Gene Symbol Genbank MCF7-T MCF7-F Description

Home , ATP11B, BCL11B, Biliverdin reductase A, COL4A3BP, CRIP2, DRAP1

Table S6. Altered expression of ERα signature genes in MCF7-T and MCF7-F Fold change (vs. MCF7) gene symbol genbank MCF7-T MCF7-F Description

Genes positively associated with ERα expression in breast tumors A1BG NM_130786 - -3.35 Alpha-1-B glycoprotein ABAT NM_020686 -3.1 -4.55 4-aminobutyrate aminotransferase AHNAK NM_024060 -2.07 - AHNAK nucleoprotein (desmoyokin) AKR7A2 NM_003689 -1.93 -2.21 Aldo-keto reductase family 7, member A2 ALCAM NM_001627 -3.72 10.55 Activated leukocyte cell adhesion molecule ALDH6A1 NM_005589 1.67 -4.27 Aldehyde dehydrogenase 6 family, member A1 ANXA9 NM_003568 -8.4 2.11 Annexin A9 APRIN NM_015928 1.47 -2.28 Androgen-induced proliferation inhibitor ARL3 NM_004311 - -5.73 ADP-ribosylation factor-like 3 AZGP1 NM_001185 -5.62 -3.22 MRNA; cDNA DKFZp762C115 (from clone DKFZp762C115) BAG3 NM_004281 -2.52 -3.55 BCL2-associated athanogene 3 BC-2 NM_198426 - -2.52 Putative breast adenocarcinoma marker (32kD) BCAS4 NM_198799 - -2.1 Breast carcinoma amplified sequence 4 BLVRA NM_000712 - -4.08 Biliverdin reductase A BTD NM_000060 -1.77 -2.11 Biotinidase BTF3 NM_001207 - -2.75 Basic transcription factor 3 C10orf116 NM_006829 -1.84 -4.06 Chromosome 10 open reading frame 116 C14orf132 NM_020215 - -3.66 Chromosome 14 open reading frame 132 C18orf1 NM_181483 2.44 -6.83 Chromosome 18 open reading frame 1 C20orf35 NM_033542 1.27 -3.13 Chromosome 20 open reading frame 35 C21orf59 NM_021254 -1.72 -2.15 Chromosome 21 open reading frame 59 C9orf46 NM_018465 - -3.17 Chromosome 9 open reading frame 46 CAP2 NM_006366 -3.23 -6.03 CAP, adenylate cyclase-associated protein, 2 (yeast) CCND1 NM_053056 -1.91 -2.52 Cyclin D1 (PRAD1: parathyroid adenomatosis 1) CGI-111 NM_016048 1.47 -3.47 CGI-111 protein CLN3 NM_000086 -2.02 - Ceroid-lipofuscinosis, neuronal 3, juvenile COL4A3BP NM_031361 - -2.16 Collagen, type IV, alpha 3 (Goodpasture antigen) binding protein COX6C NM_004374 - -2.31 Cytochrome c oxidase subunit VIc COX7A2 NM_001865 - -2.28 Cytochrome c oxidase subunit VIIa polypeptide 2 (liver) CREBL2 NM_001310 - -2.04 CAMP responsive element binding protein-like 2 CRI1 NM_014335 - -4.09 CREBBP/EP300 inhibitor 1 CRIP1 NM_001311 -3.7 -12.4 Cysteine-rich protein 1 (intestinal) CRIP2 NM_001312 -5.03 -5.3 Cysteine-rich protein 2 CTBP2 NM_022802 -1.22 -2.5 C-terminal binding protein 2 CTDSP1 NM_182642 - -2.12 CTD small phosphatase 1 CXXC5 NM_016463 -8.1 -1.62 CXXC finger 5 CYB5 NM_148923 -2.26 -4.37 Cytochrome b-5 DEAF1 NM_021008 - -2.38 Deformed epidermal autoregulatory factor 1 (Drosophila) DEPDC6 NM_022783 -2.71 -1.73 DEP domain containing 6 DHRS2 NM_182908 -2.77 4.17 Dehydrogenase/reductase (SDR family) member 2 DHRS4 NM_021004 - -2.33 Dehydrogenase/reductase (SDR family) member 4 DNAJC12 NM_201262 -3.42 -47.9 DnaJ (Hsp40) homolog, subfamily C, member 12 DRAP1 NM_006442 - -2.17 DR1-associated protein 1 (negative cofactor 2 alpha) DUSP4 NM_057158 -4.4 -1.47 Dual specificity phosphatase 4 ENSA NM_004436 1.6 -2.21 Endosulfine alpha ERBB4 NM_005235 - -2.6 V-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) ESR1 NM_000125 -2.19 -25.89 Estrogen receptor 1 ETNK2 NM_018208 - -2.04 Ethanolamine kinase 2 EVL NM_016337 1.68 -2.65 Enah/Vasp-like FBP1 NM_000507 -1.31 -2.82 Fructose-1,6-bisphosphatase 1 FER1L3 NM_133337 -2.88 3.03 Fer-1-like 3, myoferlin (C. elegans) FLJ10116 NM_018000 - -5.2 Whn-dependent transcript 2 FLJ20366 NM_017786 1.27 -5.37 Hypothetical protein FLJ20366 FOXA1 NM_004496 - -6.56 Forkhead box A1 GALNT10 NM_198321 -2.53 2.16 GalNAc-T10 GATA3 NM_032742 -1.41 -2.55 GATA binding protein 3 GFRA1 NM_145793 -3.45 -21.48 GDNF family receptor alpha 1 GLUL NM_002065 -2.15 - Glutamate-ammonia ligase (glutamine synthase) GPHN NM_020806 1.45 -2.65 Gephyrin Table S6. Altered expression of ERα signature genes in MCF7-T and MCF7-F (continued) Fold change (vs. MCF7) gene symbol genbank MCF7-T MCF7-F Description

