Supplemental Figure 1. -protein interaction network with increased expression in FTEb during the luteal phase. Supplemental Figure 2. Protein-protein interaction network with decreased expression in FTEb during luteal phase. LEGENDS TO SUPPLEMENTAL FIGURES

Supplemental Figure 1. Protein-protein interaction network with increased expression in FTEb during the luteal phase.

Submission of probe sets differentially expressed in the FTEb specimens

that clustered with SerCa as well as those specifically altered in FTEb luteal

samples to the online I2D database revealed overlapping networks of with increased expression in the four FTEb samples and/or FTEb

luteal samples overall. Proteins are represented by nodes, and known and

predicted first-degree interactions are represented by solid lines.

encoding proteins shown as large ovals highlighted in blue were

exclusively found in the first comparison (Manuscript Figure 2), whereas

those highlighted in red were only found in the second comparison

(Manuscript Figure 3). Genes encoding proteins shown as large ovals

highlighted in black were found in both comparisons. The color of each node indicates the ontology of the corresponding protein as determined by the Online Predicted Interaction Database (OPHID) link with the NAViGaTOR software.

Supplemental Figure 2. Protein-protein interaction network with decreased expression in FTEb during the luteal phase.

Submission of probe sets differentially expressed in the FTEb specimens

that clustered with SerCa as well as those specifically altered in FTEb luteal

samples to the online I2D database revealed overlapping networks of proteins with decreased expression in the four FTEb samples and/or FTEb

luteal samples overall. Proteins are represented by nodes, and known and

predicted first-degree interactions are represented by solid lines. Genes

encoding proteins shown as large ovals highlighted in blue were

exclusively found in the first comparison (Manuscript Figure 2), whereas

those highlighted in red were only found in the second comparison

(Manuscript Figure 3). Genes encoding proteins shown as large ovals

highlighted in black were found in both comparisons. The color of each node indicates the ontology of the corresponding protein as determined by the Online Predicted Human Interaction Database (OPHID) link with the NAViGaTOR software.

Supplemental Table 1. Genes differentially expressed in subset of FTEb samples.

Probe Set ID Title Symbol Fold Change* q-value**

Regulation of (106)

androgen (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy 211110_s_at disease) AR 0.2 3.7 202820_at aryl hydrocarbon receptor AHR 2.7 1.9 225490_at AT rich interactive domain 2 (ARID RFX-like) ARID2 0.7 3.5 212614_at †AT rich interactive domain 5B (MRF1-like) ARID5B 3.0 1.0 228890_at atonal homolog 8 () ATOH8 3.0 3.7 221530_s_at basic helix-loop-helix domain containing class B 3 BHLHB3 0.5 3.7 223185_s_at basic helix-loop-helix domain containing class B 3 BHLHB3 0.3 2.0 203543_s_at basic transcription element binding protein 1 BTEB1 2.8 3.1 220272_at basonuclin 2 BNC2 0.4 3.7 230722_at basonuclin 2 BNC2 0.3 3.7 222891_s_at B-cell CLL/lymphoma 11A ( protein) BCL11A 0.3 1.0 203140_at B-cell CLL/lymphoma 6 (zinc finger protein 51) BCL6 2.9 0.0 215990_s_at B-cell CLL/lymphoma 6 (zinc finger protein 51) BCL6 4.7 3.5 BTB and CNC homology 1 basic transcription 204194_at factor 1 BACH1 2.2 2.7 BTB and CNC homology 1, basic leucine zipper 236796_at 2 BACH2 8.2 3.7 218384_at regulated heat stable protein 1 24kDa CARHSP1 2.5 0.0 224910_at calcium regulated heat stable protein 1 24kDa CARHSP1 2.2 3.7 1555370_a_at binding transcription activator 1 CAMTA1 5.2 1.0 213268_at calmodulin binding transcription activator 1 CAMTA1 7.2 2.7 209967_s_at cAMP responsive element modulator CREM 3.9 3.7 214508_x_at cAMP responsive element modulator CREM 2.2 3.7 212501_at §CCAAT/enhancer binding protein (C/EBP) beta CEBPB 3.6 1.3 203973_s_at CCAAT/enhancer binding protein (C/EBP) delta CEBPD 3.6 2.1 213006_at CCAAT/enhancer binding protein (C/EBP) delta CEBPD 6.0 2.1 213003_s_at CCAAT/enhancer binding protein (C/EBP), delta CEBPD 3.8 3.1 1561181_at CDNA FLJ31194 fis clone KIDNE2000510 --- 4.1 1.3 202575_at cellular retinoic acid binding protein 2 CRABP2 0.2 3.5 235791_x_at chromodomain DNA binding protein 1 CHD1 1.5 3.7 1562673_at Clone IMAGE:5286598 mRNA --- 3.1 2.1 201160_s_at †cold shock domain protein A CSDA 1.4 3.1 1555411_a_at cyclin CCNL1 2.3 0.0 220046_s_at cyclin L1 CCNL1 2.2 0.0 E74-like factor 3 (ets domain transcription factor 201510_at epithelial-specific ) ELF3 3.4 1.9 E74-like factor 3 (ets domain transcription factor epithelial- 210827_s_at specific ) ELF3 3.1 3.7 226099_at ‡ RNA II 2 ELL2 2.9 2.1 226982_at ‡elongation factor RNA polymerase II 2 ELL2 3.5 3.5 219517_at elongation factor RNA polymerase II-like 3 ELL3 0.4 2.0 221950_at empty spiracles homolog 2 (Drosophila) EMX2 0.5 1.1 200878_at endothelial PAS domain protein 1 EPAS1 2.7 4.3 Probe Set ID Gene Title Symbol Fold Change* q-value** 225645_at ets homologous factor EHF 0.5 0.7 241397_at Ets homologous factor EHF 0.3 1.1 212024_x_at ‡flightless I homolog (Drosophila) FLII 1.4 2.7 202949_s_at ± four and a half LIM domains 2 FHL2 4.0 3.7 227613_at Full length insert cDNA clone YZ93G08 --- 4.1 2.7 226446_at hairy and enhancer of split 6 (Drosophila) HES6 0.3 4.3 204225_at 4 HDAC4 2.3 3.5 206194_at homeo box C4 HOXC4 0.4 3.7 211597_s_at homeodomain-only protein /// homeodomain-only protein HOP 6.0 3.7 218068_s_at hypothetical protein FLJ22301 FLJ22301 2.1 4.3 LOC148203 /// hypothetical protein LOC148203 /// similar to hypothetical LOC115648 /// 240155_x_at protein FLJ13659 /// zinc finger protein 493 ZNF493 0.6 1.1 ±,‡,§inhibitor of DNA binding 2 dominant negative helix-loop- 201565_s_at helix protein ID2 2.4 1.2 ‡,§inhibitor of DNA binding 2 dominant negative helix-loop- 201566_x_at helix protein ID2 2.2 3.5 ±,§inhibitor of DNA binding 2 dominant negative helix-loop- 213931_at helix protein ID2 2.9 1.5 206332_s_at interferon gamma-inducible protein 16 IFI16 2.8 1.0 208966_x_at interferon gamma-inducible protein 16 IFI16 2.8 2.1 204785_x_at interferon (alpha beta and omega) receptor 2 IFNAR2 1.8 3.7 204786_s_at interferon (alpha beta and omega) receptor 2 IFNAR2 2.1 2.1 204166_at KIAA0963 KIAA0963 1.8 1.2 231015_at Kruppel-like factor 15 KLF15 2.2 1.9 212924_s_at ‡LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM4 0.7 4.3 205101_at MHC class II transactivator MHC2TA 5.4 3.7 1555832_s_at MRNA; cDNA DKFZp564C2063 (from clone DKFZp564C2063) --- 1.9 2.1 232676_x_at myelin expression factor 2 MYEF2 0.5 2.1 204959_at myeloid cell nuclear differentiation MNDA 2.0 2.7 220184_at Nanognuclear factor of kappa polypeptide gene enhancer in NANOG 0.6 3.7 209239_at B-cells 1 (p105) NFKB1 1.9 2.1 225344_at 7 NCOA7 6.9 0.0 nuclear receptor subfamily 3 group C member 1 201865_x_at () NR3C1 1.6 3.5 202080_s_at OGT(O-Glc-NAc )-interacting protein 106 KDa OIP106 0.6 4.3 227220_at ovarian zinc finger protein HOZFP 0.4 4.3 37152_at peroxisome proliferative activated receptor delta PPARD 2.5 2.1

phosphatidylinositol glycan anchor biosynthesis, class OAF /// F /// zinc finger, FYVE domain containing 20 /// OAF PIGF /// 1553569_at homolog (Drosophila) ZFYVE20 0.7 3.5

phosphatidylinositol glycan anchor biosynthesis, class OAF /// F /// zinc finger, FYVE domain containing 20 /// OAF PIGF /// 1553570_x_at homolog (Drosophila) ZFYVE20 0.7 2.7 207109_at POU domain class 2 transcription factor 3 POU2F3 4.5 1.2 203035_s_at ‡ protein inhibitor of activated STAT 3 PIAS3 0.5 4.3 202963_at regulatory factor X 5 (influences HLA class II expression) RFX5 1.7 1.2 ±runt-related transcription factor 1 (acute myeloid leukemia 209360_s_at 1; aml1 ) RUNX1 2.6 0.0 1559946_s_at RuvB-like 2 (E. coli) RUVBL2 0.4 3.1 Probe Set ID Gene Title Symbol Fold Change* q-value** 206118_at signal transducer and activator of transcription 4 STAT4 3.0 3.7 225227_at ±, ‡SKI-like SKIL 2.5 2.1 201920_at †, ‡ 20 (phosphate transporter) member 1 SLC20A1 1.8 1.0 202761_s_at repeat containing nuclear envelope 2 SYNE2 4.0 1.3 208313_s_at splicing factor 1 SF1 1.2 1.2 214633_at SRY (sex determining region Y)-box 3 SOX3 0.1 3.5 201416_at ±,‡SRY (sex determining region Y)-box 4 SOX4 0.5 3.1 215078_at superoxide dismutase 2 mitochondrial SOD2 12.7 2.1 215223_s_at superoxide dismutase 2 mitochondrial SOD2 12.3 1.9 216841_s_at superoxideSWI/SNF related dismutase matrix 2 associatedmitochondrial dependent SOD2 10.2 3.5 204099_at regulator of subfamily d member 3 SMARCD3 6.0 0.0 204281_at TEA domain family member 4 TEAD4 5.0 4.3 41037_at TEA domain family member 4 TEAD4 5.8 3.5 212209_at thyroid associated protein 2 THRAP2 1.8 3.7 236439_at Transcribed --- 2.7 1.2 242784_at Transcribed locus --- 3.9 1.0 243469_at Transcribed locus --- 2.1 1.2 transcription factor AP-2 gamma (activating enhancer 205286_at binding protein 2 gamma) TFAP2C 2.3 2.0 238520_at transcriptional regulating factor 1 TRERF1 0.2 3.7 ±,§v-ets erythroblastosis virus E26 oncogene homolog 201328_at 2 (avian) ETS2 4.8 1.0 ±,§v-ets erythroblastosis virus E26 oncogene homolog 201329_s_at 2 (avian) ETS2 3.5 1.2 224833_at v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) ETS1 2.3 3.5 204798_at v- myeloblastosis viral oncogene homolog (avian) MYB 0.5 2.7 206035_at v- reticuloendotheliosis viral oncogene homolog (avian) REL 1.7 3.7 209431_s_at zinc finger protein 278 ZNF278 0.6 2.1 231545_at --- 1.5 4.3 240776_at --- 0.1 3.1 240798_at --- 2.7 3.7

Signal Transduction (66) 202641_at ADP-ribosylation factor-like 3 ARL3 0.4 1.1 228771_at ‡ adrenergic beta receptor 2 ADRBK2 0.4 2.0 217419_x_at agrin AGRN 0.6 2.7 205870_at bradykinin receptor B2 BDKRB2 3.5 3.5 219500_at ±cardiotrophin-like cytokine CLC 2.5 1.5 203416_at CD53 antigen CD53 2.9 3.5 203794_at CDC42 binding alpha (DMPK-like) CDC42BPA 0.8 2.1 239555_at CDNA clone IMAGE:40114646 --- 1.4 3.1 232120_at CDNA FLJ14259 fis clone PLACE1001076 --- 1.8 3.7 232290_at CDNA: FLJ20869 fis clone ADKA02377 --- 1.6 3.1 221223_x_at cytokine inducible SH2-containing protein CISH 3.1 2.1 206590_x_at dopamine receptor D2 DRD2 2.1 1.0 216938_x_at dopamine receptor D2 DRD2 1.9 4.3 endothelial differentiation lysophosphatidic acid G-protein- 231192_at coupled receptor 7 EDG7 0.4 2.0 216999_at erythropoietin receptor EPOR 0.1 1.0 Probe Set ID Gene Title Symbol Fold Change* q-value** 205650_s_at fibrinogen A alpha polypeptide FGA 5.9 3.5 237131_at hypothetical protein FLJ36032 FLJ36032 0.2 2.7 204686_at substrate 1 IRS1 1.8 1.5 205302_at ‡insulin-like growth factor binding protein 1 IGFBP1 9.7 3.7 202727_s_at interferon gamma receptor 1 IFNGR1 2.4 1.0 242903_at interferon gamma receptor 1 IFNGR1 2.1 3.5 interferon gamma receptor 1 /// interferon gamma 211676_s_at receptor 1 IFNGR1 2.4 2.0 interferon gamma receptor 2 (interferon gamma 201642_at transducer 1) IFNGR2 2.2 1.2 201887_at interleukin 13 receptor alpha 1 IL13RA1 2.3 0.0 222868_s_at interleukin 18 binding protein IL18BP 2.2 1.2 ‡interleukin 6 signal transducer (gp130 oncostatin M 212195_at receptor) IL6ST 2.3 1.9 226218_at interleukin 7 receptor IL7R 5.1 3.1 231779_at ± interleukin-1 receptor-associated kinase 2 IRAK2 8.0 1.2 229296_at LOC389793 --- 2.4 3.7 223280_x_at membrane-spanning 4-domains subfamily A member 6A MS4A6A 4.8 1.0 223922_x_at membrane-spanning 4-domains subfamily A member 6A MS4A6A 3.4 2.1 224356_x_at membrane-spanning 4-domains subfamily A member 6A MS4A6A 5.0 1.0 natriuretic peptide receptor B/ B 204310_s_at (atrionatriuretic peptide receptor B) NPR2 0.4 3.1 natriuretic peptide receptor B/guanylate cyclase B 214066_x_at (atrionatriuretic peptide receptor B) NPR2 0.3 1.9 201080_at phosphatidylinositol-4-phosphate 5-kinase type II beta PIP5K2B 0.6 3.5 4A cAMP-specific (phosphodiesterase 204735_at E2 dunce homolog Drosophila) PDE4A 1.7 2.7 ‡phosphodiesterase 4D cAMP-specific (phosphodiesterase 204491_at E3 dunce homolog Drosophila) PDE4D 2.2 1.5 209643_s_at D2 PLD2 1.9 1.0 210845_s_at ‡plasminogen activator PLAUR 3.2 3.7 1555167_s_at pre-B-cell colony enhancing factor 1 PBEF1 8.3 3.1 217738_at pre-B-cell colony enhancing factor 1 PBEF1 11.7 2.1 217739_s_at pre-B-cell colony enhancing factor 1 PBEF1 9.7 1.2 243296_at Pre-B-cell colony enhancing factor 1 PBEF1 9.5 2.7 204842_x_at protein kinase cAMP-dependent regulatory type II alpha PRKAR2A 0.8 3.5 protein 2 regulatory subunit B (B56) 202513_s_at delta isoform PPP2R5D 0.7 3.5 212587_s_at protein tyrosine phosphatase receptor type C PTPRC 2.9 3.5 212588_at protein tyrosine phosphatase receptor type C PTPRC 3.0 2.7 203910_at PTPL1-associated RhoGAP 1 PARG1 2.6 3.1 228521_s_at ‡RAB4B member RAS oncogene family RAB4B 2.0 2.1 233385_x_at ‡RAB4B member RAS oncogene family RAB4B 1.7 3.1 212122_at ras homolog gene family member Q RHOQ 3.0 4.3 202988_s_at §regulator of G-protein signalling 1 RGS1 3.5 1.0 226576_at Rho GTPase activating protein 26 ARHGAP26 0.3 3.1 205980_s_at Rho GTPase activating protein 8 ARHGAP8 0.6 3.1 204765_at Rho guanine nucleotide exchange factor (GEF) 5 ARHGEF5 1.8 2.0 1553794_at stomatin (EPB72)-like 3 STOML3 0.3 2.1 Probe Set ID Gene Title Symbol Fold Change* q-value** 227697_at ‡suppressor of cytokine signaling 3 SOCS3 3.5 3.7 236495_at Transcribed locus --- 9.1 4.3 242106_at Transcribed locus --- 3.3 3.5 242110_at Transcribed locus --- 1.8 3.7 ‡ transforming growth factor beta receptor I (activin A 224793_s_at receptor type II-like kinase 53kDa) TGFBR1 1.7 4.3 202154_x_at ‡ beta 4 TUBB4 0.3 4.3 213476_x_at ‡ tubulin beta 4 TUBB4 0.3 2.1 207907_at tumor necrosis factor (ligand) superfamily member 14 TNFSF14 1.9 1.9 ‡v-yes-1 Yamaguchi sarcoma viral related oncogene 202625_at homolog LYN 1.5 3.5 240655_at --- 0.6 3.7

