Supplementary Methods

Tissue sample process. Each tissue sample was cryosectioned, and selected sections stained with hematoxylin/eosin, and reviewed to determine tumor content, pathological status, and freedom from necrosis and freezing artifacts. Epithelial cells from all normal samples and tumor cells from HNC or CC samples with less than 80% tumor were laser capture microdissected from adjacent sections using a PixCell II LCM system (Arcturus, Mountain View, CA) (Supplementary Table 2). For guidance, an adjacent section was briefly stained with hematoxylin to visualize tissue structure.

RNA amplification and labeling. Total RNA was extracted from sectioned and/or microdissected samples as follows: 1 ml of TRIzol (Invitrogen, Carlsbad, CA) was added to each tissue sample, homogenized by passing through a 20 gauge needle, and added to 0.2 ml chloroform. After centrifugation at 20,000 xg for 20 min at 4oC, RNA in the aqueous phase was precipitated with an equal volume of isopropanol for 30 min at 4oC, pelleted, and washed twice with cold 70% ethanol. Double strand (ds) cDNA was synthesized from this RNA using a SuperScript ds cDNA synthesis kit (Invitrogen) and T7 promoter-linked oligo (dT)24. Complementary RNA (cRNA) was synthesized from T7 promoter-linked ds cDNA using a

MEGAscript high transcription kit (Ambion, Austin, TX). To obtain a sufficient cRNA for ≥2 microarray hybridizations, this amplification process was repeated. Second round cRNA was biotin labeled using a BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) and stored at -80oC until hybridized. cRNA quality and quantity was determined by gel electrophoresis and UV spectrophotometry.

HPV microarrays. HPV arrays included probes representing all 37 sequenced mucosotropic HPV genotypes (6, 11, 12, 13, 16, 17, 18, 22, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43, 44, 45, 51,

52, 53, 54, 55, 56, 57, 58, 59, 61, 66, 67, 68, 69, 70, 72, 83), human β- and GAPDH as

1 positive controls, cell differentiation markers (PCNA, K8, K1, K10, , Suprabasin, Loricrin, Sp4), known cervical cancer markers (p16, , RB1, hTERT, Cyclin D1, IFITM1, ISGF3, MCM4, MCM5, MCM6, MCM7, USP3), and selected rice genome sequences as a negative controls. NCBI BLAST Searches were used to remove probes with predicted cross- reactivity to other .

Microarray hybridization. Biotin-labeled cRNA was dissolved in fragmentation buffer (40mM Tris-Acetate, pH 8.1, 100mM potassium acetate, 30mM magnesium acetate) and incubated at 95oC for 25 min. 10 µg of cRNA was used for Affymetrix microarray hybridization and scanning at the University of Wisconsin Biotechnology Expression Center. HPV arrays were washed and blocked following the epoxy slide manufacturer’s washing and blocking protocol (Genomic Solutions). 10 µg cRNA was mixed with 200 µl of array hybridization buffer (Genomic Solutions) and added to the HPV array covered with a hybridization chamber (Schleicher & Schuell, Keene, NH). After hybridization at 50oC for 24 h, the array was washed sequentially with 0.1% SDS plus 2X SCC, 1X SCC, and 0.2X SCC at 50oC, then hybridized to streptavidin-Cy3 at room temperature for 15 min, followed by washing with 2X SCC, 1X SCC, and 0.5X SCC at room temperature. The dry array was scanned using an Agilent DNA microarray scanner (Agilent, Palo Alto, CA) and data were analyzed using Axon GenePix Pro 5.1 microarray image analysis software (Molecular

Devices, Sunnyvale, CA).

Quantitative reverse transcriptase-PCR. First strand DNA was synthesized from 15 µg of total RNA from tissues or cultured cells using oligo (dT) 15 and SuperScript reverse transcriptase. Quantitative PCR (qPCR) was performed with 0.5 µg of cDNA using a QuantiTect SYBR Green PCR kit (Qiagen, Valencia, CA) and an ABI Prism 7900 sequence detection system (Applied Biosystems, Foster City, CA). Oligonucleotide primers (Supplementary Table 1) were designed using the Primer3 primer design program (1),

2 synthesized by Integrated DNA Technologies (Coralville, IA) and used at 0.5 µM for PCR amplification for 40 cycles of 15 s denaturation at 95°C, 30 s annealing at 55°C, and 30 s polymerization at 72°C, following 10 min pre-incubation at 95°C. Plasmid standards containing each gene used in qPCR were produced by TA cloning PCR amplified fragments into pGEM-T Easy vector (Promega).

Immunohistochemistry and western blotting. All steps were at room temperature unless otherwise specified. For , cryosectioned tissue was incubated successively in 4% paraformaldehyde for 15 min, 3% H2O2/methanol for 10 min, 10 mM citrate buffer (pH6.0) at 95oC for 20 min, and 2M HCl for 20 min. Following blocking with 2.5% horse serum, tissue sections were incubated successively with mouse anti-PCNA (PC10, Chemicon International, Temecula, CA) or mouse anti-Cdc7 (DCS-341, Sigma, St. Louis, MO) for 2 hr, biotin-conjugated anti-mouse IgG (Vector Laboratories, Burlingame, CA) for 30 min, and ABC reagent (Vector Laboratories) for 30 min. Tissue sections were developed with DAB reagent (Vector Laboratories) for 2 min and counter- stained with hematoxylin. IHC images were analyzed and quantified as described previously (Zhang et al.). Briefly, the developed brown color of the PCNA signal was digitally extracted from other spectral components of the image, converted to a gray scale image, and the gray scale densities of five random fields within the tumor tissue of each sample were measured using Image J and averaged. Fig. 4 shows representative images and a plot of the numerical values for all tested samples, which included 11 HPV+ cancers (6 HPV+HNCs and 5 - HPV+CCs) and 10 HPV HNCs. Approximately one million cultured cells were used for western blotting. Cell pellets were lysed with lysis buffer (10 mM Tris, 150 mM NaCl, 0.5% NP-40, 2 mM EDTA) plus complete protease inhibitor cocktail (Roche Applied Science, Indianapolis, IN). fractionated by SDS polyacrylamide gel electrophoresis transferred to polyvinylidene difluoride paper (Amersham). SYCP2, HPV E7, and actin bands were visualized by chemiluminescence using goat anti-human SYCP2 (T-16, Santa Cruz

3 Biotechnology, Santa Cruz, CA), mouse anti-HPV16 E7 ( (ED17, Santa Cruz and 8C9, Zymed, South San Francisco, CA), and rabbit anti-actin (I-19, Santa Cruz) , respectively, and secondary antibodies (donkey anti-goat IgG (Santa Cruz), donkey anti- mouse IgG (Jackson ImmunoResearch), or goat anti-rabbit IgG (Jackson ImmunoResearch) conjugated with horseradish peroxidase.

Tissue culture. Normal human immortalized keratinocytes (NIKSTM, obtained from Lynn Allen Hoffman) that differentiate faithfully, NIKS16, 18, 31 derivatives stably transfected with the indicated HPV DNA genomes, and HaCaT cells were maintained as described (2-4). Primary cultures of human cervical epithelial cells were established from fresh human cervical tissue obtained after hysterectomy due to fibroids or endometriosis (5). Cells were maintained in serum free MCDB153-LB medium (K-SFM, Invitrogen, Carlsbad, CA). Secondary cultures were infected (6) for 3 h with retroviruses expressing the neomycin resistance gene alone (pLXSN) or with HPV16 E6, E7, or E6/E7 genes. Cells were selected in G418 (200 µg/ml for 2 days) and subcultured once prior to RNA extraction. For RNA extraction, subconfluent monolayers were washed with prewarmed PBS, lysed with Trizol (Invitrogen), and extracted with chloroform to remove protein and DNA (6). Primary cervical keratinocytes transfected with HPV16 were a kind gift from Dr. Aloysius Klingelhutz (7). - HPV array hybridization was carefully optimized using RNA from known HPV+ and HPV keratinocyte cell lines such as NIKS (previously named BC1-Ep/SL cells) (17), NIKS-16 (HPV16) (3), NIKS-18 (HPV18), NIKS-31 (HPV31), W12E clone 20850 (HPV16) (4), CaSki (HPV16) (8), and HaCaT cells (9)

References

1. Rozen, S., and Skaletsky, H.J. (2000). Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics Methods and Protocols: Methods in Molecular Biology, S. Krawetz and S. Misener, eds. (Totowa, NJ: Humana Press), pp. 365-386.

4 2. Allen-Hoffmann BL, Schlosser SJ, Ivarie CA, Sattler CA, Meisner LF, O'Connor SL. Normal growth and differentiation in a spontaneously immortalized near-diploid human keratinocyte cell line, NIKS. J Invest Dermatol 2000;114:444-55.

3. Flores ER, Allen-Hoffmann BL, Lee D, Sattler CA, Lambert PF. Establishment of the human papillomavirus type 16 (HPV-16) life cycle in an immortalized human foreskin keratinocyte cell line. Virology 1999;262:344-54.

4. Jeon S, Allen-Hoffmann BL, Lambert PF. Integration of human papillomavirus type 16 into the correlates with a selective growth advantage of cells. J Virol 1995;69:2989-97.

5. Woodworth, C. D., Bowden, P. E., Doniger, J., Pirisi, L., Barnes, W., Lancaster, W. D., and DiPaolo, J. A. Characterization of Normal Human Exocervical Epithelial Cells Immortalized in Vitro by Papillomavirus Types 16 and 18 DNA. Cancer Res, 48: 4620- 4628, 1988.

6. Nees, M., Geoghegan, J. M., Hyman, T., Frank, S., Miller, L., and Woodworth, C. D. Papillomavirus Type 16 Oncogenes Downregulate Expression of Interferon-Responsive Genes and Upregulate Proliferation-Associated and NF-{kappa}B-Responsive Genes in Cervical Keratinocytes. J. Virol., 75: 4283-4296, 2001.

7. Sprague, D. L., Phillips, S. L., Mitchell, C. J., Berger, K. L., Lace, M., Turek, L. P., and Klingelhutz, A. J. activation in cervical keratinocytes containing stably replicating human papillomavirus type 16 episomes. Virology, 301: 247-254., 2002.

8. Baker CC, Phelps WC, Lindgren V, Braun MJ, Gonda MA, Howley PM. Structural and transcriptional analysis of human papillomavirus type 16 sequences in cervical cell lines. J Virol 1987;61:962-71.

9. Boukamp P, Petrussevska RT, Breitkreutz D, Hornung J, Markham A, Fusenig NE. Normal keratinization in a spontaneously immortalized aneuploid human keratinocyte cell line. J Cell Biol 1988;106:761-71.

5 Supplementary Figure Legends

Supplementary Figure S1. LCM decision with hematoxylin and eosin staining. A frozen tissue section of each sample was stained with hematoxylin and eosin and cancer regions were determined for LCM.

Supplementary Figure S2. PCR detection of HPV DNA in host genome shows parallel results with oligonucleotide spotted HPV array. Genomic DNA was extracted from tissue samples using DNAzol (Invitrogen) and HPV signal was detected with amplification of L1 consensus sequence using primers MY09-MY11. β-actin amplification was performed as a positive control.

Supplementary Figure S3. (A) Same as Fig. 1B, but using, in place of probeset values, 2760 standardized GO categories, each mapping to ≥10 Affymetrix probesets. Each GO category fold change was calculated by averaging cancer vs. normal log2 fold changes across all probesets in that GO category, and was standardized to accommodate the variably-sized categories. GO-level correlation between HPV+HNCs and HPV+CCs was R=0.76, - approaching the 0.83 correlation of HPV+ and HPV HNC and significantly higher than GO- - level correlation between HPV+CC and HPV HNC (R = 0.59) by bootstrap analysis. (B) Heatmap displays expression of 1944 probesets that are significantly differentially expressed between the class of tumor tissues and the class of normal tissues. Standardization takes the average log2 fold change for all probe sets in each GO category, centers by the mean for all same-sized subsets, and divides by the standard deviation across all same-sized subsets, producing a normal score, which is expected in the range (-3,3) with high probability in the absence of enrichment of the GO category for altered genes. GO-averaging enhances between-cancer correlations. Gene sets I and II show significantly up- or down-regulated probesets, respectively.

6

Supplementary Figure S4. Subgroup structures. Using n=100 probesets most differentially - expressed between HPV+HNC samples and HPV HNC samples (from Figure 2a), we performed calculations to measure the strength of apparent subgrouping. (A) Results of hierarchical cluster analysis applied to the 16 HPV+HNC samples are shown and reveal a predominant split of this group into a smaller subgroup containing 6 HPV+HNCs and a larger subgroup of 10 HPV+HNCs. This split was not sensitive to the agglomeration method used for clustering, nor to the precise number of probesets used. (Note that distance is Euclidean distance over the n probesets, which is the sum of squared pairwise differences between log2 expression values.) Further, the parametric bootstrap testing method (see Experimental Procedures) assigns p-value = 0.04 to the significance of this split. (B) A hierarchical clustering of all HPV+ cancer samples is shown. Interestingly, the HPV+HNCs split as before, and two HPV+CCs group with smaller HPV+HNC subgroup, while other CCs are closer to other HNC samples. (C) Genes altered between subgroups: Shown is a heatmap of 390 probesets that are significantly differentially expressed between the two identified subgroups, now considering the whole genome. The samples in subgroup are indicated as red text.

Supplementary Figure S5. Meta-analysis. Regarding other subgroup structure in the data, a heatmap shows all HNCs using a subset of signature-defining genes reported by Chung et al.

Informally, there is some consistency between Chung's grouping and expression patterns in these HNCs. For example, `subgroup 2' shows high expression of , syndecan, collagen subunits and low expression of TGF-α, 14, gap junction protein. Subgroups reported previously are indicated on the bottom of heatmap and gene sets C through G are shown as previously presented (Chung et al., 2004, Figure 1). The genes used in this analysis are listed in Supplementary Table 7. (D) The same set of cell cycle-related genes in Figure 4A was used to analyze Slebos’ independent data comparing between - HPV+HNC and HPV HNC.

7

Supplementary Figure S6. Cell cycle-related gene expression by HPV16 E6 and E7. Real time qRT-PCR was performed with total RNA extracted from primary cervical keratinocytes lacking or transduced with HPV16 E6 and/or E7. Retrovirus without HPV16 gene was used as mock control.

8 Supplementary Figure S1

LCM Yes No

CC029 CC237

CC233 CC600

9 Supplementary Figure S2

NIKS16 (HPV16+) NIKS16 CC701 NIKS (HPV-) CC233 CC237 (HPV16+) CN001 (HPV-) CC243

HPV L1 (MY09-MY11)

β-actin

10 Supplementary Figure S3

A HPV+HNC vs. HPV-HNC HPV+HNC vs. CC HPV-HNC vs. CC

R=0.83 R=0.76 R=0.59 HNC/HNN] HNC/HNN] HNC/HNN] - + + GO [HPV GO [HPV GO [HPV

- GO [CC/CN] GO [HPV HNC/HNN] GO [CC/CN]

B

I

II

11 Supplementary Figure S4

A

α β

B

α β

12 Supplementary Figure S4

C

α β

13 Supplementary Figure S5

A

14 Supplementary Figure S5

B

+ - HPV HNC HPV HNC

15 Supplementary Figure S6

CCNB1 CCNA1

16 1.4 14 1.2 12 1 10 0.8 8 0.6 6 0.4 4 2 0.2 0 0 6 7 6 /E7 E E 6 05 05 E 1 X 05E6/E X105E7 05 C 1 C X1 HCX105E7 H X H HCX1 C C CX105Mock H HCX105Mock H H

cdc2 ORC1 Fold change

20 10 18 9 16 8 14 7 12 6 10 5 8 4 6 3 4 2 2 1 0 0 7 6 7 6 E7 /E7 E E 6 05 1 105 X X C C X105Mock H HCX105E H HCX105 C HCX105Mock HCX105E H HCX105E6/E

p16

9 8 7 6 5 4 3 2 1 0

7 6 k E c 05 105E7 05E6/E X 05Mo 1 C 1 X H HCX1 X C C H H

16 Supplementary Table S1. Patient information Anatomical Histological Accession Tissue ID Case Source* HPV† § Gender Age Stage LCM sites grade number CC010 Cervical cancer GOG + (31) Yes Cervix Female 35 Well/moderately II No GSM155645 CC028 Cervical cancer GOG + (16) No Cervix Female 27 Well/moderately IB2 Yes GSM155646 CC029 Cervical cancer GOG + (18) Yes Cervix Female 40 Well/moderately IB No GSM155647 CC034A Cervical cancer GOG + (18) Yes Cervix Female 42 Poorly/undiffer IB No GSM155648 CC034B Cervical cancer GOG + (58) No Cervix Female 44 Poorly/undiffer II/III No GSM155649 CC068 Cervical cancer GOG + (35) No Cervix Female 41 Poorly/undiffer IB Yes GSM155650 CC205 Cervical cancer GOG + (16) Yes Cervix Female 57 Well/moderately IB No GSM155651 CC225 Cervical cancer GOG + (16) Yes Cervix Female 44 Well/moderately IV ND** GSM155652 CC233 Cervical cancer GOG - Yes Cervix Female 44 Well/moderately IB No GSM155653 CC237 Cervical cancer GOG + (16) No Cervix Female 25 Well/moderately IB No GSM155654 CC243 Cervical cancer GOG - No Cervix Female 30 Poorly/undiffer IB2 No GSM155655 CC300 Cervical cancer GOG + (18) Yes Cervix Female 47 Poorly/undiffer IB2 No GSM155656 CC304 Cervical cancer GOG + (33) No Cervix Female 63 Poorly/undiffer IB No GSM155657 CC437 Cervical cancer GOG + (16) No Cervix Female 38 Poorly/undiffer IB No GSM155658 CC507 Cervical cancer GOG + (16) No Cervix Female 52 Poorly/undiffer IIIB Yes GSM155659 CC515 Cervical cancer GOG + (16) Yes Cervix Female 38 Poorly/undiffer IB2 No GSM155660 CC519 Cervical cancer GOG + (16) Yes Cervix Female 48 Well/moderately IB2 No GSM155661 CC553 Cervical cancer GOG + (35) Yes Cervix Female 53 Poorly/undiffer IB No GSM155662 CC600 Cervical cancer GOG + (66) No Cervix Female 55 Poorly/undiffer IB1 No GSM155663 CC701 Cervical cancer GOG - Yes Cervix Female 26 Poorly/undiffer IB2 Yes GSM155664 CN001 Cervical normal GOG - Yes Cervix Female 35 - - - GSM155665 CN018 Cervical normal GOG - Yes Cervix Female 44 - - - GSM155666 CN022 Cervical normal GOG - Yes Cervix Female 45 - - - GSM155667 CN206 Cervical normal GOG - Yes Cervix Female 66 - - - GSM155668 CN243 Cervical normal GOG - Yes Cervix Female 43 - - - GSM155669 CN407 Cervical normal GOG - Yes Cervix Female 56 - - - GSM155670 CN530 Cervical normal GOG - Yes Cervix Female 48 - - - GSM155671 CN543 Cervical normal GOG - Yes Cervix Female 43 - - - GSM155672 HNC001 HN cancer U. Iowa - Yes Oral Cavity Male 57 Well/moderately IV ND GSM155674 HNC004 HN cancer U. Iowa - Yes Oral Cavity Male 64 Well/moderately IV ND GSM155673 HNC005 HN cancer U. Iowa + (16) No Oropharynx Male 44 Poorly/undiffer IV ND GSM155675 HNC008 HN cancer U. Iowa + (16) No Oropharynx Female 57 Poorly/undiffer III ND GSM155676 HNC009 HN cancer U. Iowa + (16) Yes Oropharynx Female 50 Well/moderately III ND GSM155677 HNC012 HN cancer U. Iowa + (16) No Oropharynx Male 59 Poorly/undiffer IV ND GSM155678 HNC015 HN cancer U. Iowa - Yes ND ND ND ND ND ND GSM155679 HNC017 HN cancer U. Iowa - Yes Tonsil Male 54 Well/moderately IV ND GSM155680 HNC018 HN cancer U. Iowa - Yes Tonsil Female 57 Well/moderately IV ND GSM155681 HNC2551 HN cancer Harvard + (18) Yes Female 85 Well/moderately I No GSM155682 HNC2686 HN cancer Harvard - No Tongue Female 68 Well/moderately ND ND GSM155683 HNC2714 HN cancer Harvard - Yes Tongue Male 76 Well/moderately ND ND GSM155684 HNC2719 HN cancer Harvard + (16) No Tongue Male 58 Poorly/undiffer I No GSM155685 HNC2724 HN cancer Harvard - No Mouth Female 58 ND ND ND GSM155686 HNC2725 HN cancer Harvard + (33) Yes Tongue Male 69 Well/moderately ND ND GSM155687 Floor of HNC2738 HN cancer Harvard - No Male 50 Poorly/undiffer III ND GSM155688 mouth HNC2743 HN cancer Harvard - Yes Tongue Female 32 Well/moderately ND ND GSM155689 HNC2748 HN cancer Harvard - Yes Tongue Male 65 Well/moderately III No GSM155690 HNC2774 HN cancer Harvard - Yes Oropharynx Male 66 Poorly/undiffer II ND GSM155691 HNC2784 HN cancer Harvard + (16) Yes Hypopharynx Male 53 Poorly/undiffer ND ND GSM155692 HNC2814 HN cancer Harvard - Yes Tongue Male 54 Well/moderately ND ND GSM155693 Floor of HNC2816 HN cancer Harvard - No Male 57 Well/moderately ND ND GSM155694 mouth HNC2836 HN cancer Harvard - No Tongue Male 84 Well/moderately ND ND GSM155695 HNC2855 HN cancer Harvard - No Mouth Female 69 Well/moderately ND ND GSM155696 HNC2857 HN cancer Harvard - Yes Larynx Male 68 ND III ND GSM155697 HNC2885 HN cancer Harvard - Yes Tongue Female 54 ND ND ND GSM155698 Floor of HNC2887 HN cancer Harvard + (33) Yes Male 76 Poorly/undiffer II No GSM155699 mouth HNC2907 HN cancer Harvard - Yes Larynx Male 76 Well/moderately ND ND GSM155700 HNC2910 HN cancer Harvard - No Tongue Male 67 Well/moderately ND ND GSM155701 HNC2914 HN cancer Harvard + (16) Yes Pharynx Male 53 ND II No GSM155702 HNC2942 HN cancer Harvard + (16) Yes Oropharynx Male 56 Poorly/undiffer III No GSM155703 HNC2966 HN cancer Harvard - Yes Tongue Male 55 Well/moderately ND ND GSM155704

17 Floor of ND HNC2967 HN cancer Harvard - Yes ND Well/moderately ND ND GSM155705 mouth ND HNC3003 HN cancer Harvard - No Tongue Female 74 ND ND ND GSM155706 HNC3046 HN cancer Harvard + (16) Yes Tongue Male 56 Well/moderately II No GSM155707 HNC3055 HN cancer U. Iowa - Yes Tonsil Male 74 Well/moderately IV ND GSM155708 HNC3092 HN cancer U. Iowa + (16) No Tongue Male 37 Well/moderately IV ND GSM155709 Floor of HNC3687 HN cancer Harvard - No Female 54 Well/moderately ND GSM155710 mouth HNCB1 HN cancer U. Iowa + (16) Yes Tonsil Male 50 Well/moderately IV ND GSM155711 HNCS1 HN cancer U. Iowa - Yes Hypopharynx Male 56 Well/moderately III ND GSM155712 HNCS2 HN cancer U. Iowa + (16) Yes Tonsil Male 64 Poorly/undiffer IV ND GSM155713 HNCS3 HN cancer U. Iowa + (16) Yes Tonsil Male 62 Well/moderately III ND GSM155714 HNN013 HN normal U. Iowa - Yes Tonsil Female 20 - - - GSM155715 Uvula and HNN023 HN normal U. Iowa - Yes Female 24 - - - GSM155716 palate HNN039 HN normal U. Iowa - Yes Tonsil Male 66 - - - GSM155717 HNN052 HN normal U. Iowa - Yes Tonsil Male 47 - - - GSM155718 HNN053 HN normal U. Iowa - Yes Tonsil Female 18 - - - GSM155719 ND004 HN normal NDRI - Yes Oral Cavity Female 76 - - - GSM155720 ND007 HN normal NDRI - Yes Oral Cavity Female 77 - - - GSM155721 ND010 HN normal NDRI - Yes Oral Cavity Male 55 - - - GSM155722 ND011 HN normal NDRI - Yes Oral Cavity Male 62 - - - GSM155723 ND012 HN normal NDRI - Yes Oral Cavity Female 63 - - - GSM155724 ND014 HN normal NDRI - Yes Oral Cavity Female 88 - - - GSM155725 ND015 HN normal NDRI - Yes Oral Cavity Female 54 - - - GSM155726 ND017 HN normal NDRI - Yes Oral Cavity Male 84 - - - GSM155727 ND018 HN normal NDRI - Yes Oral Cavity Female 81 - - - GSM155728 * Tissue source: GOG, gynecologic oncology group; NDRI, national disease research interchange † HPV presence is indicated with detected genotypes § The samples with or without LCM are labeled as yes or no, respectively **ND No data

18 Supplementary Table S2. qPCR primers

Genes Sequence Direction SYCP2 5’-ACATCCGAGATGTGTTTGATGA Sense 5’-TGACATCAGTTCTCTGCGTACA Antisense 5’-GGCAAGCTTCAACTCAGTAACC Sense TCAM1 5’-TCAGAGACAGAACACTGGGCTA Antisense 5’-TGTGTTGGAGTTTTCTGGAGTG Sense p16 5’-ATGCTTGTCATGAAGTCGACAG Antisense 5’-GGGTTGGGAAGACAGATAATGA Sense cdc7 5’-CCCATAGGAAGTTTGATATGCTG Antisense 5’-TTGACTTCTCAGGCTTAGGTGA Sense ORC1 5’-GGTGAAGCCCTGTCTCTACAAA Antisense 5’-CAGTTAGAACTTCCGGCTTTTG Sense KNTC1 5’-AATAACCTGAGGGTCACAGGAA Antisense 5’-GGGACAGAAGTGTTTCTGGAAG Sense MCM6 5’-AGCCTGTGTTGGTATGAAACCT Antisense 5’-CTCACGCTTACCTCAACCATC Sense Cyclin D1 5’-CGATACACACAACATCCAGGAC Antisense 5’-CAGCAAGCAATTAGGGAGAAGT Sense Cyclin A1 5’-GGAAGTGCTTCCATTCAGAAAC Antisense 5’-CATGTAAGCCAAGTCATGGAGA Sense Cyclin B1 5’-AGAAACAGAAAACAGGGGGACT Antisense 5’-TTTAGAAGGCTTCCTCATTTGG Sense BUB1 5’-AGCTTTTGCCTTAACAAATCCA Antisense 5’-CAACAGGGAAGAACAGTTTTGA Sense cdc2 5’-TGACCAAGGCATAAGAATTCAC Antisense 5’-TGAACTCAAAGGTCACACATCC Sense cdc20 5’-CATAGCCTCAGGGTCTCATCTG Antisense 5’-GAGAGACCCTGTCCTCCCTAAT Sense STAG3 5’-TCCATTAAACACAGAGGTGCTG Antisense 5’-TCACCCACACTGTGCCCATCTA Sense β-actin 5’-TGAGGTAGTCAGTCAGGTCCCG Antisense

