO 217727_x_at vacuolar protein sorting 35 (yeast) VPS35 16q12 55737 217733_s_at thymosin, beta 10 TMSB1 0 2p1 1.2 9168 217739_s_at pre-B-cell colony enhancing factor 1 PBEF1 7q22.3 10135 m oo 217749_at coatomer protein complex, subunit gamma COPG 3q21 .3 22820 CO O 217767_at complement component 3 C3 19p1 3.3-p13.2 718 m m 217772_S_at mitochondrial carrier homolog 2 (C. elegans) MTCH2 11p 1 1.2 23788 217832_at synaptotagmin binding, cytoplasmic RNA interacting protein SYNCRIP 6q14-q15 10492 π T 217834_s_at synaptotagmi binding, cytoplasmic RNA interacting protein SYNCRIP 6q14-q15 10492 217835_x_at chromosome 20 open reading frame 24 C20orf24 20q1 1.23 55969 ι- m 217838_s_at Enah/Vasp-like EVL 14q32.2 5 1466 IO 217845_x_at HIG1 domain family, member 1A HIGD1A 3p22.1 25994 217894_at potassium channel tetramerisation domain containing 3 KCTD3 1q41 5 1133 217906_at kelch domain containing 2 KLHDC2 14q21 .3 23588 217938_s_at potassium channel modulatory factor 1 KCMF1 2p1 1.2 56888 217943_s_at arginϊne/proline rich coiled-coil 1 RPRC1 1p34.3 55700 217979_at Tetraspanin 13 TM4SF13 7p21 .1 27075 2 18002_s_at chemoki πe (C-X-C motif) ligand 14 CXCL14 5q31 9547 2 18005_at zinc finger protein 22 (KOX 15) ZNF22 10q1 1 7570 2 18018_at pyridoxal (pyridoxine, vitamin B6) kinase PDXK 2 1q22.3 8566 2 18019_s_at pyridoxal (pyridoxine, vitamin B6) kinase PDXK 21q22.3 8566 2 18035_s_at RNA-binding protein FLJ20273 4p13-p12 54502 218094 s at chromosome 20 open reading frame 35 C20orf35 20q1 3.12 55861 Table 8 2181 40_x_at signal recognition particle receptor, B subunit SRPRB 3q22.1 58477 2181 81_s_at mitogen-activated protein kinase kinase kinase kinase 4 MAP4K4 2q1 1.2-q12 9448 21821 1_s_at melanophilin MLPH 2q37.3 79083 2 18294_s_at nucleoporin 5OkDa NUP50 22q1 3.31 10762 2 18303_x_at hypothetical protein LOC5131 5 LOC51 315 2p1 1.2 5131 5 218309_at calcium/calmoduli π-dependent protein kinase Il inhibitor 1 CAMK2N1 1p36.12 55450 218357_s_at translocase of inner mitochondrial membrane 8 homolog B (yeast) TIMM8B 11q23.1-q23.2 26521 218398_at mitochondrial ribosomal protein S30 MRPS30 5q1 1 10884 218400_at 2'-5'-oligoadenylate synthetase 3, 10OkDa 0AS3 12q24.2 4940 2 18482_at enhancer of yellow 2 homolog (Drosophila) ENY2 8q23.1 56943 trichorhinophalangeal syndrome I CO 218502_s_at TRPS1 8q24.1 2 7227 C 218507_at hypoxia-inducible protein 2 HIG2 7q32.2 29923 CO CO 218772_x_at transmembrane protein 38B TMEM38B 9q31 .2 55151 218807_at vav 3 oncogene VAV3 1p13.3 10451 218963_s_at keratin 23 (histone deacetylase inducible) KRT23 17q21 .2 25984 π m 219032_x_at opsin 3 (encephalopsin, pa opsin) 0PN3 1q43 23596 OO 2191 17_s_at FK506 binding protein 11, 19 kDa FKBP1 1 12q1 3.1 2 5 1303 CO 219121_s_at RNA binding motif protein 35A RBM35A 8q22.1 54845 m m 2 19153_s_at hypothetical protein FLJ1 3710 FLJ1 3710 15q23 79875 2 19159_s_at SLAM family member 7 SLAMF7 1q23.1 -q24.1 57823 T 2 19197_s_at signal peptide, CUB domain, EGF-like 2 SCUBE2 11p 15.3 57758 ι- 2 19342_at putative protein product of NblaO41 96 NBLA04196 7q21 .3 64921 m 219382_at SERTA domain containing 3 SERTAD3 19q13.2 29946 IO 2 19386_s_at SLAM family member 8 SLAMF8 1q23.2 56833 219402_s_at Der1-like domain family, member 1 DERL1 8q24.1 3 79139 219414_at calsyntenin 2 CLSTN2 3q23-q24 64084 219440_at retinoic acid induced 2 RAI2 Xp22 10742 219481_at tetratricopeptide repeat domain 13 TTC1 3 1q42.2 79573 219489_s_at nucleoredoxin NXN 17p13.3 64359 219519_s_at Sialoadhesin /// Sialoadhesin SN 20p13 6614 219630_at PDZK1 interacting protein 1 PDZK1 IP1 1p33 10158 219682_s_at T-box 3 (ulnar mammary syndrome) TBX3 12q24.1 6926 219686_at serine/threonine kinase 32B STK32B 4p16.2 55351 219735_s_at transcription factor CP2-like 1 TFCP2L1 2q14 29842 219768 at V-set domain containing T cell activation inhibitor 1 VTCN 1 1p13.1 79679 Table 8 2 19850_s_at ets homologous factor EHF 11p12 26298 219956_at UDP-N-acetyl-alpha-D-galactosamineipolypeptide N- GALNT6 12q1 3 11226 acetylgalactosaminyltransferase 6 (GaINAc-T6) 220220_at hypothetical protein FLJ1 0120 FU1 0 120 17q21 .31 55073 220324_at chromosome 6 open reading frame 155 C6orf1 55 6q13 79940 220532_s_at LR8 protein LR8 7q36.1 28959 22061 3_s_at synaptotagmin-like 2 SYTL2 11q14 54843 220948_s_at ATPase, Na+/K+ transporting, alpha 1 polypeptide ATP1A 1 1p21 476 221012_s_at tripartite motif-containing 8 /// tripartite motif-containing 8 TRIM8 10q24.3 81603 221 137_at 221253_s_at thioredoxin domain containing 5 /// thioredoxin domain containing 5 TXNDC5 6p24.3 81567 CO — C 221477_s_at hypothetical protein MGC5618 MGC561 8 79099 CO 221484_at UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide B4GALT5 20q1 3.1-q13.2 9334 CO 5 221580_s_at hypothetical protein MGC5306 MGC5306 11q21 79101 221651_x_at immunoglobulin kappa constant /// immunoglobulin kappa variable IGKC /// 2p12 28299 /// 3514 m 1-5 IGKV1 -5 CO 221671_x_at immunoglobulin kappa constant /// immunoglobulin kappa variable IGKC /// 2p12 28299 /// 3514 m OO 1-5 IGKV1-5 m 221676_s_at coronin, actin binding protein, 1C C0R01 C 12q24.1 23603 221765_at UDP-glucose ceramide glucosyltransferase UGCG 9q31 7357 T 221815_at abhydrolase domain containing 2 ABHD2 15q26.1 11057 ι- 221843_s_at KIAA1 609 protein KIAA1 609 16q24.1 57707 m 221864_at hypothetical protein MGC13024 MGC1 3024 16p1 1.2 93129 IO 221874_at KIAA1324 KIAA1 324 1p 13.3 57535 221875_x_at major histocompatibility complex, class I, F HLA-F 6p21 .3 3134 221891_x_at heat shock 7OkDa protein 8 HSPA8 11q24.1 3312 221896_s_at HIG1 domain family, member 1A HIGD1A 3p22.1 25994 22191 5_s_at RAN binding protein 1 RANBP1 22q1 1.21 5902 221942_s_at guanylate cyclase 1, soluble, alpha 3 GUCY1 A3 4q31 .3-q33|4q31 .1- 2982 q31 .2 221986_s_at kelch-Iike 24 (Drosophila) KLHL24 3q27.1 54800 222027_at Nuclear casein kinase and cyclin-dependent kinase substrate 1 NUCKS 1q32.1 6471 0 222038_s_at WD repeat domain 50 CGI-48 17q21 .33 51096 222056_s_at fumarylacetoacetate hydrolase domain containing 2A FAHD2A 2p24.3-p1 1.2 5101 1 2221 35 at Zinc finger protein 587 ZNF587 19q1 3.43 8491 4 Table 8 22221 2_s_at LAG1 longevity assurance homolog 2 (S. cerevisiae) LASS2 1q21 .2 29956 222275_at Mitochondrial ribosomal protein S30 MRPS30 5q1 1 10884 222379_at Potassium voltage-gated channel, Isk-related family, member 4 KCN E4 2q36.3 23704 222385_x_at Sec61 alpha 1 subunit (S. cerevisiae) SEC61 A 1 3q21 .3 29927 222392_x_at PERP, TP53 apoptosis effector PERP 6q24 64065 222400 s at membrane-type 1 matrix metalloproteinase cytoplasmic tail binding MTCBP-1 2p25.2 55256 protein-1 222409. at coronin, actin binding protein, 1C CORO1 C 12q24.1 23603 222449. at transmembrane, prostate androgen induced RNA TMEPAI 20q1 3.31 -q1 3.33 56937 222450. at transmembrane, prostate androgen induced RNA TMEPAI 20q13.31 -q1 3.33 56937 222453. .at cytochrome b reductase 1 CYBRD1 2q31 .1 79901 CO C 222458. .s_at chromosome 1 open reading frame 108 C 1orf1 08 1p34.3 79647 CO 222474. s_at translocase of outer mitochondrial membrane 22 homolog (yeast) T0MM22 22q12-q13 56993 CO 222484. s_at chemokine (C-X-C motif) ligand 14 CXCL14 5q31 9547 222488. s_at dynactin 4 (p62) DCTN4 5q31-q32 5 1164 222496. s_at RNA-binding protein FLJ20273 4p13-p12 54502 m OO 222565. s_at protein kinase D3 PRKD3 2p21 23683 CO 222651. .s_at trichorhinophalangea! syndrome I TRPS1 8q24.12 7227 m m 222699 s at pleckstrin homology domain containing, family F (with FYVE PLEKHF2 8q22.1 79666 domain) member 2 222760_at zinc finger protein 703 ZNF703 8p12 80139 T 222771_s_at myelin expression factor 2 MYEF2 15q21 . 1 50804 ι- m 222804_x_at WD repeat domain 32 WDR32 9p13.2 79269 IO 222835_at hypothetical protein FLJ1 371 0 FLJ1 371 0 15q23 79875 222936_s_at chromosome 1 open reading frame 121 C 1orf121 1q44 5 1029 222975_s_at cold shock domain containing E 1, RNA-binding CSDE1 1p22 7812 222979_s_at surfeit 4 SURF4 9q34.2 6836 222992_s_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa NDUFB9 8q13.3 4715 222997_s_at mitochondrial ribosomal protein S21 MRPS21 — 54460 223020_at cisplati π resistance related protein CRR9p CRR9 5pter-p1 5.3 81037 223044_at solute carrier family 40 (iron-regulated transporter), member 1 SLC40A1 2q32 30061 223054_at DnaJ (Hsp40) homolog, subfamily B, member 11 DNAJB1 1 3q27.3 51726 223063_at hypothetical protein FLJ14525 FU14525 1q42.13-q43 84886 223075_s_at chromosome 9 open reading frame 58 C9orf58 9q34.13-q34.3 83543 223100_s_at nudix (nucleoside diphosphate linked moiety X)-type motif 5 NUDT5 10p14-p1 3 11164 Table 8 2231 03_at START domain containing 10 STARD10 11q13 10809 223126_s_at chromosome 1 open reading frame 2 1 C1orf21 1q25 81563 2231 30_s_at myosin regulatory light chain interacting protein MYLIP 6p23-p22.3 291 16 223251 _s_at ankyrin repeat domain 10 ANKRD10 13q34 55608 22331 3_s_at melanoma antigen family D, 4 MAGED4 — 8 1557 223361 _at chromosome 6 open reading frame 115 C6orf1 15 6q24.1 58527 223416_at splicing factor 3B, 14 kDa subunit SF3B14 2pter-p25.1 51639 223500_at complexin 1 CPLX1 4p16.3 1081 5 223551_at protein kinase (cAMP-dependent, catalytic) inhibitor beta PKIB 6q22.31 5570 223577_x_at PR01 073 protein PRO1 073 11cen-q12.3 29005