Immune Response (59) CD74 antigen (invariant polypeptide of major 209619_at histocompatibility complex class II antigen-associated) CD74 3.0 1.3 CD74 antigen (invariant polypeptide of major histocompat- 1567628_at ibility complex class II antigen-associated) CD74 4.1 1.2 CD74 molecule, major histocompatibility complex, class II 1567627_at invariant chain CD74 4.2 1.0 205758_at CD8 antigen alpha polypeptide (p32) CD8A 5.2 4.3 206337_at chemokine (C-C motif) receptor 7 CCR7 2.5 2.0 chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic 206336_at protein 2) CXCL6 8.5 1.9 complement component 1 q subcomponent gamma 225353_s_at polypeptide C1QG 4.0 1.0 212067_s_at complement component 1 r subcomponent C1R 8.5 1.2 208747_s_at complement component 1 s subcomponent C1S 3.2 3.5 205654_at ‡complement component 4 binding protein alpha C4BPA 12.9 3.5 208451_s_at complement component 4A C4A 7.4 1.2 214428_x_at complement component 4A C4A 7.7 0.0 Fc fragment of IgE high affinity I receptor for; gamma 204232_at polypeptide FCER1G 6.4 0.0 Fc fragment of IgE high affinity I receptor for; gamma 1554899_s_at polypeptide FCER1G 6.2 0.0

Fc fragment of IgG low affinity IIa receptor for (CD32) /// FCGR2A /// Fc fragment of IgG low affinity IIb receptor for (CD32) /// FCGR2B /// 210992_x_at Fc fragment of IgG low affinity IIc receptor for (CD32) FCGR2C 1.9 1.2 202748_at ±guanylate binding protein 2 interferon-inducible GBP2 2.5 3.5 201422_at interferon gamma-inducible protein 30 IFI30 3.4 2.0 201315_x_at interferon induced transmembrane protein 2 (1-8D) IFITM2 1.9 1.0 212203_x_at interferon induced transmembrane protein 3 (1-8U) IFITM3 1.6 3.5 212657_s_at ±, ‡interleukin 1 receptor antagonist IL1RN 2.9 4.3 interleukin 2 receptor gamma (severe combined 204116_at immunodeficiency) IL2RG 3.0 1.0 203233_at interleukin 4 receptor IL4R 5.5 1.0 lymphocyte cytosolic protein 2 (SH2 domain containing 205269_at leukocyte protein of 76kDa) LCP2 4.9 2.0 215313_x_at major histocompatibility complex class I A HLA-A 2.0 1.9 Probe Set ID Gene Title Symbol Fold Change* q-value** major histocompatibility complex class I A /// Clone 213932_x_at IMAGE:5214329 mRNA HLA-A 1.6 3.5 208729_x_at ‡ major histocompatibility complex class I B HLA-B 3.0 2.1 209140_x_at ‡ major histocompatibility complex class I B HLA-B 2.8 2.1 208812_x_at major histocompatibility complex class I C HLA-C 2.2 3.5 214459_x_at major histocompatibility complex class I C HLA-C 2.2 2.1 major histocompatibility complex class I C /// major 211911_x_at histocompatibility complex class I C HLA-C 3.1 3.7 200905_x_at major histocompatibility complex class I E HLA-E 2.0 2.1 217456_x_at major histocompatibility complex class I E HLA-E 1.8 1.2 204806_x_at major histocompatibility complex class I F HLA-F 2.6 3.5 221875_x_at major histocompatibility complex class I F HLA-F 2.6 2.0 221978_at major histocompatibility complex class I F HLA-F 3.2 2.0 217478_s_at major histocompatibility complex class II DM alpha HLA-DMA 4.2 2.7 203932_at major histocompatibility complex class II DM beta HLA-DMB 3.3 1.9 226878_at major histocompatibility complex class II DO alpha HLA-DOA 15.4 0.0 211991_s_at major histocompatibility complex class II DP alpha 1 HLA-DPA1 7.1 0.0 213537_at major histocompatibility complex class II DP alpha 1 HLA-DPA1 7.4 1.2 201137_s_at major histocompatibility complex class II DP beta 1 HLA-DPB1 6.2 0.0 209823_x_at majorjpypQ histocompatibility complex class II DQ beta 1 HLA-DQB1 6.2 0.0 211656_x_at major histocompatibility complex class II DQ beta 1 HLA-DQB1 4.1 1.2 208894_at major histocompatibility complex class II DR alpha HLA-DRA 5.4 1.9 210982_s_at major histocompatibility complex class II DR alpha HLA-DRA 5.1 1.9

major histocompatibility complex class II DR beta 1 /// HLA-DRB1 /// major histocompatibility complex class II DR beta 3 /// HLA-DRB3 /// 204670_x_at major histocompatibility complex class II DR beta 4 HLA-DRB4 4.8 1.2 208306_x_at major histocompatibility complex class II DR beta 3 HLA-DRB3 3.8 1.2 215193_x_at major histocompatibility complex class II DR beta 3 HLA-DRB3 4.9 1.5 216526_x_at major histocompatibility complex, class I, C HLA-C 2.4 1.2 200904_at major histocompatibility complex, class I, E HLA-E 2.3 2.0 211990_at major histocompatibility complex, class II, DP alpha 1 HLA-DPA1 5.2 1.3 209312_x_at major histocompatibility complex, class II, DR beta 1 HLA-DRB1 4.7 1.9 203828_s_at natural killer cell transcript 4 NK4 2.5 1.9 211063_s_at NCK adaptor protein 1 /// NCK adaptor protein 1 NCK1 1.8 3.7 serine (or cysteine) proteinase inhibitor clade B (ovalbumin) 210413_x_at member 4 SERPINB4 2.8 1.5 serine (or cysteine) proteinase inhibitor clade G (C1 200986_at inhibitor) member 1 (angioedema hereditary) SERPING1 4.6 0.0 204924_at toll-like receptor 2 TLR2 3.8 2.1 229937_x_at Transcribed locus --- 3.3 3.5 244485_at Transcribed locus --- 5.9 1.5

Cell Cycle/Proliferation (39) 209901_x_at allograft inflammatory factor 1 AIF1 3.2 1.0 213095_x_at allograft inflammatory factor 1 AIF1 3.4 1.0 215051_x_at allograft inflammatory factor 1 AIF1 3.4 0.0 bone morphogenetic protein receptor type II (serine/ 225144_at threonine kinase) BMPR2 1.6 3.7 214452_at † branched chain aminotransferase 1 cytosolic BCAT1 1.4 3.7 Probe Set ID Gene Title Symbol Fold Change* q-value** 202717_s_at CDC16 cell division cycle 16 homolog (S. cerevisiae) CDC16 0.6 3.5 201853_s_at ‡ cell division cycle 25B CDC25B 2.2 2.7 201220_x_at ‡C-terminal binding protein 2 CTBP2 0.6 2.0 210835_s_at ‡C-terminal binding protein 2 CTBP2 0.7 2.1 218845_at dual specificity phosphatase 22 DUSP22 2.4 1.3 204014_at dual specificity phosphatase 4 DUSP4 10.7 3.7 211485_s_at fibroblast growth factor 18 FGF18 2.4 3.1 211284_s_at †granulin GRN 1.7 3.7 202192_s_at growth arrest-specific 7 GAS7 0.3 3.5 206697_s_at haptoglobin HP 27.5 3.5 208470_s_at haptoglobin HP 14.8 4.3 218603_at ‡headcase homolog (Drosophila) HECA 1.6 3.7 hypothetical protein MGC12760 /// hypothetical protein 211038_s_at MGC12760 MGC12760 0.4 3.5 226535_at ±,§integrin beta 6 ITGB6 3.8 1.9 201601_x_at interferon induced transmembrane protein 1 (9-27) IFITM1 2.6 3.5 227013_at ‡LATS large tumor suppressor homolog 2 (Drosophila) LATS2 2.4 1.2 205011_at loss of heterozygosity 11 chromosomal region 2 gene A LOH11CR2A 3.1 2.0 223234_at MAD2 mitotic arrest deficient-like 2 (yeast) MAD2L2 1.6 3.1 223158_s_at NIMA (never in gene a)-related kinase 6 NEK6 2.4 3.1 209815_at Patched homolog (Drosophila) --- 0.6 3.5 209193_at § pim-1 oncogene PIM1 3.0 3.1 201939_at †polo-like kinase 2 (Drosophila) PLK2 3.7 3.7 221554_at protein kinase LYK5 LYK5 0.6 2.7 201408_at 1 catalytic subunit beta isoform PPP1CB 2.1 1.5 228222_at Protein phosphatase 1, catalytic subunit, beta isoform PPP1CB 1.4 2.7 ‡ (formerly 2A) regulatory subunit A 202883_s_at (PR 65) beta isoform PPP2R1B 2.2 1.3 regenerating islet-derived 1 alpha (pancreatic stone protein 209752_at pancreatic thread protein) REG1A 2.5 4.3 206392_s_at responder (tazarotene induced) 1 RARRES1 10.4 1.2 221872_at retinoic acid receptor responder (tazarotene induced) 1 RARRES1 13.1 1.9 212698_s_at septin 10 39335 2.0 3.5 203448_s_at telomeric repeat binding factor (NIMA-interacting) 1 TERF1 0.6 3.7 202241_at tribbles homolog 1 (Drosophila) TRIB1 2.0 2.1 210512_s_at §vascular endothelial growth factor VEGF 2.2 2.0 201369_s_at ‡zinc finger protein 36 C3H type-like 2 ZFP36L2 1.9 3.7

Protein Modification (34) 232592_at CDNA FLJ11982 fis clone HEMBB1001335 --- 2.3 4.3 1561705_at Clone IMAGE:5267224 mRNA --- 0.4 1.9 collagen type IV alpha 3 (Goodpasture antigen) binding 226277_at protein COL4A3BP 0.5 1.0 223402_at dual specificity phosphatase 23 DUSP23 5.3 0.0 220408_x_at family with sequence similarity 48 member A FAM48A 0.5 2.0 221774_x_at family with sequence similarity 48 member A FAM48A 0.5 2.7 226330_s_at family with sequence similarity 48 member A FAM48A 0.5 2.7 208018_s_at hemopoietic cell kinase HCK 2.3 1.2 235458_at hepatitis A virus cellular receptor 2 HAVCR2 5.1 2.7 Probe Set ID Gene Title Symbol Fold Change* q-value** 229584_at hypothetical protein DKFZp434H2111 DKFZp434H2111 2.4 3.7 225949_at hypothetical protein LOC340371 LOC340371 0.5 4.3 211339_s_at IL2-inducible T-cell kinase ITK 1.9 2.7 211108_s_at Janus kinase 3 (a protein leukocyte) JAK3 1.3 3.7 214180_at mannosidase alpha class 1C member 1 MAN1C1 3.5 2.7 202569_s_at MAP/ affinity-regulating kinase 3 MARK3 1.8 3.1 201460_at mitogen-activated protein kinase-activated protein kinase 2 MAPKAPK2 2.0 1.5 MRNA; cDNA DKFZp434O0919 (from clone 234224_at DKFZp434O0919) --- 2.4 0.0 209791_at peptidyl arginine deiminase type II PADI2 6.0 3.7 protein tyrosine phosphatase non-receptor type 22 206060_s_at (lymphoid) PTPN22 2.5 1.5 221840_at protein tyrosine phosphatase receptor type E PTPRE 3.4 2.0 206574_s_at protein tyrosine phosphatase type IVA member 3 PTP4A3 5.0 2.7 209695_at protein tyrosine phosphatase type IVA member 3 PTP4A3 4.0 1.9 226571_s_at ‡protein tyrosine phosphatase, receptor type, S PTPRS 1.5 2.0 sialyltransferase 1 (beta-galactoside alpha-2 6- 201998_at sialyltransferase) SIAT1 3.5 0.0 204595_s_at stanniocalcin 1 STC1 44.9 1.0 204597_x_at stanniocalcin 1 STC1 24.3 1.5 230746_s_at Stanniocalcin 1 STC1 15.2 0.0 243410_at Transcribed locus --- 2.3 2.7

Transcribed locus, moderately similar to XP_001067122.1 similar to zinc finger and BTB domain containing 41 229465_s_at [Rattus norvegicus] --- 1.4 2.1 202478_at tribbles homolog 2 (Drosophila) TRIB2 1.9 1.2 205890_s_at ubiquitin D UBD 3.2 1.2 UDP-GlcNAc:betaGal beta-1 3-N-acetylglucosaminyl- 1555963_x_at transferase 7 B3GNT7 6.9 2.1 UDP-GlcNAc:betaGal beta-1 3-N-acetylglucosaminyl- 1555962_at transferase 7 B3GNT7 6.7 1.5 242188_at --- 2.5 0.0