19 Table S3A. Genes highly upregulated in HPV+ cancers (red dots in Fig. 1B) Gene t-statistic t-statistic t-statistic Gene title symbol (HNC+:HNN)* (HNC-:HNN)* (CC:CN) 3'-phosphoadenosine 5'-phosphosulfate synthase 2 PAPSS2 3.48 0.75 -2.63 Amylase, alpha AMY1A -0.75 -4.9 2.27 Butyrophilin-like 9 BTNL9 2.07 -3.41 1.41 Chemokine (C-X-C motif) ligand 10 CXCL10 9.47 3.54 2.36 Chemokine (C-X-C motif) 4 CXCR4 1.57 -0.75 2.4 4 open reading frame 7 C4orf7 2.08 0.09 1.13 Chromosome Y open reading frame 15B CYorf15B 1.89 0.15 -4.26 Cyclin-dependent kinase inhibitor 2A CDKN2A 20.76 2.13 13.8 Cytochrome P450, family 1, subfamily B, polypeptide 1 CYP1B1 2.82 1.38 1.54 Cytochrome P450, family 4, subfamily X, polypeptide 1 CYP4X1 -0.33 -3.81 0.87 DKFZP56 DKFZP564O0823 protein 2.31 -1.1 -2.18 4O0823 (muscular dystrophy, Duchenne and Becker types) DMD 2.13 -0.61 1.2 Eukaryotic translation initiation factor 1A, Y-linked EIF1AY 2.24 0.41 -0.6 Full-length cDNA clone CS0DM011YC22 of Fetal liver of Homo --- 3.5 -0.18 4.91 sapiens (human) FYN binding protein (FYB-120/130) FYB 4.28 1.22 3.08 Glucuronidase, beta-like 1 /// Glucuronidase, beta-like 2 C6orf216 3.52 -0.14 4.23 Golgi autoantigen, golgin subfamily a, 1 GOLGA1 2.58 -2.41 3.11 , lymphoid-specific HELLS 4.44 1.06 2.88 Holocarboxylase synthetase HLCS 1.29 -2.38 1.73 Hypothetical gene supported by AK095200; BC042853 LOC44033 5.58 -0.39 3.73 Hypothetical gene supported by AL365406; BC034005 LOC38849 6.45 1.37 3.07 Hypothetical protein FLJ12505 FLJ12505 2.42 0.23 2.25 Hypothetical protein FLJ14503 FLJ14503 4.71 0.26 2.74 Hypothetical protein LOC285084 LOC28508 4.14 -1.96 3.43 Hypothetical protein LOC375196 LOC37519 5.05 0.01 3.05 Hypothetical protein MGC42174 MGC4217 0.85 -2.56 0.95 IQ motif containing G IQCG 4.25 1.32 6.86 KRT19 1.27 -1.98 3.85 KIAA1641 KIAA1641 4.02 0.35 2.57 Lymphocyte antigen 75 LY75 2.47 -2.32 2.35 Lymphotoxin beta (TNF superfamily, member 3) LTB 2.24 -0.69 1.69 Matrix metallopeptidase 9 MMP9 5.81 4.21 2.83 , heavy polypeptide 200kDa NEFH 2.33 -2.35 0.66 Olfactomedin 1 OLFM1 3.64 0.16 2.38 Ovostatin 2 OVOS2 2.99 -0.13 4.47 PC4 and SFRS1 interacting protein 1 PSIP1 3.05 -1.27 7.1 Sema domain, transmembrane domain (TM), and cytoplasmic domain, SEMA6A 2.37 -1.26 0.33 (semaphorin) 6A Similar to hypothetical protein LOC231503 --- 1.12 -2.91 1.32 SWI/SNF related, matrix associated, actin dependent regulator of SMARCA 1.93 -1.84 5.63 chromatin, subfamily a, member 2 2 Synaptogyrin 3 SYNGR3 3.96 0.86 4.21 Synaptonemal complex protein 2 SYCP2 5.64 0.9 7.84 Synaptopodin 2 SYNPO2 2.04 -2.73 -0.56 Testicular cell adhesion molecule 1 homolog (mouse) TCAM1 5.4 -2.9 4.98 Transmembrane protein 46 TMEM46 4.42 1.93 2.22 Ubiquitin D UBD 4.02 0.83 2.67 Vascular cell adhesion molecule 1 VCAM1 2.54 0.1 2.18 v- myeloblastosis viral oncogene homolog (avian) MYB 1.24 -5.73 3.84 + - * HNC+: HPV HNC; HNC-:HPV HNC

20 Table S3B. Genes highly downregulated in HPV+ cancers (blue dots in Fig. 1B) Gene t-statistic t-statistic t-statistic Gene Title symbol (HNC+:HNN)* (HNC-:HNN)* (CC:CN) Aldo-keto reductase family 1, member B10 (aldose reductase) AKR1B10 -1.38 3.53 -2.33 Aldo-keto reductase family 1, member C2 AKR1C2 -1.69 1.6 0.92 Aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid AKR1C3 -0.89 2.49 1.16 dehydrogenase, type II) Amphiregulin (schwannoma-derived growth factor) AREG -1.03 2.17 -1.88 ATP-binding cassette, sub-family A (ABC1), member 12 ABCA12 1.38 4.77 -0.1 Caveolin 2 CAV2 0.4 5.05 2.77 Chemokine (C-X-C motif) ligand 14 CXCL14 -0.36 3.48 -3.27 Chloride channel, calcium activated, family member 2 CLCA2 -1.86 1.18 -0.13 Chromosome 10 open reading frame 99 C10orf99 -0.92 0.97 -2.53 Chromosome 14 open reading frame 78 C14orf78 -2.05 1.79 -0.11 open reading frame 33 C19orf33 -2.67 -0.03 -1.39 Coagulation factor II (thrombin) receptor-like 1 F2RL1 -1 4.74 2.27 Cortactin CTTN -2.34 2.39 -0.7 Decay accelerating factor for complement (CD55, Cromer blood group DAF -3.06 0.65 0.17 system) Dermokine ZD52F10 -1.47 1.16 -5.78 Desmoglein 1 DSG1 -1.44 0.5 -6.1 Epiregulin EREG -2.51 0.3 -5.59 Fatty acid binding protein 5 (-associated) FABP5 -2.16 1.65 -0.5 Gap junction protein, beta 2, 26kDa (connexin 26) GJB2 -2.1 0.57 -2.36 Gap junction protein, beta 6 (connexin 30) GJB6 -2.41 0.6 -1.61 Insulin-like growth factor binding protein 6 IGFBP6 -1.92 1.09 0.64 Kallikrein 11 KLK11 -5.43 -1.8 -4.32 (epidermolysis bullosa simplex, Dowling-Meara, Koebner) KRT14 -0.85 3.3 -1.69 (focal non-epidermolytic ) KRT16 1.89 5.2 0.28 KIPV467 UNQ467 -1.64 1.09 -6.35 Malic 1, NADP(+)-dependent, cytosolic ME1 -3.05 0.31 0.39 antigen family A, 11 MAGEA11 -4.84 2.55 -1.7 Melanoma antigen family A, 3 MAGEA3 1.19 3.41 -0.03 Melanoma antigen family A, 6 MAGEA6 1.24 3.54 0.4 Parathyroid hormone-like hormone PTHLH 2.22 7.08 0.89 Peptidase inhibitor 3, skin-derived (SKALP) PI3 -0.47 2.39 -1.74 Protein tyrosine , receptor type, f polypeptide (PTPRF), PPFIA1 -0.54 3.2 1.78 interacting protein (liprin), alpha 1 Protein tyrosine phosphatase, receptor-type, Z polypeptide 1 PTPRZ1 1.34 5.66 0.88 Ring finger protein 128 RNF128 -2.11 1.09 -0.23 S100 calcium binding protein A12 (calgranulin C) S100A12 -2.56 0.19 -1.67 S100 calcium binding protein A7 (psoriasin 1) S100A7 -0.97 2.25 -1 S100 calcium binding protein A7-like 1 S100A7L1 0.96 3.79 0.52 Serpin peptidase inhibitor, clade B (ovalbumin), member 3 SERPINB3 -3.13 -1.02 -1.42 Serpin peptidase inhibitor, clade B (ovalbumin), member 4 SERPINB4 -2.75 -0.75 1.07 Small proline-rich protein 1A SPRR1A -2.67 -1.05 -1.87 Small proline-rich protein 1B (cornifin) SPRR1B -2.14 -0.06 -1.9 Small proline-rich protein 2B SPRR2B -3.31 -0.91 -1.62 Small proline-rich protein 3 SPRR3 -3.47 -1.39 -2.14 Solute carrier family 6 (amino acid transporter), member 14 SLC6A14 -0.54 2.61 1.43 Suprabasin SBSN -2.77 -0.56 -3.85 + - * HNC+: HPV HNC; HNC-:HPV HNC

21 Supplementary Table S4A. GO annotations upregulated in HPV+HNC Size: probesets included in the category; GO level: hierarchical position; Z = (X-µ)/δ, X = average log2 fold change between a tumor class and a corresponding normal, µ = average value of X, δ = standard deviation, Z > 0 means the average log2 fold on the set is above the average. Please refer to the Gene Ontology website (http://www.geneontology.org/) GO categories upregulated only in HPV+HNC and CC are indicated with pink cells and GO categories upregulated only in HNC are indicated with blue cells. ID Ontology Term z-score Number of genes GO:0004861 MF cyclin-dependent protein kinase inhibitor activity 15.84 7 GO:0006270 BP DNA replication initiation 10.76 18 GO:0007049 BP cell cycle 8.43 574 GO:0051301 BP cell division 7.56 131 GO:0000075 BP cell cycle checkpoint 7.12 29 GO:0000278 BP mitotic cell cycle 6.99 189 GO:0000279 BP M phase 6.64 165

Supplementary Table S4B. GO annotations downregulated in HPV+HNC ID Ontology Term z-score Number of genes GO:0007595 BP lactation 39.78 5 GO:0005179 MF hormone activity 11.96 94 GO:0008544 BP epidermis development 12.35 73 GO:0048609 BP reproductive organismal physiological process 12.63 57 GO:0050876 BP reproductive physiological process 12.63 57 GO:0007398 BP ectoderm development 11.24 82 GO:0004263 MF chymotrypsin activity 7.60 84 GO:0004295 MF trypsin activity 7.45 88 GO:0042742 BP defense response to bacteria 5.96 54 GO:0009888 BP tissue development 7.37 161 GO:0004252 MF serine-type endopeptidase activity 5.97 121

22 Supplementary Table S5. Differentially expressed genes in cancers vs. normals * In order as shown in Supplementary Fig. 3B. Probeset ID* Gene title Gene symbol t-stat 204475_at Matrix metalloproteinase 1 (interstitial collagenase) MMP1 13.864 220620_at open reading frame 42 C1orf42 -6.514 224329_s_at Cornifelin CNFN -5.925 214599_at Involucrin IVL -4.288 214549_x_at Small proline-rich protein 1A SPRR1A -3.49 232082_x_at ------3.765 235272_at HLAR698 UNQ698 -3.983 207602_at Airway trypsin-like protease HAT -3.752 1556793_a_at Chromosome 20 open reading frame 128 C20orf128 -4.121 219554_at Rhesus blood group, C glycoprotein RHCG -6.286 217272_s_at Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13 SERPINB13 -3.87 220431_at DESC1 protein DESC1 -4.465 218990_s_at Small proline-rich protein 3 SPRR3 -5.688 220026_at Chloride channel, calcium activated, family member 4 CLCA4 -6.456 1560712_at Hypothetical protein DKFZp686L1818 DKFZp686L1818 -11.324 204777_s_at Mal, T-cell differentiation protein MAL -10.546 223720_at cancer-related gene-2 ECG2 -7.302 220090_at Chromosome 1 open reading frame 10 C1orf10 -9.118 205185_at Serine protease inhibitor, Kazal type 5 SPINK5 -8.075 206004_at Transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase) TGM3 -5.477 213240_s_at KRT4 -12.51 207935_s_at KRT13 -7.045 207802_at Cysteine-rich secretory protein 3 CRISP3 -7.212 227174_at Hypothetical protein FLJ38736 FLJ38736 8.988 214612_x_at Melanoma antigen, family A, 6 MAGEA6 4.247 209942_x_at Melanoma antigen, family A, 3 MAGEA3 3.835 201427_s_at Selenoprotein P, plasma, 1 SEPP1 -4.27 210096_at Cytochrome P450, family 4, subfamily B, polypeptide 1 CYP4B1 -5 207039_at Cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) CDKN2A 10.585 230493_at ------5.643 205828_at Matrix metalloproteinase 3 (stromelysin 1, progelatinase) MMP3 8.1 231766_s_at Collagen, type XII, alpha 1 COL12A1 7.824 210511_s_at Inhibin, beta A (activin A, activin AB alpha polypeptide) INHBA 10.988 227140_at Inhibin, beta A (activin A, activin AB alpha polypeptide) INHBA 12.844 221805_at Neurofilament, light polypeptide 68kDa NEFL 6.47 205680_at Matrix metalloproteinase 10 (stromelysin 2) MMP10 8.613 218804_at Transmembrane protein 16A TMEM16A 6.123 204469_at Protein tyrosine phosphatase, receptor-type, Z polypeptide 1 PTPRZ1 4.209 220322_at Interleukin 1 family, member 9 IL1F9 4.676 1556773_at Parathyroid hormone-like hormone PTHLH 6.682 206300_s_at Parathyroid hormone-like hormone PTHLH 8.302 210355_at Parathyroid hormone-like hormone PTHLH 5.581 211756_at Parathyroid hormone-like hormone PTHLH 7.86 209875_s_at Secreted phosphoprotein 1 SPP1 11.045 225681_at Collagen triple helix repeat containing 1 CTHRC1 11.279 242881_x_at Hypothetical LOC389048 --- 6.059 224568_x_at Metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) MALAT1 4.017 217388_s_at Kynureninase (L-kynurenine ) KYNU 4.203 205476_at Chemokine (C-C motif) ligand 20 CCL20 4.41 210538_s_at Baculoviral IAP repeat-containing 3 BIRC3 4.854 204748_at Prostaglandin-endoperoxide synthase 2 PTGS2 5.027 1553604_at ATP binding cassette gene, sub-family A (ABC1), member 13 ABCA13 4.484 1553605_a_at ATP binding cassette gene, sub-family A (ABC1), member 13 ABCA13 5.423 203820_s_at IGF-II mRNA-binding protein 3 IMP-3 6.127 203819_s_at IGF-II mRNA-binding protein 3 IMP-3 7.706 1565162_s_at Microsomal glutathione S- 1 MGST1 3.715 202859_x_at Interleukin 8 IL8 8.283 204470_at Chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) CXCL1 6.325 228260_at ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B) ELAVL2 7.069 223642_at Zic family member 2 (odd-paired homolog, Drosophila) ZIC2 11.468 209921_at Solute carrier family 7, (cationic amino acid transporter, y+ system) member 11 SLC7A11 5.276 203184_at 2 (congenital contractural arachnodactyly) FBN2 5.194 205691_at Synaptogyrin 3 SYNGR3 5.134

23 1557570_a_at Hypothetical protein LOC285084 LOC285084 4.585 206546_at Synaptonemal complex protein 2 SYCP2 7.451 233320_at Testicular cell adhesion molecule 1 TCAM1 5.655 231164_at Hypothetical gene supported by AK095200; BC042853 --- 5.698 205347_s_at Thymosin, beta, identified in neuroblastoma cells TMSNB 4.816 202269_x_at Guanylate binding protein 1, interferon-inducible, 67kDa GBP1 6.078 231577_s_at Guanylate binding protein 1, interferon-inducible, 67kDa GBP1 5.248 202270_at Guanylate binding protein 1, interferon-inducible, 67kDa GBP1 5.961 236285_at ------8.656 206513_at Absent in melanoma 2 AIM2 8.042 201641_at Bone marrow stromal cell antigen 2 BST2 8.66 205552_s_at 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS1 4.249 234987_at SAM domain and HD domain 1 SAMHD1 3.941 205483_s_at Interferon, alpha-inducible protein (clone IFI-15K) G1P2 11.974 226702_at Hypothetical protein LOC129607 LOC129607 9.567 214453_s_at Interferon-induced protein 44 IFI44 8.917 204439_at Chromosome 1 open reading frame 29 C1orf29 8.376 218986_s_at Hypothetical protein FLJ20035 FLJ20035 9.921 203153_at Interferon-induced protein with tetratricopeptide repeats 1 IFIT1 8.237 213797_at Viperin cig5 8.609 242625_at Viperin cig5 9.441 229450_at Interferon-induced protein with tetratricopeptide repeats 3 IFIT3 7.844 226757_at Interferon-induced protein with tetratricopeptide repeats 2 IFIT2 7.216 210163_at Chemokine (C-X-C motif) ligand 11 CXCL11 6.444 211122_s_at Chemokine (C-X-C motif) ligand 11 CXCL11 7.408 204533_at Chemokine (C-X-C motif) ligand 10 CXCL10 7.214 203915_at Chemokine (C-X-C motif) ligand 9 CXCL9 6.573 229400_at Homeo box D10 HOXD10 3.798 205157_s_at KRT17 10.277 212236_x_at Keratin 17 KRT17 7.733 203423_at Retinol binding protein 1, cellular RBP1 7.127 210074_at Cathepsin L2 CTSL2 6.803 209301_at Carbonic anhydrase II CA2 6.422 1552487_a_at Basonuclin 1 BNC1 6.282 226847_at Follistatin FST 6.574 201839_s_at Tumor-associated calcium signal transducer 1 TACSTD1 6.999 205959_at Matrix metalloproteinase 13 (collagenase 3) MMP13 5.656 221872_at responder (tazarotene induced) 1 RARRES1 5.058 219295_s_at Procollagen C-endopeptidase enhancer 2 PCOLCE2 5.183 215446_s_at Lysyl oxidase LOX 10.373 204298_s_at Lysyl oxidase LOX 7.562 204259_at Matrix metalloproteinase 7 (matrilysin, uterine) MMP7 7.343 203936_s_at Matrix metalloproteinase 9 MMP9 7.232 204580_at Matrix metalloproteinase 12 (macrophage elastase) MMP12 11.977 227266_s_at FYN binding protein (FYB-120/130) FYB 4.361 205242_at Chemokine (C-X-C motif) ligand 13 (B-cell chemoattractant) CXCL13 5.129 236341_at Cytotoxic T-lymphocyte-associated protein 4 CTLA4 3.922 219607_s_at Membrane-spanning 4-domains, subfamily A, member 4 MS4A4A 4.874 220330_s_at SAM domain, SH3 domain and nuclear localisation signals, 1 SAMSN1 4.941 223343_at Membrane-spanning 4-domains, subfamily A, member 7 MS4A7 4.819 215193_x_at Major histocompatibility complex, class II, DR beta 1 HLA-DRB1 3.864 210982_s_at Major histocompatibility complex, class II, DR alpha HLA-DRA 3.906 208894_at Major histocompatibility complex, class II, DR alpha HLA-DRA 3.935 225767_at Hypothetical protein LOC284801 LOC284801 3.807 206140_at LIM 2 LHX2 7.012 228245_s_at Ovostatin OVOS 4.354 206858_s_at Homeo box C6 HOXC6 12.046 206504_at Cytochrome P450, family 24, subfamily A, polypeptide 1 CYP24A1 5.72 210809_s_at Periostin, osteoblast specific factor POSTN 3.86 202007_at Nidogen (enactin) NID 4.447 222108_at Amphoterin induced gene 2 AMIGO2 4.945 201110_s_at Thrombospondin 1 THBS1 4.639 201744_s_at Lumican LUM 5.968 37892_at Collagen, type XI, alpha 1 COL11A1 6.421 217428_s_at Collagen, type X, alpha 1(Schmid metaphyseal chondrodysplasia) COL10A1 6.031 219087_at Asporin (LRR class 1) ASPN 5.295

24 229802_at WNT1 inducible signaling pathway protein 1 WISP1 4.322 218468_s_at Gremlin 1 homolog, cysteine knot superfamily (Xenopus laevis) GREM1 6.652 218469_at Gremlin 1 homolog, cysteine knot superfamily (Xenopus laevis) GREM1 6.702 229554_at ------5.413 221731_x_at Chondroitin sulfate proteoglycan 2 (versican) CSPG2 6.335 204620_s_at Chondroitin sulfate proteoglycan 2 (versican) CSPG2 6.835 204619_s_at Chondroitin sulfate proteoglycan 2 (versican) CSPG2 4.125 207173_x_at Cadherin 11, type 2, OB-cadherin (osteoblast) CDH11 5.002 212353_at 1 SULF1 6.184 226237_at Collagen, type VIII, alpha 1 COL8A1 7.37 205547_s_at Transgelin TAGLN 4.426 212158_at Syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan) SDC2 4.544 225664_at Collagen, type XII, alpha 1 COL12A1 5.898 221729_at Collagen, type V, alpha 2 COL5A2 6.683 221730_at Collagen, type V, alpha 2 COL5A2 7.313 211980_at Collagen, type IV, alpha 1 COL4A1 9.548 200665_s_at Secreted protein, acidic, cysteine-rich (osteonectin) SPARC 7.13 211719_x_at Fibronectin 1 FN1 9.65 212464_s_at Fibronectin 1 FN1 10.048 216442_x_at Fibronectin 1 FN1 10.129 210495_x_at Fibronectin 1 FN1 10.064 202403_s_at Collagen, type I, alpha 2 COL1A2 4.148 202310_s_at Collagen, type I, alpha 1 COL1A1 4.993 202404_s_at Collagen, type I, alpha 2 COL1A2 7.068 211161_s_at Collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) COL3A1 4.024 215076_s_at Collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) COL3A1 4.889 201852_x_at Collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) COL3A1 5.756 203413_at NEL-like 2 (chicken) /// NEL-like 2 (chicken) NELL2 5.345 212977_at Chemokine orphan receptor 1 CMKOR1 7.297 224851_at Cyclin-dependent kinase 6 CDK6 4.921 209774_x_at Chemokine (C-X-C motif) ligand 2 CXCL2 5.315 214974_x_at Chemokine (C-X-C motif) ligand 5 CXCL5 4.847 232277_at Solute carrier family 28 (sodium-coupled nucleoside transporter), member 3 SLC28A3 5.693 213423_x_at Tumor suppressor candidate 3 TUSC3 5.857 209228_x_at Tumor suppressor candidate 3 TUSC3 7.045 222847_s_at Egl nine homolog 3 (C. elegans) EGLN3 4.649 229128_s_at ------5.247 213872_at ------4.25 203007_x_at I LYPLA1 4.508 1553530_a_at Integrin, beta 1 ITGB1 5.388 1553678_a_at Integrin, beta 1 ITGB1 5.532 215078_at Superoxide dismutase 2, mitochondrial SOD2 6.131 214464_at CDC42 binding protein kinase alpha (DMPK-like) CDC42BPA 4.477 201291_s_at (DNA) II alpha 170kDa TOP2A 8.407 242890_at Helicase, lymphoid-specific HELLS 4.261 220085_at helicase, lymphoid-specific HELLS 6.435 222529_at Mitochondrial solute carrier protein MSCP 3.925 230563_at RasGEF domain family, member 1A RASGEF1A 5.689 206632_s_at Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B APOBEC3B 8.081 202760_s_at PALM2-AKAP2 protein PALM2-AKAP2 4.425 204457_s_at Growth arrest-specific 1 GAS1 3.889 202238_s_at Nicotinamide N-methyltransferase NNMT 5.45 202237_at Nicotinamide N-methyltransferase NNMT 5.8 235683_at Sestrin 3 SESN3 4.762 1554018_at Glycoprotein (transmembrane) nmb GPNMB 8.675 201141_at Glycoprotein (transmembrane) nmb GPNMB 4.745 233002_at KIAA1622 KIAA1622 5.521 212190_at serine (or cysteine) proteinase inhibitor, clade E, member 2 SERPINE2 4.832 208025_s_at High mobility group AT-hook 2 /// high mobility group AT-hook 2 HMGA2 6.605 226448_at Hypothetical gene supported by BC009447 MGC15887 5.515 210138_at Regulator of G-protein signalling 20 RGS20 5.875 203324_s_at Caveolin 2 CAV2 4.614 203065_s_at Caveolin 1, caveolae protein, 22kDa CAV1 4.24 202628_s_at Serine (or cysteine) proteinase inhibitor, clade E, member 1 SERPINE1 7.897 202627_s_at Serine (or cysteine) proteinase inhibitor, clade E, member 1 SERPINE1 6.505 214456_x_at Serum amyloid A1 SAA1 6.153