Genes positively associated with ERα expression in breast tumors GREB1 NM_148903 -97.81 -59.66 GREB1 protein GSTM3 NM_000849 - -8.26 Glutathione S-transferase M3 (brain) GSTZ1 NM_145871 1.61 -6.99 Glutathione transferase zeta 1 (maleylacetoacetate isomerase) HAGH NM_005326 -1.72 -2.51 Hydroxyacylglutathione hydrolase HEBP1 NM_015987 -1.62 -2.56 Heme binding protein 1 HIST1H2BD NM_138720 -1.35 -2.68 Histone 1, H2bd HOXC6 NM_153693 2.29 -2.3 Homeo box C6 HSPA2 NM_021979 3.7 -3.36 Heat shock 70kDa protein 2 HSPB1 NM_001540 -1.57 -3.02 Heat shock 27kDa protein 1 HSPB8 NM_014365 -1.86 -7.28 Heat shock 22kDa protein 8 ICA1 NM_022308 -1.94 -2.16 Islet cell autoantigen 1, 69kDa IGBP1 NM_001551 - -3.39 Immunoglobulin (CD79A) binding protein 1 IMPACT NM_018439 1.42 -2.52 Hypothetical protein IMPACT INPP4B NM_003866 -3.24 -2.96 Inositol polyphosphate-4-phosphatase, type II, 105kDa ITPK1 NM_014216 - -2.64 Inositol 1,3,4-triphosphate 5/6 kinase KIAA1143 NM_020696 - -5.14 KIAA1143 protein KIAA1181 NM_020462 -2.49 -2.6 Endoplasmic reticulum-golgi intermediate compartment 32 kDa protein KIAA1324 NM_020775 1.59 -20.11 Maba1 KIAA1443 NM_020834 - -2.08 KIAA1443 KIF3B NM_004798 -2.33 -1.46 Kinesin family member 3B KIF9 NM_182903 -1.75 -2.82 Kinesin family member 9 KRT8 NM_002273 - -2.13 Keratin 8 LRBA NM_006726 - -2.02 LPS-responsive vesicle trafficking, beach and anchor containing LRIG1 NM_015541 2.93 -2.02 Leucine-rich repeats and immunoglobulin-like domains 1 LZTFL1 NM_020347 -1.33 -2.02 Leucine zipper transcription factor-like 1 MGC2650 NM_024108 - -2.56 Hypothetical protein MGC2650 MIPEP NM_005932 -10.63 -5.42 Mitochondrial intermediate peptidase MOAP1 NM_022151 1.47 -3.15 Modulator of apoptosis 1 MPI NM_002435 - -2.24 Mannose phosphate isomerase MRPL24 NM_145729 - -4.12 Mitochondrial ribosomal protein L24 MTL5 NM_004923 -1.61 -3.07 Metallothionein-like 5, testis-specific (tesmin) MUC1 NM_182741 -3.33 -2.38 Mucin 1, transmembrane MYB NM_005375 -1.7 -2.88 V-myb myeloblastosis viral oncogene homolog (avian) MYO6 NM_004999 -2.39 2.66 myosin VI NAT1 NM_000662 -1.75 -2.85 N-acetyltransferase 1 (arylamine N-acetyltransferase) NCDN NM_014284 - -2.09 Neurochondrin NDUFA7 NM_005001 - -2.67 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5kDa NEBL NM_006393 -1.61 -2.42 Nebulette NEDD4L NM_015277 -2.94 -3.66 Neural precursor cell expressed, developmentally down-regulated 4-like NEUGRIN NM_016645 - -2.68 Mesenchymal stem cell protein DSC92 NPY1R NM_000909 -10.26 -580.16 Neuropeptide Y receptor Y1 NUDT2 NM_147173 - -3.73 Nudix (nucleoside diphosphate linked moiety X)-type motif 2 PDZK1 NM_002614 -3.09 -15.25 PDZ domain containing 1 PECI NM_006117 - -2.19 Peroxisomal D3,D2-enoyl-CoA isomerase PEX12 NM_000286 - -2.1 Peroxisomal biogenesis factor 12 PHPT1 NM_014172 - -2.55 Phosphohistidine phosphatase 1 PLEKHA6 NM_014935 -1.7 -2.35 Pleckstrin homology domain containing, family A member 6 PLEKHF2 NM_024613 -2.21 -3.55 Pleckstrin homology domain containing, family F PLK2 NM_006622 -5.84 - Polo-like kinase 2 (Drosophila) PMVK NM_006556 - -3.6 Phosphomevalonate kinase PNMA1 NM_006029 1.54 -2.85 Paraneoplastic antigen MA1 POLB NM_002690 - -3.65 Polymerase (DNA directed), beta POLR2L NM_021128 - -6.48 Polymerase (RNA) II (DNA directed) polypeptide L, 7.6kDa PPP2R5A NM_006243 - -2.24 Protein phosphatase 2, regulatory subunit B (B56), alpha isoform PREX1 NM_020820 1.3 -40.66 Phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1 PTP4A2 NM_080392 -1.45 -2.65 Protein tyrosine phosphatase type IVA, member 2 PUNC NM_004884 -2.06 - Putative neuronal cell adhesion molecule PURA NM_005859 - -2.5 Purine-rich element binding protein A PURB NM_033224 - -3.3 Purine-rich element binding protein B Table S6. Altered expression of ERα-positive tumor signature genes in MCF7-T and MCF7-F (continued) Fold change (vs. MCF7) gene symbol genbank MCF7-T MCF7-F Description

Genes positively associated with ERα expression in breast tumors QDPR NM_000320 - -2.05 Quinoid dihydropteridine reductase RAB11A NM_004663 - -2.75 RAB11A, member RAS oncogene family RAB31 NM_006868 - -5.22 RAB31, member RAS oncogene family RAB5C NM_201434 - -4.04 RAB5C, member RAS oncogene family RARA NM_000964 - -2.66 Retinoic acid receptor, alpha RRM2B NM_015713 - -2.2 Ribonucleotide reductase M2 B (TP53 inducible) SALL2 NM_005407 - -4.43 Sal-like 2 (Drosophila) SELENBP1 NM_003944 2.06 -3.81 Selenium binding protein 1 SGKL NM_170709 1.6 -4.31 Serum/glucocorticoid regulated kinase-like SH3BGRL NM_003022 -3.92 -1.4 SH3 domain binding glutamic acid-rich protein like SIAH2 NM_005067 -1.62 -3.21 Seven in absentia homolog 2 (Drosophila) SKP1A NM_170679 1.29 -2.76 S-phase kinase-associated protein 1A (p19A) SLC9A3R1 NM_004252 -1.68 -3.42 Solute carrier family 9, isoform 3 regulator 1 SLC9A5 NM_004594 - -2.07 Solute carrier family 9 (sodium/hydrogen exchanger), isoform 5 SORD NM_003104 1.44 -4.84 Sorbitol dehydrogenase SPDEF NM_012391 - -15.48 SAM pointed domain containing ets transcription factor SRP14 NM_003134 - -3.87 Signal recognition particle 14kDa STARD10 NM_006645 -2.48 -7.07 START domain containing 10 STC2 NM_003714 - -2.54 Stanniocalcin 2 SUCLG2 NM_003848 - -2.19 Succinate-CoA ligase, GDP-forming, beta subunit TCEAL4 NM_024863 - -3.04 Transcription elongation factor A (SII)-like 4 TENC1 NM_198316 - -9.67 Tensin like C1 domain containing phosphatase TFF1 NM_003225 1.26 -7.57 Trefoil factor 1 TFF3 NM_003226 -13.71 -75.86 Trefoil factor 3 (intestinal) TNNT1 NM_003283 - -8.89 Troponin T1, skeletal, slow TNRC9 XM_941030 -27.24 -6.6 trinucleotide repeat containing 9 TOB1 NM_005749 - -5.03 Transducer of ERBB2, 1 TRPS1 NM_014112 -2.08 -2.9 Trichorhinophalangeal syndrome I TUSC2 NM_007275 - -2.15 Tumor suppressor candidate 2 UGDH NM_003359 -2 -7.49 UDP-glucose dehydrogenase VAV3 NM_006113 -8.35 6.67 Vav 3 oncogene XBP1 NM_005080 -1.95 -2.94 X-box binding protein 1 ZNF219 NM_016423 - -3.01 Zinc finger protein 219 ZNF278 NM_032052 - -3.14 Zinc finger protein 278 ZNF395 NM_017606 - -2.03 zinc finger protein 395 ZNF552 NM_024762 - -2.48 Zinc finger protein 552

Genes inversely associated with ERα expression in breast tumors ACAT2 NM_005891 2.11 -2.6 Acetyl-Coenzyme A acetyltransferase 2 ACSL4 NM_022977 21.06 8.26 Acyl-CoA synthetase long-chain family member 4 ADM NM_001124 - 3.4 Adrenomedullin ADORA2B NM_000676 - 2.45 Adenosine A2b receptor AIM1 NM_001624 - 2.82 absent in melanoma 1 ALG6 NM_013339 1.23 2.57 Asparagine-linked glycosylation 6 homolog AMY2A NM_000699 - 18.77 Amylase, alpha 2A; pancreatic ANKRD3 AP001743 - 33.91 ankyrin repeat domain 3 ANLN NM_018685 2.12 2.27 Anillin, actin binding protein (scraps homolog, Drosophila) ANXA1 NM_000700 -3.05 14.27 Annexin A1 ANXA8 NM_001630 -3 2.29 Annexin A8 ARHE NM_005168 - 3.28 Ras homolog