Table S2. Genes with altered expression in MCF7-T and MCF7-F cells Fold Change (vs. MCF7) Gene symbol Genbank MCF7-T MCF-F Description Downregulated in both MCF7-T and MCF7-F ABAT NM_020686 -3.10 -4.55 4-aminobutyrate aminotransferase ASCL2 NM_005170 -3.58 -6.11 Achaete-scute complex-like 2 (Drosophila) AZGP1 NM_001185 -29.21 -5.09 Alpha-2-glycoprotein 1, zinc CAP2 NM_006366 -3.23 -6.03 CAP, adenylate cyclase-associated protein, 2 (yeast) CD24 NM_013230 -4.20 -3.89 CD24 antigen (small cell lung carcinoma cluster 4 antigen) CDC42EP5 NM_145057 -3.89 -6.01 CDC42 effector protein (Rho GTPase binding) 5 CISH NM_145071 -4.76 -3.03 Cytokine inducible SH2-containing protein CLDN3 NM_001306 -4.24 -3.05 Claudin 3 CRIP1 NM_001311 -3.70 -12.43 Cysteine-rich protein 1 (intestinal) CRIP2 NM_001312 -5.03 -5.30 Cysteine-rich protein 2 CTXN1 Hs.250879 -3.53 -3.21 Cortexin 1 DLC1 NM_182643 -4.03 -21.61 Deleted in liver cancer 1 DNAJC12 NM_201262 -3.17 -67.76 DnaJ (Hsp40) homolog, subfamily C, member 12 EFEMP1 NM_018894 -5.30 -4.99 EGF-containing fibulin-like extracellular matrix protein 1 EFS NM_032459 -3.31 -25.59 Embryonal Fyn-associated substrate FHL1 NM_001449 -24.97 -110.29 Four and a half LIM domains 1 FLJ23548 NM_024590 -8.42 -8.30 Arylsulfatase J FOLR1 NM_016731 -4.56 -4.54 Folate receptor 1 (adult) GREB1 NM_148903 -97.58 -59.66 GREB1 protein HEY2 NM_012259 -7.29 -8.42 Hairy/enhancer-of-split related with YRPW motif 2 HRASLS3 NM_007069 -3.51 -4.84 HRAS-like suppressor 3 INHBB NM_002193 -5.74 -3.73 Inhibin, beta B (activin AB beta polypeptide) KLK10 NM_145888 -12.11 -3.81 Kallikrein 10 KLK11 NM_144947 -62.25 -16.30 Kallikrein 11 LOC387911 Hs.434541 -4.29 -10.84 Prostate collagen triple helix MAGEA1 NM_004988 -5.94 -5.59 Melanoma antigen family A, 1 (directs expression of antigen MZ2-E) MAGEA2 NM_175743 -6.61 -7.80 Melanoma antigen family A, 2 MIDN Hs.302969 -3.12 -3.21 midnolin MIPEP NM_005932 -10.64 -5.42 Mitochondrial intermediate peptidase MME NM_007289 -4.82 -6.50 Membrane metallo-endopeptidase (CALLA, CD10) MT1X NM_005952 -3.84 -3.75 Metallothionein 1X NEDD4L NM_015277 -6.07 -3.67 Neural precursor cell expressed, developmentally down-regulated 4-like NPY1R NM_000909 -10.26 -581.64 Neuropeptide Y receptor Y1 NPY5R NM_006174 -3.18 -9.30 Neuropeptide Y receptor Y5 NXPH1 NM_152745 -33.70 -3.54 Neurexophilin 1 PDZK1 NM_002614 -3.09 -15.24 PDZ domain containing 1 PKIB NM_181795 -37.26 -33.38 Protein kinase (cAMP-dependent, catalytic) inhibitor beta PLS3 NM_005032 -24.83 -3.02 Plastin 3 (T isoform) QPRT NM_014298 -5.18 -3.76 Quinolinate phosphoribosyltransferase RAB34 NM_031934 -5.69 -23.81 RAB34, member RAS oncogene family RHOD NM_014578 -3.53 -6.81 Ras homolog gene family, member D S100A13 Hs.446592 -4.02 -3.74 S100 calcium binding protein A13 S100A14 NM_020672 -7.11 -3.07 S100 calcium binding protein A14 S100A16 NM_080388 -13.05 -7.30 S100 calcium binding protein A16 SLC6A14 NM_007231 -10.30 -47.38 Solute