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