Apoptosis (29) 210538_s_at baculoviral IAP repeat-containing 3 BIRC3 8.1 4.3 202387_at BCL2-associated athanogene BAG1 1.9 0.0 211475_s_at BCL2-associated athanogene BAG1 2.0 1.2 205780_at BCL2-interacting killer (apoptosis-inducing) BIK 1.6 4.3 200838_at † cathepsin B CTSB 2.2 1.0 200839_s_at † cathepsin B CTSB 1.7 1.2 213274_s_at † cathepsin B CTSB 2.9 1.0 225656_at EF-hand domain (C-terminal) containing 1 EFHC1 0.6 2.7 215096_s_at † D/formylglutathione ESD 0.8 3.5 201631_s_at ±,§immediate early response 3 IER3 4.1 2.7 203836_s_at mitogen-activated protein kinase kinase kinase 5 MAP3K5 5.7 3.5 203837_at mitogen-activated protein kinase kinase kinase 5 MAP3K5 5.7 0.0 200798_x_at myeloid cell leukemia sequence 1 (BCL2-related) MCL1 3.4 1.5 214056_at Myeloid cell leukemia sequence 1 (BCL2-related) MCL1 3.7 0.0 Probe Set ID Gene Title Symbol Fold Change* q-value** non-metastatic cells 5 protein expressed in (nucleoside- 206197_at diphosphate kinase) NME5 0.4 1.9 200787_s_at phosphoprotein enriched in astrocytes 15 PEA15 2.6 1.0 200788_s_at phosphoprotein enriched in astrocytes 15 PEA15 2.4 0.0 205512_s_at programmed cell death 8 (apoptosis-inducing factor) PDCD8 0.5 4.3 209539_at ‡Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 ARHGEF6 2.5 1.9 221601_s_at ‡regulator of Fas-induced apoptosis TOSO 4.1 4.3 serine (or cysteine) proteinase inhibitor clade B (ovalbumin) 209723_at member 9 SERPINB9 3.0 1.9 212344_at 1 SULF1 2.6 1.2 212353_at sulfatase 1 SULF1 3.9 1.0 212354_at sulfatase 1 SULF1 4.2 3.1 202688_at ±,‡ tumor necrosis factor (ligand) superfamily member 10 TNFSF10 5.5 1.3 218856_at tumor necrosis factor receptor superfamily member 21 TNFRSF21 4.2 3.7

v-rel reticuloendotheliosis viral oncogene homolog A nuclear factor of kappa light polypeptide gene enhancer 201783_s_at in B-cells 3 p65 (avian) RELA 1.9 1.0

V-rel reticuloendotheliosis viral oncogene homolog A, nuclear factor of kappa light polypeptide gene enhancer in B-cells 3, 230202_at p65 (avian) RELA 1.9 0.0 1553538_s_at --- 0.8 2.7

Metabolism (24) 203711_s_at 3-hydroxyisobutyryl-Coenzyme A hydrolase HIBCH 0.5 3.7 202422_s_at acyl-CoA synthetase long-chain family member 4 ACSL4 2.8 2.0 201612_at aldehyde dehydrogenase 9 family member A1 ALDH9A1 0.6 1.5 ‡aldo-keto reductase family 1 member A1 (aldehyde 201900_s_at reductase) AKR1A1 0.8 2.7 203504_s_at ATP-binding cassette sub-family A (ABC1) member 1 ABCA1 2.7 4.3 203505_at ATP-binding cassette sub-family A (ABC1) member 1 ABCA1 2.8 2.1 232347_x_at CDNA FLJ11379 fis clone HEMBA1000469 --- 0.6 1.1 dodecenoyl-Coenzyme A delta (3 2 trans-enoyl- 209759_s_at Coenzyme A isomerase) DCI 0.6 1.9 209368_at epoxide hydrolase 2 cytoplasmic EPHX2 0.5 4.3 202651_at family with sequence similarity 34 member A FAM34A 1.6 1.9 202419_at follicular lymphoma variant translocation 1 FVT1 1.9 1.2 205100_at glutamine-fructose-6-phosphate transaminase 2 GFPT2 7.6 3.7 213713_s_at hypothetical protein BC008326 LOC89944 0.5 1.3 202069_s_at †isocitrate dehydrogenase 3 (NAD+) alpha IDH3A 2.5 1.9 212715_s_at KIAA0819 protein KIAA0819 0.6 1.1 225847_at KIAA1363 protein KIAA1363 4.0 3.1 235374_at ‡malate dehydrogenase 1 NAD (soluble) MDH1 0.6 3.5 238721_at malate dehydrogenase 1B NAD (soluble) MDH1B 0.4 1.1 methylene tetrahydrofolate dehydrogenase (NAD+ 201761_at dependent) methenyltetrahydrofolate cyclohydrolase MTHFD2 2.1 1.5 Microtubule associated monoxygenase, calponin and LIM 231553_s_at domain containing 3 MICAL3 0.6 1.1 208918_s_at ‡ NAD kinase FLJ13052 2.1 0.0 208919_s_at ‡ NAD kinase FLJ13052 1.5 1.3 Probe Set ID Gene Title Symbol Fold Change* q-value** 218025_s_at peroxisomal D3 D2-enoyl-CoA isomerase PECI 0.5 2.1 202739_s_at phosphorylase kinase beta PHKB 0.5 3.5

Cell Adhesion (22) 201952_at †activated leukocyte cell adhesion molecule ALCAM 0.7 3.5 203256_at cadherin 3 type 1 P-cadherin (placental) CDH3 3.8 1.2 ‡cell adhesion molecule with homology to L1CAM (close 204591_at homolog of L1) CHL1 6.0 2.1 221900_at collagen type VIII alpha 2 COL8A2 1.8 1.0 203240_at Fc fragment of IgG binding protein FCGBP 3.9 0.0 201350_at ‡flotillin 2 FLOT2 2.3 1.5 229041_s_at Hypothetical gene supported by BC040064 --- 4.6 1.2 221921_s_at immunoglobulin superfamily member 4B IGSF4B 7.4 1.2 immunoglobulin superfamily member 4B /// immunoglobulin 211677_x_at superfamily member 4B IGSF4B 3.7 0.0 210184_at (antigen CD11C (p150) alpha polypeptide) ITGAX 4.0 1.2

(antigen CD18 (p95) lymphocyte function- associated antigen 1; macrophage antigen 1 (mac-1) beta 202803_s_at subunit) ITGB2 4.4 3.1 intercellular adhesion molecule 1 (CD54) human rhinovirus 202638_s_at receptor ICAM1 4.2 3.7 234583_at MRNA; cDNA DKFZp547L174 (from clone DKFZp547L174) --- 10.0 1.9 204895_x_at mucin 4 tracheobronchial MUC4 1.7 2.1 217110_s_at mucin 4 tracheobronchial MUC4 2.5 3.1 223562_at parvin gamma PARVG 2.4 3.1 233510_s_at parvin gamma PARVG 2.4 2.0 202897_at protein tyrosine phosphatase non-receptor type substrate 1 PTPNS1 2.1 1.3 205656_at protocadherin 17 PCDH17 0.3 3.5 1552807_a_at sialic acid binding Ig-like lectin 10 SIGLEC10 1.7 2.7 †,‡transglutaminase 2 (C polypeptide protein-glutamine- 201042_at gamma-glutamyltransferase) TGM2 4.2 0.0 203868_s_at vascular cell adhesion molecule 1 VCAM1 15.7 1.0

Cell Motility (14) 201550_x_at actin gamma 1 ACTG1 1.3 4.3 211995_x_at actin gamma 1 ACTG1 1.6 1.0 212363_x_at actin gamma 1 ACTG1 1.5 1.0 212988_x_at actin gamma 1 ACTG1 1.4 3.5 201954_at actin related protein 2/3 complex subunit 1B 41kDa ARPC1B 3.9 1.9 200600_at †,‡moesin MSN 1.7 3.5 201670_s_at myristoylated alanine-rich protein kinase C substrate MARCKS 0.6 1.9 213002_at Myristoylated alanine-rich protein kinase C substrate MARCKS 0.6 3.1 1555812_a_at ‡ Rho GDP dissociation inhibitor (GDI) beta ARHGDIB 2.7 1.9 201288_at ‡Rho GDP dissociation inhibitor (GDI) beta ARHGDIB 1.8 3.1 208977_x_at tubulin beta 2 TUBB2 0.3 3.7 213726_x_at tubulin beta 2 TUBB2 0.3 4.3 205844_at vanin 1 VNN1 38.4 1.5 205922_at vanin 2 VNN2 2.8 3.5 Probe Set ID Gene Title Symbol Fold Change* q-value**

Ubiquitin Cycle (10) 227203_at F-box and leucine-rich repeat protein 17 FBXL17 0.5 3.5 228427_at F-box protein 16 FBXO16 0.3 3.1 227219_x_at microtubule-associated protein 1 light chain 3 alpha MAP1LC3A 1.6 4.3 208785_s_at ‡microtubule-associated protein 1 light chain 3 beta MAP1LC3B 2.0 4.3 232573_at MRNA full length insert cDNA clone EUROIMAGE 2004482 --- 7.6 2.7 229573_at ubiquitin specific peptidase 9, X-linked USP9X 1.9 4.3 226035_at ubiquitin specific 31 USP31 3.8 1.0 227093_at ubiquitin specific protease 36 USP36 2.2 3.7 ubiquitin specific protease 9 X-linked (fat facets-like 201099_at Drosophila) USP9X 1.3 3.5

‡ ubiquitin-conjugating E2D 1 (UBC4/5 homolog yeast) /// ubiquitin-conjugating enzyme E2D 1 (UBC4/5 211764_s_at homolog yeast) UBE2D1 2.1 2.1