25 208607_s_at Serum amyloid A1 /// serum amyloid A2 SAA1 /// SAA2 5.752 202411_at Interferon, alpha-inducible protein 27 IFI27 9.145 204567_s_at ATP-binding cassette, sub-family G (WHITE), member 1 ABCG1 8.721 227697_at Suppressor of cytokine signaling 3 SOCS3 4.128 202555_s_at , light polypeptide kinase /// myosin, light polypeptide kinase MYLK 3.755 224823_at Myosin, light polypeptide kinase MYLK 4.736 200790_at Ornithine decarboxylase 1 ODC1 5.552 227897_at ------4.136 231042_s_at ------4.441 204083_s_at 2 (beta) TPM2 6.086 212143_s_at Insulin-like growth factor binding protein 3 IGFBP3 5.459 210095_s_at Insulin-like growth factor binding protein 3 IGFBP3 5.249 225285_at Branched chain aminotransferase 1, cytosolic BCAT1 8.015 226517_at Branched chain aminotransferase 1, cytosolic BCAT1 7.966 231726_at Protocadherin beta 14 PCDHB14 7.916 201952_at ------4.995 201951_at Activated leukocyte cell adhesion molecule ALCAM 7.604 242836_at ------4.616 201860_s_at Plasminogen activator, tissue PLAT 4.434 226021_at Retinol dehydrogenase 10 (all-trans) RDH10 6.035 202626_s_at v-yes-1 Yamaguchi sarcoma viral related oncogene homolog LYN 6.027 202625_at ------4.898 201645_at Tenascin C (hexabrachion) TNC 6.741 201487_at Cathepsin C CTSC 7.751 225646_at Cathepsin C CTSC 9.642 225647_s_at Cathepsin C CTSC 8.475 230193_at Hypothetical protein MGC33630 MGC33630 19.325 201506_at Transforming growth factor, beta-induced, 68kDa TGFBI 9.644 225688_s_at Pleckstrin homology-like domain, family B, member 2 PHLDB2 8.1 Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, 203789_s_at SEMA3C 12.626 (semaphorin) 3C 221185_s_at Hypothetical protein DKFZp434B227 DKFZp434B227 5.833 204702_s_at Nuclear factor (erythroid-derived 2)-like 3 NFE2L3 7.331 235157_at ------6.179 235046_at ------3.968 226535_at ------7.008 208083_s_at Integrin, beta 6 ITGB6 6.34 202599_s_at interacting protein 1 NRIP1 5.84 202600_s_at Nuclear receptor interacting protein 1 NRIP1 5.308 236462_at ------4.596 225041_at M-phase phosphoprotein, mpp8 HSMPP8 4.691 242438_at ------5.345 235705_at Triple functional domain (PTPRF interacting) TRIO 5.561 237310_at ------4.39 230183_at ------5.7 230000_at open reading frame 27 C17orf27 3.719 1559214_at ------4.103 235911_at Hypothetical gene supported by BC034933; BC068085 --- 6.852 241036_at ------5.872 229490_s_at ------5.861 229105_at G protein-coupled receptor 39 GPR39 5.606 205289_at Bone morphogenetic protein 2 BMP2 4.908 208893_s_at Dual specificity phosphatase 6 DUSP6 6.604 208891_at Dual specificity phosphatase 6 DUSP6 4.398 208892_s_at Dual specificity phosphatase 6 DUSP6 3.844 229070_at open reading frame 105 C6orf105 5.551 214297_at ------5.67 226907_at 1, regulatory (inhibitor) subunit 14C PPP1R14C 4.822 200832_s_at Stearoyl-CoA desaturase (delta-9-desaturase) SCD 4.532 223839_s_at ------4.424 213067_at Myosin, heavy polypeptide 10, non-muscle MYH10 4.921 229975_at ------5.631 209911_x_at Histone 1, H2bd HIST1H2BD 4.284 208579_x_at H2B histone family, member S H2BFS 5.45 209806_at Histone 1, H2bk HIST1H2BK 5.955 209398_at Histone 1, H1c HIST1H1C 5.524

26 209644_x_at Cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) CDKN2A 8.723 230795_at ------5.68 235292_at LOC441069 --- 6.013 225105_at Hypothetical protein LOC387882 10.9 225202_at ------7.692 204557_s_at DAZ interacting protein 1 DZIP1 5.6 210002_at GATA binding protein 6 GATA6 5.581 228776_at Gap junction protein, alpha 7, 45kDa (connexin 45) GJA7 6.021 44783_s_at Hairy/enhancer-of-split related with YRPW motif 1 HEY1 5.514 204285_s_at Phorbol-12-myristate-13-acetate-induced protein 1 PMAIP1 5.738 204286_s_at Phorbol-12-myristate-13-acetate-induced protein 1 PMAIP1 5.117 223687_s_at cDNA for differentially expressed CO16 gene LY6K 7.346 1557578_at Pleckstrin homology-like domain, family B, member 2 PHLDB2 5.082 218847_at IGF-II mRNA-binding protein 2 IMP-2 5.84 242990_at ------5.571 Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting 202066_at PPFIA1 6.571 protein (liprin), alpha 1 202535_at Fas (TNFRSF6)-associated via death domain FADD 7.303 222803_at Phosphoribosyl transferase domain containing 1 PRTFDC1 8.572 224911_s_at Discoidin, CUB and LCCL domain containing 2 DCBLD2 7.493 230175_s_at ------7.554 219181_at , endothelial LIPG 7.079 210830_s_at 2 PON2 4.647 201616_s_at Caldesmon 1 CALD1 3.793 201617_x_at Caldesmon 1 CALD1 5.094 204222_s_at GLI pathogenesis-related 1 (glioma) GLIPR1 7.411 231202_at Hypothetical protein FLJ38508 FLJ38508 6.254 228438_at Transient receptor potential cation channel, subfamily A, member 1 TRPA1 5.825 218404_at Sorting nexin 10 SNX10 11.068 205122_at Transmembrane protein with EGF-like and two follistatin-like domains 1 TMEFF1 8.725 235296_at Eukaryotic translation initiation factor 5A2 EIF5A2 9.493 209288_s_at CDC42 effector protein (Rho GTPase binding) 3 CDC42EP3 9.025 225685_at CDC42 effector protein (Rho GTPase binding) 3 CDC42EP3 7.437 212354_at Sulfatase 1 SULF1 5.637 Full-length cDNA clone CS0DI014YH21 of Placenta Cot 25-normalized of Homo 226311_at --- 7.095 sapiens (human) 201310_s_at Chromosome 5 open reading frame 13 C5orf13 5.787 201792_at AE binding protein 1 AEBP1 4.689 211964_at Collagen, type IV, alpha 2 COL4A2 7.601 212489_at Collagen, type V, alpha 1 COL5A1 6.149 212488_at Collagen, type V, alpha 1 COL5A1 5.593 202311_s_at Collagen, type I, alpha 1 COL1A1 8.007 212012_at Melanoma associated gene D2S448 8.161 212473_s_at MICAL2 MICAL2 9.111 211651_s_at Laminin, beta 1 LAMB1 5.375 201505_at Laminin, beta 1 LAMB1 4.368 226777_at A disintegrin and metalloproteinase domain 12 (meltrin alpha) ADAM12 9.134 206025_s_at Tumor necrosis factor, alpha-induced protein 6 TNFAIP6 6.64 208747_s_at Complement component 1, s subcomponent C1S 4.399 201426_s_at Vimentin VIM 4.071 225524_at Anthrax toxin receptor 2 ANTXR2 5.714 201162_at Insulin-like growth factor binding protein 7 IGFBP7 4.126 201105_at Lectin, galactoside-binding, soluble, 1 (galectin 1) LGALS1 6.059 222449_at Transmembrane, prostate androgen induced RNA TMEPAI 10.337 222450_at Transmembrane, prostate androgen induced RNA TMEPAI 6.729 210987_x_at Tropomyosin 1 (alpha) TPM1 9.975 206116_s_at Tropomyosin 1 (alpha) TPM1 5.856 210986_s_at Tropomyosin 1 (alpha) TPM1 6.57 202458_at Protease, serine, 23 PRSS23 4.442 225288_at Collagen, type XXVII, alpha 1 COL27A1 6.217 204345_at Collagen, type XVI, alpha 1 COL16A1 4.13 218980_at Formin homology 2 domain containing 3 FHOD3 6.258 204017_at KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3 KDELR3 6.298 201313_at Enolase 2 (gamma, neuronal) ENO2 5.742 226158_at Hypothetical protein LOC339924 LOC339924 5.518 221986_s_at DRE1 protein DRE1 5.296

27 223854_at Protocadherin beta 10 PCDHB10 6.637 203650_at Protein C receptor, endothelial (EPCR) PROCR 8.027 205542_at Six transmembrane epithelial antigen of the prostate STEAP 4.689 236565_s_at Acheron FLJ11196 8.837 211725_s_at BH3 interacting domain death agonist BID 8.058 203562_at Fasciculation and elongation protein zeta 1 (zygin I) FEZ1 6.832 201579_at FAT tumor suppressor homolog 1 (Drosophila) FAT 7.971 212314_at KIAA0746 protein KIAA0746 5.484 217989_at Dehydrogenase/reductase (SDR family) member 8 DHRS8 4.799 223374_s_at UDP-Gal:betaGlcNAc beta 1,3-, polypeptide 3 B3GALT3 4.617 211379_x_at UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 B3GALT3 5.016 202149_at Neural precursor cell expressed, developmentally down-regulated 9 NEDD9 3.858 221973_at Hypothetical protein LOC150759 LOC150759 4.016 231292_at Thioredoxin reductase 1 TXNRD1 4.788 210135_s_at Short stature homeobox 2 SHOX2 6.43 228347_at Sine oculis homeobox homolog 1 (Drosophila) SIX1 7.121 229796_at ------9.414 204784_s_at Myeloid leukemia factor 1 MLF1 11.495 204783_at Myeloid leukemia factor 1 MLF1 9.614 233504_at open reading frame 84 C9orf84 6.535 229442_at Hypothetical protein MGC33382 MGC33382 6.708 1561195_at ------6.117 224320_s_at MCM8 minichromosome maintenance deficient 8 (S. cerevisiae) MCM8 8.431 230387_at ------7.203 226925_at -like 2 ACPL2 5.334 229795_at ------4.186 223513_at Centromere protein J CENPJ 4.587 229830_at ------7.966 236251_at ------7.812 232797_at CDNA FLJ11397 fis, clone HEMBA1000622 --- 7.668 241769_at ------5.076 230206_at ------3.904 227484_at Homo sapiens, clone IMAGE:3604678, mRNA --- 6.779 226320_at THO complex 4 THOC4 6.435 226319_s_at THO complex 4 THOC4 5.424 200658_s_at Prohibitin PHB 5.395 215952_s_at Ornithine decarboxylase antizyme 1 OAZ1 4.444 213187_x_at Ferritin, light polypeptide FTL 5.833 200920_s_at B-cell translocation gene 1, anti-proliferative BTG1 4.683 228204_at ------4.881 200613_at Adaptor-related protein complex 2, mu 1 subunit AP2M1 4.736 234000_s_at Butyrate-induced transcript 1 HSPC121 5.493 222404_x_at Butyrate-induced transcript 1 HSPC121 5.46 204858_s_at Endothelial cell growth factor 1 (platelet-derived) ECGF1 7.592 221972_s_at Calcium binding protein Cab45 precursor Cab45 4.408 202620_s_at Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2 PLOD2 8.942 202619_s_at Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2 PLOD2 9.743 242909_at ------9.1 243018_at ------6.92 207469_s_at Pirin (iron-binding nuclear protein) PIR 4.591 210540_s_at UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4 B4GALT4 7.148 225911_at Hypothetical protein LOC255743 LOC255743 6.186 224901_at Stearoyl-CoA desaturase 4 SCD4 7.041 201596_x_at KRT18 5.137 209008_x_at /// keratin 8 KRT8 3.822 213110_s_at Collagen, type IV, alpha 5 (Alport syndrome) COL4A5 5.757 225283_at Arrestin domain containing 4 ARRDC4 5.743 222877_at Neuropilin 2 NRP2 9.331 203304_at BMP and activin membrane-bound inhibitor homolog (Xenopus laevis) BAMBI 6.614 206247_at MHC class I polypeptide-related sequence B MICB 5.44 229390_at Similar to RIKEN cDNA A630077B13 gene; RIKEN cDNA 2810048G17 --- 5.773 229391_s_at Similar to RIKEN cDNA A630077B13 gene; RIKEN cDNA 2810048G17 --- 5.879 205488_at Granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine 3) GZMA 4.947 210164_at Granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1) GZMB 6.005 229625_at Guanylate binding protein 5 GBP5 5.856 238581_at Guanylate binding protein 5 GBP5 7.339

28 214329_x_at ------6.661 202687_s_at Tumor necrosis factor (ligand) superfamily, member 10 TNFSF10 6.672 202688_at Tumor necrosis factor (ligand) superfamily, member 10 TNFSF10 7.353 209546_s_at Apolipoprotein L, 1 APOL1 11.341 217933_s_at Leucine aminopeptidase 3 LAP3 6.69 AFFX-HUMRGE Signal recognition particle 68kDa SRP68 8.776 /M10098_3_at 205660_at 2'-5'-oligoadenylate synthetase-like OASL 7.328 204698_at Interferon stimulated gene 20kDa ISG20 5.571 33304_at Interferon stimulated gene 20kDa ISG20 5.466 1568609_s_at FLJ39739 protein FLJ39739 4.568 204122_at TYRO protein tyrosine kinase binding protein TYROBP 5.154 202953_at Complement component 1, q subcomponent, beta polypeptide C1QB 7.054 201743_at CD14 antigen CD14 4.46 203382_s_at Apolipoprotein E APOE 5.923 206214_at A2, group VII (platelet-activating factor acetylhydrolase, plasma) PLA2G7 6.911 240232_at ------7.162 224583_at Coactosin-like 1 (Dictyostelium) COTL1 5.007 221059_s_at Coactosin-like 1 (Dictyostelium) COTL1 5.21 224833_at v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) ETS1 4.239 206082_at HLA complex P5 HCP5 5.947 202307_s_at Transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) TAP1 7.514 216231_s_at Beta-2-microglobulin B2M 4.999 200905_x_at Major histocompatibility complex, class I, E HLA-E 5.115 217456_x_at Major histocompatibility complex, class I, E HLA-E 6.378 204806_x_at Major histocompatibility complex, class I, F HLA-F 7.19 221875_x_at Major histocompatibility complex, class I, F HLA-F 6.833 211799_x_at Major histocompatibility complex, class I, A, C HLA-A / HLA-C 6.776 209140_x_at Major histocompatibility complex, class I, B HLA-B 6.291 215313_x_at Major histocompatibility complex, class I, A HLA-A 6.493 214459_x_at Major histocompatibility complex, class I, C HLA-C 6.496 208812_x_at Major histocompatibility complex, class I, C, B HLA-C / HLA-B 6.187 217436_x_at ------6.122 211528_x_at HLA-G histocompatibility antigen, class I, G HLA-G 6.204 211529_x_at HLA-G histocompatibility antigen, class I, G HLA-G 6.243 209040_s_at Proteasome (prosome, macropain) subunit, beta type, 8 PSMB8 5.974 211911_x_at Major histocompatibility complex, class I, C, B HLA-C / HLA-B 7.19 208729_x_at Major histocompatibility complex, class I, B HLA-B 7.096 202659_at Proteasome (prosome, macropain) subunit, beta type, 10 PSMB10 6.113 209846_s_at Butyrophilin, subfamily 3, member A2 BTN3A2 5.713 231769_at F-box protein 6 FBXO6 6.274 201649_at Ubiquitin-conjugating enzyme E2L 6 UBE2L6 6.685 200628_s_at Tryptophanyl-tRNA synthetase WARS 8.513 200629_at Tryptophanyl-tRNA synthetase WARS 8.524 209417_s_at Interferon-induced protein 35 IFI35 9.265 204279_at Proteasome (prosome, macropain) subunit, beta type, 9 PSMB9 8.514 202357_s_at B-factor, properdin BF 6.378 38241_at Butyrophilin, subfamily 3, member A3 BTN3A3 5.35 204821_at Butyrophilin, subfamily 3, member A3 BTN3A3 5.145 219684_at 28kD interferon responsive protein IFRG28 6.143 232375_at Signal transducer and activator of transcription 1, 91kDa STAT1 8.446 203964_at N- (and STAT) interactor NMI 9.779 200887_s_at Signal transducer and activator of transcription 1, 91kDa STAT1 9.691 AFFX-HUMISGF3A Signal transducer and activator of transcription 1, 91kDa STAT1 8.82 /M97935_5_at 219209_at Interferon induced with helicase C domain 1 IFIH1 7.836 219211_at Ubiquitin specific protease 18 USP18 7.836 226603_at Chromosome 7 open reading frame 6 C7orf6 5.127 230383_x_at ------5.825 226725_at ------7.249 238430_x_at Hypothetical protein MGC19764 MGC19764 6.145 224701_at Poly (ADP-ribose) family, member 14 PARP14 7.838 225415_at Rhysin 2 BBAP 9.09 223220_s_at Poly (ADP-ribose) polymerase family, member 9 PARP9 10.247 233632_s_at 5'-3' 1 XRN1 5.777 225929_s_at Chromosome 17 open reading frame 27 C17orf27 7.062

29 218543_s_at CCCH type domain containing 1 ZC3HDC1 9.788 202864_s_at Nuclear antigen Sp100 SP100 7.541 202863_at Nuclear antigen Sp100 SP100 7.161 204070_at Retinoic acid receptor responder (tazarotene induced) 3 RARRES3 4.065 209969_s_at Signal transducer and activator of transcription 1, 91kDa STAT1 9.56 204415_at Interferon, alpha-inducible protein (clone IFI-6-16) G1P3 8.757 206133_at XIAP associated factor-1 HSXIAPAF1 8.276 228617_at XIAP associated factor-1 HSXIAPAF1 7.733 227609_at Epithelial stromal interaction 1 (breast) EPSTI1 9.573 235276_at ------6.728 202086_at Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) MX1 6.348 214059_at Interferon-induced protein 44 IFI44 6.485 218943_s_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 DDX58 7.314 218400_at 2'-5'-oligoadenylate synthetase 3, 100kDa OAS3 9.277 228152_s_at Hypothetical protein FLJ31033 FLJ31033 9.496 219863_at Hect domain and RLD 5 HERC5 8.883 205569_at Lysosomal-associated 3 LAMP3 8.111 1557236_at ------5.793 241916_at ------7.554 202446_s_at scramblase 1 PLSCR1 8.793 202430_s_at Phospholipid scramblase 1 PLSCR1 7.482 203726_s_at Laminin, alpha 3 LAMA3 8.374 202267_at Laminin, gamma 2 LAMC2 10.92 209270_at Laminin, beta 3 LAMB3 6.762 215177_s_at Integrin, alpha 6 ITGA6 6.545 201656_at Integrin, alpha 6 ITGA6 7.769 219936_s_at G protein-coupled receptor 87 GPR87 5.189 1552477_a_at Interferon regulatory factor 6 IRF6 6.301 203256_at Cadherin 3, type 1, P-cadherin (placental) CDH3 7.56 60474_at Chromosome 20 open reading frame 42 C20orf42 6.494 243754_at ------9.425 205241_at SCO cytochrome oxidase deficient homolog 2 (yeast) SCO2 5.904 228303_at ------7.411 222457_s_at Epithelial protein lost in neoplasm beta EPLIN 6.672 223276_at Putative small membrane protein NID67 NID67 6.525 65438_at KIAA1609 protein KIAA1609 5.619 208002_s_at Brain acyl-CoA hydrolase BACH 5.895 224950_at Prostaglandin F2 receptor negative regulator PTGFRN 6.825 236831_at Chromosome 3 open reading frame 6 C3orf6 4.758 227458_at ------6.882 225847_at KIAA1363 protein KIAA1363 6.126 202388_at Regulator of G-protein signalling 2, 24kDa RGS2 4.395 224973_at Family with sequence similarity 46, member A FAM46A 7.497 221766_s_at Family with sequence similarity 46, member A FAM46A 7.042 229553_at Phosphoglucomutase 2-like 1 PGM2L1 7.385 229256_at Phosphoglucomutase 2-like 1 PGM2L1 7.024 206683_at ZNF165 5.978 209218_at Squalene epoxidase SQLE 4.263 222587_s_at N-acetylgalactosaminyltransferase 7 (GalNAc-T7) GALNT7 4.76 243495_s_at KIAA0924 protein KIAA0924 4.209 229067_at ------4.648 230265_at ------5.21 AFFX-HUMGAPDH Glyceraldehyde-3-phosphate dehydrogenase GAPD 3.744 /M33197_M_at 214359_s_at Heat shock 90kDa protein 1, beta HSPCB 3.765 210338_s_at Heat shock 70kDa protein 8 HSPA8 4.247 200806_s_at Heat shock 60kDa protein 1 (chaperonin) HSPD1 6.237 200866_s_at Prosaposin (variant Gaucher disease and variant metachromatic leukodystrophy) PSAP 4.975 1555226_s_at Chromosome 1 open reading frame 43 C1orf43 4.157 213047_x_at SET translocation (myeloid leukemia-associated) SET 4.638 207791_s_at RAB1A, member RAS oncogene family RAB1A 4.886 200737_at Phosphoglycerate kinase 1 PGK1 5.708 217356_s_at Phosphoglycerate kinase 1 PGK1 4.871 203987_at Frizzled homolog 6 (Drosophila) FZD6 7.109 220199_s_at Hypothetical protein FLJ12806 FLJ12806 7.295 221428_s_at Transducin (beta)-like 1X-linked receptor 1 TBL1XR1 5.998

30 208925_at Chromosome 3 open reading frame 4 C3orf4 4.494 202089_s_at Solute carrier family 39 (zinc transporter), member 6 SLC39A6 7.672 224996_at Hypothetical protein MGC34646 MGC34646 5.235 210896_s_at Aspartate beta-hydroxylase ASPH 4.035 212040_at Trans-golgi network protein 2 TGOLN2 5.823 222549_at Claudin 1 CLDN1 5.197 216841_s_at Superoxide dismutase 2, mitochondrial SOD2 5.89 215223_s_at Superoxide dismutase 2, mitochondrial SOD2 6.179 224847_at Cyclin-dependent kinase 6 CDK6 5.324 231899_at KIAA1726 protein KIAA1726 6.947 209015_s_at DnaJ (Hsp40) homolog, subfamily B, member 6 DNAJB6 4.069 1563182_at CDNA clone IMAGE:4796641, partial cds --- 8.702 223138_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 36 DHX36 5.838 208859_s_at Alpha thalassemia/mental retardation syndrome X-linked ATRX 5.296 219507_at BM-011 protein MGC12197 7.599 208965_s_at Interferon, gamma-inducible protein 16 IFI16 6.003 239002_at Asp (abnormal spindle)-like, microcephaly associated (Drosophila) ASPM 5.581 210180_s_at Splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila) SFRS10 5.584 235266_at ATPase family, AAA domain containing 2 ATAD2 6.781 1555772_a_at Cell division cycle 25A CDC25A 5.991 235425_at Shugoshin-like 2 (S. pombe) SGOL2 4.687 204324_s_at Golgi phosphoprotein 4 GOLPH4 7.328 213668_s_at SRY (sex determining region Y)-box 4 SOX4 5.768 234326_at ------5.943 1553186_x_at RAS and EF hand domain containing RASEF 4.189 214055_x_at HBxAg transactivated protein 2 XTP2 4.427 219221_at Hypothetical protein FLJ35036 FLJ35036 4.933 227740_at Kinase interacting with leukemia-associated gene () KIS 5.516 242853_at ------5.591 236879_at ------4.802 226763_at SEC14 and domains 1 SESTD1 6.542 205091_x_at RecQ protein-like (DNA helicase Q1-like) RECQL 6.898 212917_x_at RecQ protein-like (DNA helicase Q1-like) RECQL 9.013 208809_s_at Chromosome 6 open reading frame 62 C6orf62 7.699 235003_at Kinase interacting with leukemia-associated gene (stathmin) KIS 8.376 225267_at Karyopherin alpha 4 (importin alpha 3) KPNA4 7.001 224642_at Hypothetical protein DKFZp761B1514 DKFZp761B1514 7.053 212720_at Poly(A) polymerase alpha PAPOLA 7.048 218349_s_at Zwilch FLJ10036 6.612 1555797_a_at Actin related protein 2/3 complex, subunit 5, 16kDa ARPC5 9.323 208670_s_at CREBBP/EP300 inhibitor 1 CRI1 6.375 224595_at CDW92 antigen CDW92 7.698 1555948_s_at Chromosome 9 open reading frame 10 C9orf10 6.561 201456_s_at BUB3 budding uninhibited by benzimidazoles 3 homolog (yeast) BUB3 6.351 222850_s_at Hypothetical protein FLJ14281 FLJ14281 5.958 201151_s_at Muscleblind-like (Drosophila) MBNL1 4.411 1558111_at Muscleblind-like (Drosophila) MBNL1 4.347 217299_s_at Nijmegen breakage syndrome 1 (nibrin) NBS1 7.282 222420_s_at Ubiquitin-conjugating enzyme E2H (UBC8 homolog, yeast) UBE2H 5.389 222679_s_at RP42 homolog RP42 5.572 209678_s_at Protein kinase C, iota PRKCI 5.041 212702_s_at Bicaudal D homolog 2 (Drosophila) BICD2 5.735 225100_at F-box protein 45 FBXO45 10.226 225099_at F-box protein 45 FBXO45 9.08 200598_s_at Tumor rejection antigen (gp96) 1 TRA1 6.83 211968_s_at Heat shock 90kDa protein 1, alpha HSPCA 5.912 215780_s_at SET translocation (myeloid leukemia-associated) SET 6.95 200900_s_at Mannose-6-phosphate receptor (cation dependent) M6PR 6.919 222619_at Zinc finger protein 281 ZNF281 7.459 200616_s_at KIAA0152 gene product KIAA0152 6.459 216449_x_at Tumor rejection antigen (gp96) 1 TRA1 6.388 201901_s_at YY1 YY1 4.841 200607_s_at RAD21 homolog (S. pombe) RAD21 5.937 223254_s_at KIAA1333 KIAA1333 6.662 229115_at , cytoplasmic, heavy polypeptide 1 DNCH1 5.704 222633_at Transducin (beta)-like 1X-linked receptor 1 TBL1XR1 5.617