CO 223578_x_at PR01 073 protein PRO1 073 11cen-q12.3 29005 C 223696_at arylsulfatase D ARSD Xp22.3 414 CO CO 223701 _s_at ubiquitin specific peptidase 47 USP47 11p 15.3 55031 223864_at ankyrin repeat domain 3OA ANKRD30A 10p1 1.21 9 1074 223940_x_at metastasis associated lung adenocarcinoma transcript 1 (non- MALAT1 11q 13.1 378938 m coding RNA) 223958_s_at chromosome 14 open reading frame 168 C 14orf1 68 14q24.3 83544 CO 223961 _s_at cytokine inducible SH2-containing protein CISH 3p21 .3 1154 m o m 223993_s_at cornichon homolog 4 (Drosophila) CNIH4 1q42.12 29097 22401 6_at homeodomain interacting protein kinase 2 HIPK2 7q32-q34 28996 T 224046_s_at phosphodiesterase 7A PDE7A 8q13 5 150 ι- 224131_at G protein-coupled receptor 8 1 GPR81 12q24.31 27198 m 224187_x_at heat shock 7OkDa protein 8 HSPA8 11q24.1 3312 IO 2241 89_x_at ets homologous factor EHF 11p12 26298 22421 8_s_at trichorhinophalangeal syndrome I TRPS1 8q24.1 2 7227 224221 _s_at vav 3 oncogene VAV3 1p13.3 10451 224342_x_at (clone 9F2L) Ig rearranged L-chain mRNA V-region, 5' end /// (clone 9F2L) Ig rearranged L-chain mRNA V-region, 5' end 224346_at 224516_s_at CXXC finger 5 /// CXXC finger 5 CXXC5 5q31 .2 5 1523 224558_s_at metastasis associated lung adenocarcinoma transcript 1 (non- MALAT1 11q13.1 378938 coding RNA) 224559_at metastasis associated lung adenocarcinoma transcript 1 (non- MALAT1 11q13.1 378938 coding RNA) 224568_x_at metastasis associated lung adenocarcinoma transcript 1 (non- MALAT1 11q1 3.1 378938 coding RNA) Table 8 224576_at endoplasmic reticulum-golgi intermediate compartment 32 kDa KIAA1 181 5q35.1 57222 protein 224583_at coactosin-like 1 (Dictyostelium) C0TL1 16q24.1 23406 224795_x_at immunoglobulin kappa constant /// immunoglobulin kappa variable IGKC/// 2p12 28299 /// 3514 1-5 IGKV1 -5 224838_at forkhead box P1 F0XP1 3p14.1 27086 224851 _at cyclin-dependent kinase 6 CDK6 7q21-q22 1021 22491 8_x_at microsomal glutathione S-transferase 1 MGST1 12p12.3-p12.1 4257 224967_at UDP-glucose ceramide glucosyltransferase UGCG 9q31 7357 224989_at Hypothetical protein LOC201 895 LOC201 895 4p14 201 895 22501 7_at coiled-coil domain containing 14 CCDC14 3q21 .1 64770 CO C 225036_at Src homology 2 domain containing adaptor protein B /// SHB /// 9p12-p1 1 /// 9p1 3.1 401 505 /// CO chromosome 9 open reading frame 105 C9orf105 6461 CO 225070_at Chromosome 6 open reading frame 68 C6orf68 6q22.1 1161 50 225079_at epithelial membrane protein 2 EMP2 16p13.2 2013 225081_s_at cell division cycle associated 7-like CDCA7L 7p1 5.3 55536 m 225092_at rabaptin, RAB GTPase binding effector protein 1 RABEP1 17p1 3.2 9135 CO 225155_at chromosome 6 open reading frame 160 C6orf160 6q14.3 387066 m 225157_at Mix interactor MONDOA 12q21 .31 22877 m 225177_at RAB1 1 family interacting protein 1 (class I) RAB1 1FIP1 8p1 1.22 80223 225237_s_at musashi homolog 2 (Drosophila) MSI2 17q23.2 124540 T 225238_at musashi homolog 2 (Drosophila) MSI2 17q23.2 124540 ι- m 225240_s_at musashi homolog 2 (Drosophila) MSI2 17q23.2 124540 IO 225269_s_at chromosome 2 open reading frame 12 C2orf12 2q24.3 192137 225288_at Collagen, type XXVII, alpha 1 COL27A1 9q32 85301 225293_at collagen, type XXVII, alpha 1 COL27A1 9q32 85301 225356_at CDNA FU34896 fis, clone NT2NE2018180 225496_s_at synaptotagmin-like 2 SYTL2 11q14 54843 225498_at chromatin modifying protein 4B CHMP4B 20q1 1.22 128866 225515_s_at hypothetical protein LOC220906 LOC220906 10p12.1 220906 22551 6_at solute carrier family 7 (cationic amino acid transporter, y+ system), SLC7A2 8p22-p21 .3 6542 member 2 225525_at KIAA1671 protein KIAA1 671 ... 85379 225547_at Chromosome 8 open reading frame 45 FLJ25692 8q13.1 157777 225585_at RAP2A, member of RAS oncogene family RAP2A 13q34 591 1 225604 s at chromosome 9 open reading frame 19 C9orf19 9p1 3-p12 152007 Table 8 22561 1_at microtubule associated serine/threonine kinase family member 4 MAST4 5q12.3 23227 22561 3_at microtubule associated serine/threonine kinase family member 4 MAST4 5q12.3 23227 225645_at Ets homologous factor EHF 11p12 26298 225647_s_at cathepsin C CTSC 11q1 4.1-q14.3 1075 225649_s_at serine/threonine kinase 35 STK35 20p13 140901 225692_at calmodulin binding transcription activator 1 CAMTA1 1p36.31 -p36.23 23261 225759_x_at calmin (calponin-like, transmembrane) CLMN 14q32.1 3 79789 225852_at ankyrin repeat domain 17 ANKRD17 4q13.3 26057 225864_at family with sequence similarity 84, member B FAM84B 8q24.21 157638 225897_at Myristoylated alanine-rich protein