Unknown/Other (483) 224938_at ‡82-kD FMRP Interacting Protein 182-FIP 1.7 3.7 a disintegrin and metalloproteinase domain 17 (tumor 205745_x_at necrosis factor alpha converting enzyme) ADAM17 1.6 2.7 a disintegrin and metalloproteinase domain 17 (tumor 213532_at necrosis factor alpha converting enzyme) ADAM17 1.7 3.7 232007_at acid acyltransferase-epsilon LPAAT-e 3.0 1.0 225917_at activating transcription factor 7 interacting protein ATF7IP 0.7 3.1 205639_at acyloxyacyl hydrolase (neutrophil) AOAH 1.9 2.0 202442_at adaptor-related protein complex 3 sigma 1 subunit AP3S1 0.8 4.3 203741_s_at adenylate cyclase 7 ADCY7 1.6 3.5 221761_at adenylosuccinate synthase ADSS 1.7 3.5 209596_at adlican DKFZp564I1922 8.8 3.5 200011_s_at ‡ ADP-ribosylation factor 3 /// ADP-ribosylation factor 3 ARF3 1.4 2.1 200761_s_at ADP-ribosylation-like factor 6 interacting protein 5 ARL6IP5 0.7 3.5 212285_s_at agrin AGRN 0.6 3.7 Alport syndrome mental retardation midface hypoplasia 204976_s_at and elliptocytosis chromosomal region gene 1 AMMECR1 0.4 1.9 214707_x_at Alstrom syndrome 1 /// LOC200420 LOC200420 0.7 2.7 200714_x_at amplified in osteosarcoma OS-9 0.7 3.7 ‡angiotensinogen (serine (or cysteine) proteinase inhibitor 202834_at clade A (alpha-1 antiproteinase antitrypsin) member 8) AGT 4.1 1.2 209442_x_at 3 node of Ranvier (ankyrin G) ANK3 0.5 3.7 238538_at ankyrin repeat domain 11 ANKRD11 0.6 2.1 209173_at anterior gradient 2 homolog (Xenopus laevis) AGR2 0.1 1.0 228969_at anterior gradient 2 homolog (Xenopus laevis) AGR2 0.1 2.1 224694_at anthrax toxin receptor 1 ANTXR1 2.2 4.3 204561_x_at apolipoprotein C-II APOC2 6.3 0.0 231561_s_at Apolipoprotein C-II APOC2 6.3 1.0 203382_s_at ‡ apolipoprotein E APOE 2.0 0.0 205568_at 9 AQP9 5.9 0.0 223794_at armadillo repeat containing 4 ARMC4 0.3 2.1 226055_at arrestin domain containing 2 ARRDC2 2.0 4.3 Probe Set ID Gene Title Symbol Fold Change* q-value** ATP synthase H+ transporting mitochondrial F1 complex 203926_x_at delta subunit ATP5D 0.7 2.1 201242_s_at ATPase Na+/K+ transporting beta 1 polypeptide ATP1B1 0.4 3.5 208836_at ATPase Na+/K+ transporting beta 3 polypeptide ATP1B3 2.6 3.7 202850_at ATP-binding cassette sub-family D (ALD) member 3 ABCD3 0.7 3.5 212599_at autism susceptibility candidate 2 AUTS2 2.6 3.7 B double prime 1 subunit of RNA polymerase III transcription 226290_at initiation factor IIIB BDP1 0.4 4.3 202357_s_at B-factor properdin BF 6.3 1.0 †biogenesis of lysosome-related organelles complex-1 202592_at subunit 1 BLOC1S1 0.6 2.7 1569001_at †,‡bone morphogenetic protein 1 BMP1 1.4 3.7 226580_at breast cancer metastasis-suppressor 1-like BRMS1L 1.9 4.3 202103_at bromodomain containing 4 BRD4 2.2 3.7 34726_at ‡ voltage-dependent beta 3 subunit CACNB3 0.4 2.0 231729_s_at calcyphosine CAPS 0.3 1.5 200653_s_at calmodulin 1 (phosphorylase kinase delta) CALM1 0.5 1.3 200655_s_at calmodulin 1 (phosphorylase kinase delta) CALM1 0.4 3.7 209563_x_at calmodulin 1 (phosphorylase kinase delta) CALM1 0.4 2.0 203044_at carbohydrate (chondroitin) synthase 1 CHSY1 1.8 3.1 -related cell adhesion molecule 1 209498_at (biliary glycoprotein) CEACAM1 7.6 0.0 239753_at CDNA clone IMAGE:30352956 partial cds --- 0.7 2.1 1564424_at CDNA clone IMAGE:4689616 --- 2.3 3.5 1556362_at CDNA clone IMAGE:5541046 partial cds --- 1.9 1.2 222294_s_at CDNA clone IMAGE:5745639 --- 2.5 1.2 232406_at CDNA clone IMAGE:6184587 partial cds --- 0.2 3.1 210608_s_at CDNA clone MGC:2062 IMAGE:3534501 complete cds --- 4.0 1.3 225785_at CDNA clone MGC:24463 IMAGE:4082362 complete cds --- 1.9 3.5 232355_at CDNA FLJ10247 fis clone HEMBB1000705 --- 2.6 2.1 233912_x_at CDNA FLJ11463 fis clone HEMBA1001608 --- 0.7 2.7 227498_at CDNA FLJ11723 fis clone HEMBA1005314 --- 0.5 2.1 233908_x_at CDNA FLJ12050 fis clone HEMBB1002002 --- 0.5 3.7 214967_at CDNA FLJ12055 fis clone HEMBB1002049 --- 6.0 3.7 227051_at CDNA FLJ13585 fis clone PLACE1009150 --- 4.0 2.0 233176_at CDNA FLJ14181 fis clone NT2RP2004300 --- 2.5 2.7 1560622_at CDNA FLJ20196 fis clone COLF0944 --- 2.2 2.1 1556364_at CDNA FLJ25194 fis clone REC04095 --- 2.5 3.5 224989_at CDNA FLJ26764 fis clone PRS02668 --- 0.4 2.1 227052_at CDNA FLJ26764 fis clone PRS02668 --- 0.7 2.1 1564299_at CDNA FLJ33307 fis, clone BNGH42004076 --- 26.6 0.0 226773_at CDNA FLJ35131 fis clone PLACE6008824 --- 0.3 2.7 239768_x_at CDNA FLJ41751 fis clone HSYRA2008154 --- 0.5 1.0 1562275_at CDNA FLJ43544 fis clone PROST2009388 --- 5.1 4.3 229699_at CDNA FLJ45384 fis clone BRHIP3021987 --- 2.3 1.2 1563259_at CDNA: FLJ21185 fis clone CAS11646 --- 0.4 2.7 233506_at CDNA: FLJ21531 fis clone COL06036 --- 2.8 3.5 232161_x_at CDNA: FLJ21893 fis clone HEP03412 --- 0.5 2.0 227792_at CDNA: FLJ22994 fis clone KAT11918 --- 2.3 1.0 Probe Set ID Gene Title Symbol Fold Change* q-value** 233935_at CDNA: FLJ23051 fis clone LNG02642 --- 2.1 3.7 CDP-diacylglycerol synthase (phosphatidate 226187_at cytidylyltransferase) 1 CDS1 0.4 2.7 212477_at centaurin, beta 2 CENTB2 0.5 3.1 ceroid-lipofuscinosis neuronal 2 late infantile (Jansky- 200743_s_at Bielschowsky disease) CLN2 1.7 2.0 1558034_s_at ceruloplasmin (ferroxidase) CP 6.0 1.2 214282_at ceruloplasmin (ferroxidase) CP 4.0 1.2 228143_at ceruloplasmin (ferroxidase) CP 5.4 2.7 205308_at CGI-62 protein CGI-62 0.4 3.5 209395_at chitinase 3-like 1 (cartilage glycoprotein-39) CHI3L1 12.8 1.2 209396_s_at chitinase 3-like 1 (cartilage glycoprotein-39) CHI3L1 10.5 1.2 218177_at CHMP1.5 protein CHMP1.5 2.5 1.5 236979_at 1 178 C1orf178 7.3 1.2 217967_s_at open reading frame 24 C1orf24 9.0 0.0 228100_at chromosome 1 open reading frame 88 C1orf88 0.4 3.7 202808_at open reading frame 26 C10orf26 1.4 3.5 237314_at chromosome 10 open reading frame 63 C10orf63 0.4 2.0 232291_at chromosome 13 open reading frame 25 C13orf25 2.4 2.0 222809_x_at open reading frame 65 C14orf65 1.6 3.5 219051_x_at open reading frame 23 C16orf23 0.4 4.3 232269_x_at chromosome 16 open reading frame 23 C16orf23 0.4 4.3 219951_s_at chromosome 20 open reading frame 12 C20orf12 0.5 3.7 229672_at Chromosome 20 open reading frame 44 C20orf44 0.6 3.7 222044_at ‡chromosome 20 open reading frame 67 C20orf67 3.0 2.0 89948_at ‡chromosome 20 open reading frame 67 C20orf67 1.8 3.1 240068_at open reading frame 130 C21orf130 3.2 2.7 227188_at chromosome 21 open reading frame 63 C21orf63 2.6 1.0 226109_at chromosome 21 open reading frame 91 C21orf91 0.6 3.7 229260_at open reading frame 15 C5orf15 0.8 3.7 220614_s_at open reading frame 103 C6orf103 0.3 4.3 226301_at chromosome 6 open reading frame 192 C6orf192 1.5 3.1 226386_at open reading frame 30 C7orf30 2.3 1.9 229976_at open reading frame 18 C9orf18 0.2 2.7 232000_at chromosome 9 open reading frame 52 C9orf52 2.0 1.3 227520_at chromosome X open reading frame 15 CXorf15 1.6 3.5 238875_at Clone HLS_IMAGE_731119 mRNA sequence --- 0.3 3.5 229599_at Clone IMAGE:5166045 mRNA --- 0.7 3.5 229899_s_at Clone IMAGE:5285034 mRNA --- 2.1 2.0 221059_s_at coactosin-like 1 (Dictyostelium) COTL1 3.6 0.0 224583_at coactosin-like 1 (Dictyostelium) COTL1 4.9 1.9 201359_at ‡coatomer protein complex subunit beta COPB 0.7 3.1 201098_at coatomer protein complex subunit beta 2 (beta prime) COPB2 0.6 3.5 complement component 1 q subcomponent alpha 218232_at polypeptide C1QA 2.9 0.0 218983_at complement component 1 r subcomponent-like C1RL 3.7 2.1 217767_at complement component 3 C3 8.1 0.0 214782_at cortactin CTTN 1.9 3.5 219767_s_at crystallin zeta (quinone reductase)-like 1 CRYZL1 0.6 1.0 Probe Set ID Gene Title Symbol Fold Change* q-value** ±C-type (calcium dependent carbohydrate-recognition 1556209_at domain) lectin superfamily member 2 (activation-induced) CLECSF2 4.4 4.3 ± C-type (calcium dependent carbohydrate-recognition 209732_at domain) lectin superfamily member 2 (activation-induced) CLECSF2 4.0 3.7 222453_at cytochrome b reductase 1 CYBRD1 2.5 3.1 cytochrome b-245 beta polypeptide (chronic granulomatous 203922_s_at disease) CYBB 2.6 1.2 207986_x_at cytochrome b-561 CYB561 0.5 1.1 209164_s_at cytochrome b-561 CYB561 0.3 0.7 217200_x_at cytochrome b-561 CYB561 0.4 1.1 223377_x_at cytokine inducible SH2-containing protein CISH 3.5 4.3 †,‡DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 /// DEAD 208152_s_at (Asp-Glu-Ala-Asp) box polypeptide 21 DDX21 2.3 3.5 205003_at dedicator of cytokinesis 4 DOCK4 2.2 2.1 232843_s_at ± dedicator of cytokinesis 8 DOCK8 2.1 2.0 212538_at dedicator of cytokinesis 9 DOCK9 2.0 3.7 degenerative spermatocyte homolog lipid desaturase 207431_s_at (Drosophila) DEGS 2.3 2.0 degenerative spermatocyte homolog lipid desaturase 209250_at (Drosophila) DEGS 1.6 3.1 1558742_at dexamethasone-induced transcript DEXI 7.9 1.0 209190_s_at diaphanous homolog 1 (Drosophila) DIAPH1 2.5 1.2 201430_s_at ‡dihydropyrimidinase-like 3 DPYSL3 5.1 2.7 201431_s_at ‡dihydropyrimidinase-like 3 DPYSL3 4.6 1.2 209094_at dimethylarginine dimethylaminohydrolase 1 DDAH1 0.6 1.5 210006_at DKFZP564O243 protein DKFZP564O243 0.5 2.7 222925_at doublecortin domain containing 2 DCDC2 0.3 2.0 218424_s_at dudulin 2 TSAP6 3.2 0.0 237804_at , axonemal, heavy chain 11 DNAH11 0.5 3.1 E74-like factor 3 (ets domain transcription factor, epithelial- 229842_at specific ) ELF3 3.3 1.2 212830_at EGF-like-domain multiple 5 EGFL5 0.3 3.7 232531_at empty spiracles homolog 2 (Drosophila) opposite strand EMX2OS 0.5 3.1 201769_at enthoprotin ENTH 1.2 3.7 202023_at ephrin-A1 EFNA1 2.4 3.7 218498_s_at ERO1-like (S. cerevisiae) ERO1L 2.0 2.0 225750_at ERO1-like (S. cerevisiae) ERO1L 2.2 1.0 226722_at family with sequence similarity 20 member C FAM20C 8.3 0.0 225684_at family with sequence similarity 33 member A FAM33A 0.5 1.1 217916_s_at family with sequence similarity 49 member B FAM49B 2.1 2.7 230276_at family with sequence similarity 49, member A FAM49A 2.8 3.1 228587_at Family with sequence similarity 83, member G FAM83G 1.7 2.1 216080_s_at fatty acid desaturase 3 FADS3 1.8 3.1 F-box and WD-40 domain protein 7 (archipelago homolog 218751_s_at Drosophila) FBXW7 0.4 3.7 F-box and WD-40 domain protein 7 (archipelago homolog 222729_at Drosophila) FBXW7 0.3 3.7 231382_at Fibroblast growth factor 18 FGF18 1.7 2.1 Probe Set ID Gene Title Symbol Fold Change* q-value** fibroblast growth factor receptor 3 (achondroplasia 204379_s_at thanatophoric dwarfism) FGFR3 2.7 1.3 212169_at ‡FK506 binding protein 9 63 kDa FKBP9 0.6 2.7 206263_at flavin containing monooxygenase 4 FMO4 0.6 3.5 1563369_at FLJ42957 protein FLJ42957 6.7 0.0 237591_at FLJ42957 protein FLJ42957 3.3 3.5 230757_at FLJ44796 protein FLJ44796 0.4 3.7 205860_x_at hydrolase (prostate-specific membrane antigen) 1 FOLH1 0.1 2.0 215363_x_at folate hydrolase (prostate-specific membrane antigen) 1 FOLH1 0.1 2.0 204437_s_at folate receptor 1 (adult) FOLR1 0.1 2.1 204789_at formin-like 1 FMNL1 1.6 0.0 225520_at formyltetrahydrofolate synthetase domain containing 1 FTHFSDC1 2.5 0.0 228188_at FOS-like antigen 2 FOSL2 2.3 1.2 229850_at Full length insert cDNA clone YX81F03 --- 1.6 1.2 Full-length cDNA clone CS0DJ004YB09 of T cells (Jurkat cell 226546_at line) Cot 10-normalized of Homo sapiens (human) --- 0.4 3.1 226985_at FYVE RhoGEF and PH domain containing 5 FGD5 5.2 1.9 208868_s_at †GABA(A) receptor-associated protein like 1 GABARAPL1 2.1 1.5 208869_s_at †GABA(A) receptor-associated protein like 1 GABARAPL1 1.7 3.1 211458_s_at †GABA(A) receptor-associated protein like 1 GABARAPL1 1.4 3.7 204537_s_at gamma-aminobutyric acid (GABA) A receptor epsilon GABRE 4.6 2.1 201667_at protein alpha 1 43kDa ( 43) GJA1 2.8 1.2 201816_s_at glioblastoma amplified sequence GBAS 0.5 1.1 201348_at glutathione peroxidase 3 (plasma) GPX3 19.5 2.1 225609_at glutathione reductase GSR 0.5 0.7 235405_at †glutathione S-transferase A4 GSTA4 0.3 2.0 218146_at glycosyltransferase AD-017 AD-017 0.4 0.7 218147_s_at glycosyltransferase AD-017 AD-017 0.4 1.3 230828_at GRAM domain containing 2 GRAMD2 2.5 1.0 224997_x_at H19 imprinted maternally expressed untranslated mRNA H19 6.1 4.3 117_at ‡heat shock 70kDa protein 6 (HSP70B') HSPA6 2.3 2.7 213418_at ‡heat shock 70kDa protein 6 (HSP70B') HSPA6 3.2 3.5 203665_at heme oxygenase (decycling) 1 HMOX1 4.5 1.0 218120_s_at heme oxygenase (decycling) 2 HMOX2 0.5 3.5 220491_at hepcidin antimicrobial peptide HAMP 3.9 2.7 227139_s_at Hermansky-Pudlak syndrome 3 HPS3 2.7 2.1 ‡hexose-6-phosphate dehydrogenase (glucose 221892_at 1-dehydrogenase) H6PD 2.7 3.5 209377_s_at high mobility group nucleosomal binding domain 3 HMGN3 0.7 2.1 205579_at histamine receptor H1 HRH1 2.9 0.0 ‡HIV-1 Rev binding protein-like /// insulin receptor HRBL /// 222126_at substrate 3-like IRS3L 2.2 0.0 Homo sapiens, Similar to RIKEN cDNA E130308A19 gene, 235112_at clone IMAGE:6198463, mRNA --- 0.4 3.7 229356_x_at homolog of yeast INO80 INO80 1.5 4.3 219284_at HSPB (heat shock 27kDa) associated protein 1 HSPBAP1 1.9 2.0 229238_at Hypothetical gene supported by AK128660 --- 0.5 4.3 227388_at hypothetical gene supported by BC017510; BC046919 LOC389708 1.8 2.7 Probe Set ID Gene Title Symbol Fold Change* q-value** Hypothetical gene supported by BC019073; BC036842; 215185_at BC044229 --- 2.3 1.2 Hypothetical gene supported by BC019073; BC036842; 217625_x_at BC044229 --- 1.9 1.5 226179_at Hypothetical gene supported by BC062364; BX647289 --- 1.6 3.5 224723_x_at Hypothetical gene supported by BX537645 --- 0.5 3.7 241910_x_at hypothetical LOC400590 LOC400590 0.6 3.1 231847_at hypothetical protein BC014641 LOC129138 0.5 1.1 hypothetical protein BC016861 /// hypothetical protein LOC90557 /// 227966_s_at DKFZp434E2321 DKFZp434E2321 0.5 3.7 229973_at hypothetical protein DKFZp547I048 DKFZp547I048 0.4 3.1 225355_at hypothetical protein DKFZP761M1511 DKFZP761M1511 0.4 3.1 228574_at hypothetical protein DKFZp762A217 DKFZp762A217 0.3 1.5 218815_s_at hypothetical protein FLJ10199 FLJ10199 2.4 3.1 231851_at hypothetical protein FLJ10770 KIAA1579 0.5 1.3 218824_at hypothetical protein FLJ10781 FLJ10781 0.3 3.7 220003_at hypothetical protein FLJ11004 FLJ11004 0.3 2.0 225316_at hypothetical protein FLJ14490 FLJ14490 4.0 4.3 225846_at hypothetical protein FLJ20171 FLJ20171 0.5 1.5 229918_at hypothetical protein FLJ20753 FLJ20753 0.5 3.5 218584_at hypothetical protein FLJ21127 FLJ21127 0.6 3.5 220072_at hypothetical protein FLJ22490 FLJ22490 0.5 2.1 218810_at hypothetical protein FLJ23231 FLJ23231 4.7 0.0 223583_at hypothetical protein FLJ23467 FLJ23467 1.5 3.1 220141_at hypothetical protein FLJ23554 FLJ23554 0.3 3.5 1555866_a_at hypothetical protein FLJ23825 FLJ23825 2.2 3.5 1554298_a_at hypothetical protein FLJ33620 FLJ33620 0.4 3.7 236745_at hypothetical protein FLJ34512 FLJ34512 0.3 4.3 223128_at hypothetical protein H17 H17 0.4 3.7 231849_at hypothetical protein LOC144501 LOC144501 4.5 2.0 238864_at hypothetical protein LOC146177 LOC146177 0.3 3.1 227956_at Hypothetical protein LOC162073 LOC162073 1.8 4.3 229616_s_at hypothetical protein LOC196996 LOC196996 3.0 0.0 238625_at hypothetical protein LOC199920 LOC199920 0.3 1.9 213195_at hypothetical protein LOC201229 LOC201229 0.5 2.0 hypothetical protein LOC222967 /// hypothetical protein LOC222967 /// 1557417_s_at LOC285927 LOC285927 0.4 3.5 238018_at hypothetical protein LOC285016 LOC285016 5.2 0.0 230621_at hypothetical protein LOC285148 LOC285148 1.6 1.2 236465_at hypothetical protein LOC285533 LOC285533 3.4 3.5 236523_at hypothetical protein LOC285556 LOC285556 0.1 2.7 230179_at hypothetical protein LOC285812 LOC285812 1.9 3.7 1562698_x_at hypothetical protein LOC339988 LOC339988 1.7 3.7 hypothetical protein LOC730399 /// hypothetical protein LOC730399 /// 217436_x_at LOC731974 LOC731974 1.9 0.0 243021_at hypothetical protein LOC730496 LOC730496 3.2 2.1 233198_at hypothetical protein LOC92497 LOC92497 0.4 4.3 223363_at hypothetical protein MGC10911 MGC10911 0.4 3.1 236085_at hypothetical protein MGC26610 MGC26610 0.4 3.7 Probe Set ID Gene Title Symbol Fold Change* q-value** 1562371_s_at hypothetical protein MGC26733 MGC26733 0.3 3.7 214965_at hypothetical protein MGC26885 MGC26885 3.3 1.9 242963_at hypothetical protein MGC26963 MGC26963 2.7 2.7 219097_x_at hypothetical protein MGC2747 MGC2747 0.6 2.0 231430_at hypothetical protein MGC33846 MGC33846 0.3 4.3 200995_at 7 IPO7 1.3 3.5 213076_at inositol 1 4 5-trisphosphate 3-kinase C ITPKC 2.8 3.5 204912_at ‡interleukin 10 receptor alpha IL10RA 2.8 3.7 230966_at interleukin 4 induced 1 IL4I1 4.1 2.0 238584_at IQ motif containing with AAA domain IQCA 0.3 1.0 225832_s_at ‡KCCR13L LOC221955 1.6 2.0 228377_at kelch-like 14 (Drosophila) KLHL14 0.3 3.5 228325_at KIAA0146 protein KIAA0146 4.4 1.2 202181_at KIAA0247 KIAA0247 2.2 0.0 212487_at KIAA0553 protein KIAA0553 0.5 1.1 213185_at KIAA0556 protein KIAA0556 0.3 2.1 212314_at KIAA0746 protein KIAA0746 2.5 1.2 234936_s_at KIAA1345 protein KIAA1345 0.5 3.7 233536_at KIAA1713 protein KIAA1713 0.3 1.1 200650_s_at lactate dehydrogenase A LDHA 2.4 1.0 244881_at † leishmanolysin-like (metallopeptidase M8 family) LMLN 0.3 2.1 228648_at leucine-rich alpha-2-glycoprotein 1 LRG1 3.1 2.1 231897_at leukotrienee y o t o ogB4 o12-hydroxydehydrogenase ouse tu o ec os s a p a duced LTB4DH 0.6 3.7 225987_at adipose-related protein FLJ23153 5.9 3.5 224917_at ±,‡likely ortholog of rat vacuole 1 VMP1 3.2 1.2 220990_s_at ±,‡likely ortholog of rat vacuole membrane protein 1 VMP1 3.1 1.2 225904_at LOC126731 LOC126731 3.0 0.0 241353_s_at LOC402617 --- 4.2 0.0 LPS-responsive vesicle trafficking beach and anchor 214109_at containing LRBA 0.5 2.0 203042_at †,‡lysosomal-associated membrane protein 2 LAMP2 0.6 3.5 major histocompatibility complex class II DR beta 6 217362_x_at () HLA-DRB6 3.6 1.0 202180_s_at major vault protein MVP 1.9 1.9 1558077_s_at malate dehydrogenase 1B NAD (soluble) MDH1B 0.5 2.7 mannosyl (alpha-1 3-)-glycoprotein beta-1 225409_at 4-N-acetylglucosaminyltransferase isoenzyme A MGAT4A 0.6 2.1 204259_at matrix metallopeptidase 7 (matrilysin, uterine) MMP7 11.9 0.0 213627_at melanoma antigen family D 2 MAGED2 0.7 3.7 201421_s_at MEP50 protein MEP50 0.2 3.1 213924_at Metallophosphoesterase 1 MPPE1 4.0 4.3 226238_at methylmalonyl CoA epimerase MCEE 0.5 3.7 201403_s_at ‡microsomal glutathione S-transferase 3 MGST3 0.6 3.7 203151_at microtubule-associated protein 1A MAP1A 0.4 4.3 228943_at ‡ microtubule-associated protein 6 MAP6 0.4 2.1 232296_s_at ‡mitochondrial elongation factor G1 EFG1 2.0 3.5 230034_x_at Mitochondrial ribosomal protein L41 MRPL41 1.6 3.7 223356_s_at mitochondrial translational initiation factor 3 MTIF3 0.6 2.0 227066_at MOB1 Mps One Binder kinase activator-like 2C (yeast) MOBKL2C 1.7 3.7 Probe Set ID Gene Title Symbol Fold Change* q-value** 203414_at †,‡ monocyte to macrophage differentiation-associated MMD 1.9 4.3 218853_s_at ‡ motile sperm domain containing 1 MOSPD1 0.3 2.0 218774_at mRNA decapping enzyme DCPS 2.5 4.3 231051_at MRNA of muscle specific gene M1. --- 0.4 3.7 MRNA; cDNA DKFZp564C203 (from clone 1563357_at DKFZp564C203) --- 2.8 2.1 226863_at MRNA; cDNA DKFZp586L2424 (from clone DKFZp586L2424) --- 3.5 1.2 MRNA; cDNA DKFZp667O1523 (from clone 1558385_at DKFZp667O1523) --- 2.7 2.1 228554_at MRNA; cDNA DKFZp686A0815 (from clone DKFZp686A0815) --- 0.2 2.0 238432_at MRNA; cDNA DKFZp686I0115 (from clone DKFZp686I0115) --- 2.5 3.1 223731_at MYCBP associated protein MYCBPAP 0.3 3.7 244364_at IIIA MYO3A 3.0 3.7 224656_s_at ‡myotrophin MTPN 0.7 3.7 226616_s_at NADH dehydrogenase (ubiquinone) flavoprotein 3 10kDa NDUFV3 0.5 3.7 232226_at netrin-G1 ligand NGL-1 1.8 4.3 212298_at ‡ 1 NRP1 3.1 2.0 202237_at ‡ nicotinamide N-methyltransferase NNMT 9.0 0.0 202238_s_at ‡ nicotinamide N-methyltransferase NNMT 4.6 0.0 231559_at ‡ nicotinamide N-methyltransferase NNMT 3.4 2.7 228090_at nicotinamide nucleotide adenylyltransferase 3 NMNAT3 0.4 3.5 200701_at † Niemann-Pick disease type C2 NPC2 2.1 2.7 229306_at Nuclear localized factor 2 NLF2 4.3 1.5 203675_at nucleobindin 2 NUCB2 0.2 3.1 209073_s_at numb homolog (Drosophila) NUMB 0.6 2.0 1552321_a_at NYD-SP28 protein NYD-SP28 0.4 1.1 227379_at O-acyltransferase (membrane bound) domain containing 1 OACT1 0.7 3.1 227321_at opposite strand transcription unit to STAG3 GATS 0.7 2.7 205432_at oviductal glycoprotein 1 120kDa (mucin 9 oviductin) OVGP1 0.0 3.5 214204_at PARK2 co-regulated PACRG 0.3 3.5 1558164_s_at peroxisome biogenesis factor 13 PEX13 2.5 4.3 †peroxisome proliferative activated receptor gamma 203737_s_at coactivator-related 1 PPRC1 2.2 3.5 224658_x_at phosphofurin acidic cluster sorting protein 1 PACS1 1.7 1.3 225366_at phosphoglucomutase 2 PGM2 2.1 4.3 202430_s_at 1 PLSCR1 2.0 3.1 202446_s_at phospholipid scramblase 1 PLSCR1 2.5 3.1 205325_at phytanoyl-CoA hydroxylase interacting protein PHYHIP 3.8 3.5 pleckstrin homology domain containing family A 226247_at (phosphoinositide binding specific) member 1 PLEKHA1 1.7 1.9 pleckstrin homology domain containing family B (evectins) 209504_s_at member 1 PLEKHB1 0.4 3.7 225688_s_at pleckstrin homology-like domain family B member 2 PHLDB2 6.4 2.0 201064_s_at poly(A) binding protein cytoplasmic 4 (inducible form) PABPC4 1.8 3.7 222839_s_at poly(A) polymerase gamma PAPOLG 3.1 3.5 217929_s_at polycystic kidney disease 1-like PKD1-like 0.5 3.5 226245_at tetramerisation domain containing 1 KCTD1 0.5 1.9 206765_at potassium inwardly-rectifying channel subfamily J member 2 KCNJ2 0.3 3.7 Probe Set ID Gene Title Symbol Fold Change* q-value** potassium voltage-gated channel KQT-like subfamily 204487_s_at member 1 KCNQ1 3.6 2.0 217730_at PP1201 protein PP1201 3.1 0.0 225373_at PP2135 protein PP2135 2.3 3.5 ‡procollagen-proline 2-oxoglutarate 4-dioxygenase (proline 4- 202733_at hydroxylase) alpha polypeptide II P4HA2 0.5 4.3 210367_s_at PTGES 4.1 3.5 211303_x_at prostate-specific membrane antigen-like protein PSMAL/GCP III 0.1 1.1 226790_at protein containing single MORN motif in testis MOPT 0.4 3.5 201214_s_at protein phosphatase 1 regulatory subunit 7 PPP1R7 0.4 1.1 207808_s_at protein S (alpha) PROS1 2.4 3.5 201858_s_at proteoglycan 1 secretory granule PRG1 3.3 3.7 201859_at proteoglycan 1 secretory granule PRG1 3.4 1.0 202793_at putative protein similar to nessy (Drosophila) C3F 1.8 3.5 225207_at pyruvate dehydrogenase kinase, isozyme 4 PDK4 2.5 4.3 212636_at quaking homolog KH domain RNA binding (mouse) QKI 2.2 1.9 quinolinate phosphoribosyltransferase (nicotinate-nucleotide 204044_at pyrophosphorylase (carboxylating)) QPRT 0.4 3.7 quinolinate phosphoribosyltransferase (nicotinate-nucleotide 242414_at pyrophosphorylase (carboxylating)) QPRT 0.1 2.0 219681_s_at RAB11 family interacting protein 1 (class I) RAB11FIP1 2.5 1.2 217763_s_at RAB31 member RAS oncogene family RAB31 2.7 4.3 206137_at regulating synaptic membrane exocytosis 2 RIMS2 0.2 4.3 233409_at rhomboid veinlet-like 4 (Drosophila) RHBDL4 0.4 3.7 219202_at rhomboid 5 homolog 2 (Drosophila) RHBDF2 2.3 2.1 213566_at RNase A family k6 RNASE6 3.5 3.5 224450_s_at RIO kinase 1 (yeast) /// RIO kinase 1 (yeast) RIOK1 1.7 2.7 236613_at RNA binding motif protein 25 RBM25 2.3 3.1 220330_s_at SAM domain SH3 domain and nuclear localisation signals 1 SAMSN1 3.4 1.9 217977_at selenoprotein X 1 SEPX1 2.0 3.7 serine (or cysteine) proteinase inhibitor clade B (ovalbumin) 212268_at member 1 SERPINB1 3.5 1.2 serine (or cysteine) proteinase inhibitor clade B (ovalbumin) 213572_s_at member 1 SERPINB1 2.7 1.9 229674_at ±SERTA domain containing 4 SERTAD4 0.3 1.0 213307_at SH3 and multiple ankyrin repeat domains 2 SHANK2 0.3 1.0 242064_at sidekick homolog 2 (chicken) SDK2 0.2 3.5