gene family, member E ARL6IP2 NM_022374 - 6.57 ADP-ribosylation factor-like 6 interacting protein 2 ATP11B NM_014616 1.31 2.19 ATPase, Class VI, type 11B ATP2C1 NM_014382 1.47 2.31 ATPase, Ca++ transporting, type 2C, member 1 BACE2 NM_138992 1.65 3.73 Beta-site APP-cleaving enzyme 2 BCL11B NM_138576 2.53 -2.62 B-cell CLL/lymphoma 11B (zinc finger protein) BENE NM_005434 - 10.2 BENE protein BIRC5 NM_001168 2.08 -3.47 Baculoviral IAP repeat-containing 5 (survivin) BM039 NM_018455 2.19 -3.48 Uncharacterized bone marrow protein BM039 BUB1 NM_004336 1.82 2.29 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) Table S6. Altered expression of ERα signature genes in MCF7-T and MCF7-F (continued) Fold change (vs. MCF7) gene symbol genbank MCF7-T MCF7-F Description

Genes inversely associated with ERα expression in breast tumors C3 NM_000064 - 13.3 Complement component 3 CASP4 NM_033307 - 3.08 Caspase 4, apoptosis-related cysteine protease CBFB NM_022845 -1.22 3.29 Core-binding factor, beta subunit CCNA2 NM_001237 2.1 1.43 Cyclin A2 CCNB2 NM_004701 2 -1.67 Cyclin B2 CDC2 NM_033379 2.78 1.98 Cell division cycle 2, G1 to S and G2 to M CDKN2C NM_078626 2.7 -2.51 Cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) CENPF NM_016343 2.2 2.16 Centromere protein F, 350/400ka (mitosin) CGI-141 NM_016072 - 2.13 CGI-141 protein CKAP4 NM_006825 -1.58 2.39 Cytoskeleton-associated protein 4 CLDN4 NM_001305 -2.47 2.64 Claudin 4 CLIC4 NM_013943 - 2.26 Chloride intracellular channel 4 CNGA1 NM_000087 - 4.18 Cyclic nucleotide gated channel alpha 1 CP NM_000096 - 3.48 Ceruloplasmin (ferroxidase) CRLF1 NM_004750 1.62 3.93 Cytokine receptor-like factor 1 CSDA NM_003651 -1.56 2.62 Cold shock domain protein A CSPG6 NM_005445 - 4.31 Chondroitin sulfate proteoglycan 6 (bamacan) CSRP2 NM_001321 4.38 - Cysteine and glycine-rich protein 2 CTSC NM_148170 - 43.2 Cathepsin C CTSL2 NM_001333 2.2 2.17 Cathepsin L2 CXADR NM_001338 1.88 2.81 Coxsackie virus and adenovirus receptor CXCL11 NM_005409 - 10.09 Chemokine (C-X-C motif) ligand 11 CXCR4 NM_003467 5.15 2.29 Chemokine (C-X-C motif) receptor 4 CYBA NM_000101 -3.55 2.27 Cytochrome b-245, alpha polypeptide CYP1B1 NM_000104 4.19 14.36 Cytochrome P450, family 1, subfamily B, polypeptide 1 DEGS NM_144780 - 3.26 Degenerative spermatocyte homolog, lipid desaturase (Drosophila) DEPDC1 NM_017779 3.04 3.85 DEP domain containing 1 DHCR7 NM_001360 2.43 3.19 7-dehydrocholesterol reductase DIAPH2 NM_007309 3.64 3.09 Diaphanous homolog 2 (Drosophila) DKFZp762E1312 NM_018410 2.68 2.08 Hypothetical protein DKFZp762E1312 DKK1 NM_012242 1.53 2.28 Dickkopf homolog 1 (Xenopus laevis) DLG7 NM_014750 2.94 - Discs, large homolog 7 (Drosophila) DNM1L NM_012063 - 2.43 Dynamin 1-like DSC2 NM_024422 -1.41 3.56 Desmocollin 2 DSG2 NM_001943 2.92 3.07 Desmoglein 2 ECHDC1 NM_018479 -2.41 5.22 Enoyl Coenzyme A hydratase domain containing 1 EDN2 NM_001956 - 3.18 Endothelin 2 EED NM_152991 1.3 9.33 Embryonic ectoderm development EGFR NM_201284 - 9.91 Epidermal growth factor receptor EIF2C2 NM_012154 -1.81 3.33 Eukaryotic translation initiation factor 2C, 2 EML4 NM_019063 1.36 5.36 Echinoderm microtubule associated protein like 4 ENO1 NM_005945 - 17.51 enolase 1, (alpha) EPHA2 NM_004431 - 5.83 EPH receptor A2 EPHA4 NM_004438 -1.37 4.39 EPH receptor A4 EPHB2 NM_017449 - 2.53 EPH receptor B2 EPHB3 NM_004443 - 3.22 EPH receptor B3 EXT1 NM_000127 - 5.65 Exostoses (multiple) 1 FABP5 NM_001444 2.22 -1.91 Fatty acid binding protein 5 (psoriasis-associated) FAD104 NM_022763 -1.91 3.05 Factor for adipocyte differentiation 104 FADS1 NM_013402 3.35 2.09 