31 212468_at Sperm associated antigen 9 SPAG9 4.749 212107_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 9 DHX9 5.686 209024_s_at Synaptotagmin binding, cytoplasmic RNA interacting protein SYNCRIP 3.913 209127_s_at Squamous cell carcinoma antigen recognised by T cells 3 SART3 5.556 201946_s_at Chaperonin containing TCP1, subunit 2 (beta) CCT2 5.412 1557910_at Heat shock 90kDa protein 1, beta HSPCB 4.941 209896_s_at Protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) PTPN11 4.286 218859_s_at Chromosome 20 open reading frame 6 C20orf6 5.754 242665_at Forming-like 2 FMNL2 5.803 1555920_at Chromobox homolog 3 (HP1 gamma homolog, Drosophila) CBX3 6.158 200907_s_at Paladin KIAA0992 5.024 209529_at Phosphatidic acid phosphatase type 2C PPAP2C 5.79 223038_s_at open reading frame 14 C12orf14 5.916 202071_at Syndecan 4 (amphiglycan, ryudocan) SDC4 4.49 207983_s_at Stromal antigen 2 STAG2 4.41 209023_s_at Stromal antigen 2 STAG2 3.915 210371_s_at Retinoblastoma binding protein 4 RBBP4 4.155 1556060_a_at KIAA1702 protein KIAA1702 5.081 201737_s_at Membrane-associated RING-CH protein VI MARCH-VI 5.062 212840_at KIAA0794 protein KIAA0794 6.324 236000_s_at ------3.899 201917_s_at Hypothetical protein FLJ10618 FLJ10618 5.256 228545_at ------4.553 236696_at U2-associated SR140 protein SR140 6.058 201918_at Hypothetical protein FLJ10618 FLJ10618 6.374 202412_s_at Ubiquitin specific protease 1 USP1 5.642 227748_at Kynurenine aminotransferase III KAT3 3.92 200956_s_at Structure specific recognition protein 1 SSRP1 6.067 208974_x_at Karyopherin (importin) beta 1 KPNB1 4.344 208765_s_at Heterogeneous nuclear ribonucleoprotein R HNRPR 5.219 1566509_s_at F-box protein 9 FBXO9 4.277 203319_s_at Zinc finger protein 148 (pHZ-52) ZNF148 6.074 222158_s_at CGI-146 protein PNAS-4 4.449 223139_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 36 DHX36 6.392 231716_at Membrane associated DNA binding protein MNAB 5.663 224687_at repeat and IBR domain containing 1 ANKIB1 5.711 225127_at KIAA1423 KIAA1423 5.331 236381_s_at WD repeat domain 8 WDR8 4.862 224578_at RCC1-like TD-60 5.329 212300_at Taxilin DKFZp451J0118 5.141 208663_s_at Tetratricopeptide repeat domain 3 TTC3 4.695 209932_s_at dUTP pyrophosphatase DUT 4.467 209579_s_at Methyl-CpG binding domain protein 4 MBD4 6.751 227801_at Tripartite motif-containing 59 TRIM59 6.342 210115_at Ribosomal protein L39-like RPL39L 8.181 200748_s_at Ferritin, heavy polypeptide 1 FTH1 5.47 226269_at Ganglioside-induced differentiation-associated protein 1 GDAP1 5.273 205479_s_at Plasminogen activator, urokinase PLAU 12.455 212501_at CCAAT/enhancer binding protein (C/EBP), beta CEBPB 8.167 219474_at Hypothetical protein FLJ23186 FLJ23186 11.696 203313_s_at TGFB-induced factor (TALE family homeobox) TGIF 7.62 218396_at Vacuolar protein sorting 13C (yeast) VPS13C 6.207 225512_at Hypothetical protein FLJ35036 FLJ35036 5.963 226756_at Hypothetical protein FLJ36031 FLJ36031 7.124 212820_at Rabconnectin-3 RC3 6.165 209267_s_at Solute carrier family 39 (zinc transporter), member 8 SLC39A8 4.577 Regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing 218352_at RCBTB1 4.396 protein 1 202052_s_at Retinoic acid induced 14 RAI14 7.838 203362_s_at MAD2 mitotic arrest deficient-like 1 (yeast) MAD2L1 6.649 219148_at T-LAK cell-originated protein kinase TOPK 5.779 203302_at Deoxycytidine kinase DCK 5.402 207332_s_at Transferring receptor (p90, CD71) TFRC 6.601 204900_x_at Sin3-associated polypeptide, 30kDa SAP30 4.865 229551_x_at Zinc finger protein 367 ZNF367 6.634 222848_at protein FKSG14 FKSG14 5.959

32 227350_at Helicase, lymphoid-specific HELLS 4.818 204146_at RAD51 associated protein 1 RAD51AP1 7.248 205034_at Cyclin E2 CCNE2 6.334 222680_s_at RA-regulated nuclear matrix-associated protein RAMP 9.935 218585_s_at RA-regulated nuclear matrix-associated protein RAMP 8.186 204023_at (activator 1) 4, 37kDa RFC4 10.081 206316_s_at Kinetochore associated 1 KNTC1 6.249 201555_at MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) MCM3 6.315 221677_s_at Downstream neighbor of SON DONSON 7.605 204510_at CDC7 cell division cycle 7 (S. cerevisiae) CDC7 5.455 225655_at Ubiquitin-like, containing PHD and RING finger domains, 1 UHRF1 6.978 228401_at ------5.901 235609_at ------5.721 226350_at Choroideremia-like (Rab escort protein 2) CHML 7.053 223542_at Ankyrin repeat domain 32 ANKRD32 5.567 212621_at KIAA0286 protein KIAA0286 7.029 228597_at Chromosome 21 open reading frame 45 C21orf45 5.633 226747_at KIAA1344 KIAA1344 4.686 204444_at family member 11 KIF11 4.511 219918_s_at Asp (abnormal spindle)-like, microcephaly associated (Drosophila) ASPM 5.974 203213_at Cell division cycle 2, G1 to S and G2 to M CDC2 7.823 201664_at SMC4 structural maintenance of 4-like 1 (yeast) SMC4L1 6.355 201663_s_at SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SMC4L1 5.918 226980_at DEP domain containing 1B DEPDC1B 6.988 218542_at Chromosome 10 open reading frame 3 C10orf3 6.852 222608_s_at Anillin, actin binding protein (scraps homolog, Drosophila) ANLN 6.461 228033_at transcription factor 7 E2F7 7.588 223381_at Cell division cycle associated 1 CDCA1 5.685 225834_at Similar to RIKEN cDNA 2700049P18 gene MGC57827 6.534 236641_at ------7.615 219787_s_at Epithelial cell transforming sequence 2 oncogene ECT2 9.56 202589_at Thymidylate synthetase TYMS 6.925 204162_at Kinetochore associated 2 KNTC2 5.595 201237_at Capping protein (actin filament) muscle Z-line, alpha 2 CAPZA2 3.839 220235_s_at Receptor-interacting factor 1 RIF1 5.078 1556283_s_at FGFR1 oncogene partner 2 FGFR1OP2 5.463 224663_s_at Cofilin 2 (muscle) CFL2 4.821 219654_at Protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a PTPLA 5.12 204992_s_at Profiling 2 PFN2 8.819 219631_at low density lipoprotein-related protein 12 LRP12 7.091 220253_s_at low density lipoprotein-related protein 12 LRP12 6.673 201266_at Thioredoxin reductase 1 TXNRD1 8.449 201272_at Aldo-keto reductase family 1, member B1 (aldose reductase) AKR1B1 7.515 202235_at Solute carrier family 16 (monocarboxylic acid transporters), member 1 SLC16A1 8.17 202234_s_at Solute carrier family 16 (monocarboxylic acid transporters), member 1 SLC16A1 7.432 209900_s_at Solute carrier family 16 (monocarboxylic acid transporters), member 1 SLC16A1 8.308 202236_s_at Solute carrier family 16 (monocarboxylic acid transporters), member 1 SLC16A1 5.157 203695_s_at Deafness, autosomal dominant 5 DFNA5 7.671 222433_at Enabled homolog (Drosophila) ENAH 8.335 217820_s_at Enabled homolog (Drosophila) ENAH 9.609 217892_s_at Epithelial protein lost in neoplasm beta EPLIN 6.326 224747_at Hypothetical protein LOC92912 LOC92912 6.475 209576_at Guanine nucleotide binding protein, alpha inhibiting activity polypeptide 1 GNAI1 7.087 223991_s_at N-acetylgalactosaminyltransferase 2 (GalNAc-T2) GALNT2 8.417 217787_s_at N-acetylgalactosaminyltransferase 2 (GalNAc-T2) GALNT2 7.655 223151_at Hypothetical protein MGC2714 MGC2714 7.307 204715_at Pannexin 1 PANX1 8.758 208456_s_at Related RAS viral (r-ras) oncogene homolog 2 RRAS2 8.289 212590_at Related RAS viral (r-ras) oncogene homolog 2 RRAS2 6.289 212365_at Myosin IB MYO1B 6.522 1555420_a_at Kruppel-like factor 7 (ubiquitous) KLF7 8.994 202693_s_at Serine/threonine kinase 17a (apoptosis-inducing) STK17A 7.643 204527_at Myosin VA (heavy polypeptide 12, myoxin) MYO5A 7.895 226184_at Forming-like 2 FMNL2 6.979 213139_at Snail homolog 2 (Drosophila) SNAI2 7.997 235072_s_at ------6.276

33 225806_at Jub, ajuba homolog (Xenopus laevis) JUB 5.689 203510_at Met proto-oncogene (hepatocyte growth factor receptor) MET 9.357 212364_at Myosin IB MYO1B 11.915 226609_at Discoidin, CUB and LCCL domain containing 1 DCBLD1 9.18 225520_at Formyltetrahydrofolate synthetase domain containing 1 FTHFSDC1 10.543 202856_s_at Solute carrier family 16 (monocarboxylic acid transporters), member 3 SLC16A3 5.584 217763_s_at RAB31, member RAS oncogene family RAB31 6.007 217764_s_at RAB31, member RAS oncogene family RAB31 6.348 217762_s_at RAB31, member RAS oncogene family RAB31 7.531 213988_s_at Spermidine/spermine N1-acetyltransferase SAT 6.036 224917_at Likely ortholog of rat vacuole membrane protein 1 VMP1 5.328 213262_at Spastic ataxia of Charlevoix-Saguenay (sacsin) SACS 5.576 203196_at ATP-binding cassette, sub-family C (CFTR/MRP), member 4 ABCC4 5.138 225295_at Solute carrier family 39 (zinc transporter), member 10 SLC39A10 5.223 211953_s_at RAN binding protein 5 RANBP5 5.191 209406_at BCL2-associated athanogene 2 BAG2 7.786 201109_s_at Thrombospondin 1 THBS1 5.952 202558_s_at Stress 70 protein chaperone, microsome-associated, 60kDa STCH 5.558 221561_at Sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1 SOAT1 8.112 223079_s_at Glutaminase GLS 6.923 221510_s_at Glutaminase GLS 6.791 225946_at Chromosome 12 open reading frame 2 C12orf2 5.213 223519_at ------5.553 225665_at Sterile alpha motif and leucine zipper containing kinase AZK ZAK 5.711 232231_at Runt-related transcription factor 2 RUNX2 4.516 223065_s_at STARD3 N-terminal like STARD3NL 5.413 202644_s_at Tumor necrosis factor, alpha-induced protein 3 TNFAIP3 5.668 202643_s_at Tumor necrosis factor, alpha-induced protein 3 TNFAIP3 10.295 204924_at Toll-like receptor 2 TLR2 8.831 209949_at Neutrophil cytosolic factor 2 (65kDa, chronic granulomatous disease, autosomal 2) NCF2 8.81 37512_at 3-hydroxysteroid epimerase RODH 6.825 225227_at Homo sapiens, clone IMAGE:5299642, mRNA --- 8.423 206675_s_at SKI-like SKIL 7.898 204779_s_at Homeo box B7 HOXB7 7.537 216973_s_at Homeo box B7 HOXB7 8.32 214806_at Bicaudal D homolog 1 (Drosophila) BICD1 8.64 231964_at MRNA; cDNA DKFZp564H1663 (from clone DKFZp564H1663) --- 6.811 201417_at SRY (sex determining region Y)-box 4 SOX4 8.552 218618_s_at Factor for adipocyte differentiation 104 FAD104 10.481 238841_at Protein tyrosine phosphatase domain containing 1 PTPDC1 10.321 241706_at Copine VIII CPNE8 7.88 222634_s_at Transducin (beta)-like 1X-linked receptor 1 TBL1XR1 7.507 213457_at Malignant fibrous histiocytoma amplified sequence 1 MFHAS1 9.34 225478_at Malignant fibrous histiocytoma amplified sequence 1 MFHAS1 9.269 222258_s_at SH3-domain binding protein 4 SH3BP4 8.87 219557_s_at Nuclear receptor interacting protein 3 NRIP3 9.152 210845_s_at Plasminogen activator, urokinase receptor PLAUR 8.37 200644_at MARCKS-like protein MLP 9.476 206307_s_at FOXD1 8.538 239138_at ------6.076 209295_at Tumor necrosis factor receptor superfamily, member 10b TNFRSF10B 6.404 201416_at SRY (sex determining region Y)-box 4 SOX4 6.696 208942_s_at Translocation protein 1 TLOC1 6.297 214104_at G protein-coupled receptor 161 GPR161 5.346 208964_s_at Fatty acid desaturase 1 FADS1 9.641 208962_s_at Fatty acid desaturase 1 FADS1 8.126 226936_at CDNA clone IMAGE:4452583, partial cds --- 6.269 216237_s_at MCM5 minichromosome maintenance deficient 5, cell division cycle 46 MCM5 6.217 201755_at MCM5 minichromosome maintenance deficient 5, cell division cycle 46 MCM5 6.482 202107_s_at MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae) MCM2 9.025 203262_s_at Family with sequence similarity 50, member A FAM50A 6.295 218308_at Transforming, acidic coiled-coil containing protein 3 TACC3 6.192 209053_s_at Wolf-Hirschhorn syndrome candidate 1 WHSC1 5.307 221521_s_at DNA replication complex GINS protein PSF2 Pfs2 6.47 212022_s_at Antigen identified by monoclonal antibody Ki-67 MKI67 5.736 202870_s_at CDC20 cell division cycle 20 homolog (S. cerevisiae) CDC20 5.056

34 205449_at Likely ortholog of mouse Sac3 homology domain 1 (S. cerevisiae) SHD1 4.198 235521_at Homeo box A3 HOXA3 7.285 225841_at Hypothetical protein FLJ30525 FLJ30525 8.201 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, 202983_at SMARCA3 8.478 subfamily a, member 3 213836_s_at WD40 repeat protein Interacting with phosphoInositides of 49kDa WIPI49 5.187 203827_at WD40 repeat protein Interacting with phosphoInositides of 49kDa WIPI49 5.645 218340_s_at Hypothetical protein FLJ10808 FLJ10808 4.456 222774_s_at Neuropilin (NRP) and tolloid (TLL)-like 2 NETO2 5.172 218888_s_at Neuropilin (NRP) and tolloid (TLL)-like 2 NETO2 6.504 205063_at Survival of motor neuron protein interacting protein 1 SIP1 5.785 214830_at Solute carrier family 38, member 6 SLC38A6 9.649 227133_at Chromosome X open reading frame 39 CXorf39 5.695 205246_at Peroxisome biogenesis factor 13 PEX13 5.382 1556009_at Peroxisome biogenesis factor 13 PEX13 4.82 202543_s_at Glia maturation factor, beta GMFB 4.849 214697_s_at ROD1 regulator of differentiation 1 (S. pombe) ROD1 4.375 200798_x_at Myeloid cell leukemia sequence 1 (BCL2-related) MCL1 4.252 212460_at Chromosome 14 open reading frame 147 C14orf147 5.911 204030_s_at Schwannomin interacting protein 1 SCHIP1 10.445 235391_at Similar to CG6405 gene product LOC137392 7.606 202016_at Mesoderm specific transcript homolog (mouse) MEST 6.294 225018_at Spire homolog 1 (Drosophila) SPIRE1 5.163 219201_s_at Twisted gastrulation homolog 1 (Drosophila) TWSG1 7.764 229865_at PRO1310 --- 8.318 222692_s_at Factor for adipocyte differentiation 104 FAD104 15.237 222693_at Factor for adipocyte differentiation 104 FAD104 11.639 212110_at Solute carrier family 39 (zinc transporter), member 14 SLC39A14 6.612 238787_at ------5.61 230793_at ------6.776 203203_s_at HIV-1 rev binding protein 2 HRB2 6.532 204956_at Methylthioadenosine MTAP 7.81 219959_at Molybdenum cofactor sulfurase MOCOS 7.479 228365_at Copine VIII CPNE8 7.108 225114_at Alkylglycerone phosphate synthase AGPS 7.603 225113_at Alkylglycerone phosphate synthase AGPS 6.628 205401_at Alkylglycerone phosphate synthase AGPS 6.327 219493_at SHC SH2-domain binding protein 1 SHCBP1 7.969 219161_s_at Chemokine-like factor CKLF 5.113 223451_s_at Chemokine-like factor CKLF 5.548 225297_at Coiled-coil domain containing 5 (spindle associated) CCDC5 6.198 208687_x_at Heat shock 70kDa protein 8 HSPA8 4.829 224187_x_at Heat shock 70kDa protein 8 HSPA8 4.888 201274_at Proteasome (prosome, macropain) subunit, alpha type, 5 PSMA5 6.451 202675_at Succinate dehydrogenase complex, subunit B, iron sulfur (Ip) SDHB 4.81 221531_at Recombination protein REC14 REC14 3.793 201923_at Peroxiredoxin 4 PRDX4 5.056 1557915_s_at Glutathione S-transferase omega 1 GSTO1 6.198 222714_s_at Lactamase, beta 2 LACTB2 8.511 203560_at Gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase) GGH 9.176 218049_s_at Mitochondrial ribosomal protein L13 MRPL13 7.452 218027_at Mitochondrial ribosomal protein L15 MRPL15 6.517 227787_s_at Thyroid associated protein 6 THRAP6 7.387 213246_at Chromosome 14 open reading frame 109 C14orf109 6.789 208029_s_at Lysosomal associated protein transmembrane 4 beta LAPTM4B 7.748 212788_x_at Ferritin, light polypeptide FTL 6.433 222988_s_at Transmembrane protein 9 TMEM9 5.069 218459_at Torsin family 3, member A TOR3A 5.529 225583_at UDP-glucuronate decarboxylase 1 UXS1 7.278 200921_s_at B-cell translocation gene 1, anti-proliferative BTG1 6.178 202243_s_at Proteasome (prosome, macropain) subunit, beta type, 4 PSMB4 5.064 225390_s_at Kruppel-like factor 13 KLF13 4.763 200903_s_at S-adenosylhomocysteine hydrolase AHCY 3.91 213104_at Hypothetical protein MGC24381 MGC24381 4.814 208074_s_at Adaptor-related protein complex 2, sigma 1 subunit AP2S1 3.985 222155_s_at G protein-coupled receptor 172A GPR172A 5.491

35 218187_s_at Hypothetical protein FLJ20989 FLJ20989 6.73 208308_s_at Glucose phosphate isomerase GPI 5.037 226621_at ------9.764 203476_at Trophoblast glycoprotein TPBG 10.485 225314_at OCIA domain containing 2 OCIAD2 9.235 202733_at Procollagen-proline, 2-oxoglutarate 4-dioxygenase, alpha polypeptide II P4HA2 8.406 225898_at Hypothetical protein FLJ12953 similar to Mus musculus D3Mm3e FLJ12953 7.082 214512_s_at Activated RNA polymerase II transcription cofactor 4 PC4 6.093 201954_at Actin related protein 2/3 complex, subunit 1B, 41kDa ARPC1B 8.204 201462_at Secernin 1 SCRN1 8.38 204647_at Homer homolog 3 (Drosophila) HOMER3 9.086 1554079_at N-acetylgalactosaminyltransferase-like 4 GALNTL4 6.421 203417_at Microfibrillar-associated protein 2 MFAP2 6.863 227256_at Ubiquitin specific protease 31 USP31 6.466 227249_at Myosin, heavy polypeptide 11, smooth muscle MYH11 8.926 220643_s_at Fas apoptotic inhibitory molecule FAIM 6.843 1558956_s_at KIAA1374 protein KIAA1374 4.371 203164_at Solute carrier family 33 (acetyl-CoA transporter), member 1 SLC33A1 4.972 227139_s_at Hermansky-Pudlak syndrome 3 HPS3 6.281 205548_s_at BTG family, member 3 BTG3 5.846 230352_at ------5.554 203401_at Phosphoribosyl pyrophosphate synthetase 2 PRPS2 7.051 211208_s_at Calcium/calmodulin-dependent serine protein kinase (MAGUK family) CASK 8.542 227156_at Trinucleotide repeat containing 8 TNRC8 6.322 225021_at Zinc finger protein 532 ZNF532 5.492 209360_s_at Runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) RUNX1 7.676 213951_s_at GT198, complete ORF HUMGT198A 6.402 212730_at Desmuslin DMN 6.276 228987_at ------5.534 212523_s_at KIAA0146 protein KIAA0146 4.904 201970_s_at Nuclear autoantigenic sperm protein (histone-binding) NASP 5.071 212200_at KIAA0692 protein KIAA0692 6.663 216952_s_at B2 LMNB2 5.319 226715_at Homo sapiens, clone IMAGE:4747087, mRNA --- 5.284 200867_at Zinc finger protein 313 ZNF313 5.398 231772_x_at Centromere protein H CENPH 7.322 222036_s_at MCM4 minichromosome maintenance deficient 4 (S. cerevisiae) MCM4 9.926 222037_at MCM4 minichromosome maintenance deficient 4 (S. cerevisiae) MCM4 8.192 224720_at Mindbomb homolog 1 (Drosophila) MIB1 5.704 208694_at Protein kinase, DNA-activated, catalytic polypeptide PRKDC 7.197 210543_s_at Protein kinase, DNA-activated, catalytic polypeptide PRKDC 6.035 1552619_a_at Anillin, actin binding protein (scraps homolog, Drosophila) ANLN 6.644 218782_s_at ATPase family, AAA domain containing 2 ATAD2 8.322 222740_at ATPase family, AAA domain containing 2 ATAD2 7.128 221245_s_at open reading frame 31 C2orf31 4.958 224764_at Rho GTPase activating protein 21 ARHGAP21 6.038 226545_at CD109 antigen (Gov platelet alloantigens) CD109 4.741 222572_at Protein phosphatase 2C, magnesium-dependent, catalytic subunit PPM2C 6.594 222581_at Xenotropic and polytropic retrovirus receptor XPR1 8.774 1554020_at Bicaudal D homolog 1 (Drosophila) BICD1 8.274 201920_at Solute carrier family 20 (phosphate transporter), member 1 SLC20A1 5.109 202043_s_at Spermine synthase SMS 8.378 223358_s_at 7A PDE7A 8.034 226463_at ------4.788 202679_at Niemann-Pick disease, type C1 NPC1 4.582 212445_s_at Neural precursor cell expressed, developmentally down-regulated 4-like NEDD4L 5.186 200762_at Dihydropyrimidinase-like 2 DPYSL2 4.555 225045_at KIAA1212 KIAA1212 6.251 225710_at CDNA FLJ34013 fis, clone FCBBF2002111 --- 5.352 202651_at Family with sequence similarity 34, member A FAM34A 5.684 212981_s_at KIAA0738 gene product KIAA0738 5.186 229075_at ------6.421 215629_s_at Deleted in lymphocytic leukemia, 2 DLEU2 5.343 225644_at Hypothetical protein FLJ33814 FLJ33814 4.178 212579_at KIAA0650 protein KIAA0650 5.235 213017_at Abhydrolase domain containing 3 ABHD3 5.331

36 224521_s_at Hypothetical protein MGC13183 /// hypothetical protein MGC13183 MGC13183 4.754 222201_s_at CASP8 associated protein 2 CASP8AP2 4.541 218979_at Chromosome 9 open reading frame 76 C9orf76 6.389 213372_at Progestin and adipoQ receptor family member III PAQR3 5.139 225406_at Twisted gastrulation homolog 1 (Drosophila) TWSG1 5.598 225904_at LOC126731 LOC126731 6.393 206364_at Kinesin family member 14 KIF14 8.418 202749_at Tryptophan rich basic protein WRB 4.617 218772_x_at Chromosome 9 open reading frame 87 C9orf87 7.246 202557_at Stress 70 protein chaperone, microsome-associated, 60kDa STCH 5.664 209451_at TRAF family member-associated NFKB activator TANK 5.688 212918_at RecQ protein-like (DNA helicase Q1-like) RECQL 5.827 225174_at DnaJ (Hsp40) homolog, subfamily C, member 10 DNAJC10 5.53 213294_at ------8.743 218602_s_at Family with sequence similarity 29, member A FAM29A 6.204 235158_at Hypothetical protein FLJ14803 FLJ14803 7.647 222685_at Family with sequence similarity 29, member A FAM29A 5.806 227539_at Guanine nucleotide binding protein (G protein), alpha 13 GNA13 5.85 212792_at KIAA0877 protein KIAA0877 7.108 228812_at ------7.158 228201_at ADP-ribosylation factor-like 2-like 1 ARL2L1 5.333 217901_at Desmoglein 2 DSG2 9.014 223471_at RAB3A interacting protein (rabin3) RAB3IP 8.99 202963_at Regulatory factor X, 5 (influences HLA class II expression) RFX5 5.619 222512_at NEDD8 ultimate buster-1 NYREN18 6.671 208091_s_at Hypothetical protein DKFZp564K0822 DKFZP564K0822 6.117 201422_at Interferon, gamma-inducible protein 30 IFI30 8.42 213698_at Zinc finger protein 258 ZNF258 6.883 203414_at Monocyte to macrophage differentiation-associated MMD 9.813 214130_s_at Phosphodiesterase 4D interacting protein (myomegalin) PDE4DIP 6.27 214129_at Phosphodiesterase 4D interacting protein (myomegalin) PDE4DIP 6.637 223085_at Ring finger protein 19 RNF19 7.523 203066_at B cell RAG associated protein GALNAC4S-6ST 6.909 227565_at ------7.296 1552417_a_at Neural precursor cell expressed, developmentally down-regulated 1 NEDD1 8.317 234984_at Neural precursor cell expressed, developmentally down-regulated 1 NEDD1 7.547 1558105_a_at Homo sapiens, Similar to LOC169932, clone IMAGE:4499203, mRNA --- 7.408 200704_at Lipopolysaccharide-induced TNF factor LITAF 7.509 200706_s_at Lipopolysaccharide-induced TNF factor LITAF 7.417 209524_at Hepatoma-derived growth factor, related protein 3 HDGFRP3 9.239 219099_at Chromosome 12 open reading frame 5 C12orf5 8.081 226001_at Kelch-like 5 (Drosophila) KLHL5 8.381 202351_at Integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51) ITGAV 9.468 218401_s_at Zinc finger protein 281 ZNF281 7.64 217771_at Golgi phosphoprotein 2 GOLPH2 8.002 202087_s_at Cathepsin L CTSL 8.673 225799_at Hypothetical protein MGC4677 MGC4677 8.733 219479_at KDEL (Lys-Asp-Glu-Leu) containing 1 KDELC1 7.562 211981_at Collagen, type IV, alpha 1 COL4A1 8.359 205120_s_at Sarcoglycan, beta (43kDa dystrophin-associated glycoprotein) SGCB 6.33 209585_s_at Multiple inositol polyphosphate histidine phosphatase, 1 MINPP1 8.862 236249_at ------8.425 204140_at Tyrosylprotein sulfotransferase 1 TPST1 9.237 Transcribed , moderately similar to XP_215486.2 similar to RIKEN cDNA 227628_at --- 8.13 2310016C16 [Rattus norvegicus] 207714_s_at Serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1 SERPINH1 8.978 221782_at DnaJ (Hsp40) homolog, subfamily C, member 10 DNAJC10 6.253 221781_s_at DnaJ (Hsp40) homolog, subfamily C, member 10 DNAJC10 7.028 227295_at IKK interacting protein IKIP 7.526 201560_at Chloride intracellular channel 4 CLIC4 9.55 223463_at RAB23, member RAS oncogene family RAB23 8.631 228785_at Zinc finger protein 281 ZNF281 8.486 222235_s_at Chondroitin sulfate GalNAcT-2 GALNACT-2 7.008 218871_x_at Chondroitin sulfate GalNAcT-2 GALNACT-2 6.191 224759_s_at Hypothetical protein MGC17943 MGC17943 7.292 225579_at Chromosome 2 open reading frame 22 C2orf22 4.579