carrier family 6 (amino acid transporter), member 14 SOX3 NM_005634 -10.04 -18.76 SRY (sex determining region Y)-box 3 SPANXA1 NM_013453 -53.76 -28.43 SPANX family, member A2 SPANXC NM_022661 -9.81 -13.17 SPANX family, member C SUSD3 NM_145006 -3.39 -3.05 Sushi domain containing 3 SYTL4 NM_080737 -5.33 -6.06 Synaptotagmin-like 4 (granuphilin-a) TFF3 NM_003226 -13.72 -75.86 Trefoil factor 3 (intestinal) TNFRSF19 NM_148957 -21.63 -13.63 Tumor necrosis factor receptor superfamily, member 19 TNFSF13 NM_172089 -4.23 -7.18 Tumor necrosis factor (ligand) superfamily, member 12 TNRC9 Hs.110826 -45.48 -5.30 trinucleotide repeat containing 9 TOSO NM_005449 -3.50 -11.57 Fas apoptotic inhibitory molecule 3 VGLL1 NM_016267 -118.86 -5.64 Vestigial like 1 (Drosophila) WWP1 NM_007013 -3.27 -5.49 WW domain containing E3 ubiquitin protein ligase 1 1 Table S2. Genes with altered expression in MCF7-T and MCF7-F cells (continued) Fold Change (vs. MCF7) Gene symbol Genbank MCF7-T MCF-F Description Upregulated in both MCF7-T and MCF7-F cells ABCG1 NM_016818 3.10 4.99 ATP-binding cassette, sub-family G (WHITE), member 1 ABCG2 NM_004827 4.10 7.40 ATP-binding cassette, sub-family G (WHITE), member 2 ANAPC7 NM_016238 3.10 5.40 Anaphase promoting complex subunit 7 APOE NM_000041 6.04 4.07 Apolipoprotein E AUTS2 NM_015570 3.99 4.32 Autism susceptibility candidate 2 AXIN2 NM_004655 5.72 3.01 Axin 2 (conductin, axil) B4GALT6 NM_004775 4.90 3.79 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6 BRIP1 NM_032043 3.31 7.30 BRCA1 interacting protein C-terminal helicase 1 C1GALT1 NM_020156 5.92 13.20 glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 CD109 NM_133493 3.14 3.99 CD109 antigen (Gov platelet alloantigens) CHD5 NM_015557 3.24 6.28 Chromodomain helicase DNA binding protein 5 CILP2 NM_153221 5.25 4.53 Cartilage intermediate layer protein 2 COL6A2 NM_058175 3.49 6.32 Collagen, type VI, alpha 2 CPE NM_001873 3.28 5.49 Carboxypeptidase E CXCR4 Hs.421986 5.15 4.35 Chemokine (C-X-C motif) receptor 4 CYBRD1 NM_024843 7.95 16.82 Cytochrome b reductase 1 CYP1B1 NM_000104 3.76 6.58 Cytochrome P450, family 1, subfamily B, polypeptide 1 DEPDC1 NM_017779 3.04 3.85 DEP domain containing 1 DIAPH2 NM_007309 3.64 3.09 Early lymphoid activation protein ENPP4 Hs.54037 3.95 4.36 Ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative function) ENPP5 NM_021572 4.55 3.47 Ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative function) ERO1LB NM_019891 5.97 12.48 ERO1-like beta (S. cerevisiae) FACL2 NM_021122 3.01 4.68 fatty-acid-Coenzyme A ligase, long-chain 2 FBN1 NM_000138 3.69 3.69 Fibrillin 1 (Marfan syndrome) FBXL10 NM_032590 4.97 4.04 F-box and leucine-rich repeat protein 10 FHOD3 Hs.444746 6.67 10.75 formin homology 2 domain containing 3 FLJ14490 Hs.75668 3.48 5.18 Major facilitator superfamily domain containing 2 FLJ20406 NM_017806 3.12 5.17 Lck interacting transmembrane adaptor 1 FLJ31842 NM_152487 4.04 5.75 Transmembrane