Fatty acid desaturase 1 FANCA NM_000135 2.38 3.85 Fanconi anemia, complementation group A FAT NM_005245 2.14 2.9 FAT tumor suppressor homolog 1 (Drosophila) FLJ10154 NM_018011 1.53 2.87 Hypothetical protein FLJ10154 FLJ10156 NM_019013 1.67 2.14 Hypothetical protein FLJ10156 FLJ10199 NM_018022 - 2.35 Hypothetical protein FLJ10199 FLJ10407 NM_018087 1.5 3.7 Hypothetical protein FLJ10407 FLJ10706 NM_018186 1.67 3.26 Hypothetical protein FLJ10706 FLJ10996 NM_031447 - 2.08 hypothetical protein FLJ10996 FLJ11000 NM_018295 - 26.4 Hypothetical protein FLJ11000 Table S6. Altered expression of ERα signature genes in MCF7-T and MCF7-F (continued) Fold change (vs. MCF7) gene symbol genbank MCF7-T MCF7-F Description

Genes inversely associated with ERα expression in breast tumors FLJ11036 NM_018306 - 2.95 Hypothetical protein FLJ11036 FLJ22833 NM_022837 1.86 5.06 Hypothetical protein FLJ22833 FLJ23518 NM_024725 - 13.95 Hypothetical protein FLJ23518 FOXD1 NM_004472 2.02 - Forkhead box D1 FOXM1 NM_021953 2 2.35 Forkhead box M1 FUT4 NM_002033 3.01 -2.68 Fucosyltransferase 4 FYB NM_199335 - 5.74 FYN binding protein (FYB-120/130) FZD3 NM_017412 -1.38 2.52 Frizzled homolog 3 (Drosophila) GALNT3 NM_004482 - 2.79 GalNAc-T3 GBP1 NM_002053 - 55.88 Guanylate binding protein 1, interferon-inducible, 67kDa GBP2 NM_004120 - 3.86 Guanylate binding protein 2, interferon-inducible GDI2 NM_001494 - 2.04 GDP dissociation inhibitor 2 GGH NM_003878 1.49 2.67 Gamma-glutamyl hydrolase GLS NM_014905 - 9.54 Glutaminase GPM6B NM_005278 - 2.58 Glycoprotein M6B GPNMB NM_002510 -2.88 4.65 Glycoprotein (transmembrane) nmb GPR109B NM_006018 1.87 2.11 G protein-coupled receptor 109B HECA NM_016217 - 4.42 Headcase homolog (Drosophila) HLA-A NM_002116 3.98 11.57 Major histocompatibility complex, class I, A HLA-B NM_005514 2.01 16.66 Major histocompatibility complex, class I, B HRB NM_004504 -1.32 5.46 HIV-1 Rev binding protein HSPC049 NM_014149 2.11 1.96 HSPC049 protein IFI30 NM_006332 -1.48 3.27 Interferon, gamma-inducible protein 30 IFI44 NM_006417 - 260.82 Interferon-induced protein 44 IFNGR1 NM_000416 - 8.7 Interferon gamma receptor 1 IFRD1 NM_001550 - 2.05 Interferon-related developmental regulator 1 IL8 NM_000584 - 3.32 Interleukin 8 IMPA2 NM_014214 2.01 -1.87 Inositol(myo)-1(or 4)-monophosphatase 2 IRF5 NM_032643 - 2.2 Interferon regulatory factor 5 ITGB4 NM_000213 - 9.93 Integrin, beta 4 ITM1 NM_152713 - 3.64 Integral membrane protein 1 ITM2B NM_021999 -1.26 2.08 Integral membrane protein 2B ITSN2 NM_147152 - 2.09 Intersectin 2 KCNK1 NM_002245 - 7.61 Potassium channel, subfamily K, member 1 KCNN4 NM_002250 - 7.86 Potassium intermediate/small conductance calcium-activated channel, N4 KIAA0092 NM_014679 - 3.3 Translokin KIAA0922 NM_015196 - 2.35 KIAA0922 protein KLF5 NM_001730 - 2.28 Kruppel-like factor 5 (intestinal) KLK5 NM_012427 - 3.44 Kallikrein 5 KLK6 NM_002774 - 7.27 Kallikrein 6 (neurosin, zyme) KNTC2 NM_006101 3.32 - Kinetochore associated 2 KRT17 NM_000422 - 2.03 Keratin 17 KRT5 NM_000424 - 55.6 Keratin 5 LAMC2 NM_018891 - 17.18 Laminin, gamma 2 LAMP2 NM_013995 -1.29 2.08 Lysosomal-associated membrane protein 2 LAMP3 NM_014398 - 24.01 Lysosomal-associated membrane protein 3 LAPTM5 NM_006762 - 7.15 Lysosomal associated multispanning membrane protein 5 LCN2 NM_005564 - 3.39 Lipocalin 2 (oncogene 24p3) LCP1 NM_002298 3.09 1.65 Lymphocyte cytosolic protein 1 (L-plastin) LDHB NM_002300 14.92 - Lactate dehydrogenase B LIPG NM_006033 - 8.95 Lipase, endothelial LISCH7 NM_015925 - 4.25 Liver-specific bHLH-Zip transcription factor LOC55971 NM_018842 1.55 4.73 Insulin receptor tyrosine kinase substrate LPIN1 NM_145693 3.43 3.03 Lipin 1 LPXN NM_004811 - 2.39 Leupaxin LRP8 NM_033300 2.33 2.4 Low density lipoprotein receptor-related protein 8 LTBR NM_002342 -2.04 2.31 Lymphotoxin beta receptor (TNFR superfamily, member 3) LXN NM_020169 1.66 3.16 Latexin LY6E NM_002346 -4.82 3.82 Lymphocyte antigen 6 complex, locus E Table S6. Altered expression of ERα signature genes in MCF7-T and MCF7-F (continued) Fold change (vs. MCF7) gene symbol genbank MCF7-T MCF7-F Description