‡signal recognition particle 14kDa (homologous Alu RNA binding protein) /// signal recognition particle 14kDa 200007_at (homologous Alu RNA binding protein) SRP14 0.8 3.7 231044_at Similar to CG5435-PA --- 0.3 1.5 239150_at Similar to hypothetical protein A430083B19 --- 0.3 3.5 230033_at similar to hypothetical testis protein from macaque LOC352909 0.4 1.9 similar to Interferon-induced transmembrane protein 3 216565_x_at (Interferon-inducible protein 1-8U) LOC391020 1.6 1.9 228953_at similar to junction-mediating and regulatory protein p300 JMY KIAA1971 2.0 2.7 239921_at Similar to matrilin 2 precursor --- 0.3 3.7 230753_at Similar to RIKEN cDNA 4930424G05 --- 1.9 1.5 222068_s_at similar to RIKEN cDNA 4930457P18 LOC123872 0.5 2.1 Probe Set ID Gene Title Symbol Fold Change* q-value** 1560676_at similar to seven in absentia 2 LOC283514 0.2 1.3 218194_at ‡small fragment DKFZP566E144 2.2 0.0 solute carrier family 11 (proton-coupled divalent metal ion 210423_s_at transporters) member 1 SLC11A1 1.7 3.7 solute carrier family 11 (proton-coupled divalent metal ion 210047_at transporters) member 2 SLC11A2 1.5 3.7 ‡solute carrier family 16 (monocarboxylic acid transporters) 202856_s_at member 3 SLC16A3 4.9 1.0 ‡solute carrier family 16 (monocarboxylic acid transporters) 217691_x_at member 3 SLC16A3 2.9 0.0 ‡solute carrier family 16 (monocarboxylic acid transporters) 213522_s_at member 3 SLC16A3 3.8 1.0 solute carrier family 22 (organic cation transporter) 205074_at member 5 SLC22A5 0.7 3.7 223732_at solute carrier family 23 (nucleobase transporters) member 1 SLC23A1 0.1 1.9 204204_at solute carrier family 31 (copper transporters) member 2 SLC31A2 2.6 3.5 204124_at solute carrier family 34 (sodium phosphate) member 2 SLC34A2 2.4 1.9 212110_at solute carrier family 39 (zinc transporter) member 14 SLC39A14 3.9 3.1 solute carrier family 40 (iron-regulated transporter) 223044_at member 1 SLC40A1 1.8 1.2 solute carrier family 7 (cationic transporter y+ 201195_s_at system) member 5 SLC7A5 3.3 2.1 ‡solute carrier family 7 (cationic amino acid transporter y+ 203580_s_at system) member 6 SLC7A6 2.0 3.1 219229_at solute carrier organic anion transporter family member 3A1 SLCO3A1 2.0 3.7 212560_at sortilin-related receptor L(DLR class) A repeats-containing SORL1 0.5 3.5 230707_at sortilin-related receptor, L(DLR class) A repeats-containing SORL1 0.2 1.0 218404_at sorting nexin 10 SNX10 2.4 3.1 213262_at spastic ataxia of Charlevoix-Saguenay (sacsin) SACS 1.9 2.0 215235_at ‡ spectrin alpha non-erythrocytic 1 (alpha-fodrin) SPTAN1 0.6 4.3 206815_at sperm associated antigen 8 SPAG8 0.2 3.1 206816_s_at sperm associated antigen 8 SPAG8 0.3 1.1 219677_at SPRY domain-containing SOCS box protein SSB-1 SSB1 2.1 1.3 226075_at SPRY domain-containing SOCS box protein SSB-1 SSB1 3.5 0.0 203760_s_at Src-like-adaptor SLA 1.9 2.7 221477_s_at superoxide dismutase 2 mitochondrial SOD2 14.8 0.0 1566342_at Superoxide dismutase 2, mitochondrial SOD2 4.6 0.0 202796_at synaptopodin SYNPO 2.9 1.0 200958_s_at syndecan binding protein (syntenin) SDCBP 1.4 3.7 218763_at ‡ syntaxin 18 STX18 0.2 2.0 1555392_at Testin-related protein TRG mRNA complete cds --- 2.2 4.3 208662_s_at tetratricopeptide repeat domain 3 TTC3 0.4 3.7 226120_at tetratricopeptide repeat domain 8 TTC8 0.5 3.7 237252_at ‡ THBD 2.9 1.2 202011_at tight junction protein 1 (zona occludens 1) TJP1 1.4 4.3 210886_x_at TP53 activated protein 1 TP53AP1 0.5 3.7 226192_at Transcribed locus --- 0.3 2.0 226197_at Transcribed locus --- 0.4 1.1 226621_at Transcribed locus --- 6.2 1.0 Probe Set ID Gene Title Symbol Fold Change* q-value** 227126_at Transcribed locus --- 2.0 2.1 228726_at Transcribed locus --- 2.0 0.0 229689_s_at Transcribed locus --- 2.1 3.7 230527_at Transcribed locus --- 5.8 1.2 230640_at Transcribed locus --- 1.5 2.0 230772_at Transcribed locus --- 0.2 3.5 230943_at Transcribed locus --- 0.2 3.7 231317_at Transcribed locus --- 1.8 2.7 235571_at Transcribed locus --- 2.7 1.2 237212_at Transcribed locus --- 4.1 4.3 237661_at Transcribed locus --- 1.3 4.3 238577_s_at Transcribed locus --- 3.7 1.0 238668_at Transcribed locus --- 1.6 3.7 239294_at Transcribed locus --- 2.0 2.7 239780_at Transcribed locus --- 2.3 4.3 240418_at Transcribed locus --- 3.7 1.2 241722_x_at Transcribed locus --- 1.7 3.1 241958_at Transcribed locus --- 0.3 3.1 241991_at Transcribed locus --- 0.3 2.0 242657_at Transcribed locus --- 4.8 3.5 243383_at Transcribed locus --- 2.7 3.7 243462_s_at Transcribed locus --- 0.4 1.3 243504_at Transcribed locus --- 0.3 3.5 243868_at Transcribed locus --- 0.6 1.0 244521_at Transcribed locus --- 3.7 1.9 Transcribed locus, strongly similar to XP_531081.2 238016_s_at hypothetical protein [Pan troglodytes] --- 2.1 3.7 200916_at transgelin 2 TAGLN2 2.3 2.0 222904_s_at †transmembrane channel-like 5 TMC5 2.2 2.0 218960_at transmembrane protease serine 4 TMPRSS4 2.3 0.0 1569003_at transmembrane protein 49 TMEM49 3.3 2.7 231697_s_at Transmembrane protein 49 TMEM49 2.5 2.7 202341_s_at tripartite motif-containing 2 TRIM2 0.3 4.3 224566_at trophoblast-derived noncoding RNA TncRNA 2.1 2.1 203661_s_at 1 TMOD1 2.9 1.2 203662_s_at TMOD1 1.8 3.7 209118_s_at ‡ tubulin alpha 3 TUBA3 0.2 3.1 207643_s_at tumor necrosis factor receptor superfamily member 1A TNFRSF1A 1.6 4.3 219415_at tweety homolog 1 (Drosophila) TTYH1 0.4 3.5 ‡tyrosine 3-monooxygenase/tryptophan 5-monooxygenase 214848_at activation protein zeta polypeptide YWHAZ 1.5 2.7 202090_s_at ubiquinol-cytochrome c reductase (6.4kD) subunit UQCR 0.6 3.5 218190_s_at ubiquinol-cytochrome c reductase complex (7.2 kD) HSPC051 0.5 3.7 203870_at ubiquitin specific protease 46 USP46 0.5 3.1 ‡ubiquitin-activating enzyme E1 (A1S9T and BN75 200964_at temperature sensitivity complementing) UBE1 0.7 1.9 204881_s_at UDP-glucose glucosyltransferase UGCG 2.5 0.0 221765_at UDP-glucose ceramide glucosyltransferase UGCG 2.6 3.7 224967_at UDP-glucose ceramide glucosyltransferase UGCG 2.6 0.0 Probe Set ID Gene Title Symbol Fold Change* q-value** UDP-N-acetyl-alpha-D-galactosamine:polypeptide 219271_at N-acetylgalactosaminyltransferase 14 (GalNAc-T14) GALNT14 5.5 4.3 208998_at uncoupling protein 2 (mitochondrial proton carrier) UCP2 0.5 1.0 225093_at (homologous to ) UTRN 0.7 3.5 229492_at vang-like 1 (van gogh, Drosophila) VANGL1 0.4 1.1 1558549_s_at vanin 1 VNN1 23.8 1.2 220528_at vanin 3 VNN3 14.7 2.1 220744_s_at WD repeat domain 10 WDR10 0.6 2.1 205667_at Werner syndrome WRN 0.6 2.1 220933_s_at zinc finger CCHC domain containing 6 ZCCHC6 1.6 3.7 230494_at --- 2.8 1.0 230537_at --- 0.2 3.5 222303_at --- 4.4 4.3 224348_s_at --- 2.1 3.5 237292_at --- 3.6 3.5 238742_x_at --- 1.8 2.1 240205_x_at --- 0.6 3.7 240765_at --- 3.1 1.5 241321_at --- 1.9 1.0 242189_at --- 2.0 3.1 242967_at --- 2.0 4.3 243252_at --- 0.3 4.3 244007_at --- 0.8 2.0