kinase C substrate MARCKS 6q22.2 4082 π CO 22591 1_at nephro ectin NPNT 4q24 255743 C 22591 2_at tumor protein p53 inducible nuclear protein 1 TP53INP1 8q22 94241 CO 4214 CO 225927_at mitogen-activated protein kinase kinase kinase 1 MAP3K1 5q1 1.2 225996_at MRNA; cDNA DKFZp686N1 345 {from clone DKFZp686N1345) 226034_at Homo sapiens, clone IMAGE:3881 549, mRNA m 226061_s_at Nudix (nucleoside diphosphate linked moiety X)-type motif 3 NUDT3 6p21 .2 11165 226065_at prickle-like 1 (Drosophila) PRICKLE1 12q1 2 1441 65 CO 226086_at synaptotagmin XIII SYT1 3 11p12-p1 1 57586 m m 2261 19_at protein-L-isoaspartate (D-aspartate) O-methyltransferase domain PCMTD 1 8q1 1.23 115294 containing 1 T 226179_at solute carrier family 25, member 37 SLC25A37 8p21 .2 5131 2 ι- 226192_at Transcribed locus, strongly similar to XP_496055.1 PREDICTED: m similar to p40 [Homo sapiens] IO 226197_at Transcribed locus, strongly similar to XP_496055.1 PREDICTED: similar to p40 [Homo sapiens] 226208_at zinc finger, SWIM-type containing 6 ZSWIM6 5q12.1 57688 226213_at v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) ERBB3 12q1 3 2065 226248_s_at KIAA1 324 KIAA1324 1p13.3 57535 226363_at ATP-binding cassette, sub-family C (CFTR/MRP), member 5 ABCC5 3q27 10057 226407_at Pp13759 /// CDNA FLJ45662 fis, clone CTONG20271 50 226408_at TEA domain family member 2 TEAD2 19q13.3 8463 226436_at Ras association (RalGDS/AF-6) domain family 4 RASSF4 10q1 1.21 83937 226440_at Dual specificity phosphatase 22 DUSP22 6p25.3 56940 226452_at pyruvate dehydrogenase kinase, isoenzyme 1 PDK1 2q31 .1 5163 226465 s at SON DNA binding protein SON 21q22.1 - 6651 q22.2[21q22.1 1 Table 8 226474_at nucleotide-binding oligomerization domains 27 NOD27 16q1 3 841 66 226575_at zinc finger protein 462 ZNF462 9q31 .2 58499 226676_at zinc finger protein 521 ZNF521 18q1 1.2 25925 226827_at 226845_s_at myeloma overexpressed 2 MYE0V2 2q37.3 150678 226933_s_at Inhibitor of DNA binding 4, dominant negative helix-loop-helix ID4 6p22-p21 3400 protein 227052_at Hypothetical protein LOC201895 LOC201 895 4p14 201 895 2271 75_at Myeloid cell leukemia sequence 1 (BCL2-related) MCL1 1q21 4170 227204_at par-6 partitioning defective 6 homolog gamma (C. elegans) PARD6G 18q23 84552 22721 4_at golgi associated PDZ and coiled-coil motif containing GOPC 6q21 571 20 CO C 227232_at Enah/Vasp-like EVL 14q32.2 51466 CO 227266_s_at FYN binding protein (FYB-120/1 30) FYB 5p13.1 2533 CO 227272_at FLJ43339 protein FLJ43339 15q1 5.1 3881 15 22731 0_at Adenylosuccinate synthase ADSS 1cen-q1 2 159 m 227369_at SERPINE1 mRNA binding protein 1 SERBP1 1p31 261 35 227492_at Transcribed locus, moderately similar to NP_689672.2 hypothetical CO O protein MGC45438 [Homo sapiens] m OJ m 227519_at placenta-specific 4 PLAC4 2 1q22.3 191585 227550_at hypothetical protein L0C1 43381 L0C1 43381 10q26.1 1 143381 227558_at chromobox homolog 4 (Pc class homolog, Drosophila) CBX4 17q25.3 8535 T 227582_at kelch/ankyrin repeat containing cyclin A 1 interacting protein KARCA1 1q23.3 126823 ι- m 227600_at Mitochondrial ribosomal protein S30 MRPS30 5q1 1 10884 IO 227641_at F-box and leucine-rich repeat protein 16 FBXL16 16p13.3 146330 227663_at CDNA FLJ40901 fis, clone UTERU2003704 227703_s_at synaptotagmin-like 4 (granuphilin-a) SYTL4 94121 227741_at protein tyrosine phosphatase-like (proline instead of catalytic PTPLB 3q21 .1 201562 arginine), member b 227742_at chloride intracellular channel 6 CLIC6 21q22.12 54102 227838_at CDNA FU12425 fis, clone MAMMA10031 04 227926_s_at KIAA1245 /// hypothetical protein LOC200030 /// hypothetical KIAA1245 /// 1q21 .2 /// 1q21 .1 149013 /// protein MGC8902 LOC200030 /// 200030 /// MGC8902 284565 2281 03_s_at Neuropilin 2 NRP2 2q33.3 8828 2281 16_at Hypothetical protein LOC283028 ... 10q1 1.21 283029 2281 79 at hyaluronan synthase 3 HAS3 16q22.1 3038 Table 8 228196_s_at La ribonucleoprotein domain family, member 5 KIAA0217 10p15.3 231 85 228204_at Proteasome (prosome, macropain) subunit, beta type, 4 PSMB4 1q21 5692 228241_at breast cancer membrane protein 11 BCMP1 1 7p21 .1 155465 228245_s_at ovostatin 2 OVOS2 12p1 1.21 144203 228297_at Calponin 3, acidic CNN3 1p22-p21 1266 22831 8_s_at hypothetical protein FLJ34443 FU34443 4p1 6.3 285464 228490_at abhydrolase domain containing 2 ABHD2 15q26.1 11057 228553_at Enabled homolog (Drosophila) ENAH 1q42.12 55740 228582_x_at Metastasis associated lung adenocarcinoma transcript 1 (non- MALAT1 11q13.1 378938 coding RNA) 228592_at membrane-spanning 