37 208788_at ELOVL family member 5, elongation of long chain fatty acids ELOVL5 6.16 203935_at Activin A receptor, type I ACVR1 7.616 201889_at Family with sequence similarity 3, member C FAM3C 6.675 225158_at Mitochondrial elongation factor G1 EFG1 6.962 222412_s_at Signal sequence receptor, gamma (translocon-associated protein gamma) SSR3 8.673 221477_s_at Transcribed locus, weakly similar to NP_079012.2 gasdermin domain containing 1 --- 5.996 222035_s_at Poly(A) polymerase alpha PAPOLA 4.86 203166_at Craniofacial development protein 1 CFDP1 5.497 218224_at Paraneoplastic antigen MA1 PNMA1 6.71 210983_s_at MCM7 minichromosome maintenance deficient 7 (S. cerevisiae) MCM7 5.448 200072_s_at Heterogeneous nuclear ribonucleoprotein M HNRPM 5.172 200959_at Fusion (involved in t(12;16) in malignant liposarcoma) FUS 5.065 204050_s_at Clathrin, light polypeptide (Lca) CLTA 4.983 200837_at B-cell receptor-associated protein 31 BCAP31 4.661 208649_s_at Valosin-containing protein VCP 4.718 202671_s_at Pyridoxal (pyridoxine, vitamin B6) kinase PDXK 4.744 213026_at APG12 autophagy 12-like (S. cerevisiae) APG12L 5.622 203048_s_at KIAA0372 KIAA0372 5.801 212506_at Phosphatidylinositol binding clathrin assembly protein PICALM 4.77 200775_s_at Heterogeneous nuclear ribonucleoprotein K HNRPK 5.021 209669_s_at PAI-1 mRNA-binding protein PAI-RBP1 6.024 200728_at ARP2 actin-related protein 2 homolog (yeast) ACTR2 5.295 224914_s_at Cytokine induced protein 29 kDa CIP29 4.494 202483_s_at RAN binding protein 1 RANBP1 8.57 214437_s_at Serine hydroxymethyltransferase 2 (mitochondrial) SHMT2 5.896 201478_s_at 1, DKC1 6.689 211501_s_at Eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa EIF3S9 4.657 208627_s_at sensitive element binding protein 1 NSEP1 6.97 200064_at Heat shock 90kDa protein 1, beta /// heat shock 90kDa protein 1, beta HSPCB 4.657 200751_s_at Heterogeneous nuclear ribonucleoprotein C (C1/C2) HNRPC 4.036 201267_s_at Proteasome (prosome, macropain) 26S subunit, ATPase, 3 PSMC3 4.566 212878_s_at Kinesin 2 60/70kDa KNS2 4.489 1555427_s_at Synaptotagmin binding, cytoplasmic RNA interacting protein SYNCRIP 5.512 1554678_s_at Heterogeneous nuclear ribonucleoprotein D-like HNRPDL 5.776 209067_s_at Heterogeneous nuclear ribonucleoprotein D-like HNRPDL 5.211 Tyrosine 3-/tryptophan 5-monooxygenase activation protein, beta 217717_s_at YWHAB 4.912 polypeptide 213798_s_at CAP, adenylate cyclase-associated protein 1 (yeast) CAP1 5.576 208689_s_at Ribophorin II RPN2 5.597 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta 208743_s_at YWHAB 5.541 polypeptide 222975_s_at Upstream of NRAS UNR 4.95 211969_at Heat shock 90kDa protein 1, alpha HSPCA 7.593 214730_s_at Golgi apparatus protein 1 GLG1 7.545 219031_s_at ------6.176 221553_at Implantation-associated protein DKFZp564K142 5.611 209226_s_at Transportin 1 TNPO1 4.756 208828_at Polymerase (DNA directed), epsilon 3 (p17 subunit) POLE3 4.943 208675_s_at Dolichyl-diphosphooligosaccharide-protein DDOST 6.097 210131_x_at ------5.824 213175_s_at Small nuclear ribonucleoprotein polypeptides B and B1 SNRPB 4.551 201411_s_at Pleckstrin homology domain containing, family B (evectins) member 2 PLEKHB2 5.847 221473_x_at Tumor differentially expressed 1 TDE1 4.996 211769_x_at Tumor differentially expressed 1 /// tumor differentially expressed 1 TDE1 4.905 203497_at PPAR binding protein PPARBP 4.127 200967_at Peptidylprolyl isomerase B (cyclophilin B) PPIB 5.454 200968_s_at Peptidylprolyl isomerase B (cyclophilin B) PPIB 5.153 223020_at Cisplatin resistance related protein CRR9p CRR9 5.959 214741_at Zinc finger protein 131 (clone pHZ-10) ZNF131 5.956 225716_at ------5.206 208846_s_at Voltage-dependent anion channel 3 VDAC3 4.276 209471_s_at Farnesyltransferase, CAAX box, alpha FNTA 4.409 214949_at Similar to family with sequence similarity 9, member C --- 5.247 222559_s_at Hypothetical protein FLJ10656 P15RS 5.008 1558233_s_at Activating transcription factor 1 ATF1 4.611 218640_s_at Pleckstrin homology domain containing, family F (with FYVE domain) member 2 PLEKHF2 5.521

38 205573_s_at Sorting nexin 7 SNX7 5.504 208669_s_at CREBBP/EP300 inhibitor 1 CRI1 4.375 208671_at Tumor differentially expressed 2 TDE2 4.279 212530_at NIMA (never in mitosis gene a)-related kinase 7 NEK7 5.303 212887_at Sec23 homolog A (S. cerevisiae) SEC23A 5.805 202266_at TRAF and TNF receptor associated protein TTRAP 6.974 218195_at Chromosome 6 open reading frame 211 C6orf211 6.377 209307_at ------5.372 225144_at Bone morphogenetic protein receptor, type II (serine/threonine kinase) BMPR2 5.047 225658_at Hypothetical protein LOC339745 LOC339745 6.48 235940_at Chromosome 9 open reading frame 64 C9orf64 5.271 208848_at Alcohol dehydrogenase 5 (class III), chi polypeptide ADH5 5.657 1553113_s_at Cyclin-dependent kinase 8 CDK8 4.52 201485_s_at Reticulocalbin 2, EF-hand calcium binding domain RCN2 7.165 201486_at Reticulocalbin 2, EF-hand calcium binding domain RCN2 6.196 221452_s_at Transmembrane protein 14B /// transmembrane protein 14B TMEM14B 5.66 1555780_a_at Ras homolog enriched in brain RHEB 6.777 203138_at Histone acetyltransferase 1 HAT1 7.788 209580_s_at Methyl-CpG binding domain protein 4 MBD4 6.386 218172_s_at Der1-like domain family, member 1 DERL1 6.161 200052_s_at Interleukin enhancer binding factor 2, 45kDa ILF2 5.177 201529_s_at , 70kDa RPA1 4.642 224787_s_at RAB18, member RAS oncogene family RAB18 3.762 212749_s_at Ring finger and CHY zinc finger domain containing 1 RCHY1 3.848 209095_at Dihydrolipoamide dehydrogenase DLD 4.017 208310_s_at Chromosome 7 open reading frame 28B C7orf28B 4.499 200723_s_at Membrane component, chromosome 11, surface marker 1 M11S1 5.718 222417_s_at Sorting nexin 5 SNX5 6.504 Phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole 201014_s_at PAICS 6.69 succinocarboxamide synthetase 202113_s_at Sorting nexin 2 SNX2 5.048 212038_s_at Voltage-dependent anion channel 1 VDAC1 4.545 208852_s_at Calnexin CANX 5.883 200692_s_at Heat shock 70kDa protein 9B (mortalin-2) HSPA9B 4.633 Transcribed locus, moderately similar to XP_375099.1 hypothetical protein 225435_at --- 4.356 LOC283585 [Homo sapiens] 209882_at Ras-like without CAAX 1 RIT1 4.475 217755_at Hematological and neurological expressed 1 HN1 4.735 223040_at N-acetyltransferase 5 (ARD1 homolog, S. cerevisiae) NAT5 4.22 211671_s_at Nuclear receptor subfamily 3, group C, member 1 () NR3C1 5.931 226050_at Chromosome 13 open reading frame 11 C13orf11 6.084 Procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 207543_s_at P4HA1 7.963 polypeptide I 201636_at ------6.844 205072_s_at X-ray repair complementing defective repair in Chinese hamster cells 4 XRCC4 7.261 221563_at Dual specificity phosphatase 10 DUSP10 5.952 202874_s_at ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1 ATP6V1C1 9.059 202872_at ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1 ATP6V1C1 7.356 201399_s_at Translocation associated membrane protein 1 TRAM1 6.729 218185_s_at Armadillo repeat containing 1 ARMC1 7.256 208097_s_at Thioredoxin domain containing TXNDC 7.058 217811_at Selenoprotein T SELT 6.684 225161_at Mitochondrial elongation factor G1 EFG1 7.497 222393_s_at Mak3 homolog (S. cerevisiae) MAK3 6.901 203165_s_at Solute carrier family 33 (acetyl-CoA transporter), member 1 SLC33A1 6.614 211075_s_at CD47 antigen (Rh-related antigen, integrin-associated signal transducer) CD47 5.441 208767_s_at Lysosomal associated protein transmembrane 4 beta LAPTM4B 7.358 1554679_a_at Lysosomal associated protein transmembrane 4 beta LAPTM4B 5.682 203207_s_at Likely ortholog of chicken chondrocyte protein with a poly-proline region CHPPR 5.733 203208_s_at Likely ortholog of chicken chondrocyte protein with a poly-proline region CHPPR 7.688 222698_s_at Hypothetical protein IMPACT IMPACT 5.858 200973_s_at Transmembrane 4 superfamily member 8 TM4SF8 4.624 200712_s_at -associated protein, RP/EB family, member 1 MAPRE1 8.616 223021_x_at Chromosome 6 open reading frame 55 C6orf55 5.837 223650_s_at Nuclear receptor binding factor 2 NRBF2 7.088 221803_s_at Nuclear receptor binding factor 2 NRBF2 7.581

39 230656_s_at Cirrhosis, autosomal recessive 1A (cirhin) CIRH1A 6.13 218156_s_at Hypothetical protein FLJ10534 FLJ10534 5.011 218193_s_at CGI-141 protein CGI-141 6.794 221676_s_at Coronin, actin binding protein, 1C CORO1C 6.115 200929_at Transmembrane trafficking protein TMP21 5.887 200700_s_at KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 KDELR2 6.032 202195_s_at CGI-100 protein CGI-100 6.035 204203_at CCAAT/enhancer binding protein (C/EBP), gamma CEBPG 7.795 208290_s_at Eukaryotic translation initiation factor 5 EIF5 7.488 208708_x_at Eukaryotic translation initiation factor 5 EIF5 6.363 202918_s_at Preimplantation protein 3 PREI3 4.544 226686_at Transcribed locus, highly similar to NP_080178.1 RIKEN cDNA 1500009M05 gene --- 6.258 226276_at Hypothetical protein MGC23909 MGC23909 5.186 204186_s_at Peptidylprolyl isomerase D (cyclophilin D) PPID 6.197 218699_at RAB7, member RAS oncogene family-like 1 RAB7L1 6.676 210041_s_at Phosphoglucomutase 3 PGM3 5.66 201554_x_at Glycogenin GYG 6.211 201847_at Lipase A, lysosomal acid, cholesterol esterase (Wolman disease) LIPA 5.12 212335_at Glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID) GNS 6.723 203574_at Nuclear factor, interleukin 3 regulated NFIL3 6.729 200838_at Cathepsin B CTSB 6.174 218092_s_at HIV-1 Rev binding protein HRB 6.376 218135_at PTX1 protein PTX1 8.114 228095_at PHD finger protein 14 PHF14 5.997 202906_s_at Nijmegen breakage syndrome 1 (nibrin) NBS1 6.699 228543_at CSRP2 binding protein CSRP2BP 6.387 228544_s_at CSRP2 binding protein CSRP2BP 8.047 226479_at Kelch repeat and BTB (POZ) domain containing 6 KBTBD6 5.91 222765_x_at Chromosome 20 open reading frame 6 C20orf6 5.961 213391_at Hypothetical protein LOC286148 LOC286148 5.614 222654_at Hypothetical protein FLJ20421 FLJ20421 6.816 221020_s_at Mitochondrial folate transporter/carrier MFTC 8.103 204068_at Serine/threonine kinase 3 (STE20 homolog, yeast) STK3 12.322 202904_s_at LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM5 6.695 205361_s_at Prefoldin 4 PFDN4 6.19 208103_s_at Acidic (leucine-rich) nuclear phosphoprotein 32 family, member E ANP32E 7.395 1555501_s_at BM-011 protein MGC12197 8.391 206302_s_at Nudix (nucleoside diphosphate linked moiety X)-type motif 4 NUDT4 6.823 220239_at Kelch-like 7 (Drosophila) KLHL7 5.603 223700_at GAJ protein GAJ 5.963 205394_at CHK1 checkpoint homolog (S. pombe) CHEK1 6.516 205393_s_at CHK1 checkpoint homolog (S. pombe) CHEK1 8.623 203087_s_at Kinesin heavy chain member 2 KIF2 5.457 218911_at YEATS domain containing 4 YEATS4 6.401 218842_at Hypothetical protein FLJ21908 FLJ21908 6.096 225766_s_at Transportin 1 TNPO1 6.001 203177_x_at Transcription factor A, mitochondrial TFAM 5.841 218875_s_at F-box protein 5 FBXO5 6.18 213253_at ------5.155 202413_s_at Ubiquitin specific protease 1 USP1 6.322 219588_s_at More than blood homolog MTB 8.266 218252_at associated protein 2 CKAP2 5.062 225578_at Similar to RIKEN cDNA 2410129H14 --- 7.305 204127_at Replication factor C (activator 1) 3, 38kDa RFC3 5.968 204244_s_at Activator of S phase kinase ASK 9.035 Methylene tetrahydrofolate dehydrogenase (NAD+ dependent), 201761_at MTHFD2 10.01 methenyltetrahydrofolate cyclohydrolase 204240_s_at SMC2 structural maintenance of chromosomes 2-like 1 (yeast) SMC2L1 6.929 220651_s_at MCM10 minichromosome maintenance deficient 10 (S. cerevisiae) MCM10 8.145 221258_s_at Kinesin family member 18A /// kinesin family member 18A KIF18A 9.293 201307_at Septin 11 SEP11 6.279 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, 213859_x_at SMARCA5 7.28 subfamily a, member 5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, 202303_x_at SMARCA5 8.243 subfamily a, member 5 209421_at mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli) MSH2 6.518

40 209520_s_at Nuclear cap binding protein subunit 1, 80kDa NCBP1 6.533 203856_at Vaccinia related kinase 1 VRK1 5.791 213092_x_at DnaJ (Hsp40) homolog, subfamily C, member 9 DNAJC9 6.712 203214_x_at Cell division cycle 2, G1 to S and G2 to M CDC2 6.888 210559_s_at Cell division cycle 2, G1 to S and G2 to M CDC2 7.189 226642_s_at Similar to RIKEN cDNA 2700047N05 LOC134492 5.793 223490_s_at Exosome component 3 EXOSC3 6.288 227916_x_at Exosome component 3 EXOSC3 6.44 223229_at HSPC150 protein similar to ubiquitin-conjugating enzyme HSPC150 6.478 210052_s_at TPX2, microtubule-associated protein homolog (Xenopus laevis) TPX2 8.144 209714_s_at Cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) CDKN3 6.533 1555758_a_at Cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) CDKN3 6.85 209507_at , 14kDa RPA3 6.969 213599_at Opa-interacting protein 5 OIP5 7.94 219555_s_at Uncharacterized bone marrow protein BM039 BM039 6.731 222118_at Uncharacterized bone marrow protein BM039 BM039 9.001 204728_s_at WD repeat and HMG-box DNA binding protein 1 WDHD1 8.196 216228_s_at WD repeat and HMG-box DNA binding protein 1 WDHD1 11.09 214804_at FSH primary response (LRPR1 homolog, rat) 1 FSHPRH1 6.658 203744_at High-mobility group box 3 HMGB3 7.734 223556_at Helicase, lymphoid-specific HELLS 6.581 222843_at Fidgetin-like 1 FIGNL1 5.085 226456_at Hypothetical protein MGC24665 MGC24665 7.446 206102_at KIAA0186 gene product KIAA0186 8.377 219258_at Timeless-interacting protein FLJ20516 6.199 203968_s_at cell division cycle 6 homolog (S. cerevisiae) CDC6 8.628 222606_at ------7.299 235113_at Peptidylprolyl isomerase (cyclophilin)-like 5 PPIL5 7.005 205909_at Polymerase (DNA directed), epsilon 2 (p59 subunit) POLE2 7.091 202580_x_at Forkhead box M1 FOXM1 8.33 203145_at Sperm associated antigen 5 SPAG5 8.148 224753_at Cell division cycle associated 5 CDCA5 8.919 203046_s_at Timeless homolog (Drosophila) TIMELESS 8.985 201697_s_at DNA (cytosine-5-)-methyltransferase 1 DNMT1 6.598 213007_at Hypothetical protein FLJ10719 FLJ10719 7.871 222077_s_at Rac GTPase activating protein 1 RACGAP1 6.36 205339_at TAL1 (SCL) interrupting locus SIL 7.676 218355_at Kinesin family member 4A KIF4A 8.488 209408_at Kinesin family member 2C KIF2C 8.053 204026_s_at ZW10 interactor ZWINT 5.86 218350_s_at Geminin, DNA replication inhibitor GMNN 7.022 204767_s_at Flap structure-specific 1 FEN1 9.248 203209_at Replication factor C (activator 1) 5, 36.5kDa RFC5 7.447 201930_at MCM6 minichromosome maintenance deficient 6 (S. cerevisiae) MCM6 6.531 201202_at Proliferating cell nuclear antigen PCNA 6.935 202911_at mutS homolog 6 (E. coli) MSH6 8.398 207165_at Hyaluronan-mediated motility receptor (RHAMM) HMMR 4.394 204092_s_at Serine/threonine kinase 6 STK6 6.398 208079_s_at Serine/threonine kinase 6 STK6 5.504 228273_at ------5.574 228069_at DUF729 domain containing 1 DUFD1 5.38 204822_at TTK protein kinase TTK 5.39 218662_s_at Chromosome condensation protein G HCAP-G 4.874 218663_at Chromosome condensation protein G HCAP-G 6.772 204641_at NIMA (never in mitosis gene a)-related kinase 2 NEK2 6.574 209172_s_at Centromere protein F, 350/400ka (mitosin) CENPF 5.842 218755_at Kinesin family member 20A KIF20A 4.841 207828_s_at Centromere protein F, 350/400ka (mitosin) CENPF 4.883 201292_at Topoisomerase (DNA) II alpha 170kDa TOP2A 5.241 230165_at ------5.455 228729_at Cyclin B1 CCNB1 4.828 218009_s_at Protein regulator of cytokinesis 1 PRC1 6.473 203755_at BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) BUB1B 5.499 228323_at AF15q14 protein AF15Q14 4.979 201890_at Ribonucleotide reductase M2 polypeptide RRM2 5.88 204825_at Maternal embryonic leucine zipper kinase MELK 7.182

41 202503_s_at KIAA0101 KIAA0101 5.526 204709_s_at Kinesin family member 23 KIF23 7.251 203764_at Discs, large homolog 7 (Drosophila) DLG7 6.32 209642_at BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1 7.016 204962_s_at Centromere protein A, 17kDa CENPA 7.378 204170_s_at CDC28 protein kinase regulatory subunit 2 CKS2 6.022 214710_s_at Cyclin B1 CCNB1 5.005 209773_s_at Ribonucleotide reductase M2 polypeptide RRM2 5.102 224413_s_at BBP-like protein 1 BLP1 7.415 202381_at A disintegrin and metalloproteinase domain 9 (meltrin gamma) ADAM9 6.371 221808_at RAB9A, member RAS oncogene family RAB9A 4.456 223361_at Chromosome 6 open reading frame 115 C6orf115 4.779 216194_s_at Cytoskeleton associated protein 1 CKAP1 4.753 1567214_a_at , desmosome associated protein PNN 4.735 212036_s_at Pinin, desmosome associated protein PNN 3.888 223181_at HSPC154 protein HSPC154 4.527 203880_at COX17 homolog, cytochrome c oxidase assembly protein (yeast) COX17 6.744 218286_s_at Ring finger protein 7 RNF7 6.146 201637_s_at Fragile X mental retardation, autosomal homolog 1 FXR1 8.028 223480_s_at Mitochondrial ribosomal protein L47 MRPL47 8.501 201521_s_at Nuclear cap binding protein subunit 2, 20kDa NCBP2 8.787 200830_at Proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 PSMD2 9.624 225657_at Hypothetical protein BC007882 LOC152217 6.37 218271_s_at Presenilin associated, rhomboid-like PSARL 7.479 214431_at Guanine monphosphate synthetase GMPS 10.068 225268_at Karyopherin alpha 4 (importin alpha 3) KPNA4 7.646 205222_at Enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase EHHADH 6.997 221203_s_at YEATS domain containing 2 YEATS2 7.733 227814_at Hypothetical protein MGC64882 MGC64882 10.157 221536_s_at Hypothetical protein FLJ11301 FLJ11301 6.987 226556_at Homo sapiens, clone IMAGE:4294444, mRNA --- 9.46 218728_s_at HSPC163 protein HSPC163 5.83 238879_at ------5.71 203621_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa NDUFB5 6.353 210907_s_at Programmed cell death 10 PDCD10 6.99 223491_at COMM domain containing 2 COMMD2 7.703 209448_at HIV-1 Tat interactive protein 2, 30kDa HTATIP2 6.323 202352_s_at Proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 PSMD12 5.991 207098_s_at Mitofusin 1 MFN1 4.51 202166_s_at , regulatory (inhibitor) subunit 2 PPP1R2 6.544 211137_s_at ATPase, Ca++ transporting, type 2C, member 1 ATP2C1 6.872 201780_s_at Ring finger protein 13 RNF13 5.11 225561_at Selenoprotein T SELT 6.166 204369_at Phosphoinositide-3-kinase, catalytic, alpha polypeptide PIK3CA 8.474 225032_at Factor for adipocyte differentiation 104 FAD104 10.362 208943_s_at Translocation protein 1 TLOC1 7.991 201517_at Nuclear cap binding protein subunit 2, 20kDa NCBP2 7.864 208877_at p21 (CDKN1A)-activated kinase 2 PAK2 8.353 202666_s_at Actin-like 6A ACTL6A 11.442 212297_at ATPase family homolog up-regulated in senescence cells AFURS1 8.485 222624_s_at zinc finger protein 639 ZNF639 6.475 222623_s_at zinc finger protein 639 ZNF639 7.569 57703_at SUMO1/sentrin specific protease 5 SENP5 8.274 208875_s_at p21 (CDKN1A)-activated kinase 2 PAK2 10.029 226832_at Hypothetical LOC389188 --- 7.18 1563111_a_at GPI- subunit FLJ20522 7.707 1552291_at GPI-mannosyltransferase subunit FLJ20522 8.174 200600_at Moesin MSN 7.753 214953_s_at Amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) APP 8.487 201300_s_at Prion protein (p27-30) PRNP 8.775 Transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 224793_s_at TGFBR1 6.732 53kDa) 224906_at Transmembrane protein 16F TMEM16F 7.057 203102_s_at Mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase MGAT2 6.451 223215_s_at Chromosome 14 open reading frame 100 C14orf100 5.477 218852_at Chromosome 14 open reading frame 10 C14orf10 6.723

42 200782_at Annexin A5 ANXA5 6.8 208857_s_at Protein-L-isoaspartate (D-aspartate) O-methyltransferase PCMT1 5.018 218196_at Osteopetrosis associated transmembrane protein 1 OSTM1 6.916 213061_s_at N-terminal asparagine amidase NTAN1 7.65 209935_at ATPase, Ca++ transporting, type 2C, member 1 ATP2C1 7.572 209934_s_at ATPase, Ca++ transporting, type 2C, member 1 ATP2C1 12.342 1552277_a_at Similar to RIKEN cDNA 5730528L13 gene MGC17337 10.84 226893_at ------10.173 208636_at , alpha 1 ACTN1 7.22 227534_at Chromosome 9 open reading frame 21 C9orf21 8.435 224896_s_at tyrosine ligase TTL 5.113 225278_at Protein kinase, AMP-activated, beta 2 non-catalytic subunit PRKAB2 5.201 203428_s_at ASF1 anti-silencing function 1 homolog A (S. cerevisiae) ASF1A 6.001 225384_at dedicator of cytokinesis 7 DOCK7 6.817 204137_at Transmembrane 7 superfamily member 1 (upregulated in kidney) TM7SF1 8.038 225638_at Chromosome 1 open reading frame 31 C1orf31 8.606 222752_s_at Hypothetical protein FLJ10874 FLJ10874 7.143 218909_at Ribosomal protein S6 kinase, 52kDa, polypeptide 1 RPS6KC1 7.358 224584_at Chromosome 20 open reading frame 30 C20orf30 8.145 206656_s_at Chromosome 20 open reading frame 3 C20orf3 7.991 225884_s_at Zinc finger protein 336 ZNF336 5.889 200975_at Palmitoyl-protein 1 (ceroid-lipofuscinosis, neuronal 1, infantile) PPT1 8.79 202088_at Solute carrier family 39 (zinc transporter), member 6 SLC39A6 8.06 227798_at SMAD, mothers against DPP homolog 1 (Drosophila) SMAD1 5.367 221559_s_at MIS12 homolog (yeast) MIS12 5.459 219913_s_at Crn, crooked neck-like 1 (Drosophila) CRNKL1 5.765 200593_s_at Heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) HNRPU 7.028 212591_at KIAA0117 protein KIAA0117 6.917 223068_at Echinoderm microtubule associated protein like 4 EML4 6.705 217908_s_at IQ motif and WD repeats 1 IQWD1 5.101 201023_at TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor TAF7 5.474 202211_at ADP-ribosylation factor GTPase activating protein 3 ARFGAP3 6.287 224827_at Dendritic cell-derived ubiquitin-like protein DC-UbP 8.532 209786_at High mobility group nucleosomal binding domain 4 HMGN4 5.413 200833_s_at RAP1B, member of RAS oncogene family RAP1B 6.387 201515_s_at Translin TSN 6.656 211754_s_at Solute carrier family 25, member 17 SLC25A17 6.612 225086_at Hypothetical protein FLJ38426 FLJ38426 6.326 218395_at ARP6 actin-related protein 6 homolog (yeast) ACTR6 5.075 201020_at Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein YWHAH 7.587 222204_s_at RRN3 RNA polymerase I transcription factor homolog (yeast) RRN3 5.477 211935_at ADP-ribosylation factor-like 6 interacting protein ARL6IP 6.388 201458_s_at BUB3 budding uninhibited by benzimidazoles 3 homolog (yeast) BUB3 6.61 212006_at UBX domain containing 2 UBXD2 6.937 212180_at v-crk sarcoma virus CT10 oncogene homolog (avian)-like CRKL 5.125 224635_s_at Baculoviral IAP repeat-containing 6 (apollon) BIRC6 4.172 221761_at Adenylosuccinate synthase ADSS 5.805 225479_at ------6.201 212163_at Likely homolog of rat kinase D-interacting substance of 220 kDa KIDINS220 5.323 224830_at ------4.28 212428_at KIAA0368 KIAA0368 4.404 201386_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 15 DHX15 4.426 225179_at Huntingtin interacting protein 2 HIP2 4.65 210092_at Mago-nashi homolog, proliferation-associated (Drosophila) MAGOH 6.938 210093_s_at Mago-nashi homolog, proliferation-associated (Drosophila) MAGOH 6.498 218348_s_at Zinc finger CCCH type domain containing 7 ZC3HDC7 4.634 208863_s_at Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) SFRS1 4.201 200608_s_at RAD21 homolog (S. pombe) RAD21 6.163 200892_s_at Splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila) SFRS10 5.818 206854_s_at Mitogen-activated protein kinase kinase kinase 7 MAP3K7 6.843 201177_s_at SUMO-1 activating enzyme subunit 2 UBA2 7.621 201376_s_at Heterogeneous nuclear ribonucleoprotein F HNRPF 5.93 209330_s_at Heterogeneous nuclear ribonucleoprotein D HNRPD 5.055 205292_s_at Heterogeneous nuclear ribonucleoprotein A2/B1 HNRPA2B1 5.659 1555844_s_at Heterogeneous nuclear ribonucleoprotein M HNRPM 4.585 226161_at ------5.466