* corresponds to the relative expression of the specific probe set in the FTEb samples grouping with serous carcinomas compared to those grouping with normal controls (decreased expression <0, increased expression >0). ** corresponds to the significance level of this differential expression. Italicized genes represent those probe sets also differentiating SerCa and FTEn specimens in the same direction. † indicates TGF-β target genes identified in mouse fibroblasts (47). ± indicates TGF-β target genes identified in immortalized human keratinocytes and pancreatic tumor cells (48). ‡ indicates TGF-β target genes identified in human lung adenocarcinoma cells and immortalized lung epithelial cells (49). § indicates TGF-β target genes reviewed by Massague et al (50). Supplemental Table 2. Genes differentially expressed between the luteal and follicular phase in carriers.

Probe Set ID Gene Title Symbol Fold Change* q-value**

Regulation of Transcription (34) 231090_s_at AT rich interactive domain 2 (ARID, RFX-like) ARID2 0.7 4.6 222891_s_at B-cell CLL/lymphoma 11A (zinc finger protein) BCL11A 0.5 8.5 212953_x_at CALR 0.5 1.3 214315_x_at calreticulin CALR 0.5 0.0 234014_at CDNA FLJ10003 fis, clone HEMBA1000050 --- 0.4 5.5 215619_at CDNA FLJ14152 fis, clone MAMMA1003089 --- 0.3 9.8 222867_s_at CGI-125 protein CGI-125 0.6 3.3 208807_s_at †,‡ chromodomain helicase DNA binding protein 3 CHD3 0.6 6.8 219325_s_at ‡elaC homolog 1 (E. coli) ELAC1 0.4 9.8 219517_at elongation factor RNA polymerase II-like 3 ELL3 0.5 0.0 219518_s_at elongation factor RNA polymerase II-like 3 ELL3 0.4 0.0 209214_s_at Ewing sarcoma breakpoint region 1 EWSR1 0.7 1.3 210719_s_at high-mobility group 20B HMG20B 0.3 6.1 205601_s_at homeo box B5 HOXB5 0.5 8.5 1560258_a_at Homo sapiens, clone IMAGE:5590287, mRNA --- 0.3 9.8 242915_at hypothetical ZNF-like protein LOC91120 0.4 4.0 235106_at mastermind-like 2 (Drosophila) MAML2 1.9 9.8 221820_s_at MYST histone acetyltransferase 1 MYST1 0.5 6.1 230412_at Neuronal PAS domain protein 3 NPAS3 0.4 3.3 202599_s_at nuclear receptor interacting protein 1 NRIP1 0.4 9.8 208305_at PGR 0.2 0.0 230533_at †,‡protein kinase C binding protein 1 PRKCBP1 2.2 9.8 217301_x_at retinoblastoma binding protein 4 RBBP4 0.7 8.5 213442_x_at SAM pointed domain containing ets transcription factor SPDEF 0.5 9.8 214403_x_at SAM pointed domain containing ets transcription factor SPDEF 0.3 6.1 214404_x_at SAM pointed domain containing ets transcription factor SPDEF 0.3 6.8 219993_at SRY (sex determining region Y)-box 17 SOX17 0.4 4.6 214633_at SRY (sex determining region Y)-box 3 SOX3 0.2 0.0 240089_at Transcribed locus --- 4.2 4.6

V-rel reticuloendotheliosis viral oncogene homolog A, nuclear factor of kappa light polypeptide gene enhancer in B-cells 3, 230202_at p65 (avian) RELA 1.8 8.5 226807_at zinc finger protein 1 homolog (mouse) ZFP1 0.4 9.8 226754_at zinc finger protein 251 ZNF251 0.6 1.8 240776_at --- 0.2 1.3 243652_at --- 0.4 9.8

Immune Response (21) 201891_s_at beta-2-microglobulin B2M 1.9 3.2 CD59 antigen p18-20 (antigen identified by monoclonal 212463_at 16.3A5 EJ16 EJ30 EL32 and G344) CD59 2.0 3.2 CD74 antigen (invariant polypeptide of major 1567628_at histocompatibility complex class II antigen-associated) CD74 5.7 4.6 CD74 antigen (invariant polypeptide of major 209619_at histocompatibility complex class II antigen-associated) CD74 3.5 5.5 Probe Set ID Gene Title Symbol Fold Change* q-value** CD74 molecule, major histocompatibility complex, class II 1567627_at invariant chain CD74 5.4 4.6 222484_s_at chemokine (C-X-C motif) ligand 14 CXCL14 0.3 9.8 223454_at chemokine (C-X-C motif) ligand 16 CXCL16 2.3 8.5 Fc fragment of IgE high affinity I receptor for; gamma 204232_at polypeptide FCER1G 8.8 8.5 202748_at ±guanylate binding protein 2 interferon-inducible GBP2 3.1 4.6 215313_x_at major histocompatibility complex class I A HLA-A 2.0 5.5 major histocompatibility complex class I A /// Clone 213932_x_at IMAGE:5214329 mRNA HLA-A 1.7 3.3 200905_x_at major histocompatibility complex class I E HLA-E 2.1 3.3 217456_x_at major histocompatibility complex class I E HLA-E 1.8 6.8 203932_at major histocompatibility complex class II DM beta HLA-DMB 4.3 4.6

major histocompatibility complex class II DR beta 1 /// HLA-DRB1 /// major histocompatibility complex class II DR beta 3 /// HLA-DRB3 /// 204670_x_at major histocompatibility complex class II DR beta 4 HLA-DRB4 7.4 4.6 208306_x_at major histocompatibility complex class II DR beta 3 HLA-DRB3 5.2 4.6 215193_x_at major histocompatibility complex class II DR beta 3 HLA-DRB3 8.3 5.5 200904_at major histocompatibility complex, class I, E HLA-E 2.6 4.6 211990_at major histocompatibility complex, class II, DP alpha 1 HLA-DPA1 8.8 6.1 209312_x_at major histocompatibility complex, class II, DR beta 1 HLA-DRB1 8.8 4.6

Signal Transduction (17) 201657_at ADP-ribosylation factor-like 1 ARL1 0.4 3.3 236618_at chromosome 20 open reading frame 132 C20orf132 0.4 8.5 colony stimulating factor 1 receptor formerly McDonough feline 203104_at sarcoma viral (v-fms) oncogene homolog CSF1R 2.5 8.5 208600_s_at -coupled receptor 39 GPR39 7.2 3.2 213880_at G protein-coupled receptor 49 GPR49 0.3 4.6 208612_at ‡glucose regulated protein 58kDa GRP58 0.3 0.0 227033_at ‡glucose regulated protein 58kDa GRP58 0.3 1.8 209002_s_at KIAA1536 protein KIAA1536 2.1 3.2 205876_at leukemia inhibitory factor receptor LIFR 1.7 4.6 201080_at phosphatidylinositol-4-phosphate 5-kinase type II beta PIP5K2B 0.7 4.0 229453_at Protein disulfide isomerase family A, member 3 PDIA3 0.3 0.0 218657_at Rap guanine nucleotide exchange factor (GEF)-like 1 RAPGEFL1 0.2 1.8 209885_at ‡ras homolog gene family member D RHOD 0.7 8.5 202988_s_at regulator of G-protein signalling 1 RGS1 3.8 8.5 204319_s_at regulator of G-protein signalling 10 RGS10 1.7 4.6 214000_s_at Regulator of G-protein signalling 10 RGS10 1.7 8.5 213476_x_at tubulin beta 4 TUBB4 0.4 6.8