Genes inversely associated with ERα expression in breast tumors MAP3K14 NM_003954 - 3.1 Mitogen-activated protein kinase kinase kinase 14 MAP3K5 NM_005923 - 3.6 Mitogen-activated protein kinase kinase kinase 5 MCM4 NM_182746 - 2.63 MCM4 minichromosome maintenance deficient 4 (S. cerevisiae) MCM5 NM_006739 - 2.23 MCM5 minichromosome maintenance deficient 5, cdc46 ME1 BC025246 - 5.17 Malic enzyme 1, NADP(+)-dependent, cytosolic MID1 NM_033291 3.73 -2.77 Midline 1 (Opitz/BBB syndrome) MIG-6 NM_018948 -1.86 2.17 Mitogen-inducible gene 6 MMP1 NM_002421 - 22.26 Matrix metalloproteinase 1 (interstitial collagenase) MRAS NM_012219 - 2.39 Muscle RAS oncogene homolog NEK2 NM_002497 1.84 2.77 NIMA (never in mitosis gene a)-related kinase 2 NFE2L3 NM_004289 - 3.32 Nuclear factor (erythroid-derived 2)-like 3 NMI NM_004688 -2.68 5.37 N-myc (and STAT) interactor NPC1 NM_000271 3.27 3.88 Niemann-Pick disease, type C1 OAS2 NM_016817 - 6.58 2'-5'-oligoadenylate synthetase 2, 69/71kDa PARC NM_015089 - 2.02 P53-associated parkin-like cytoplasmic protein PCDH8 NM_032949 6.64 - Protocadherin 8 PCOLCE2 NM_013363 12.47 3.77 Procollagen C-endopeptidase enhancer 2 PDCD5 NM_004708 2.61 - Programmed cell death 5 PELI1 NM_020651 2.26 2.48 Pellino homolog 1 (Drosophila) PGK1 NM_000291 -1.33 9.53 Phosphoglycerate kinase 1 PGM1 NM_002633 - 2.07 Phosphoglucomutase 1 PHGDH NM_006623 4.28 1.75 Phosphoglycerate dehydrogenase PITRM1 NM_014889 - 2.35 Pitrilysin metalloproteinase 1 PLA2G7 NM_005084 4.57 - Phospholipase A2, group VII PLAUR NM_002659 - 6.89 Plasminogen activator, urokinase receptor PLCG2 NM_002661 - 2.01 Phospholipase C, gamma 2 (phosphatidylinositol-specific) PLD1 NM_002662 - 4.25 Phospholipase D1, phophatidylcholine-specific PLEKHG1 NM_001029884 - 2.37 pleckstrin homology domain containing, family G PLSCR1 NM_021105 -1.76 19.96 Phospholipid scramblase 1 PRC1 NM_199414 2.56 - Protein regulator of cytokinesis 1 PRIM2A NM_000947 - 2.83 Primase, polypeptide 2A, 58kDa PRKCI NM_002740 -1.4 3.28 Protein kinase C, iota PRKD3 NM_005813 1.91 15.67 Protein kinase D3 PRNP NM_183079 - 4.43 Prion protein (p27-30) PROM1 NM_006017 3.37 - Prominin 1 PSMB9 NM_148954 1.78 4.99 Proteasome (prosome, macropain) subunit, beta type, 9 PSME4 NM_014614 - 4.41 Proteasome (prosome, macropain) activator subunit 4 PTTG1IP NM_004339 - 2.3 Pituitary tumor-transforming 1 interacting protein RAD54L NM_003579 2.06 1.49 RAD54-like (S. cerevisiae) RCN1 NM_002901 1.56 2.19 Reticulocalbin 1, EF-hand calcium binding domain RGL1 NM_015149 2.23 3.48 Ral guanine nucleotide dissociation stimulator-like 1 RIOK3 NM_145906 1.69 4.18 RIO kinase 3 (yeast) RNF138 NM_198128 2.21 - Ring finger protein 138 ROR1 NM_005012 - 14.85 Receptor tyrosine kinase-like orphan receptor 1 RPN1 NM_002950 - 3.22 Ribophorin I RRAGD NM_021244 3.07 - Ras-related GTP binding D RRBP1 NM_004587 - 21.29 Ribosome binding protein 1 homolog 180kDa (dog) RYK NM_001005861 - 5.24 RYK receptor-like tyrosine kinase S100A2 NM_005978 - 14.73 S100 calcium binding protein A2 S100A8 NM_002964 - 51.37 S100 calcium binding protein A8 (calgranulin A) S100A9 NM_002965 - 30.39 S100 calcium binding protein A9 (calgranulin B) S100P NM_005980 -4.18 3.4 S100 calcium binding protein P SAMD4 NM_015589 1.39 5.54 Sterile alpha motif domain containing 4 SCPEP1 NM_021626 2.53 7.79 Serine carboxypeptidase 1 SDC1 NM_002997 1.57 4.32 Syndecan 1 SDCBP NM_005625 1.31 3.02 Syndecan binding protein (syntenin) SERPINB5 NM_002639 - 33.84 Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5 SFN NM_006142 2.58 -1.37 Stratifin SFRS7 NM_006276 - 7.31 Splicing factor, arginine/serine-rich 7, 35kDa Table S6. Altered expression of ERα signature genes in MCF7-T and MCF7-F (continued) Fold change (vs. MCF7) gene symbol genbank MCF7-T MCF7-F Description

Genes inversely associated with ERα expression in breast tumors NEK2 NM_002497 1.84 2.77 NIMA (never in mitosis gene a)-related kinase 2 NFE2L3 NM_004289 - 3.32 Nuclear factor (erythroid-derived 2)-like 3 NMI NM_004688 -2.68 5.37 N-myc (and STAT) interactor NMT2 NM_004808 1.4 -3.14 N-myristoyltransferase 2 NMU NM_006681 1.81 -1.37 Neuromedin U NPC1 NM_000271 3.27 3.88 Niemann-Pick disease, type C1 NRAS NM_002524 - 1.78 Neuroblastoma RAS viral (v-ras) oncogene homolog NUMBL NM_004756 - 1.67 Numb homolog (Drosophila)-like NUP155 NM_153485 - 1.74 Nucleoporin 155kDa OAS2 NM_016817 - 6.58 2'-5'-oligoadenylate synthetase 2, 69/71kDa ORC6L NM_014321 - 1.58 Origin recognition complex, subunit 6 homolog-like (yeast) PARC NM_015089 - 2.02 P53-associated parkin-like cytoplasmic protein PCDH8 NM_032949 6.64 - Protocadherin 8 PCOLCE2 NM_013363 12.47 3.77 Procollagen C-endopeptidase enhancer 2 PDCD5 NM_004708 2.61 - Programmed cell death 5 PELI1 NM_020651 2.26 2.48 Pellino homolog 1 (Drosophila) PEX13 NM_002618 1.52 -4.09 Peroxisome biogenesis factor 13 PFKL NM_002626 1.45 - Phosphofructokinase, liver PFKP NM_002627 1.51 1.4 Phosphofructokinase, platelet PGK1 NM_000291 -1.33 9.53 Phosphoglycerate kinase 1 PGM1 NM_002633 - 2.07 Phosphoglucomutase 1 PHGDH NM_006623 4.28 1.75 Phosphoglycerate dehydrogenase PIM1 NM_002648 - 1.71 Pim-1 oncogene PIR NM_003662 1.58 -1.34 Pirin (iron-binding nuclear protein) PITRM1 NM_014889 - 2.35 Pitrilysin metalloproteinase 1 PLA2G7 NM_005084 4.57 - Phospholipase A2, group VII PLAUR NM_002659 - 6.89 Plasminogen activator, urokinase receptor PLCG2 NM_002661 - 2.01 Phospholipase C, gamma 2 (phosphatidylinositol-specific) PLD1 NM_002662 - 4.25 Phospholipase D1, phophatidylcholine-specific PLEKHG1 NM_001029884 - 2.37 pleckstrin homology domain containing, family G PLSCR1 NM_021105 -1.76 19.96 Phospholipid scramblase 1 POLA2 NM_002689 1.74 -1.34 Polymerase (DNA-directed), alpha (70kD) PPP2R1B NM_181699 1.28 - Protein phosphatase 2, regulatory subunit A, beta PRC1 NM_199414 2.56 - Protein regulator of cytokinesis 1 PRIM2A NM_000947 - 2.83 Primase, polypeptide 2A, 58kDa PRKCI NM_002740 -1.4 3.28 Protein kinase C, iota PRKD3 NM_005813 1.91 15.67 Protein kinase D3 PRNP NM_183079 - 4.43 Prion protein (p27-30) PROM1 NM_006017 3.37 - Prominin 1 PSAT1 NM_058179 1.78 1.92 Phosphoserine aminotransferase 1 PSCD1 NM_017456 - 1.92 Pleckstrin homology, Sec7 and coiled-coil domains 1(cytohesin 1) PSMB9 NM_148954 1.78 4.99 Proteasome (prosome, macropain) subunit, beta type, 9 PSME4 NM_014614 - 4.41 Proteasome (prosome, macropain) activator subunit 4 PTK7 NM_152883 1.3 1.61 PTK7 protein tyrosine kinase 7 PTPNS1 NM_080792 - 1.88 Protein tyrosine phosphatase, non-receptor type substrate 1 PTTG1 NM_004219 1.98 -1.6 Pituitary tumor-transforming 1 PTTG1IP NM_004339 - 2.3 Pituitary tumor-transforming 1 interacting protein PTTG3 NM_021000 1.55 -2.61 