43 218167_at Hypothetical protein LOC51321 LOC51321 5.382 201518_at Chromobox homolog 1 (HP1 beta homolog Drosophila ) CBX1 6.014 223054_at DnaJ (Hsp40) homolog, subfamily B, member 11 DNAJB11 7.045 200881_s_at DnaJ (Hsp40) homolog, subfamily A, member 1 DNAJA1 6.555 200599_s_at Tumor rejection antigen (gp96) 1 TRA1 5.761 201944_at Hexosaminidase B (beta polypeptide) HEXB 7.48 206332_s_at Interferon, gamma-inducible protein 16 IFI16 9.442 208966_x_at Interferon, gamma-inducible protein 16 IFI16 8.867 219530_at Hypothetical protein FLJ21816 FLJ21816 6.865 212740_at Phosphoinositide-3-kinase, regulatory subunit 4, p150 PIK3R4 6.624 214047_s_at Methyl-CpG binding domain protein 4 MBD4 6.679 202633_at Topoisomerase (DNA) II binding protein 1 TOPBP1 5.375 228583_at Chromosome 14 open reading frame 46 C14orf46 5.46 218827_s_at Centrosomal protein 192 kDa Cep192 5.807 225890_at Chromosome 20 open reading frame 72 C20orf72 7.484 204172_at Coproporphyrinogen oxidase CPOX 5.51 228386_s_at Hypothetical protein DKFZp564B1023 DKFZP564B1023 4.932 218768_at Nucleoporin 107kDa NUP107 6.697 212058_at U2-associated SR140 protein SR140 8.162 209902_at Ataxia telangiectasia and Rad3 related ATR 7.967 218336_at Prefoldin 2 PFDN2 7.121 203693_s_at E2F transcription factor 3 8.065 212474_at KIAA0241 protein KIAA0241 6.136 226962_at FRBZ1 protein FRBZ1 4.975 221505_at Acidic (leucine-rich) nuclear phosphoprotein 32 family, member E ANP32E 5.508 212060_at U2-associated SR140 protein SR140 7.031 218304_s_at Oxysterol binding protein-like 11 OSBPL11 7.356 206613_s_at TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa TAF1A 6.21 204299_at FUS interacting protein (serine-arginine rich) 1 FUSIP1 5.956 209566_at Insulin induced gene 2 INSIG2 5.289 219303_at Chromosome 13 open reading frame 7 C13orf7 4.775 228189_at ------5.352 221478_at BCL2/adenovirus E1B 19kDa interacting protein 3-like BNIP3L 5.448 207338_s_at Zinc finger protein 200 ZNF200 7.258 219037_at CGI-115 protein CGI-115 6.233 226608_at Similar to RIKEN cDNA 4921524J17 LOC388272 6.124 220083_x_at Ubiquitin carboxyl-terminal hydrolase L5 UCHL5 6.168 203465_at Mitochondrial ribosomal protein L19 MRPL19 5.734 218398_at Mitochondrial ribosomal protein S30 MRPS30 5.439 225260_s_at Mitochondrial ribosomal protein L32 MRPL32 5.603 201263_at Threonyl-tRNA synthetase TARS 6.862 200681_at glyoxalase I GLO1 5.995 200698_at KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 KDELR2 7.087 225853_at Glucosamine-phosphate N-acetyltransferase 1 GNPNAT1 8.105 209096_at Ubiquitin-conjugating enzyme E2 variant 2 UBE2V2 7.23 201091_s_at Chromobox homolog 3 (HP1 gamma homolog, Drosophila) CBX3 8.168 201327_s_at Chaperonin containing TCP1, subunit 6A (zeta 1) CCT6A 6.396 200037_s_at Chromobox homolog 3 (HP1 gamma homolog, Drosophila) CBX3 7.183 201976_s_at Myosin X MYO10 10.212 206550_s_at Nucleoporin 155kDa NUP155 10.491 219177_at BRIX BRIX 8.662 222203_s_at Retinol dehydrogenase 14 (all-trans and 9-cis) RDH14 6.578 213754_s_at Poly(A) binding protein interacting protein 1 PAIP1 8.351 219200_at Hypothetical protein MGC5297 MGC5297 5.98 204033_at interactor 13 TRIP13 8.742 222602_at Hypothetical protein FLJ10808 FLJ10808 7.162 225686_at Family with sequence similarity 33, member A FAM33A 6.467 219294_at Chromosome 6 open reading frame 139 C6orf139 8.684 234295_at Debranching enzyme homolog 1 (S. cerevisiae) DBR1 8.316 226041_at N-acyl-phosphatidylethanolamine-hydrolyzing NAPE-PLD 7.812 218894_s_at mago-nashi homolog FLJ10292 7.334 204354_at POT1 protection of 1 homolog (S. pombe) POT1 7.041 225424_at Glycerol-3-phosphate acyltransferase, mitochondrial GPAM 7.076 226178_at Suppressor of cytokine signaling 4 SOCS4 7.128 213137_s_at Protein tyrosine phosphatase, non-receptor type 2 PTPN2 8.507 221570_s_at HSPC133 protein HSPC133 6.349

44 208628_s_at Nuclease sensitive element binding protein 1 NSEP1 8.096 225419_at ------7.847 211747_s_at LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM5 6.295 218982_s_at Mitochondrial ribosomal protein S17 MRPS17 7.025 226087_at Leucine zipper and CTNNBIP1 domain containing LZIC 7.434 201629_s_at Acid phosphatase 1, soluble ACP1 8.33 203336_s_at Integrin beta 1 binding protein 1 ITGB1BP1 7.549 208447_s_at Phosphoribosyl pyrophosphate synthetase 1 PRPS1 9.792 203105_s_at 1-like DNM1L 8.247 218497_s_at H1 RNASEH1 9.704 215227_x_at Acid phosphatase 1, soluble ACP1 6.883 225737_s_at F-box protein 22 FBXO22 6.612 205329_s_at Sorting nexin 4 SNX4 8.336 203484_at Sec61 gamma subunit SEC61G 5.241 222411_s_at Signal sequence receptor, gamma (translocon-associated protein gamma) SSR3 6.458 211375_s_at Interleukin enhancer binding factor 3, 90kDa ILF3 6.81 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, 211989_at SMARCE1 5.663 subfamily e, member 1 Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex- 202491_s_at IKBKAP 5.69 associated protein 218014_at Pericentrin 1 PCNT1 4.74 202858_at U2(RNU2) small nuclear RNA auxiliary factor 1 U2AF1 5.168 201209_at 1 HDAC1 5.065 201275_at Farnesyl diphosphate synthase FDPS 4.666 203345_s_at Likely ortholog of mouse metal response element binding transcription factor 2 M96 6.228 201756_at , 32kDa RPA2 6.509 203022_at Ribonuclease H2, large subunit RNASEH2A 9.232 217946_s_at ------6.549 208795_s_at MCM7 minichromosome maintenance deficient 7 (S. cerevisiae) MCM7 6.018 202737_s_at LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM4 5.577 201011_at Ribophorin I RPN1 7.768 208612_at Glucose regulated protein, 58kDa GRP58 6.258 212202_s_at DKFZP564G2022 protein DKFZP564G2022 8.477 224281_s_at Mesenchymal stem cell protein DSC92 NEUGRIN 6.585 209132_s_at COMM domain containing 4 COMMD4 5.907 221007_s_at FIP1 like 1 (S. cerevisiae) /// FIP1 like 1 (S. cerevisiae) FIP1L1 8.008 221853_s_at Nodal modulator 2 /// nodal modulator 1 /// nodal modulator 3 NOMO2 5.72 209326_at Solute carrier family 35 (UDP-galactose transporter), member A2 SLC35A2 6.065 218493_at open reading frame 33 C16orf33 6.217 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP 208758_at ATIC 5.9 cyclohydrolase 218946_at HIRA interacting protein 5 HIRIP5 5.106 208921_s_at Sorcin SRI 5.059 218239_s_at GTP binding protein 4 GTPBP4 6.228 218238_at GTP binding protein 4 GTPBP4 6.124 203405_at Down syndrome critical region gene 2 DSCR2 5.44 201323_at EBNA1 binding protein 2 EBNA1BP2 7.164 210097_s_at Nucleolar protein 7, 27kDa NOL7 6.813 202882_x_at Nucleolar protein 7, 27kDa NOL7 7.168 201114_x_at Proteasome (prosome, macropain) subunit, alpha type, 7 PSMA7 7.446 216088_s_at Proteasome (prosome, macropain) subunit, alpha type, 7 PSMA7 7.464 202613_at CTP synthase CTPS 9.375 201157_s_at N-myristoyltransferase 1 NMT1 5.752 207805_s_at Proteasome (prosome, macropain) 26S subunit, non-ATPase, 9 PSMD9 6.889 200039_s_at Proteasome (prosome, macropain) subunit, beta type, 2 PSMB2 8.213 208799_at Proteasome (prosome, macropain) subunit, beta type, 5 PSMB5 6.464 202868_s_at Processing of precursor 4, /MRP subunit (S. cerevisiae) POP4 5.959 223060_at Chromosome 14 open reading frame 119 C14orf119 6.035 208777_s_at Proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 PSMD11 8.201 200786_at Proteasome (prosome, macropain) subunit, beta type, 7 PSMB7 6.691 201090_x_at Tubulin, alpha, ubiquitous K-ALPHA-1 5.44 213646_x_at Tubulin, alpha, ubiquitous K-ALPHA-1 5.241 212639_x_at Tubulin, alpha 3 TUBA3 5.237 211750_x_at Tubulin alpha 6 /// tubulin alpha 6 TUBA6 5.305 211787_s_at eukaryotic translation initiation factor 4A, isoform 1 EIF4A1 3.734 200079_s_at Lysyl-tRNA synthetase KARS 6.709

45 217774_s_at Hypothetical protein HSPC152 HSPC152 5 209233_at C2f protein C2F 4.929 210211_s_at Heat shock 90kDa protein 1, alpha HSPCA 5.663 201491_at AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast) AHSA1 6.293 208805_at Proteasome (prosome, macropain) subunit, alpha type, 6 PSMA6 6.98 201614_s_at RuvB-like 1 (E. coli) RUVBL1 7.918 202706_s_at Uridine monophosphate synthetase UMPS 7.472 215165_x_at Uridine monophosphate synthetase UMPS 8.901 209026_x_at Beta 5-tubulin OK/SW-cl.56 5.524 211714_x_at Beta 5-tubulin /// beta 5-tubulin OK/SW-cl.56 5.687 201232_s_at Proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 PSMD13 5.413 210574_s_at Nuclear distribution gene C homolog (A. nidulans) NUDC 5.897 224913_s_at Translocase of inner mitochondrial membrane 50 homolog (yeast) TIMM50 6.148 211609_x_at Proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 PSMD4 5.704 210460_s_at Proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 PSMD4 5.839 200910_at Chaperonin containing TCP1, subunit 3 (gamma) CCT3 5.733 222993_at Mitochondrial ribosomal protein L37 MRPL37 4.976 211928_at Dynein, cytoplasmic, heavy polypeptide 1 DNCH1 5.434 209452_s_at Vesicle transport through interaction with t-SNAREs homolog 1B (yeast) VTI1B 5.703 COBW-like placental protein /// COBW domain containing 2 /// COBW-like protein 226193_x_at DC36 6.08 /// dopamine responsive protein 223004_s_at Chromosome 3 open reading frame 1 C3orf1 7.213 221492_s_at APG3 autophagy 3-like (S. cerevisiae) APG3L 7.209 224129_s_at dpy-30-like protein LOC84661 7.315 201301_s_at Annexin A4 ANXA4 6.76 233124_s_at Enoyl Coenzyme A hydratase domain containing 1 ECHDC1 6.306 200934_at DEK oncogene (DNA binding) DEK 7.575 209056_s_at CDC5 cell division cycle 5-like (S. pombe) CDC5L 8.377 213088_s_at DnaJ (Hsp40) homolog, subfamily C, member 9 DNAJC9 6.217 218462_at RNA processing factor 1 RPF1 6.058 Phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide 212378_at GART 7.224 synthetase, phosphoribosylaminoimidazole synthetase 219043_s_at Hypothetical protein FLJ12205 /// phosducin-like 3 PDCL3 6.161 211594_s_at Mitochondrial ribosomal protein L9 /// mitochondrial ribosomal protein L9 MRPL9 6.913 203664_s_at Polymerase (RNA) II (DNA directed) polypeptide D POLR2D 7.305 203396_at Proteasome (prosome, macropain) subunit, alpha type, 4 PSMA4 7.891 201648_at Janus kinase 1 (a protein tyrosine kinase) JAK1 5.412 234926_s_at Chromosome 20 open reading frame 43 C20orf43 6.105 217722_s_at Mesenchymal stem cell protein DSC92 NEUGRIN 6.561 218333_at Der1-like domain family, member 2 DERL2 4.79 223209_s_at Selenoprotein S SELS 4.675 217907_at Mitochondrial ribosomal protein L18 MRPL18 4.131 202567_at Small nuclear ribonucleoprotein D3 polypeptide 18kDa SNRPD3 4.954 201068_s_at Proteasome (prosome, macropain) 26S subunit, ATPase, 2 PSMC2 5.586 202469_s_at Cleavage and polyadenylation specific factor 6, 68kDa CPSF6 5.813 202276_at Split hand/foot malformation (ectrodactyly) type 1 SHFM1 6.151 212219_at Proteasome (prosome, macropain) activator subunit 4 PSME4 5.211 226749_at Mitochondrial ribosomal protein S9 MRPS9 4.078 222443_s_at RNA binding motif protein 8A RBM8A 3.838 202078_at COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis) COPS3 4.941 219030_at CGI-121 protein CGI-121 5.5 212544_at Thyroid hormone receptor interactor 3 TRIP3 5.491 205133_s_at Heat shock 10kDa protein 1 (chaperonin 10) HSPE1 4.728 202690_s_at Small nuclear ribonucleoprotein D1 polypeptide 16kDa SNRPD1 5.521 201577_at Non-metastatic cells 1, protein (NM23A) expressed in NME1 5.218 223076_s_at NOL1/NOP2/Sun domain family 2 NSUN2 6.316 201817_at Ubiquitin protein ligase E3C UBE3C 4.848 224675_at Mesoderm development candidate 2 MESDC2 6.388 1552426_a_at BBP-like protein 2 BLP2 5.404 Protein disulfide isomerase related protein (calcium-binding protein, intestinal- 211048_s_at ERP70 6.609 related) 213404_s_at Ras homolog enriched in brain RHEB 7.554 220948_s_at ATPase, Na+/K+ transporting, alpha 1 polypeptide ATP1A1 4.523 208739_x_at SMT3 suppressor of mif two 3 homolog 2 (yeast) SUMO2 5.569 211997_x_at H3 histone, family 3B (H3.3B) H3F3B 4.525 209069_s_at H3 histone, family 3B (H3.3B) H3F3B 4.035

46 1553587_a_at Polymerase (DNA-directed), epsilon 4 (p12 subunit) POLE4 6.137 202487_s_at H2A histone family, member V H2AFV 6.759 204766_s_at Nudix (nucleoside diphosphate linked moiety X)-type motif 1 NUDT1 7.435 200744_s_at Guanine nucleotide binding protein (G protein), beta polypeptide 1 GNB1 8.581 219253_at Family with sequence similarity 11, member B FAM11B 7.26 214039_s_at Lysosomal associated protein transmembrane 4 beta LAPTM4B 8.779 218472_s_at Pelota homolog (Drosophila) PELO 6.343 202246_s_at Cyclin-dependent kinase 4 CDK4 6.958 202857_at Transmembrane protein 4 TMEM4 5.19 209796_s_at Transmembrane protein 4 TMEM4 4.912 210296_s_at Peroxisomal membrane protein 3, 35kDa (Zellweger syndrome) PXMP3 6.188 212150_at KIAA0143 protein KIAA0143 7.04 222543_at ------5.622 212250_at LYRIC/3D3 LYRIC 5.591 227836_at ------5.442 219819_s_at Mitochondrial ribosomal protein S28 MRPS28 5.076 203584_at KIAA0103 KIAA0103 5.813 201652_at COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis) COPS5 6.746 225676_s_at DKFZP564O0463 protein DKFZP564O0463 6.905 218482_at e(y)2 protein e(y)2 8.207 202635_s_at Polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa POLR2K 8.603 219060_at Hypothetical protein FLJ10204 FLJ10204 7.014 202823_at ------5.239 219449_s_at Hypothetical protein FLJ20533 FLJ20533 5.142 210260_s_at Tumor necrosis factor, alpha-induced protein 8 TNFAIP8 5.248 208296_x_at Tumor necrosis factor, alpha-induced protein 8 TNFAIP8 4.75 223047_at Chemokine-like factor super family 6 CKLFSF6 4.545 211758_x_at Thioredoxin domain containing 9 TXNDC9 6.193 203008_x_at Thioredoxin domain containing 9 TXNDC9 6.233 225580_at Mitochondrial ribosomal protein L50 MRPL50 6.076 225581_s_at Mitochondrial ribosomal protein L50 MRPL50 7.343 205763_s_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 DDX18 4.964 200996_at ARP3 actin-related protein 3 homolog (yeast) ACTR3 4.889 211936_at Heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) HSPA5 4.106 217743_s_at Transmembrane protein 30A TMEM30A 5.347 216988_s_at Protein tyrosine phosphatase type IVA, member 2 PTP4A2 6.304 201444_s_at ATPase, H+ transporting, lysosomal accessory protein 2 ATP6AP2 6.391 201653_at Cornichon homolog (Drosophila) CNIH 5.56 209476_at Thioredoxin domain containing TXNDC 5.747 224899_s_at Implantation-associated protein DKFZp564K142 5.216 219485_s_at Proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 PSMD10 5.658 200713_s_at Microtubule-associated protein, RP/EB family, member 1 MAPRE1 7.147 211963_s_at Actin related protein 2/3 complex, subunit 5, 16kDa ARPC5 6.647 200970_s_at Stress-associated endoplasmic reticulum protein 1 SERP1 5.685 201698_s_at Splicing factor, arginine/serine-rich 9 SFRS9 3.862 202680_at General transcription factor IIE, polypeptide 2, beta 34kDa GTF2E2 5.767 217745_s_at Mak3 homolog (S. cerevisiae) MAK3 6.328 200627_at Unactive , 23 kD TEBP 6.017 200794_x_at DAZ associated protein 2 DAZAP2 4.392 225194_at Pleiotropic regulator 1 (PRL1homolog, Arabidopsis) PLRG1 5.054 225538_at Zinc finger, CCHC domain containing 9 ZCCHC9 5.238 211727_s_at COX11 homolog, cytochrome c oxidase assembly protein (yeast) COX11 7.057 212168_at RNA binding motif protein 12 RBM12 6.384 201472_at von Hippel-Lindau binding protein 1 VBP1 6.69 201112_s_at CSE1 chromosome segregation 1-like (yeast) CSE1L 6.326 201699_at Proteasome (prosome, macropain) 26S subunit, ATPase, 6 PSMC6 4.919 203605_at Signal recognition particle 54kDa SRP54 6.608 223001_at DC2 protein DC2 5.083 217987_at HCV NS3-transactivated protein 1 NS3TP1 4.904 201676_x_at Proteasome (prosome, macropain) subunit, alpha type, 1 PSMA1 5.556 211746_x_at Proteasome (prosome, macropain) subunit, alpha type, 1 PSMA1 5.443 210759_s_at Proteasome (prosome, macropain) subunit, alpha type, 1 PSMA1 5.343 208761_s_at SMT3 suppressor of mif two 3 homolog 1 (yeast) SUMO1 5.386 201520_s_at G-rich RNA sequence binding factor 1 GRSF1 5.366 207668_x_at Thioredoxin domain containing 7 (protein disulfide isomerase) TXNDC7 7.354 208639_x_at Thioredoxin domain containing 7 (protein disulfide isomerase) TXNDC7 7.239

47 216640_s_at Thioredoxin domain containing 7 (protein disulfide isomerase) TXNDC7 6.595 200096_s_at ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e ATP6V0E 5.095 225850_at Chromosome 6 open reading frame 83 C6orf83 5.083 221381_s_at Mortality factor 4 /// mortality factor 4 like 1 MORF4 5.46 201821_s_at Translocase of inner mitochondrial membrane 17 homolog A (yeast) TIMM17A 6.484 202899_s_at Splicing factor, arginine/serine-rich 3 SFRS3 5.56 223002_s_at 5'-3' exoribonuclease 2 XRN2 7.835 201583_s_at Sec23 homolog B (S. cerevisiae) SEC23B 5.559 209861_s_at Methionyl aminopeptidase 2 METAP2 5.127 225253_s_at Methyltransferase like 2 /// hypothetical protein FLJ12760 METTL2 6.886 223273_at Chromosome 14 open reading frame 142 C14orf142 6.121 201947_s_at Chaperonin containing TCP1, subunit 2 (beta) CCT2 5.301 208726_s_at Eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa EIF2S2 7.028 201457_x_at BUB3 budding uninhibited by benzimidazoles 3 homolog (yeast) BUB3 7.089 218622_at Nucleoporin 37kDa NUP37 6.795 209080_x_at Thioredoxin-like 2 TXNL2 5.953 201897_s_at CDC28 protein kinase regulatory subunit 1B CKS1B 8.815 210691_s_at Siah-interacting protein SIP 7.388 200853_at H2A histone family, member Z H2AFZ 5.308 206052_s_at Stem-loop (histone) binding protein SLBP 5.986 223156_at Mitochondrial ribosomal protein S23 MRPS23 6.649 201317_s_at Proteasome (prosome, macropain) subunit, alpha type, 2 PSMA2 6.532 200750_s_at RAN, member RAS oncogene family RAN 5.013 223043_at Hypothetical protein LOC51234 LOC51234 5.329 202591_s_at Single-stranded DNA binding protein 1 SSBP1 4.575 200876_s_at Proteasome (prosome, macropain) subunit, beta type, 1 PSMB1 4.978 211762_s_at Karyopherin alpha 2 (RAG cohort 1, importin alpha 1) KPNA2 5.997 201532_at Proteasome (prosome, macropain) subunit, alpha type, 3 PSMA3 5.75 216274_s_at Signal peptidase complex (18kD) SPC18 5.37 207483_s_at TBP-interacting protein TIP120A 5.473 203857_s_at For protein disulfide isomerase-related PDIR 8.314 221641_s_at Likely ortholog of mouse acyl-Coenzyme A thioesterase 2, mitochondrial ACATE2 10.795 223120_at Fucosidase, alpha-L- 2, plasma FUCA2 9.835 226722_at Family with sequence similarity 20, member C FAM20C 8.986 209087_x_at Melanoma cell adhesion molecule MCAM 7.417 217788_s_at N-acetylgalactosaminyltransferase 2 (GalNAc-T2) GALNT2 7.243 209012_at Triple functional domain (PTPRF interacting) TRIO 7.29 201818_at Hypothetical protein FLJ12443 FLJ12443 9.962 212898_at KIAA0406 gene product KIAA0406 8.308 200739_s_at SMT3 suppressor of mif two 3 homolog 3 (yeast) SUMO3 8.082 217733_s_at Thymosin, beta 10 TMSB10 8.234 208674_x_at Dolichyl-diphosphooligosaccharide-protein glycosyltransferase DDOST 6.121 201762_s_at Proteasome (prosome, macropain) activator subunit 2 (PA28 beta) PSME2 5.568 202144_s_at Adenylosuccinate lyase ADSL 5.289 200875_s_at Nucleolar protein 5A (56kDa with KKE/D repeat) NOL5A 6.049 201853_s_at Cell division cycle 25B CDC25B 7.279 41037_at TEA domain family member 4 TEAD4 10.089 204278_s_at binding site associated, antigen, 9 EBAG9 7.701 203448_s_at Telomeric repeat binding factor (NIMA-interacting) 1 TERF1 10 218684_at Leucine rich repeat containing 5 LRRC5 9.107 208820_at PTK2 protein tyrosine kinase 2 PTK2 11.487 218611_at Immediate early response 5 IER5 5.244 204461_x_at RAD1 homolog (S. pombe) RAD1 7.46 201935_s_at Eukaryotic translation initiation factor 4 gamma, 3 EIF4G3 4.982 223586_at Aryl hydrocarbon receptor nuclear translocator-like 2 ARNTL2 6.456 213086_s_at Casein kinase 1, alpha 1 CSNK1A1 5.869 203582_s_at RAB4A, member RAS oncogene family RAB4A 4.91 200950_at Actin related protein 2/3 complex, subunit 1A, 41kDa ARPC1A 4.89 208811_s_at DnaJ (Hsp40) homolog, subfamily B, member 6 DNAJB6 6.099 208810_at DnaJ (Hsp40) homolog, subfamily B, member 6 DNAJB6 6.082 213012_at Neural precursor cell expressed, developmentally down-regulated 4 NEDD4 6.223 206976_s_at Heat shock 105kDa/110kDa protein 1 HSPH1 8.348 203403_s_at Ring finger protein (C3H2C3 type) 6 RNF6 5.578 222402_at Chromosome 13 open reading frame 12 C13orf12 6.326 217196_s_at KIAA1078 protein KIAA1078 5.401 206414_s_at Development and differentiation enhancing factor 2 DDEF2 6.235