Cell Cycle/Proliferation (16) 204998_s_at activating transcription factor 5 ATF5 2.3 3.2 218333_at derlin-2 F-LANa 0.6 4.0 †,‡disabled homolog 2 mitogen-responsive phosphoprotein 201280_s_at (Drosophila) DAB2 0.4 8.5 †, ‡ disabled homolog 2 mitogen-responsive phosphoprotein 201278_at (Drosophila) /// CDNA FLJ35517 fis clone SPLEN2000698 DAB2 0.4 0.0 212727_at discs large homolog 3 (neuroendocrine-dlg Drosophila) DLG3 0.5 4.6 Probe Set ID Gene Title Symbol Fold Change* q-value** 208891_at dual specificity phosphatase 6 DUSP6 0.5 5.5 208892_s_at dual specificity phosphatase 6 DUSP6 0.5 3.2 219454_at EGF-like-domain multiple 6 EGFL6 0.2 8.5 Full-length cDNA clone CS0DF022YN12 of Fetal brain of 226534_at Homo sapiens (human) --- 0.3 4.6 201626_at insulin induced gene 1 INSIG1 0.5 9.8 204454_at leucine zipper down-regulated in cancer 1 LDOC1 0.5 4.6 ‡pleiotrophin (heparin binding growth factor 8 neurite 209465_x_at growth-promoting factor 1) PTN 0.2 3.2 225662_at sterile alpha motif and leucine zipper containing kinase AZK ZAK 0.5 1.3 226157_at transcription factor Dp-2 ( dimerization partner 2) TFDP2 2.0 9.8 210021_s_at uracil-DNA glycosylase 2 UNG2 0.3 5.5 201368_at zinc finger protein 36 C3H type-like 2 ZFP36L2 2.1 5.5

Protein Transport (14) 202120_x_at adaptor-related protein complex 2 sigma 1 subunit AP2S1 0.6 1.3 201359_at ‡coatomer protein complex subunit beta COPB 0.7 9.8 201098_at coatomer protein complex subunit beta 2 (beta prime) COPB2 0.6 4.6 218436_at chaperone SIL1 homolog of yeast SIL1 0.7 8.5 ‡KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein 200698_at retention receptor 2 KDELR2 0.7 8.5 ‡KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein 200699_at retention receptor 2 KDELR2 0.6 3.3 200805_at lectin mannose-binding 2 LMAN2 0.7 6.1 206137_at regulating synaptic membrane exocytosis 2 RIMS2 0.3 6.8 202375_at SEC24 related gene family member D (S. cerevisiae) SEC24D 0.5 3.3 217716_s_at Sec61 alpha 1 subunit (S. cerevisiae) SEC61A1 0.5 8.5 203484_at Sec61 gamma subunit SEC61G 0.4 1.8 ‡signal sequence receptor delta (translocon-associated 201004_at protein delta) SSR4 0.5 4.6 218763_at ‡ syntaxin 18 STX18 0.3 0.0 200929_at transmembrane trafficking protein TMP21 0.7 3.3

Apoptosis (13) heat shock 70kDa protein 5 (glucose-regulated protein 211936_at 78kDa) HSPA5 0.3 0.0 heat shock 70kDa protein 5 (glucose-regulated protein 230031_at 78kDa) HSPA5 0.2 1.3 216450_x_at heat shock protein 90kDa beta (Grp94), member 1 HSP90B1 0.3 4.0 nerve growth factor receptor (TNFRSF16) associated 217963_s_at protein 1 NGFRAP1 0.8 8.5 39729_at peroxiredoxin 2 PRDX2 0.6 6.1 205512_s_at programmed cell death 8 (apoptosis-inducing factor) PDCD8 0.5 3.3 217839_at TRK-fused gene TFG 0.8 4.6 202687_s_at ±,‡tumor necrosis factor (ligand) superfamily member 10 TNFSF10 7.1 3.3 202688_at ±,‡ tumor necrosis factor (ligand) superfamily member 10 TNFSF10 11.3 4.6 200598_s_at ‡ tumor rejection antigen (gp96) 1 TRA1 0.3 8.5 200599_s_at ‡tumor rejection antigen (gp96) 1 TRA1 0.4 1.3 216449_x_at ‡ tumor rejection antigen (gp96) 1 TRA1 0.4 4.0 202893_at unc-13 homolog B (C. elegans) UNC13B 0.6 9.8 Probe Set ID Gene Title Symbol Fold Change* q-value**

Proteolysis (13) 227463_at ‡angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 ACE 0.7 9.8 206100_at ‡ carboxypeptidase M CPM 0.2 4.0 235019_at ‡ carboxypeptidase M CPM 0.2 0.0 241765_at ‡ carboxypeptidase M CPM 0.2 6.8 243403_x_at ‡ carboxypeptidase M CPM 0.2 0.0 205860_x_at folate hydrolase (prostate-specific membrane antigen) 1 FOLH1 0.2 1.3 215363_x_at folate hydrolase (prostate-specific membrane antigen) 1 FOLH1 0.3 1.3 Full-length cDNA clone CS0DB004YO04 of Neuroblastoma 213802_at Cot 10-normalized of Homo sapiens (human) --- 0.2 9.8 222161_at N-acetylated alpha-linked acidic dipeptidase 2 NAALAD2 0.4 5.5 211303_x_at prostate-specific membrane antigen-like protein PSMAL/GCP III 0.3 1.3 1552349_a_at protease serine 33 PRSS33 0.1 0.0

similar to ADAMTS-10 precursor (A disintegrin and metalloproteinase with thrombospondin motifs 10) 237411_at (ADAM-TS 10) (ADAM-TS10) LOC345667 0.2 6.1 209045_at X-prolyl aminopeptidase (aminopeptidase P) 1 soluble XPNPEP1 0.8 9.8

Steroid Biosynthesis & Metabolism (11) 205822_s_at 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) HMGCS1 0.4 4.6 221750_at 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) HMGCS1 0.4 1.8 203504_s_at ATP-binding cassette sub-family A (ABC1) member 1 ABCA1 3.6 4.6 203505_at ATP-binding cassette sub-family A (ABC1) member 1 ABCA1 3.6 3.3 202562_s_at chromosome 14 open reading frame 1 C14orf1 0.7 1.8 205765_at ‡cytochrome P450 family 3 subfamily A polypeptide 5 CYP3A5 7.0 5.5 214234_s_at ‡cytochrome P450 family 3 subfamily A polypeptide 5 CYP3A5 6.9 6.1 202735_at emopamil binding protein (sterol isomerase) EBP 0.5 8.5 203515_s_at PMVK 0.6 8.5 226390_at † START domain containing 4 sterol regulated STARD4 0.2 6.8 209146_at sterol-C4-methyl oxidase-like SC4MOL 0.5 1.8

Cell Adhesion (10) 209186_at ATPase Ca++ transporting cardiac muscle slow twitch 2 ATP2A2 0.7 3.3 234077_at CDNA FLJ11664 fis clone HEMBA1004632 --- 0.3 9.8 221328_at claudin 17 CLDN17 0.8 6.1 1553418_a_at contactin associated protein-like 5 CNTNAP5 1.3 4.6 230964_at hypothetical protein DKFZp686J0811 DKFZp686J0811 0.4 4.6 201656_at ITGA6 0.5 0.0 222454_s_at parvin alpha PARVA 0.5 0.0 225246_at stromal interaction molecule 2 STIM2 0.4 6.8 212703_at 2 TLN2 0.4 0.0 240655_at --- 0.6 1.8

Microtubule-Based Movement (10) 209026_x_at beta 5-tubulin OK/SW-cl.56 0.3 5.5 211714_x_at beta 5-tubulin /// beta 5-tubulin OK/SW-cl.56 0.3 4.6 201090_x_at tubulin alpha ubiquitous K-ALPHA-1 0.4 0.0 212639_x_at tubulin alpha ubiquitous K-ALPHA-1 0.4 1.8 Probe Set ID Gene Title Symbol Fold Change* q-value** 213646_x_at tubulin alpha ubiquitous K-ALPHA-1 0.4 1.3 211058_x_at tubulin alpha ubiquitous /// tubulin alpha ubiquitous K-ALPHA-1 0.4 0.0 211072_x_at tubulin alpha ubiquitous /// tubulin alpha ubiquitous K-ALPHA-1 0.4 0.0 209251_x_at tubulin alpha 6 TUBA6 0.4 3.3 211750_x_at tubulin alpha 6 /// tubulin alpha 6 TUBA6 0.4 4.0 210527_x_at tubulin, alpha 3c TUBA3C 0.6 3.2

Protein Modification (8) 209135_at aspartate beta-hydroxylase ASPH 0.6 0.0 208674_x_at ‡dolichyl-diphosphooligosaccharide-protein glycosyltransferase DDOST 0.6 1.3 ‡homocysteine-inducible endoplasmic reticulum stress- 217168_s_at inducible ubiquitin-like domain member 1 HERPUD1 0.4 1.8 221553_at implantation-associated protein DKFZp564K142 0.3 8.5 211320_s_at protein tyrosine phosphatase receptor type U PTPRU 1.9 8.5 sialyltransferase 1 (beta-galactoside alpha-2 201998_at 6-sialyltransferase) SIAT1 3.7 9.8 243410_at Transcribed locus --- 2.5 5.5 205139_s_at uronyl-2-sulfotransferase UST 0.4 1.8