4-domains, subfamily A, member 1 MS4A1 11q12 931 CO C 228617_at XIAP associated factor-1 BIRC4BP 17p13.1 54739 co 228658_at hypothetical protein L0C1 50271 L0C1 50271 22q12.1 150271 CO 228673_s_at Echinoderm microtubule associated protein like 4 EML4 2p22-p21 27436 228699_at Neuropilin 2 NRP2 2q33.3 8828 228834_at transducer of ERBB2, 1 TOB1 17q21 10140 m 228924_s_at Ubiquitin-conjugating enzyme E2, J 1 (UBC6 homolog, yeast) UBE2J1 6q1 5 5 1465 CO 228993_s_at hypothetical protein LOC92482 LOC92482 10q25.2 92482 m m VO 229030_at calpain 8 (nCL-2) CAPN8 1q32-q41 10754 2291 28_S_at Acidic (leucine-rich) nuclear phosphoprotein 32 family, member E ANP32E 1q21.2 8161 1 2291 50_at Melanophili π MLPH 2q37.3 79083 c 2291 52_at chromosome 4 open reading frame 7 C4orf7 4q13|4q13 260436 m 2291 63_at calcium/caimodulin-dependent protein kinase Il inhibitor 1 CAMK2N1 1p36.12 55450 IO 229221_at CD44 antigen (homing function and Indian blood group system) CD44 11p13 960 229268_at hypothetical protein BC007706 LOC90268 5p1 5.2 90268 229329_s_at Ssu72 RNA polymerase Il CTD phosphatase homolog (yeast) HSPC182 1p36.33 29101 229353_s_at nuclear casein kinase and cyclin-dependent kinase substrate 1 NUCKS1 1q32.1 64710 229538_s_at IQ motif containing GTPase activating protein 3 IQGAP3 1q22 128239 229565_x_at T-box 3 (ulnar mammary syndrome) TBX3 12q24.1 6926 229580_at Transcribed locus 229623_at Similar to hypothetical protein LOC231 503 4 441027 229630_s_at Wilms tumor 1 associated protein WTAP 6q25-q27 9589 229638_at iroquois homeobox protein 3 IRX3 16q12.2 79191 22971 1_s_at hypothetical protein MGC5370 MGC5370 12q14.3 84825 229764 at family with sequence similarity 79, member B FAM79B 3q28 285386 Table 8 229975_at Bone morphogenetic protein receptor, type IB BMPR1 B 4q22-q24 658 230126_s_at Jumonji domain containing 2B JMJD2B 19p13.3 23030 2301 63_at GDNF family receptor alpha 1 GFRA1 10q26 2674 230291_s_at Nuclear factor !/B NFIB 9p24.1 4781 230333_at Spermidine/spermine N1-acetyltransferase SAT Xp22.1 6303 230468_s_at Chromosome 1 open reading frame 56 FU20519 1q21 .2 54964 230559_x_at FVVE, RhoGEF and PH domain containing 4 FGD4 12p1 1.21 121 512 230658_at Solute carrier family 7 (cationic amino acid transporter, y+ system), SLC7A2 8p22-p21 .3 6542 member 2 230746_s_at Stanniocaicin 1 STC1 8p21-p1 1.2 6781 230757_at FLJ44796 protein FU44796 5q31 .1 401209 CO C 230788_at glucosaminyl (N-acetyl) transferase 2, l-branching enzyme GCNT2 6p24 2651 co 230795_at Histone 2, H4 HIST2H4 1q21 8370 CO 230894_s_at Musashi homolog 2 (Drosophila) MSI2 17q23.2 124540 231031_at Transcribed locus 231038_s_at Transcribed locus, strongly similar to NP_078795.2 hypothetical m protein FLJ13725 [Homo sapiens] CO 231211_s_at hypothetical LOC541 469 protein LOC541 469 19q13.2 541469 m m 231577_s_at guanylate binding protein 1, interferon-inducible, 67kDa GBP1 1p22.2 2633 231736_x_at microsomal glutathione S-transferase 1 MGST1 12p12.3-p12.1 4257 231823_s_at KIAA1295 KIAA1 295 5q35.1 285590 c 231882_at LOC4401 56 — 14q1 1.1 4401 56 m 232052_at THUMP domain containing 3 THUMPD3 3p25.3 25917 IO 232081_at EST from clone 208499, full insert 2321 97_x_at arylsulfatase B ARSB 5p1 1-q13(5q1 1-q13 4 11 23221 0_at B-cell CLL/lymphoma 2 BCL2 18q21 .33 596 232307_at Thyroid hormone receptor associated protein 2 THRAP2 12q24.21 23389 232361_s_at ets homologous factor EHF 11p12 26298 232481_s_at SLIT and NTRK-like family, member 6 SLITRK6 13q31 .1 84189 232614_at B-cell CLL/lymphoma 2 BCL2 18q21 .33 596 232653_at Trichorhinophalangeal syndrome I TRPS1 8q24.1 2 7227 232668_at Chromosome 8 open reading frame 72 MGC39325 8q12.1 90362 232889_at hypothetical protein L0C1 53561 L0C1 53561 5q1 3.2 153561 233030_at adiponutrin ADPN 22q13.31 80339 233138 at chromosome 18 open reading frame 1 C18orf1 18p1 1.2 753 Table 8 233449_at LOC440283 15q22.2 440283 233494_at V-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) ERBB4 2q33.3-q34 2066 233498_at V-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) ERBB4 2q33.3-q34 2066 233744_at RAS-like, estrogen-regulated, growth inhibitor RERG 12p12.3 85004 233793_at ST6 (alpha-N-acetyl-neuraminyl^.S-beta-galactosyl-i ,3)-N- SIAT7E 1p31 .1 81849 acetylgafactosaminide alpha-2,6-sialyltransferase 5 233864_s_at vacuolar protein sorting 35 (yeast) VPS35 16q12 55737 233893_s_at KIAA1 530 protein KIAA1 530 4p16.3 57654 233955_x_at CXXC finger 5 CXXC5 5q31 .2 51523 234056_at Full-length cDNA clone CS0DF027YC20 of Fetal brain of Homo