48 212765_at KIAA1078 protein KIAA1078 7.324 202506_at Sperm specific antigen 2 SSFA2 6.038 202932_at v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 YES1 4.995 203885_at RAB21, member RAS oncogene family RAB21 4.778 224740_at LOC441075 --- 4.714 217851_s_at Chromosome 20 open reading frame 45 C20orf45 5.317 201132_at Heterogeneous nuclear ribonucleoprotein H2 (H') HNRPH2 4.606 1558254_s_at SFRS protein kinase 2 SRPK2 4.883 203182_s_at SFRS protein kinase 2 SRPK2 5.609 201634_s_at Cytochrome b5 outer mitochondrial membrane precursor CYB5-M 5.005 225084_at SEC10-like 1 (S. cerevisiae) SEC10L1 6.974 202854_at Hypoxanthine phosphoribosyltransferase 1 (Lesch-Nyhan syndrome) HPRT1 7.348 203338_at , regulatory subunit B (B56), epsilon isoform PPP2R5E 5.439 203594_at RNA terminal phosphate cyclase domain 1 RTCD1 4.97 204194_at BTB and CNC homology 1, basic leucine zipper transcription factor 1 BACH1 5.075 204496_at Striatin, calmodulin binding protein 3 STRN3 6.305 218545_at GGA binding partner FLJ11088 7.427 202006_at Protein tyrosine phosphatase, non-receptor type 12 PTPN12 6.639 208654_s_at CD164 antigen, sialomucin CD164 5.064 212589_at Related RAS viral (r-ras) oncogene homolog 2 RRAS2 8.125 209666_s_at Conserved helix-loop-helix ubiquitous kinase CHUK 5.847 218331_s_at Chromosome 10 open reading frame 18 C10orf18 7.426 202603_at A disintegrin and metalloproteinase domain 10 ADAM10 6.596 221482_s_at Cyclic AMP phosphoprotein, 19 kD ARPP-19 5.903 204079_at Tyrosylprotein sulfotransferase 2 TPST2 6.86 226561_at Hypothetical protein LOC285086 LOC285086 4.396 211676_s_at Interferon gamma receptor 1 /// interferon gamma receptor 1 IFNGR1 5.604 212944_at Mitochondrial ribosomal protein S6 MRPS6 5.705 202946_s_at BTB (POZ) domain containing 3 BTBD3 4.505 208370_s_at Down syndrome critical region gene 1 DSCR1 5.169 217975_at WW domain binding protein 5 WBP5 6.202 212958_x_at Peptidylglycine alpha-amidating monooxygenase PAM 6.814 202336_s_at Peptidylglycine alpha-amidating monooxygenase PAM 5.984 203038_at Protein tyrosine phosphatase, receptor type, K PTPRK 5.387 238002_at Golgi phosphoprotein 4 GOLPH4 7.093 202729_s_at Latent transforming growth factor beta binding protein 1 LTBP1 6.696 211372_s_at Interleukin 1 receptor, type II IL1R2 -4.608 205403_at Interleukin 1 receptor, type II IL1R2 -7.142 204734_at KRT15 -3.651 227194_at Family with sequence similarity 3, member B FAM3B -6.516 229290_at ------5.766 211959_at Insulin-like growth factor binding protein 5 IGFBP5 -3.981 225381_at Hypothetical gene supported by BX647608 --- -4.249 202746_at Integral membrane protein 2A ITM2A -4.844 223395_at Target of Nesh-SH3 TARSH -7.182 218353_at Regulator of G-protein signalling 5 RGS5 -3.666 200795_at SPARC-like 1 (mast9, hevin) SPARCL1 -4.468 209318_x_at Pleiomorphic adenoma gene-like 1 PLAGL1 -4.218 207943_x_at ------6.886 207002_s_at Pleiomorphic adenoma gene-like 1 PLAGL1 -7.293 203178_at Glycine amidinotransferase (L-arginine:glycine amidinotransferase) GATM -4.097 209291_at Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein ID4 -5.799 butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine 205363_at BBOX1 -4.627 hydroxylase) 1 204284_at Protein phosphatase 1, regulatory (inhibitor) subunit 3C PPP1R3C -7.429 214091_s_at Glutathione peroxidase 3 (plasma) GPX3 -4.262 201348_at Glutathione peroxidase 3 (plasma) GPX3 -4.81 ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, 204256_at ELOVL6 -4.295 SUR4/Elo3-like, yeast) 205559_s_at Proprotein convertase subtilisin/kexin type 5 PCSK5 -4.364 214598_at Claudin 8 CLDN8 -4.116 1552365_at Scinderin SCIN -5.191 203913_s_at Hydroxyprostaglandin dehydrogenase 15-(NAD) HPGD -5.445 203914_x_at Hydroxyprostaglandin dehydrogenase 15-(NAD) HPGD -6.251 211548_s_at Hydroxyprostaglandin dehydrogenase 15-(NAD) HPGD -6.239 203453_at Sodium channel, nonvoltage-gated 1 alpha SCNN1A -5.562

49 213572_s_at Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1 SERPINB1 -5.667 228726_at ------4.987 228698_at SRY (sex determining region Y)-box 7 SOX7 -4.918 223832_s_at Calpain, small subunit 2 CAPNS2 -5.756 238778_at Membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7) MPP7 -4.886 91826_at EPS8-like 1 EPS8L1 -4.17 206877_at MAX dimerization protein 1 MAD -3.722 206482_at PTK6 protein tyrosine kinase 6 PTK6 -5.392 209667_at 2 (intestine, liver) CES2 -6.058 203407_at PPL -7.128 222892_s_at Hypothetical protein FLJ11036 FLJ11036 -5.083 205759_s_at Sulfotransferase family, cytosolic, 2B, member 1 SULT2B1 -5.617 1569144_a_at Similar to RIKEN cDNA 2310002J15 gene MGC59937 -7.74 228865_at Specifically androgen-regulated protein SARG -6.303 219476_at Specifically androgen-regulated protein SARG -6.987 218180_s_at EPS8-like 2 EPS8L2 -7.293 219597_s_at Dual oxidase 1 DUOX1 -5.758 235651_at ------5.787 236534_at BCL2/adenovirus E1B 19kD interacting protein like BNIPL -6.947 229518_at Family with sequence similarity 46, member B FAM46B -4.711 214536_at ARS component B ARS -4.947 242998_at Retinol dehydrogenase 12 (all-trans and 9-cis) RDH12 -4.805 207206_s_at Arachidonate 12-lipoxygenase ALOX12 -6.892 201324_at Epithelial membrane protein 1 EMP1 -7.777 201325_s_at Epithelial membrane protein 1 EMP1 -4.971 213895_at Epithelial membrane protein 1 EMP1 -7.772 229011_at ------9.52 212657_s_at Interleukin 1 receptor antagonist IL1RN -3.631 223739_at Peptidyl arginine deiminase, type I PADI1 -4.93 232074_at Pancreasin MPN -6.592 1553213_a_at Keratin 5b K5B -6.504 1553212_at Keratin 5b K5B -6.672 1563894_at Hypothetical protein LOC154222 LOC154222 -7.836 1561685_a_at Hypothetical protein LOC154222 LOC154222 -9.131 209365_s_at Extracellular matrix protein 1 ECM1 -5.149 244056_at GSGL541 UNQ541 -5.277 1552532_a_at ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2 ATP6V1C2 -3.457 1553924_at Hypothetical protein BC014341 LOC116123 -3.475 231929_at MRNA; cDNA DKFZp586O0724 (from clone DKFZp586O0724) --- -4.783 228256_s_at TIGA1 TIGA1 -6.377 204069_at Meis1, myeloid ecotropic viral integration site 1 homolog (mouse) MEIS1 -4.46 229130_at Hypothetical protein LOC285535 LOC285535 -5.001 230748_at Solute carrier family 16 (monocarboxylic acid transporters), member 6 SLC16A6 -6.892 203845_at p300/CBP-associated factor PCAF -5.874 213929_at Transcribed locus, weakly similar to XP_375099.1 hypothetical protein LOC283585 --- -5.596 226022_at SAM and SH3 domain containing 1 SASH1 -5.829 207655_s_at B-cell linker BLNK -6.072 220403_s_at p53-regulated apoptosis-inducing protein 1 P53AIP1 -4.87 238763_at RNA binding motif protein 20 RBM20 -5.697 204754_at Hepatic leukemia factor HLF -6.09 204755_x_at Hepatic leukemia factor HLF -5.866 204753_s_at Hepatic leukemia factor HLF -3.673 205666_at Flavin containing monooxygenase 1 FMO1 -4.552 209242_at Paternally expressed 3 PEG3 -7.736 225728_at Importin 9 IPO9 -6.101 227826_s_at ------5.204 204041_at Monoamine oxidase B MAOB -6.919 225817_at Likely ortholog of mouse junction-associated coiled-coil protein JACOP -8.308 225990_at Brother of CDO BOC -7.58 238066_at retinol binding protein 7, cellular RBP7 -6.143 239624_at LOC440885 --- -3.522 1569607_s_at Chromosome 21 open reading frame 81 /// ankyrin repeat domain 20A C21orf81 -7.344 241233_x_at Chromosome 21 open reading frame 81 C21orf81 -6.364 228538_at FLJ45880 protein FLJ45880 -6.782 Similar to c439A6.1 (novel protein similar to heparan sulfate (glucosamine) 3-O- 239547_at --- -6.256 sulfotransferases)

50 209250_at Degenerative spermatocyte homolog, lipid desaturase (Drosophila) DEGS -4.832 219908_at Dickkopf homolog 2 (Xenopus laevis) DKK2 -4.478 219304_s_at Platelet derived growth factor D PDGFD -4.588 1566140_at Homeodomain-only protein HOP -4.728 208399_s_at Endothelin 3 EDN3 -4.176 232855_at MRNA full length insert cDNA clone EUROIMAGE 980547 --- -5.459 210262_at Cysteine-rich secretory protein 2 CRISP2 -4.455 220518_at Target of Nesh-SH3 TARSH -5.273 226197_at ------9.124 226192_at ------6.314 226933_s_at ------4.93 211748_x_at Prostaglandin D2 synthase 21kDa (brain) PTGDS -3.564 229839_at Hypothetical protein MGC45780 MGC45780 -5.118 209047_at Aquaporin 1 (channel-forming integral protein, 28kDa) AQP1 -5.092 205392_s_at Chemokine (C-C motif) ligand 14 /// chemokine (C-C motif) ligand 15 CCL14 / CCL15 -6.433 204731_at Transforming growth factor, beta receptor III (betaglycan, 300kDa) TGFBR3 -5.343 226625_at ------6.075 236480_at CDNA FLJ41489 fis, clone BRTHA2004582 --- -4.83 240458_at ------4.801 202660_at Inositol 1,4,5-triphosphate receptor, type 2 ITPR2 -7.17 205554_s_at I-like 3 DNASE1L3 -6.404 227782_at Similar to B230208J24Rik protein --- -7.4 231118_at Hypothetical protein FLJ25124 FLJ25124 -4.928 218312_s_at Hypothetical protein FLJ12895 FLJ12895 -6.859 209869_at Adrenergic, alpha-2A-, receptor /// adrenergic, alpha-2A-, receptor ADRA2A -5.339 212594_at Programmed cell death 4 (neoplastic transformation inhibitor) PDCD4 -7.451 239250_at Zinc finger protein 542 ZNF542 -8.885 228974_at Hypothetical protein MGC48625 MGC48625 -7.803 219932_at Solute carrier family 27 (fatty acid transporter), member 6 SLC27A6 -6.642 229584_at Leucine-rich repeat kinase 2 LRRK2 -6.036 1554547_at Family with sequence similarity 13, member C1 FAM13C1 -4.974 232136_s_at Cortactin binding protein 2 CTTNBP2 -4.83 230451_at CDNA FLJ41269 fis, clone BRAMY2036079 --- -4.475 230866_at ------5.123 228376_at Glycoprotein, alpha-galactosyltransferase 1 GGTA1 -6.437 1561368_at ------5.197 227985_at ------4.094 1552463_at Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11 SERPINB11 -4.543 227676_at Family with sequence similarity 3, member D FAM3D -8.336 225354_s_at SH3 domain binding glutamic acid-rich protein like 2 SH3BGRL2 -4.479 228653_at ------8.064 215239_x_at Zinc finger protein 273 ZNF273 -6.411 214624_at Uroplakin 1A UPK1A -6.606 234359_at Similar to cSH-PTP2 --- -9.212 1553114_a_at PTK6 protein tyrosine kinase 6 PTK6 -8.515 220149_at Hypothetical protein FLJ22671 FLJ22671 -8.931 1557016_a_at Hypothetical protein FLJ40201 FLJ40201 -7.192 225671_at Hypothetical protein LOC124976 LOC124976 -7.829 225914_s_at Calcium binding protein 39-like CAB39L -6.069 1561777_at Hypothetical gene supported by AF486622 C21orf34 -7.557 237351_at Hypothetical protein LOC284825 LOC284825 -5.645 242009_at ------5.659 240734_at Homo sapiens, clone IMAGE:4826738, mRNA --- -4.318 225618_at Rho GTPase activating protein 27 ARHGAP27 -6.188 213236_at SAM and SH3 domain containing 1 SASH1 -6.075 41644_at SAM and SH3 domain containing 1 SASH1 -8.488 241417_at ------7.745 219930_at Kruppel-like factor 8 KLF8 -7.296 217508_s_at Chromosome 18 open reading frame 25 C18orf25 -5.911 214621_at 2 (liver) GYS2 -6.896 229252_at Endothelial antisense SONE -6.624 1553505_at Hypothetical protein FLJ25179 FLJ25179 -5.377 207008_at Interleukin 8 receptor, beta IL8RB -6.429 chromosome 11 open reading frame 17 /// likely ortholog of rat SNF1/AMP- 220987_s_at C11orf17 -6.821 activated protein kinase 222271_at ------7.374

51 229740_at RecQ protein-like 5 /// PP12104 RECQL5 -8.392 218858_at DEP domain containing 6 DEPDC6 -9.555 228568_at GRINL1A complex upstream protein Gup1 -8.162 1554921_a_at Sciellin SCEL -4.799 236225_at Hypothetical protein FLJ90165 FLJ90165 -6.346 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group 214088_s_at FUT3 -5.629 included) 219722_s_at Hypothetical protein MGC4171 MGC4171 -6.154 204393_s_at Acid phosphatase, prostate ACPP -4.503 231711_at ------5.104 225102_at Monoglyceride lipase MGLL -9.422 211026_s_at Monoglyceride lipase /// monoglyceride lipase MGLL -6.782 241782_at ------5.603 203961_at Nebulette NEBL -6.008 229764_at FLJ41238 protein FLJ41238 -6.19 236129_at ------5.521 205765_at Cytochrome P450, family 3, subfamily A, polypeptide 5 CYP3A5 -6.647 214235_at Cytochrome P450, family 3, subfamily A, polypeptide 5 CYP3A5 -5.58 214234_s_at Cytochrome P450, family 3, subfamily A, polypeptide 5 CYP3A5 -5.924 240242_at ------4.351 1557136_at Hypothetical protein DKFZp761I1011 DKFZp761I1011 -4.909 232360_at Ets homologous factor EHF -4.013 239999_at ------4.833 230003_at ------3.943 207057_at ------5.296 204237_at GULP, engulfment adaptor PTB domain containing 1 GULP1 -7.448 204235_s_at GULP, engulfment adaptor PTB domain containing 1 GULP1 -5.105 228821_at ------3.832 214399_s_at ------4.31 222249_at ------3.949 222835_at Hypothetical protein FLJ13710 FLJ13710 -5.262 204719_at ATP-binding cassette, sub-family A (ABC1), member 8 ABCA8 -5.551 211734_s_at Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide FCER1A -5.116 206199_at Carcinoembryonic antigen-related cell adhesion molecule 7 CEACAM7 -3.604 211712_s_at Annexin A9 ANXA9 -3.833 201884_at Carcinoembryonic antigen-related cell adhesion molecule 5 CEACAM5 -4.371 206023_at Neuromedin U NMU -4.128 236444_x_at Hypothetical LOC389328 --- -4.55 214063_s_at Transferring TF -3.941 228067_at Similar to 2010300C02Rik protein MGC42367 -4.976 230986_at Transcribed locus, moderately similar to NP_689573.2 zinc finger protein 573 --- -5.823 211726_s_at Flavin containing monooxygenase 2 FMO2 -5.107 228268_at Flavin containing monooxygenase 2 FMO2 -5.805 220723_s_at Hypothetical protein FLJ21511 FLJ21511 -4.033 242871_at Membrane progestin receptor gamma MPRG -4.894 1559607_s_at Hypothetical protein DKFZp686G0786 DKFZp686G0786 -7.512 227238_at ------4.174 215103_at ------4.078 208126_s_at Cytochrome P450, family 2, subfamily C, polypeptide 18 CYP2C18 -5.529 230323_s_at Hypothetical protein BC016153 LOC120224 -3.61 206605_at 26 serine protease P11 -8.525 220782_x_at Kallikrein 12 KLK12 -4.381 233586_s_at Kallikrein 12 KLK12 -4.535 205783_at Kallikrein 13 KLK13 -5.004 207463_x_at Protease, serine, 3 (mesotrypsin) PRSS3 -4.658 205470_s_at Kallikrein 11 KLK11 -6.833 219529_at Chloride intracellular channel 3 CLIC3 -4.533 1564307_a_at Hypothetical protein FLJ25179 FLJ25179 -4.326 206884_s_at Sciellin SCEL -5.965 232056_at Sciellin SCEL -5.94 211597_s_at Homeodomain-only protein HOP -7.578 238654_at Hypothetical protein LOC147645 LOC147645 -6.107

52 Supplementary Table S6. Differentially expressed genes in CCs vs. HNCs * In order as shown in Fig. 2B. Probeset ID* Gene title Gene symbol t-statistic 212990_at 1 SYNJ1 5.238 227375_at Hypothetical protein DKFZp566D1346 DKFZP566D1346 5.318 212061_at U2-associated SR140 protein SR140 5.115 225216_at Chromosome X open reading frame 39 CXorf39 4.849 227471_at HECT domain and ankyrin repeat containing, E3 ubiquitin protein ligase 1 HACE1 5.366 213387_at KIAA1240 protein KIAA1240 6.097 226894_at ------6.056 209187_at Down-regulator of transcription 1, TBP-binding (negative cofactor 2) DR1 5.601 233898_s_at FGFR1 oncogene partner 2 FGFR1OP2 4.697 229173_at ------5.926 225539_at Zinc finger protein 295 ZNF295 6.652 214820_at Chromosome 21 open reading frame 107 C21orf107 5.467 230427_s_at ------6.054 204727_at WD repeat and HMG-box DNA binding protein 1 WDHD1 6.172 203689_s_at Fragile X mental retardation 1 FMR1 5.614 212836_at Polymerase (DNA-directed), delta 3, accessory subunit POLD3 5.813 203347_s_at Likely ortholog of mouse metal response element binding transcription factor 2 M96 5.724 234995_at Hypothetical protein AY099107 LOC152185 6.488 202293_at Stromal antigen 1 STAG1 7.607 229027_at ------6.052 228334_x_at KIAA1712 KIAA1712 5.785 204634_at NIMA (never in mitosis gene a)-related kinase 4 NEK4 6.113 219171_s_at Zinc finger protein 236 ZNF236 4.82 234997_x_at ------4.747 226115_at ELYS transcription factor-like protein TMBS62 ELYS 5.106 202294_at ------8.547 229022_at ------6.763 204835_at Polymerase (DNA directed), alpha POLA 6.672 203401_at Phosphoribosyl pyrophosphate synthetase 2 PRPS2 6.139 225021_at Zinc finger protein 532 ZNF532 5.759 220617_s_at Zinc finger protein 532 ZNF532 6.463 203482_at Chromosome 10 open reading frame 6 C10orf6 6.155 226730_s_at Ubiquitin specific protease 37 USP37 6.055 218515_at Chromosome 21 open reading frame 66 C21orf66 5.504 212943_at KIAA0528 gene product KIAA0528 5.973 218397_at Fanconi anemia, complementation group L FANCL 6.272 225017_at Hypothetical protein FLJ12892 FLJ12892 5.375 228286_at Hypothetical protein FLJ40869 FLJ40869 5.694 229303_at ------5.471 232362_at Sarcoma antigen NY-SAR-41 NY-SAR-41 5.009 225318_at DDHD domain containing 2 DDHD2 4.732 214306_at Optic atrophy 1 (autosomal dominant) OPA1 5.141 222629_at REV1-like (yeast) REV1L 6.239 224974_at Likely ortholog of mouse Sds3 SDS3 6.108 213140_s_at Synovial sarcoma translocation gene on chromosome 18-like 1 SS18L1 5.802 208798_x_at Golgin-67 GOLGIN-67 5.185 210425_x_at ------5.537 227199_at Chromosome 21 open reading frame 106 C21orf106 6.379 236910_at Mitochondrial ribosomal protein L39 MRPL39 6.352 228940_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa NDUFB4 5.908 230516_at Chromosome 7 open reading frame 30 C7orf30 5.057 243332_at ------5.676 225595_at MRNA; cDNA DKFZp566P1124 (from clone DKFZp566P1124) --- 4.672 225594_at MRNA; cDNA DKFZp566P1124 (from clone DKFZp566P1124) --- 5.378 218793_s_at Sex comb on midleg-like 1 (Drosophila) SCML1 5.387 239577_at ------4.466 222201_s_at CASP8 associated protein 2 CASP8AP2 5.367 218979_at Chromosome 9 open reading frame 76 C9orf76 5.468 218757_s_at UPF3 regulator of nonsense transcripts homolog B (yeast) UPF3B 7.293 202633_at Topoisomerase (DNA) II binding protein 1 TOPBP1 7.354 227255_at Casein kinase LOC149420 4.722 201555_at MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) MCM3 7.992 239413_at KIAA0912 protein Cep152 7.158

53 206316_s_at Kinetochore associated 1 KNTC1 7.584 228859_at Prematurely terminated mRNA decay factor-like LOC91431 6.037 221677_s_at Downstream neighbor of SON DONSON 8.188 225655_at Ubiquitin-like, containing PHD and RING finger domains, 1 UHRF1 8.055 228401_at ------7.279 219306_at Kinesin-like 7 KNSL7 6.072 235609_at ------6.233 203209_at Replication factor C (activator 1) 5, 36.5kDa RFC5 5.279 203432_at Thymopoietin TMPO 4.836 206102_at KIAA0186 gene product KIAA0186 5.766 204510_at CDC7 cell division cycle 7 (S. cerevisiae) CDC7 7.611 203358_s_at Enhancer of zeste homolog 2 (Drosophila) EZH2 6.571 218783_at DKFZP434B168 protein DKFZP434B168 5.005 224428_s_at Cell division cycle associated 7 CDCA7 4.567 214804_at FSH primary response (LRPR1 homolog, rat) 1 FSHPRH1 5.661 203744_at High-mobility group box 3 HMGB3 6.469 212060_at U2-associated SR140 protein SR140 5.261 218304_s_at Oxysterol binding protein-like 11 OSBPL11 5.936 228386_s_at Hypothetical protein DKFZp564B1023 DKFZP564B1023 5.527 215009_s_at SEC31-like 1 (S. cerevisiae) SEC31L1 5.184 226350_at Choroideremia-like (Rab escort protein 2) CHML 6.435 1565951_s_at Choroideremia-like (Rab escort protein 2) CHML 5.487 242923_at Hypothetical protein MGC15634 MGC15634 4.925 205296_at Retinoblastoma-like 1 (p107) RBL1 4.687 203276_at LMNB1 5.178 238756_at Growth arrest-specific 2 like 3 GAS2L3 4.914 228577_x_at KIAA1229 protein KIAA1229 5.562 231909_x_at KIAA1229 protein KIAA1229 5.05 226164_x_at KIAA1238 protein KIAA1238 4.309 228397_at ------4.259 239680_at ------6.372 236513_at ------5.773 231931_at PR domain containing 15 PRDM15 6.115 230777_s_at PR domain containing 15 PRDM15 5.542 208174_x_at U2(RNU2) small nuclear RNA auxiliary factor 1-like 2 U2AF1L2 5.364 213876_x_at U2(RNU2) small nuclear RNA auxiliary factor 1-like 2 U2AF1L2 5.517 42361_g_at Chromosome 6 open reading frame 18 C6orf18 4.599 64408_s_at Calmodulin-like 4 CALML4 4.377 220969_s_at ------4.24 230209_at Hypothetical protein MGC11349 MGC11349 4.501 203262_s_at Family with sequence similarity 50, member A FAM50A 6.106 213947_s_at Nucleoporin 210 NUP210 5.367 230395_at DORA reverse strand protein 1 DREV1 4.248 1562497_at MKL/myocardin-like 2 MKL2 5.24 223797_at ------4.519 244625_at ------4.668 235646_at ------5.002 242737_at ------6.262 219280_at Chromosome 21 open reading frame 107 C21orf107 7.491 222343_at BCL2-like 11 (apoptosis facilitator) BCL2L11 6.325 230534_at Hypothetical protein MGC15634 MGC15634 5.384 238699_s_at Calcium/calmodulin-dependent serine protein kinase (MAGUK family) CASK 4.742 232370_at Hypothetical protein LOC254057 LOC254057 4.482 204143_s_at rTS beta protein HSRTSBETA 4.634 237246_at ------4.651 215623_x_at SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SMC4L1 5.25 241954_at ------4.48 204224_s_at GTP cyclohydrolase 1 (dopa-responsive dystonia) GCH1 4.677 222603_at KIAA1815 KIAA1815 5.974 223275_at HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae) HRMT1L6 4.656 228778_at ------6.636 203991_s_at Ubiquitously transcribed tetratricopeptide repeat, UTX 6.092 214678_x_at ------5.425 203992_s_at Ubiquitously transcribed tetratricopeptide repeat, X chromosome UTX 6.441 204061_at Protein kinase, X-linked PRKX 4.969 229305_at MLF1 interacting protein MLF1IP 4.709