Pituitary tumor-transforming 3 PWP2H NM_005049 - 1.55 PWP2 periodic tryptophan protein homolog (yeast) RAD54L NM_003579 2.06 1.49 RAD54-like (S. cerevisiae) RCN1 NM_002901 1.56 2.19 Reticulocalbin 1, EF-hand calcium binding domain RDX NM_002906 -4.07 1.97 Radixin RFC4 NM_181573 1.31 -1.43 Replication factor C (activator 1) 4, 37kDa RGL1 NM_015149 2.23 3.48 Ral guanine nucleotide dissociation stimulator-like 1 RGS10 NM_002925 1.96 -3.81 Regulator of G-protein signalling 10 RIOK3 NM_145906 1.69 4.18 RIO kinase 3 (yeast) RIT1 NM_006912 1.37 -2.49 Ras-like without CAAX 1 RNF138 NM_198128 2.21 - Ring finger protein 138 ROR1 NM_005012 - 14.85 Receptor tyrosine kinase-like orphan receptor 1 Table S6. Altered expression of ERα signature genes in MCF7-T and MCF7-F (continued) Fold change (vs. MCF7) gene symbol genbank MCF7-T MCF7-F Description

Genes inversely associated with ERα expression in breast tumors SLC1A3 NM_004172 - 36.64 DKFZP547J0410 protein SLC2A6 NM_017585 - 4.07 Solute carrier family 2 (facilitated glucose transporter), member 6 SLC7A5 NM_015923 3.25 2.97 solute carrier family 7, member 5 SLPI NM_003064 - 19.98 Secretory leukocyte protease inhibitor (antileukoproteinase) SMC4L1 NM_005496 1.99 3.85 SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SNRPA1 NM_003090 1.71 5.98 Small nuclear ribonucleoprotein polypeptide A' SOAT1 NM_003101 - 3.01 Sterol O-acyltransferase SOX9 NM_000346 -4.53 3.24 SRY (sex determining region Y)-box 9 SRD5A1 NM_001047 1.28 2.36 Steroid-5-alpha-reductase, alpha polypeptide 1 SREBF2 NM_004599 1.53 2.22 Sterol regulatory element binding transcription factor 2 SRPRB NM_021203 -1.36 2.07 Signal recognition particle receptor, B subunit SSR1 NM_003144 1.29 3.56 Signal sequence receptor, alpha (translocon-associated protein alpha) ST14 NM_021978 -2.28 2.91 Suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin) STAT1 NM_139266 -1.3 10.88 Signal transducer and activator of transcription 1, 91kDa SYK NM_003177 -1.41 14.96 Spleen tyrosine kinase TAP1 NM_000593 1.28 8.42 Transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) TGFA NM_003236 - 2.47 Transforming growth factor, alpha TGFBI NM_000358 - 11.6 Transforming growth factor, beta-induced, 68kDa TIA1 NM_022173 - 10.34 TIA1 cytotoxic granule-associated RNA binding protein TLE4 NM_007005 - 8.64 Transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) TM4SF1 NM_014220 -16.82 4.38 Transmembrane 4 superfamily member 1 TMEFF1 NM_003692 1.42 2.14 Transmembrane protein with EGF-like and two follistatin-like domains 1 TMPO NM_003276 2.06 - Thymopoietin TMSNB NM_021992 3.22 -2.18 Thymosin, beta, identified in neuroblastoma cells TNFAIP2 NM_006291 - 3.89 Tumor necrosis factor, alpha-induced protein 2 TNFSF13B NM_006573 - 2.52 Tumor necrosis factor (ligand) superfamily, member 13b TPX2 NM_012112 2.17 1.26 TPX2, microtubule-associated protein homolog (Xenopus laevis) TRIM16 NM_006470 - 3.25 Tripartite motif-containing 16 TRIM2 NM_015271 - 2.48 Tripartite motif-containing 2 TRIP13 NM_004237 1.42 3.73 Thyroid hormone receptor interactor 13 TTK NM_003318 2.19 - TTK protein kinase TTLL4 NM_014640 - 3.86 Tubulin tyrosine ligase-like family, member 4 TTYH3 NM_025250 - 2.38 Tweety homolog 3 (Drosophila) TYMS NM_001071 2.28 3.76 Thymidylate synthetase USP1 NM_003368 1.27 2.48 Ubiquitin specific protease 1 USP10 NM_005153 - 7.64 Ubiquitin specific protease 10 USP18 NM_017414 - 3.8 Ubiquitin specific protease 18 VEGF NM_003376 1.2 3.05 Vascular endothelial growth factor WDR5 NM_052821 - 3.42 WD repeat domain 5 ZNF532 NM_018181 - 2.97 Zinc finger protein 532