CO sapiens (human) Cσ 234057_at FIAS-like, estrogen-regulated, growth inhibitor RERG 12p12.3 85004 o 234275_at ESR1 6q25.1 2099 CO Estrogen receptor 1 234328_at 234351_x_at trichorhinophalangeal syndrome I TRPS1 8q24.12 7227 23441 8_x_at CD44 antigen (homing function and Indian blood group system) CD44 11p 13 960 m 234612_at CDNA: FU21346 fis, clone COL02705 CO VO 234707_x_at Ig lambda mRNA V-region (V-J) heterohybridoma m O N m 234723_x_at CDNA: FU21228 fis, clone COL00739 234764_x_at Ig lambda mRNA V-region (V-J) heterohybridoma /// IGLC2 22q1 1.2 3538 73 Immunoglobulin lambda joining 3 /// Immunoglobulin lambda c constant 1 (Meg marker) m 234825_at MRNA; cDNA DKFZp434P1 019 (from clone DKFZp434P1 0 19) 234854_at MDN1 , midasin homolog (yeast) MDN1 6q15 23195 235059_at RAB12, member RAS oncogene family RAB12 18p1 1.22 201475 235086_at Thrombospondin 1 THBS1 15q15 7057 2351 10_at HRAS-like suppressor 3 HRASLS3 11q12.3-q13.1 11145 2351 23_at Transcribed locus 235141_at MARVEL domain containing 2 MARVELD2 5q13.2 153562 235153_at ring finger protein 183 RNF183 9q32 138065 235193_at Hypothetical protein FLJ10980 FU 10980 15q21 .2-q21 .3 56204 235538_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 235598_at SMAD, mothers against DPP homolog 2 (Drosophila) SMAD2 18q21 .1 4087 235626_at calcium/calmodulin-depende πt protein kinase ID CAMK1 D 10p13 571 18 235643_at sterile alpha motif domain containing 9-like SAMD9L 7q21 .3 219285 235759 at EF-hand calcium binding protein 1 EFCBP1 8q21 .3 64168 Table 8 235789_at jumonji domain containing 2B JMJD2B 19p1 3.3 23030 235856_at Transcribed locus 235977_at MRNA; cDNA DKFZp686N1345 (from clone DKFZp686N1 345) 236173_s_at Leucine-rich repeats and immunoglobulin-like domains 1 LRIG1 3p14 2601 8 236237_at Hypothetical protein FLJ1 0980 FU1 0980 15q21 .2-q21 .3 56204 236301 _at Putative ORB3 gene, 5' 236769_at hypothetical protein L0C1 58402 LOC1 58402 9q32 158402 236934_at Insulin-like growth factor 1 receptor IGF1 R 15q26.3 3480 237091_at 237301 _at Transcribed locus CO 237339_at Transcribed locus — — — C co 237625_s_at Immunoglobulin kappa variable 1-5 IGKC 2p12 3514 CO 237871 _x_at 237963_x_at KIAA1529 KIAA1529 9q22.33 57653 238021 _s_at hypothetical gene supported by AF275804 LOC388279 16q12.2 388279 m 238323_at TEA domain family member 2 TEAD2 19q13.3 8463 CO 238330_s_at Myosin phosphatase- Rho interacting protein M-RlP 17p1 1.2 231 64 m 238339_x_at leucine-rich repeats and immunoglobulin-like domains 1 LRIG 1 3p14 2601 8 m 238368_at Pvt1 oncogene homolog, MYC activator (mouse) PVT1 8q24 5820 23881 1_at ATPase, Class VI, type 11B ATP1 1B 3q27 23200 c 238853_at Glioma amplified sequence 64 2391 55_at Coxsackie virus and adenovirus receptor CXADR 2 1q21 . 1 1525 m 239210_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 IO 239336_at Thrombospondin 1 THBS1 15q15 7057 239466_at hypothetical LOC344595 LOC344595 3q13.12 344595 239944_at CDNA FU42561 fis, clone BRACE3006463 24001 0_at LIM homeobox transcription factor 1, beta LMX1 B 9q34 401 0 240475_at Inositol 1,4,5-triphosphate receptor, type 1 ITPR1 3p26-p25 3708 240736_at 240838_s_at hypothetical protein LOC1 45837 LOC1 45837 15q23 145837 241376_at CDNA clone IMAG&4821 290 241464_s_at Transcribed locus, weakly similar to NP_997360.1 FLJ27365 protein [Homo sapiens] 241 505_at Transcribed locus 241581 at V-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) ERBB4 2q33.3-q34 2066 Table 8 241681_at Musdeblind-Iike (Drosophila) MBNL1 3q25 4 154 241701_at Rho GTPase activating protein 2 1 ARHGAP21 10p12.1 57584 241762_at 242004_x_at KIAA1 324 KIAA1 324 1p 13.3 57535 242022_at Pre-B-cell leukemia transcription factor 1 PBX1 1q23 5087 242301 _at cerebellin 2 precursor CBLN2 18q22.3 147381 242323_at 242335_at solute carrier family 25, member 37 SLC25A37 8p21 .2 5131 2 242338_at transmembrane protein 64 TMEM64 8q21 .3 169200 242434_at CDNA FU31093 fis, clone IMR3210001 6 1