54 218883_s_at MLF1 interacting protein MLF1IP 6.342 219990_at FLJ23311 protein FLJ23311 4.99 210371_s_at Retinoblastoma binding protein 4 RBBP4 6.888 218733_at Hypothetical protein FLJ10546 FLJ10546 5.501 233841_s_at Likely ortholog of mouse Sds3 SDS3 5.987 221919_at Heterogeneous nuclear ribonucleoprotein A1 HNRPA1 5.492 212515_s_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked DDX3X 4.514 220553_s_at PRP39 pre-mRNA processing factor 39 homolog (yeast) PRPF39 4.995 201970_s_at Nuclear autoantigenic sperm protein (histone-binding) NASP 5.843 212200_at KIAA0692 protein KIAA0692 5.66 215017_s_at Chromosome 1 open reading frame 39 C1orf39 4.318 235142_at Zinc finger and BTB domain containing 8 ZBTB8 4.617 219157_at Kelch-like 2, Mayven (Drosophila) KLHL2 6.137 236769_at Hypothetical protein LOC158402 LOC158402 5.643 227133_at Chromosome X open reading frame 39 CXorf39 4.437 220520_s_at Hypothetical protein FLJ20130 FLJ20130 5.257 217936_at Rho GTPase activating protein 5 ARHGAP5 5.74 223167_s_at Ubiquitin specific protease 25 USP25 5.464 205281_s_at Phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria) PIGA 5.451 226302_at ------4.823 213285_at Transmembrane protein 30B TMEM30B 4.978 228565_at Mixed lineage kinase 4 KIAA1804 4.999 227356_at CDNA: FLJ22198 fis, clone HRC01218 --- 4.591 228201_at ADP-ribosylation factor-like 2-like 1 ARL2L1 4.742 228812_at ------4.625 225227_at Homo sapiens, clone IMAGE:5299642, mRNA --- 4.459 232398_at Hypothetical protein DKFZp434P055 DKFZp434P055 5.822 233504_at Chromosome 9 open reading frame 84 C9orf84 5.832 1554447_at CDNA clone MGC:32876 IMAGE:4734912, complete cds --- 5.544 218966_at Myosin VC MYO5C 6.466 1556105_at Par-3 partitioning defective 3 homolog (C. elegans) PARD3 7.135 235635_at ------4.637 228455_at CDNA FLJ43677 fis, clone SYNOV4009295 --- 5.957 225786_at Family with sequence similarity 36, member A FAM36A 4.716 223513_at Centromere protein J CENPJ 4.285 217894_at Potassium channel tetramerisation domain containing 3 KCTD3 6.689 204146_at RAD51 associated protein 1 RAD51AP1 4.219 203213_at Cell division cycle 2, G1 to S and G2 to M CDC2 5.255 201663_s_at SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SMC4L1 4.65 201664_at SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SMC4L1 6.127 225834_at Similar to RIKEN cDNA 2700049P18 gene MGC57827 7.226 228323_at AF15q14 protein AF15Q14 5.322 223381_at Cell division cycle associated 1 CDCA1 4.969 228033_at E2F transcription factor 7 E2F7 6.759 204641_at NIMA (never in mitosis gene a)-related kinase 2 NEK2 4.905 209172_s_at Centromere protein F, 350/400ka (mitosin) CENPF 4.919 218585_s_at RA-regulated nuclear matrix-associated protein RAMP 5.95 222680_s_at RA-regulated nuclear matrix-associated protein RAMP 6.996 222740_at ATPase family, AAA domain containing 2 ATAD2 5.314 222848_at leucine zipper protein FKSG14 FKSG14 5.878 229551_x_at Zinc finger protein 367 ZNF367 8.85 227350_at Helicase, lymphoid-specific HELLS 6.363 205034_at Cyclin E2 CCNE2 7.033 223542_at Ankyrin repeat domain 32 ANKRD32 7.339 216228_s_at WD repeat and HMG-box DNA binding protein 1 WDHD1 4.689 226747_at KIAA1344 KIAA1344 5.709 228597_at Chromosome 21 open reading frame 45 C21orf45 5.181 209337_at PC4 and SFRS1 interacting protein 1 PSIP1 5.364 205961_s_at PC4 and SFRS1 interacting protein 1 PSIP1 4.401 226925_at acid phosphatase-like 2 ACPL2 4.686 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, 202983_at SMARCA3 4.929 subfamily a, member 3 225768_at Nuclear receptor subfamily 1, group D, member 2 NR1D2 5.387 229442_at Hypothetical protein MGC33382 MGC33382 5.117 212840_at KIAA0794 protein KIAA0794 4.926 201329_s_at v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) ETS2 6.218

55 201328_at v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) ETS2 4.879 208078_s_at SNF1-like kinase \ SNF1LK 4.865 1555411_a_at Cyclin L1 CCNL1 6.615 1555827_at Cyclin L1 CCNL1 5.578 241495_at Cyclin L1 CCNL1 4.355 241903_at ------5.813 243030_at ------5.475 205345_at BRCA1 associated RING domain 1 BARD1 4.352 213353_at ATP-binding cassette, sub-family A (ABC1), member 5 ABCA5 5.381 240452_at ------4.398 230097_at ------4.269 236322_at ------4.201 242146_at ------5.106 1559156_at Protein inhibitor of activated STAT, 1 PIAS1 4.832 235926_at ------4.262 244753_at ------4.129 232058_at Actinin, alpha 4 ACTN4 4.419 203767_s_at (microsomal), C, isozyme S STS 4.633 213150_at Homeo box A10 HOXA10 4.669 235292_at LOC441069 --- 4.149 226374_at ------4.552 204286_s_at Phorbol-12-myristate-13-acetate-induced protein 1 PMAIP1 4.648 210540_s_at UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4 B4GALT4 4.992 237269_at ------4.908 226420_at Ecotropic viral integration site 1 EVI1 5.871 218901_at Phospholipid scramblase 4 PLSCR4 6.1 235165_at Par-6 partitioning defective 6 homolog beta (C. elegans) PARD6B 4.241 221045_s_at Period homolog 3 (Drosophila) PER3 4.957 221973_at Hypothetical protein LOC150759 LOC150759 4.445 238593_at Hypothetical protein FLJ22531 FLJ22531 4.248 216248_s_at Nuclear receptor subfamily 4, group A, member 2 NR4A2 4.868 204622_x_at Nuclear receptor subfamily 4, group A, member 2 NR4A2 4.882 206698_at Kell blood group precursor (McLeod phenotype) XK 4.927 227492_at ------6.648 1562921_at E1A binding protein p300 EP300 4.238 235144_at RAS and EF hand domain containing RASEF 6.912 1553986_at RAS and EF hand domain containing RASEF 4.273 229842_at ------4.773 209692_at Eyes absent homolog 2 (Drosophila) EYA2 6.153 219313_at Hypothetical protein DKFZp434C0328 DKFZp434C0328 5.167 204069_at Meis1, myeloid ecotropic viral integration site 1 homolog (mouse) MEIS1 4.556 214464_at CDC42 binding protein kinase alpha (DMPK-like) CDC42BPA 4.303 214723_x_at KIAA1641 KIAA1641 5.208 HSPA1A /// 200800_s_at Heat shock 70kDa protein 1A /// heat shock 70kDa protein 1B 5.342 HSPA1B 201169_s_at Basic helix-loop-helix domain containing, class B, 2 BHLHB2 4.172 214651_s_at Homeo box A9 HOXA9 7.526 209905_at Homeo box A9 HOXA9 7.791 228904_at ------5.333 206546_at Synaptonemal complex protein 2 SYCP2 5.824 233320_at Testicular cell adhesion molecule 1 TCAM1 4.918 229400_at Homeo box D10 HOXD10 5.335 227671_at X (inactive)-specific transcript XIST 5.623 231592_at ------4.565 224589_at X (inactive)-specific transcript XIST 4.966 205778_at Kallikrein 7 (chymotryptic, stratum corneum) KLK7 -4.171 206125_s_at Kallikrein 8 (neuropsin/ovasin) KLK8 -4.858 206192_at CDSN -4.747 235514_at Hypothetical protein FLJ25084 FLJ25084 -4.359 223582_at Monogenic, audiogenic seizure susceptibility 1 homolog (mouse) MASS1 -4.856 239352_at ------4.807 207356_at Defensin, beta 4 DEFB4 -4.625 205054_at Nebulin NEB -6.402 203562_at Fasciculation and elongation protein zeta 1 (zygin I) FEZ1 -4.482 221898_at Lung type-I cell membrane-associated glycoprotein T1A-2 -4.543 228492_at Ubiquitin specific protease 9, Y-linked (fat facets-like, Drosophila) USP9Y -6.254

56 223646_s_at Chromosome Y open reading frame 15B CYorf15B -7.48 204410_at Eukaryotic translation initiation factor 1A, Y-linked EIF1AY -5.799 206700_s_at Jumonji, AT rich interactive domain 1D (RBP2-like) JARID1D -8.832 223645_s_at Chromosome Y open reading frame 15B CYorf15B -7.22 230760_at Zinc finger protein, Y-linked ZFY -6.432 213068_at Dermatopontin DPT -6.491 213909_at Leucine rich repeat containing 15 LRRC15 -5.414 201893_x_at Decorin DCN -4.228 223475_at CocoaCrisp LOC83690 -4.253 210467_x_at Melanoma antigen, family A, 12 MAGEA12 -4.686 232523_at MEGF10 protein MEGF10 -5.346 206584_at Lymphocyte antigen 96 LY96 -4.524 236313_at Cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) CDKN2B 4.437 205225_at Estrogen receptor 1 ESR1 4.321 207039_at Cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) CDKN2A 4.922 232170_at S100 calcium binding protein A7-like 1 S100A7L1 -4.32 207324_s_at Desmocollin 1 DSC1 -3.977 224646_x_at ------4.37 224997_x_at H19, imprinted maternally expressed untranslated mRNA H19 -4.791 224348_s_at ------4.566 205403_at Interleukin 1 receptor, type II IL1R2 -5.361 211372_s_at Interleukin 1 receptor, type II IL1R2 -4.172 205000_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked DDX3Y -8.052 214131_at Chromosome Y open reading frame 15B CYorf15B -6.626 204409_s_at Eukaryotic translation initiation factor 1A, Y-linked EIF1AY -5.951 201909_at Ribosomal protein S4, Y-linked 1 RPS4Y1 -8.251 201650_at Keratin 19 KRT19 4.223 224588_at X (inactive)-specific transcript XIST 9.351 224590_at X (inactive)-specific transcript XIST 8.602 214218_s_at X (inactive)-specific transcript XIST 9.127 221728_x_at X (inactive)-specific transcript XIST 9.808 230835_at KIPV467 UNQ467 -4.315

57 + Supplementary Table S7. Probesets upregulated in the subgroup of HPV cancers These 390 genes are ordered as in Suppl. Fig. 4C. Differentially expressed genes between the two HNC HPV+ subgroups are indicated with t-statistics as significance of changes. Gene symbol t-stat Gene symbol t-stat Gene symbol t-stat Gene symbol t-stat PCM1 5.36 DDHD2 5.32 BCL11A 5.63 OVOS 5.99 PCM1 7.09 * 236513_at 4.97 BCL11A 6.7 HOXC6 6.58 LIPT1 6.21 SMARCA2 5.45 PELI1 4.63 BTNL9 5.35 MYST3 6.07 SMARCA2 5.26 * 213158_at 4.62 * 229623_at 5.14 FLJ11342 5.33 LOC56757 4.59 * 1559026_at 5.45 SEMA6A 8.02 ZNF161 4.53 NT5C2L1 5.37 SLC12A7 4.44 DKFZP564O0823 5.69 LOC58486 5.35 * 228709_at 4.9 * 229242_at 4.71 MEGF10 5.92 NAP1L1 5.24 PDE4DIP 4.63 CD8B1 8.22 BIRC3 5.66 WDR35 4.51 RNF19 4.72 RNF150 4.54 * 226612_at 4.56 DCP2 4.42 MGC22679 4.59 C18orf23 5.42 AMY2A 5 FRS2 4.74 * 65472_at 5.11 KIAA1889 5.8 ZNF83 5 * 235556_at 5.09 * 221878_at 4.89 BTNL9 6 CEACAM6 -4.5 HNRPDL 5.91 * 230653_at 4.73 FRMD4A 4.8 CEACAM6 -5.17 * 228959_at 4.7 * 235561_at 4.93 PRPF18 4.45 S100P -4.37 * 235470_at 5.18 * 229705_at 4.98 KIT 7.14 LOC147645 -5.04 SEPHS1 4.98 SMARCE1 5.07 ZNF228 4.81 G1P2 -4.57 LNX 4.49 ALS2CR4 5.51 PARP11 4.96 OAS3 -4.48 LOC286161 6.49 * 229303_at 5.79 PRKD1 6.31 HERC6 -4.98 USP47 5.43 * 235603_at 6.18 C10orf38 5.01 PTHLH -4.64 * 230072_at 5.44 UBE2V2 4.88 * 228557_at 4.86 CA12 -4.45 KIAA0368 4.8 SFRS11 4.51 * 217665_at 5.02 FGFBP1 -6.04 * 230304_at 4.93 ENAH 4.78 * 230499_at 5.45 MGC34923 -4.58 * 238620_at 5.48 CLK4 6.63 STAR 5.34 MAP17 -4.54 ZNF84 5.76 CLK4 5.27 ALS2CR19 4.67 CST6 -4.47 ANKRA2 5.21 * 229243_at 9.16 LOC339535 6.63 PROS1 -4.64 SMAD5 5.36 CYP4V2 5.22 MGC16291 8.07 TNFAIP9 -4.46 FLJ44216 4.61 TAF15 5.3 FRMD4A 5.5 MAGED4 -4.38 LOC285002 5.01 PRKRA 5.35 * 229968_at 7.48 CAPNS2 -4.36 * 238492_at 6.41 * 238651_at 4.81 ARNT2 5.32 MAOA -6.45 * 228240_at 6.67 * 241460_at 5.15 SYNPO2 6.19 MAOA -5.55 SMARCA2 5.25 * 222266_at 6.48 * 1563414_at 6.12 PFN2 -4.42 * 237419_at 5.91 CBR4 4.66 INM01 6.27 NQO1 -5 C1orf37 6.3 * 238875_at 4.55 INM01 5.6 NQO1 -5.4 SAP18 4.72 * 235138_at 4.41 * 1558404_at 5.75 NHLH2 -4.42 FLJ10154 4.9 * 240498_at 6.11 LRIG3 4.49 SLC7A5 -5.38 RBBP9 5.01 * 242208_at 5.46 CENPJ 4.83 DUOX2 -6.25 FLJ30726 4.81 * 229434_at 4.9 FUBP1 4.57 DUOX1 -5.96 SENP7 4.87 * 229470_at 4.82 * 227921_at 5.1 BNIPL -5.55 LPAAT-e 4.87 RUNX3 4.87 * 225046_at 5.34 DKFZp686G0786 -5.05 * 244198_at 4.44 * 243417_at 5.07 * 225062_at 4.42 ALDH3B2 -5.1 * 240344_x_at 5.43 FRMD4A 5.55 LOC150759 4.55 * 235651_at -5.65 * 244548_at 4.88 * 235123_at 4.7 * 229796_at 5.28 SAMD9 -4.72 * 236922_at 5.23 ETV6 5.31 BCL2 4.64 SAMD9 -5.22 C3orf6 4.68 * 1565786_x_at 5.31 BCL2 5.4 FAM46B -5.26 CPSF6 4.9 SMA4 5.24 BCL2 6.99 D4S234E -4.58 CD47 4.46 * 239449_at 5.6 * 235122_at 4.86 LASS3 -7.97 MSH6 4.54 MBNL2 5.86 * 229985_at 6.01 C10orf99 -8.58 RNF138 4.66 * 239954_at 4.53 * 230599_at 6.05 * 239155_at -4.54 NFYB 4.43 * 227565_at 5.81 DCBLD2 5.14 GABRE -4.43 * 224944_at 4.63 * 226974_at 6.25 NFE2L3 6.73 MN1 -7.92 SFRS7 5.01 PSIP1 4.67 NFE2L3 8.28 CRABP2 -4.43 LOC126731 5.43 PSIP1 4.7 CG018 5.31 GPR115 -4.86 FANCL 5.15 RAMP 4.7 ABCC4 5.42 PYGL -5.79 ZNF84 4.98 * 235919_at 4.98 * 213817_at 4.44 BTBD11 -5.86 ZFP62 9.01 TRIB2 5.87 * 1559410_at 4.65 RAI3 -4.82 * 238154_at 4.49 MCM8 6.17 * 241903_at 4.82 RAI3 -6.98 C6orf111 5.27 * 227663_at 5.88 NFIB 5.08 ZNF185 -4.67 NAP1L1 5.61 DPYSL2 4.47 NFIB 4.54 BENE -4.43 HNRPA3 5.19 ZNF238 5.92 NFIB 4.61 MPP7 -7.35 FAM36A 5.73 * 242968_at 5.35 * 243933_at 4.88 EMP1 -4.7 * 236619_at 5.08 BCL11A 6.7 NFIB 6.35 MAD -4.87

58 Gene symbol t-stat Gene symbol t-stat Gene symbol t-stat Gene symbol t-stat MAD -5.5 ITPKC -4.5 * 227970_at -4.51 AKR1C2 -6.04 SARG -5.8 FLJ21918 -4.54 MGC3234 -5.09 AKR1C2/AKR1C1 -5.57 SARG -7.22 NIP -6.75 FLJ23867 -4.51 AKR1C1 -6.92 ECM1 -4.71 NIP -6.26 PPARD -5.1 S100A7 -5.91 MPN -4.38 EVPL -4.96 MICAL-L1 -4.83 GJB6 -7.84 MGC59937 -4.39 PHLDA2 -5.01 ANXA11 -4.46 AKR1B10 -6.54 * 234973_at -4.51 PCYT1A -4.63 GTF3C1 -5.21 FABP5 -10.19 BJ-TSA-9 -7.47 EHD1 -4.43 CMIP -5.43 GJB2 -7.07 BJ-TSA-9 -5.74 YKT6 -4.48 * 236078_at -4.45 KRT6B -4.45 BJ-TSA-9 -7.58 PPP2R3A -5.32 HOMER2 -4.74 KRT16 -4.41 CDH3 -4.41 KIAA1145 -4.65 ARF4L -4.6 SERPINB13 -5.42 PROM2 -4.95 CA12 -4.4 FLNB -4.54 CLCA2 -4.89 TDE2L -6.59 PCYT1A -4.45 ZDHHC5 -4.88 CLCA2 -6.13 KIAA1609 -4.49 MAPK13 -4.37 FBLP-1 -5.43 CLCA2 -4.54 KIAA1609 -5.49 PVR -4.51 PKP3 -4.36 CLCA2 -4.58 CARD6 -5.23 KIAA0431 -6.49 RHOD -4.93 SPRR1B -9.49 BNC1 -4.65 PSCD3 -4.74 SARG -5.72 SPRR1A -5.8 BCL2L10 -4.47 * 228951_at -5.19 S100A16 -5.02 RHCG -4.63 SH3RF2 -4.91 OIP106 -4.54 ANXA1 -4.94 C10orf99 -8.14 HSPC159 -4.51 GPT2 -4.68 * 223596_at -4.68 CNFN -4.69 P2RY1 -6.14 SCOTIN -5.45 TJP1 -5.06 UNQ698 -6.36 PERP -5.32 MGC35097 -10.76 OVOL1 -6.59 C1orf42 -4.73 LASS3 -6.73 CDCP1 -5.2 TPM4 /// TPM3 -4.46 HAT -5.04 GM2A -5.48 ABHD6 -4.57 TPM4 -6.13 S100A12 -7.2 MLZE -6.53 ABHD6 -4.81 BDKRB1 -5.54 FLJ25179 -4.61 EVA1 -5.88 HN1 -5.98 BDKRB2 -4.62 IVL -8.71 DSG3 -5.76 C14orf65 -4.59 * 242196_at -4.78 SPRR1A -8.77 FLJ32028 -7.69 LOC284207 -5.05 OACT2 -4.69 SPRR2A -6.48 TUBA1 -4.66 SEPX1 -6.17 RASAL2 -5.4 * 232082_x_at -7.21 MGC13102 -8.36 H2AFJ -5.46 RAB10 -4.46 SYNPO2 7.91 TPD52L1 -6.12 H2AFJ -6.06 SLC6A14 -4.63 SYNPO2 6.82 SLC2A1 -4.68 PLD1 -4.42 SERPINB4 -5.05 VCAM1 4.89 TPD52L1 -5.85 * 214056_at -4.76 SERPINB4 -4.95 * 230493_at 7.09 AQP3 -5.25 ABHD5 -7.63 SERPINB3 -5.34 DMD 4.68 AQP3 -5.55 GAN -5.2 SERPINB3 -5.29 UNQ467 -6.61 * 238028_at -4.42 FLJ14490 -4.91 AKR1C3 -5.3 * 241455_at -5.37 MAFB -4.69 AKR1C2 -4.91

59 Supplementary Table S8. Probesets used in subgroup classification

Gene Group C 213702_x_at ASAH1 207121_s_at MAPK6 202998_s_at LOXL2 symbol 213902_at ASAH1 204469_at PTPRZ1 202999_s_at LOXL2 1566267_at LTBP1 218342_s_at KIAA1815 209792_s_at KLK10 201105_at LGALS1 1566268_at LTBP1 203279_at EDEM1 215808_at KLK10 203989_x_at F2R 202728_s_at LTBP1 217870_s_at CMPK 204451_at FZD1 202729_s_at LTBP1 222448_s_at CMPK Gene 204452_s_at FZD1 204475_at MMP1 Group F 202850_at ABCD3 symbol 204472_at GEM 1560078_at LAMA3 1555938_x_at VIM 1555056_at CCNG2 1563772_a_at LAMA3 201426_s_at VIM 202769_at CCNG2 Gene 1568879_a_at LAMA3 212154_at SDC2 Group G 202770_s_at CCNG2 symbol 203726_s_at LAMA3 212157_at SDC2 1554093_a_at SNAPC5 211559_s_at CCNG2 234608_at LAMA3 212158_at SDC2 213203_at SNAPC5 228081_at CCNG2 234719_at LAMA3 200755_s_at CALU 204058_at ME1 209089_at RAB5A 202267_at LAMC2 200756_x_at CALU 204059_s_at ME1 218171_at VPS4B 207517_at LAMC2 200757_s_at CALU 211204_at ME1 201339_s_at SCP2 209270_at LAMB3 1555433_at SLC39A14 240788_at ME1 209115_at UBE1C 204636_at COL17A1 1555434_a_at SLC39A14 201467_s_at NQO1 202704_at TOB1 203256_at CDH3 212110_at SLC39A14 201468_s_at NQO1 209027_s_at ABI1 201667_at GJA1 1561739_at --- 202554_s_at GSTM3 209028_s_at ABI1 203234_at UPP1 203876_s_at MMP11 201266_at TXNRD1 202730_s_at PDCD4 231376_at UPP2 203878_s_at MMP11 202831_at GPX2 202731_at PDCD4 233155_at UPP2 235908_at MMP11 239595_at GPX2 220026_at CLCA4 201481_s_at PYGB 204320_at COL11A1 204151_x_at AKR1C1 204734_at KRT15 243238_at PYGB 37892_at COL11A1 TALDO1 208771_s_at LTA4H 224915_x_at 202990_at PYGL 201852_x_at COL3A1 /// HSUP1 203431_s_at RICS TALDO1 232958_at PYGL 211161_s_at COL3A1 226227_x_at 210791_s_at RICS /// HSUP1 205577_at PYGM 215076_s_at COL3A1 TALDO1 202481_at DHRS3 226835_s_at 210074_at CTSL2 232458_at COL3A1 /// HSUP1 202701_at BMP1 209576_at GNAI1 1556499_s_at COL1A1 207152_at NTRK2 204168_at MGST2 227692_at GNAI1 202310_s_at COL1A1 214680_at NTRK2

221795_at NTRK2 201040_at GNAI2 Gene 202311_s_at COL1A1 Group E 201179_s_at GNAI3 symbol 202312_s_at COL1A1 221796_at NTRK2 201180_s_at GNAI3 205015_s_at TGFA 217430_x_at COL1A1 229463_at NTRK2 201181_at GNAI3 205016_at TGFA 204051_s_at SFRP4 236095_at NTRK2 201300_s_at PRNP 211258_s_at TGFA 204052_s_at SFRP4 201118_at PGD 215707_s_at PRNP 202345_s_at FABP5 203083_at THBS2 214430_at GLA 204750_s_at DSC2 204463_s_at EDNRA 212788_x_at FTL Gene 213187_x_at FTL Group D 204751_x_at DSC2 204464_s_at EDNRA symbol 226817_at DSC2 216235_s_at EDNRA 213813_x_at FTL 213240_s_at KRT4 205595_at DSG3 243555_at EDNRA 203343_at UGDH 201324_at EMP1 235075_at DSG3 244832_at EDNRA 204992_s_at PFN2 208911_s_at PDHB 210419_at BARX2 221729_at COL5A2 237116_at PFN2 1555419_a_at ASAH1 209351_at KRT14 221730_at COL5A2 210979_at ASAH1 223278_at GJB2 202997_s_at LOXL2 210980_s_at ASAH1

60 Supplementary Table S9. Probesets used in subgroup classification Spearman = Spearman (i.e. rank) correlation between RMA values for cell cycle gene and IHC values, across the 21 IHC'ed tumors p-value assuming sqrt(n-3)*atanh(sp) is N(0,1) Spearman p-value EREG -0.6 0 KLK10 -0.486 0 CCND1 -0.569 0 CCND2 -0.475 0 SESN3 -0.194 0.096 CCNA1 -0.392 0 SESN3 -0.418 0 CDKN2A 0.732 0 SYCP2 0.748 0 CDKN2C 0.722 0 CDC7 0.712 0 KNTC1 0.704 0 ORC1L 0.592 0 TP53 0.713 0 MCM8 0.742 0 PARC 0.552 0 MCM10 0.481 0 MCM3 0.679 0 MCM6 0.827 0 TFDP1 0.362 0.001 0.652 0 GADD45G 0.018 0.877 CCDC5 0.681 0 GAS1 0.37 0.001 E2F7 0.642 0 CDK2 0.496 0 ORC3L 0.773 0 KIF2C 0.768 0 CENPF 0.731 0 LUZP5 0.582 0 E2F3 0.514 0 HCAP-G 0.682 0 MCM2 0.717 0 MCM7 0.575 0 SMC4L1 0.732 0 PCNA 0.656 0 CDC2 0.665 0 SMC2L1 0.364 0.001 CCNE2 0.586 0 CHEK1 0.388 0.001 CCNB1 0.477 0 BUB1B 0.723 0

61