Other/Unknown (222) acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme 209608_s_at A thiolase) ACAT2 0.5 9.8 234312_s_at acetyl-Coenzyme A synthetase 2 (ADP forming) ACAS2 0.3 9.8 219986_s_at acyl-Coenzyme A dehydrogenase family member 10 ACAD10 0.6 0.0 227962_at acyl-Coenzyme A oxidase 1 palmitoyl ACOX1 0.7 6.1 237336_at adducin 2 (beta) ADD2 1.3 6.1 215783_s_at liver/bone/kidney ALPL 0.6 6.1 202740_at aminoacylase 1 ACY1 0.6 4.6 †amphiphysin (Stiff-Man syndrome with breast cancer 128kDa 205257_s_at autoantigen) AMPH 0.2 0.0 204408_at APEX nuclease (apurinic/apyrimidinic ) 2 APEX2 0.7 6.1 202655_at arginine-rich mutated in early stage tumors ARMET 0.3 0.0 240318_at Arylformamidase AFMID 2.1 5.5 201128_s_at ATP citrate ACLY 0.8 6.8 ATP synthase H+ transporting mitochondrial F0 complex 209492_x_at subunit e ATP5I 0.6 8.5 ATP synthase H+ transporting mitochondrial F0 complex 207573_x_at subunit g ATP5L 0.7 0.0 ATP synthase H+ transporting mitochondrial F0 complex 208746_x_at subunit g ATP5L 0.7 0.0 ATP synthase H+ transporting mitochondrial F0 complex 210453_x_at subunit g ATP5L 0.7 0.0 ATP synthase H+ transporting mitochondrial F1 complex 213738_s_at alpha subunit isoform 1 cardiac muscle ATP5A1 0.7 9.8 ATP synthase H+ transporting mitochondrial F1 complex 217801_at epsilon subunit ATP5E 0.7 8.5 ATP synthase H+ transporting mitochondrial F1 complex O 200818_at subunit (oligomycin sensitivity conferring protein) ATP5O 0.6 6.8 ‡ ATP synthase, H+ transporting, mitochondrial F1 complex, 205711_x_at gamma polypeptide 1 ATP5C1 0.7 4.6 Probe Set ID Gene Title Symbol Fold Change* q-value** ‡ATP synthase, H+ transporting, mitochondrial F1 complex, 208870_x_at gamma polypeptide 1 ATP5C1 0.7 8.5 204685_s_at ATPase Ca++ transporting plasma membrane 2 ATP2B2 0.2 1.8 205662_at B9 protein EPPB9 0.6 6.1 †biogenesis of lysosome-related organelles complex-1 202592_at subunit 1 BLOC1S1 0.6 8.5 212952_at Calreticulin CALR 0.6 0.0 214316_x_at Calreticulin CALR 0.7 4.0 231102_at carnitine O-octanoyltransferase CROT 0.6 8.5 219505_at cat eye syndrome chromosome region candidate 1 CECR1 0.4 4.0 227498_at CDNA FLJ11723 fis clone HEMBA1005314 --- 0.5 3.3 228108_at CDNA FLJ30761 fis clone FEBRA2000538 --- 0.2 4.0 228457_at CDNA FLJ30761 fis clone FEBRA2000538 --- 0.2 0.0 226773_at CDNA FLJ35131 fis clone PLACE6008824 --- 0.4 3.3 239768_x_at CDNA FLJ41751 fis clone HSYRA2008154 --- 0.6 5.5 232161_x_at CDNA: FLJ21893 fis clone HEP03412 --- 0.6 8.5 218298_s_at chromosome 14 open reading frame 159 C14orf159 0.5 6.8 210532_s_at chromosome 14 open reading frame 2 C14orf2 0.7 8.5 225300_at open reading frame 23 C15orf23 0.6 8.5 225981_at open reading frame 28 C17orf28 0.4 3.2 221587_s_at open reading frame 24 C19orf24 0.6 6.1 240068_at chromosome 21 open reading frame 130 C21orf130 4.2 4.6 225182_at chromosome 21 open reading frame 4 C21orf4 0.7 1.8 228510_at chromosome 6 open reading frame 134 C6orf134 0.7 6.8 203259_s_at ‡chromosome 6 open reading frame 74 C6orf74 0.7 8.5 229585_at chromosome 9 open reading frame 94 C9orf94 0.1 3.2 239909_at chromosome 9 open reading frame 94 C9orf94 0.4 9.8 202403_s_at collagen type I alpha 2 COL1A2 0.2 1.8 234950_s_at constitutive photomorphogenic protein COP1 0.6 9.8 218358_at cysteine-rich with EGF-like domains 2 CRELD2 0.2 0.0 subunit IV isoform 1 /// cytochrome c 200086_s_at oxidase subunit IV isoform 1 COX4I1 0.7 4.0 200925_at cytochrome c oxidase subunit VIa polypeptide 1 COX6A1 0.6 5.5 201754_at cytochrome c oxidase subunit VIc COX6C 0.5 3.3 201597_at cytochrome c oxidase subunit VIIa polypeptide 2 (liver) COX7A2 0.8 4.6 DEAD (Asp-Glu-Ala-As) box polypeptide 19 /// FLJ11126 DDX19 /// 202576_s_at protein FLJ11126 0.6 9.8 232843_s_at ±dedicator of cytokinesis 8 DOCK8 2.3 4.6 216060_s_at dishevelled associated activator of morphogenesis 1 DAAM1 0.7 4.0 223054_at DnaJ (Hsp40) homolog subfamily B member 11 DNAJB11 0.5 4.6 229588_at DnaJ (Hsp40) homolog subfamily C member 10 DNAJC10 0.3 1.3 212830_at EGF-like-domain multiple 5 EGFL5 0.4 3.2 212831_at EGF-like-domain multiple 5 EGFL5 0.3 1.8 ‡ELOVL family member 6 elongation of long chain fatty acids 204256_at (FEN1/Elo2 SUR4/Elo3-like yeast) ELOVL6 0.3 1.8 201718_s_at erythrocyte membrane protein band 4.1-like 2 EPB41L2 0.3 8.5 201719_s_at erythrocyte membrane protein band 4.1-like 2 EPB41L2 0.5 0.0 †eukaryotic translation initiation factor 2B subunit 3 gamma 218488_at 58kDa EIF2B3 0.7 6.8 225684_at family with sequence similarity 33 member A FAM33A 0.6 3.3 Probe Set ID Gene Title Symbol Fold Change* q-value** 226811_at family with sequence similarity 46 member C FAM46C 0.5 9.8 222854_s_at family with sequence similarity 51 member A1 FAM51A1 0.5 4.0 227203_at F-box and leucine-rich repeat protein 17 FBXL17 0.5 0.0 203240_at Fc fragment of IgG binding protein FCGBP 5.1 3.3 ferritin heavy polypeptide pseudogene 1 /// ferritin heavy 211628_x_at polypeptide pseudogene 1 FTHP1 1.4 8.5 212788_x_at ‡ ferritin light polypeptide FTL 2.0 8.5 202709_at fibromodulin FMOD 0.6 0.0 225480_at FLJ45459 protein FLJ45459 0.5 6.8 237262_at Full length insert cDNA clone ZE05E03 --- 1.8 6.1 Full-length cDNA clone CS0DI067YF23 of Placenta Cot 229182_at 25-normalized of Homo sapiens (human) --- 0.4 5.5 222710_at GDP-mannose pyrophosphorylase B GMPPB 0.5 8.5 225853_at glucosamine-phosphate N-acetyltransferase 1 GNPNAT1 0.7 9.8 221759_at glucose 6 phosphatase catalytic 3 G6PC3 0.8 6.8 202922_at glutamate-cysteine catalytic subunit GCLC 0.3 1.3 202923_s_at glutamate-cysteine ligase catalytic subunit GCLC 0.2 5.5 202722_s_at glutamine-fructose-6-phosphate transaminase 1 GFPT1 0.5 6.8 AFFX- HUMGAPDH/ M33197_3_at ‡glyceraldehyde-3-phosphate dehydrogenase GAPD 0.7 4.6 213129_s_at glycine cleavage system protein H (aminomethyl carrier) GCSH 0.5 1.3 209169_at glycoprotein M6B GPM6B 0.6 1.3 218706_s_at HCV NS3-transactivated protein 2 NS3TP2 1.6 6.1 242451_x_at homolog of yeast INO80 INO80 1.6 6.8 221880_s_at hypothetical gene supported by AK075564; BC060873 LOC400451 0.5 4.6 222085_at Hypothetical gene supported by AK075564; BC060873 LOC400451 0.5 4.6 51158_at hypothetical gene supported by AK075564; BC060873 LOC400451 0.5 4.0 203897_at hypothetical protein A-211C6.1 LOC57149 2.0 3.2 213658_at hypothetical protein DKFZp547K1113 DKFZp547K1113 0.5 4.6 hypothetical protein DKFZp547K1113 /// MRNA full length 37590_g_at insert cDNA clone EUROIMAGE 375854 DKFZp547K1113 0.4 4.6 225355_at hypothetical protein DKFZP761M1511 DKFZP761M1511 0.4 3.2 219331_s_at hypothetical protein FLJ10748 FLJ10748 0.3 4.0 222871_at hypothetical protein FLJ10748 FLJ10748 0.2 4.6 227245_at hypothetical protein FLJ13089 FLJ13089 0.6 8.5 hypothetical protein FLJ22649 similar to signal peptidase 222753_s_at SPC22/23 FLJ22649 0.6 6.8 225284_at hypothetical protein LOC144871 LOC144871 0.6 0.0 212708_at hypothetical protein LOC339287 LOC339287 0.5 0.0 228532_at hypothetical protein MGC24133 MGC24133 0.4 3.3 212909_at ±hypothetical protein MGC29643 MGC29643 7.0 3.2 221939_at hypothetical protein MGC3262 MGC3262 0.8 9.8 231430_at hypothetical protein MGC33846 MGC33846 0.4 3.3 218756_s_at hypothetical protein MGC4172 MGC4172 0.6 8.5 200825_s_at ‡hypoxia up-regulated 1 HYOU1 0.3 3.3 210970_s_at inhibitor of Bruton agammaglobulinemia tyrosine kinase IBTK 0.7 1.3 220741_s_at inorganic 2 PPA2 0.7 0.0 202718_at ‡insulin-like growth factor binding protein 2 36kDa IGFBP2 0.4 4.6 212832_s_at KIAA0097 gene product ch-TOG 0.7 9.8 201240_s_at ‡KIAA0102 gene product KIAA0102 0.7 4.0 Probe Set ID Gene Title Symbol Fold Change* q-value** 225611_at KIAA0303 protein KIAA0303 2.1 8.5 212946_at KIAA0564 protein KIAA0564 0.4 1.3 1565866_a_at KIAA0663 gene product KIAA0663 0.6 1.3 1565867_a_at KIAA0663 gene product KIAA0663 0.7 5.5 212792_at ‡ KIAA0877 protein KIAA0877 0.4 4.6 1559409_a_at KIAA1345 protein KIAA1345 1.6 9.8 233002_at KIAA1622 KIAA1622 0.2 1.8 227638_at KIAA1632 protein KIAA1632 1.9 4.6 201036_s_at L-3-hydroxyacyl-Coenzyme A dehydrogenase short chain HADHSC 0.7 9.8 leucine-rich repeats and immunoglobulin-like domains 1 /// 211596_s_at leucine-rich repeats and immunoglobulin-like domains 1 LRIG1 0.6 6.8 230717_at lipocalin 12 LCN12 0.4 8.5 201721_s_at Lysosomal-associated multispanning membrane protein-5 LAPTM5 4.2 4.6 major histocompatibility complex class II DR beta 6 217362_x_at (pseudogene) HLA-DRB6 4.1 5.5 235374_at ‡malate dehydrogenase 1 NAD (soluble) MDH1 0.7 8.5 1552481_s_at mannosidase alpha class 1A member 2 MAN1A2 0.5 1.8 220945_x_at MANSC domain containing 1 MANSC1 0.8 3.3 209014_at †melanoma antigen family D 1 MAGED1 0.5 0.0 201420_s_at MEP50 protein MEP50 0.2 0.0 201421_s_at MEP50 protein MEP50 0.2 0.0 224675_at mesoderm development candidate 2 MESDC2 0.7 4.0 205442_at microfibrillar-associated protein 3-like MFAP3L 0.3 0.0 243_g_at ‡microtubule-associated protein 4 MAP4 0.6 9.8 203781_at mitochondrial ribosomal protein L33 MRPL33 0.6 8.5 228554_at MRNA; cDNA DKFZp686A0815 (from clone DKFZp686A0815) --- 0.2 0.0 229569_at MRNA; cDNA DKFZp686C1090 (from clone DKFZp686C1090) --- 0.4 4.0 204173_at 1 slow a MLC1SA 0.5 5.5 224656_s_at ‡myotrophin MTPN 0.7 6.1 201670_s_at myristoylated alanine-rich protein kinase C substrate MARCKS 0.7 5.5 225897_at myristoylated alanine-rich protein kinase C substrate MARCKS 0.4 9.8 218189_s_at N-acetylneuraminic acid synthase (sialic acid synthase) NANS 0.4 4.6 231934_at N-acetylneuraminic acid synthase (sialic acid synthase) NANS 0.5 4.6 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 1 202298_at 7.5kDa NDUFA1 0.6 1.8 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4 217773_s_at 9kDa NDUFA4 0.7 1.8 NADH dehydrogenase (ubiquinone) Fe-S protein 5 15kDa 201757_at (NADH-coenzyme Q reductase) NDUFS5 0.6 3.3 226616_s_at NADH dehydrogenase (ubiquinone) flavoprotein 3 10kDa NDUFV3 0.6 8.5 224248_x_at NEFA-interacting nuclear protein NIP30 NIP30 0.7 6.8 209556_at ‡ neurochondrin NCDN 0.5 1.8 229838_at nucleobindin 2 NUCB2 0.4 5.5 213599_at Opa-interacting protein 5 OIP5 0.7 8.5 205432_at oviductal glycoprotein 1 120kDa (mucin 9 oviductin) OVGP1 0.1 0.0 232304_at pellino homolog 1 (Drosophila) PELI1 0.6 3.2 202739_s_at phosphorylase kinase beta PHKB 0.5 1.3 218718_at platelet derived growth factor C PDGFC 1.4 9.8 † polycystic kidney and hepatic disease 1 (autosomal recessive)- 230673_at like 1 PKHD1L1 0.2 8.5 Probe Set ID Gene Title Symbol Fold Change* q-value** 221889_at ‡ potassium channel tetramerisation domain containing 13 KCTD13 0.5 9.8 45653_at ‡ potassium channel tetramerisation domain containing 13 KCTD13 0.5 5.5 219545_at potassium channel tetramerisation domain containing 14 KCTD14 0.4 3.2 58916_at potassium channel tetramerisation domain containing 14 KCTD14 0.3 8.5 potassium voltage-gated channel Shaw-related subfamily 230531_at member 3 KCNC3 0.4 1.8

procollagen-proline 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase) beta polypeptide (protein disulfide isomerase; 200654_at thyroid hormone binding protein p55) P4HB 0.6 8.5 ‡protein disulfide isomerase related protein (calcium-binding 208658_at protein intestinal-related) ERP70 0.3 0.0 231830_x_at RAB11 family interacting protein 1 (class I) RAB11FIP1 1.8 6.8 205645_at †RALBP1 associated Eps domain containing 2 REPS2 0.4 8.5 210106_at retinol dehydrogenase 5 (11-cis and 9-cis) RDH5 0.5 3.3 201288_at ‡Rho GDP dissociation inhibitor (GDI) beta ARHGDIB 1.9 4.6 226576_at Rho GTPase activating protein 26 ARHGAP26 0.4 4.0 205980_s_at Rho GTPase activating protein 8 ARHGAP8 0.6 8.5 37117_at Rho GTPase activating protein 8 ARHGAP8 0.6 4.0 230755_at rhomboid veinlet-like 4 (Drosophila) RHBDL4 0.3 5.5 233409_at rhomboid veinlet-like 4 (Drosophila) RHBDL4 0.4 1.8 218007_s_at ‡ribosomal protein S27-like RPS27L 1.5 5.5

‡signal recognition particle 14kDa (homologous Alu RNA binding protein) /// signal recognition particle 14kDa 200007_at (homologous Alu RNA binding protein) SRP14 0.8 3.3 signal sequence receptor gamma (translocon-associated 222411_s_at protein gamma) SSR3 0.5 1.3 236064_at similar to 1810012H11Rik FLJ40217 0.1 1.3 240312_at Similar to MGC68553 protein --- 0.4 1.8 224867_at Similar to ribosomal protein S14 --- 0.7 3.3 solute carrier family 12 (sodium/potassium/chloride 225835_at transporters) member 2 SLC12A2 0.4 6.1 228836_at solute carrier family 25, member 35 SLC25A35 0.3 1.3 202433_at solute carrier family 35 member B1 SLC35B1 0.5 1.8 226444_at †solute carrier family 39 (zinc transporter) member 10 SLC39A10 2.3 8.5 202667_s_at solute carrier family 39 (zinc transporter) member 7 SLC39A7 0.5 9.8 223044_at solute carrier family 40 (iron-regulated transporter) member 1 SLC40A1 1.8 8.5 233123_at solute carrier family 40 (iron-regulated transporter) member 1 SLC40A1 2.9 4.6 † solute carrier family 9 (sodium/hydrogen exchanger) isoform 201349_at 3 regulator 1 SLC9A3R1 0.4 4.0 200795_at ‡ SPARC-like 1 (mast9 hevin) SPARCL1 0.5 6.8 206816_s_at sperm associated antigen 8 SPAG8 0.4 6.8 229744_at sperm specific antigen 2 SSFA2 0.4 8.5 212321_at sphingosine-1-phosphate lyase 1 SGPL1 2.0 3.2 201247_at ‡sterol regulatory element binding transcription factor 2 SREBF2 0.6 8.5 231521_at Stromal antigen 3-like FLJ13195 0.6 4.0 223395_at target of Nesh-SH3 TARSH 0.3 1.3 222011_s_at †t-complex 1 TCP1 0.5 6.1 208073_x_at tetratricopeptide repeat domain 3 TTC3 0.7 4.0 208959_s_at thioredoxin domain containing 4 (endoplasmic reticulum) TXNDC4 0.5 1.8 207668_x_at thioredoxin domain containing 7 (protein disulfide isomerase) TXNDC7 0.6 0.0 Probe Set ID Gene Title Symbol Fold Change* q-value** 208639_x_at thioredoxin domain containing 7 (protein disulfide isomerase) TXNDC7 0.5 0.0 222315_at Transcribed locus --- 0.3 3.2 229823_at Transcribed locus --- 0.3 3.2 230580_at Transcribed locus --- 0.5 4.0 230943_at Transcribed locus --- 0.3 1.3 231174_s_at Transcribed locus --- 0.4 1.8 235901_at Transcribed locus --- 0.6 8.5 238115_at Transcribed locus --- 0.5 1.8 244671_at Transcribed locus --- 0.7 6.8 244690_at Transcribed locus --- 0.1 0.0 transient receptor potential cation channel subfamily M 219360_s_at member 4 TRPM4 0.5 4.0 of inner mitochondrial membrane 17 homolog A 215171_s_at (yeast) TIMM17A 0.5 4.6 212352_s_at transmembrane trafficking protein TMP21 0.8 5.5 210705_s_at tripartite motif-containing 5 TRIM5 0.5 6.8 203252_at tumor suppressor deleted in oral cancer-related 1 DOC-1R 0.3 4.0 202090_s_at ubiquinol-cytochrome c reductase (6.4kD) subunit UQCR 0.6 3.2 218190_s_at ubiquinol-cytochrome c reductase complex (7.2 kD) HSPC051 0.6 6.8 222578_s_at ubiquitin-activating enzyme E1-domain containing 1 UBE1DC1 0.6 6.8 UDP-N-acetyl-alpha-D-galactosamine:polypeptide 218885_s_at N-acetylgalactosaminyltransferase 12 (GalNAc-T12) GALNT12 0.3 4.0 215200_x_at UG0651E06 --- 0.8 9.8 210064_s_at uroplakin 1B UPK1B 0.2 4.6 220744_s_at WD repeat domain 10 WDR10 0.6 8.5 222503_s_at WD repeat domain 41 WDR41 0.4 1.8 213813_x_at --- 1.9 8.5 217557_s_at --- 0.1 0.0 222096_x_at --- 0.5 5.5 230537_at --- 0.2 1.3 244075_at --- 0.5 8.5

* corresponds to the relative expression of the specific probe set in FTEb luteal compared to FTEb follicular samples (decreased expression <0, increased expression >0). ** corresponds to the significance level of this differential expression. Italicized genes represent those probe sets also differentiating SerCa and FTEn specimens in the same direction. † indicates TGF-β target genes identified in mouse fibroblasts (47). ± indicates TGF-β target genes identified in immortalized human keratinocytes and pancreatic tumor cells (48). ‡ indicates TGF-β target genes identified in human lung adenocarcinoma cells and immortalized lung epithelial cells (49). § indicates TGF-β target genes reviewed by Massague et al (50).