CO 24251 6_x_at hypothetical protein MGC2701 6 MGC27016 4q32.1 166863 C 24251 7_at G protein-coupled receptor 54 GPR54 19p13.3 84634 co CO 242579_at Bone morphogenetic protein receptor, type IB BMPR1 B 4q22-q24 658 242874_at CDNA FLJ37931 fis, clone CTONG2004397 24291 1_at thyroid hormone receptor associated protein 2 THRAP2 12q24.21 23389 m 24291 2_at CDNA FU43851 fis, clone TESTI4006728 242974_at CD47 antigen (Rh-related antigen, integrin-associated signal CD47 3q13.1-q13.2 961 CO m transducer) m 24301 0_at musashi homolog 2 (Drosophila) MSI2 17q23.2 124540 243241 at hypothetical gene supported by AY338954 /// hypothetical gene LOC400880 /// 22q1 1.1 /// 14q1 1.1 400880 /// OO supported by AY338954 /// hypothetical gene supported by LOC440155 /// /// 14q1 1.2 4401 55 /// c AY338954 LOC440161 440161 m 243349_at KIAA1 324 KIAA1 324 1p13.3 57535 IO 243358_at hypothetical protein MGC18216 MGC1821 6 15q26.3 145815 24351 3_at Hypothetical protein MGC20481 MGC20481 15q1 5.1 90416 243837_x_at 243929_at Zinc finger protein 533 ZNF533 2q31 .2-q31.3 151126 243967_at AF4/FMR2 family, member 3 AFF3 2q1 1.2-q12 3899 244478 at Transcribed locus, weakly similar to XP_51 8226.1 PREDICTED: similar to signal-transducing adaptor protein-2; brk kinase substrate [Pan troglodytes] 244489_at 244533_at 244579_at Trichorhinophalangeal syndrome I TRPS1 8q24.12 7227 244696_at AF4/FMR2 family, member 3 LAF4 2q1 1.2-q12 3899 244891 _x_at Transcribed locus Table 8 266_s_at CD24 antigen (small cell lung carcinoma cluster 4 antigen) CD24 6q21 934 3 1874_at growth arrest-specific 2 like 1 GAS2L1 22q12.2 10634 33323_r_at stratifin SFN 1p36.1 1 2810 33646_g_at GM2 ganglioside activator GM2A 5q31 .3-q33.1 2760 35666_at sema domain, immunoglobulin domain (Ig), short basic domain, SEMA3F 3p21 .3 6405 secreted, (semaphorin) 3F 37793_r_at RAD51-like 3 (S. cerevisiae) RAD51 L3 17q1 1 5892 37892_at collagen, type Xl, alpha 1 C0L1 1A 1 1p21 1301 38241_at butyrophilin, subfamily 3, member A3 BTN3A3 6p21 .3 10384 4001 6_g_at microtubule associated serine/threonine kinase family member 4 MAST4 5q12.3 23227

CO 40148_at amyloid beta (A4) precursor protein-binding, family B, member 2 APBB2 4p14 323 C (Fe65-like) CO 4 1660_at cadherin, EGF LAG seven-pass G-type receptor 1 (flamingo CELSR1 22q13.3 9620 CO homolog, Drosophila) 46323_at calcium activated nucleotidase 1 CANT1 17q25.3 124583 87100_at Abhydrolase domain containing 2 ABHD2 15q26.1 11057 m AFFX-HSAC07/ actin, beta ACTB 7p15-p12 60 CO X00351_5_at m AFFX-HSAC07/ actin, beta ACTB 7p1 5-p12 60 m X00351_M_at AFFX-HUMGAPDH/ glyceraldehyde-3-phosphate dehydrogenase GAPDH 12p1 3 2597 T M33197_3_at ι- AFFX-HUMGAPDH/ glyceraldehyde-3-phosphate dehydrogenase GAPDH 12p1 3 2597 m M331 97_5_at IO AFFX-HUMGAPDH/ glyceraldehyde-3-phosphate dehydrogenase GAPDH 12p13 2597 M33197_M_at AFFX-HUMISGF3A/ signal transducer and activator of transcription 1, 9 1kDa STAT1 2q32.2 6772 M97935_MA_at AFFX-r2-Ec-bioB-3 at Biotin synthase /// biotin synthesis, sulfur insertion? bioB ... What is claimed:

1. A method for analyzing gene expression levels from a formalin-fixed, paraffin-embedded tissue sample, comprising pre-hybridizing a labeled nucleic acid sample prepared from the formalin-fixed, paraffin-embedded tissue sample with a first microarray, hybridizing the unbound labeled nucleic acid sample with a second microarray, and detecting the labeled nucleic acid sample bound to the second microarray.

2. The method of claim 1 wherein the first microarray is a previously used microarray.

3. The method of claim 1, wherein the formalin-fixed, paraffin-embedded tissue sample comprises diseased tissue.

4. The method of claim 3, wherein the formalin-fixed, paraffin-embedded tissue sample comprises a tumor.

5. The method of claim 1, wherein the labeled nucleic acid sample is prepared from RNA isolated from the formalin-fixed, paraffin-embedded tissue sample.

6. The method of claim 5, wherein the RNA is isolated from a section prepared from the formalin-fixed, paraffin-embedded tissue sample.

7. The method of claim 6, wherein the section prepared from the formalin-fixed, paraffin-embedded tissue sample is between about 1 and about 10 microns thick.

8. The method of claim 3, wherein RNA is isolated from the diseased tissue in the formalin-fixed, paraffin-embedded tissue sample.

9. The method of claim 8, wherein the diseased tissue is identified by staining the formalin-fixed, paraffin-embedded tissue sample.

10. The method of claim 4, wherein RNA is isolated from the tumor in the formalin-fixed, paraffin-embedded tissue sample.

11. The method of claim 10, wherein the tumor in the formalin-fixed, paraffin-embedded tissue sample is identified by staining the formalin-fixed, paraffin-embedded tissue sample.

12. The method of claim 11, wherein the tumor in the formalin-fixed, paraffin-embedded tissue sample is identified by hematoxylin and eosin staining the formalin-fixed, paraffin-embedded tissue sample.

13. The method of claim 5, wherein the RNA isolated from the formalin-fixed, paraffin-embedded tissue sample is amplified. 14. The method of claim 13, wherein the RNA isolated from the formalin-fixed, paraffin-embedded tissue sample is converted into an amplified cDNA sample.

15. The method of claim 14, wherein the labeled nucleic acid sample is prepared by labeling the amplified cDNA sample.

16. The method of claim 15, wherein the amplified cDNA sample is labeled with BIO- ULS.

17. The method of claim 15, wherein the labeled amplified cDNA sample is purified.

18. The method of claim 17, wherein the purified labeled amplified cDNA sample is fragmented.

19. The method of claim 18, wherein the fragmented labeled amplified cDNA sample is purified subsequent to fragmentation.

20. A method for analyzing gene expression levels from a formalin-fixed, paraffin-embedded tissue sample, comprising identifying a disease area within the formalin-fixed, paraffin-embedded tissue sample, dissecting the identified disease area to obtain at least a first section of the diseased area, isolating RNA from the at least a first section of the diseased area, converting the RNA into an amplified cDNA sample, labeling the amplified cDNA sample, purifying the labeled cDNA sample, fragmenting the purified and labeled cDNA sample, purifying the fragmented cDNA sample, pre-hybridizing the fragmented cDNA sample with a first microarray, hybridizing the unbound fragmented cDNA sample with a second microarray, and detecting the fragmented cDNA sample bound to the second microarray.