protein 56 FLJ37927 Hs.289044 3.16 3.03 CDC20-like protein FN1 NM_054034 3.20 14.43 Fibronectin 1 FRAS1 NM_025074 8.28 8.74 Fraser syndrome 1 GSTA4 NM_001512 3.68 5.39 Glutathione S-transferase A4 HECTD2 NM_182765 3.87 19.28 HECT domain containing 2 HLA-A NM_002116 3.01 10.06 Major histocompatibility complex, class I, A HLA-C NM_002117 3.95 7.13 Major histocompatibility complex, class I, C JAG2 NM_145159 3.89 3.09 Jagged 2 KIAA2028 Hs.255938 3.37 4.96 similar to PH (pleckstrin homology) domain LDLR NM_000527 3.07 3.58 Low density lipoprotein receptor (familial hypercholesterolemia) LIPG NM_006033 3.66 8.92 Lipase, endothelial LOC85028 Hs.40092 6.62 7.64 PNAS-123 LPIN1 NM_145693 3.43 3.03 Lipin 1 LSS NM_002340 4.20 5.53 Lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) MARK3 Hs.35828 3.64 5.07 MAP/microtubule affinity-regulating kinase 3 MEF2C NM_002397 12.79 37.53 MADS box transcription enhancer factor 2, polypeptide C MEIS1 NM_002398 3.08 5.81 Meis1, myeloid ecotropic viral integration site 1 homolog (mouse) MVD NM_002461 5.52 3.34 Mevalonate (diphospho) decarboxylase NPC1 NM_000271 3.27 3.88 Niemann-Pick disease, type C1 NR3C1 NM_000176 3.03 18.66 Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) OSMR NM_003999 3.69 5.61 Oncostatin M receptor PCOLCE2 NM_013363 12.47 3.77 Procollagen C-endopeptidase enhancer 2 PGAP1 NM_024989 4.29 4.03 GPI deacylase PRKACB NM_182948 5.10 4.26 Protein kinase, cAMP-dependent, catalytic, beta PRKAR2B NM_002736 10.39 3.39 Protein kinase, cAMP-dependent, regulatory, type II, beta PTGER4 NM_000958 11.44 7.95 Prostaglandin E receptor 4 (subtype EP4) RGS6 NM_004296 4.87 4.97 Regulator of G-protein signalling 6 RPL17 NM_000985 4.42 4.64 Ribosomal protein L17 SAT NM_002970 3.62 5.37 Spermidine/spermine N1-acetyltransferase SC4MOL Hs.105269 3.82 8.08 Sterol-C4-methyl oxidase-like 2 Table S2. Genes with altered expression in MCF7-T and MCF7-F cells (continued) Fold Change (vs. MCF7) Gene symbol Genbank MCF7-T MCF-F Description Upregulated in both MCF7-T and MCF7-F cells SCD NM_005063 3.86 4.20 Stearoyl-CoA desaturase (delta-9-desaturase) SCML1 NM_006746 4.11 3.20 Sex comb on midleg-like 1 (Drosophila) SFRS3 NM_003017 3.01 7.24 Splicing factor, arginine/serine-rich 3 SIAT9 NM_003896 6.92 11.07 ST3 beta-galactoside alpha-2,3-sialyltransferase 5 SLC2A6 NM_017585 3.00 4.08 Solute carrier family 2 (facilitated glucose transporter), member 6 SLC35B4 NM_032826 3.45 4.64 Solute carrier family 35, member B4 SREBF1 NM_004176 3.18 5.01 Sterol regulatory element binding transcription factor 1 SSBP1 NM_003143 3.79 4.72 Single-stranded DNA binding protein 1 STX16 NM_003763 3.07 6.72 Syntaxin 16 TFAP2A NM_003220 5.05 6.15 Transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha) TGFBR3 NM_003243 4.14 4.36 Transforming growth factor, beta receptor III (betaglycan, 300kDa) TIMP3 NM_000362 5.17 15.78 Tissue inhibitor of metalloproteinase 3 TM7SF1 NM_003272 3.61 7.41 Transmembrane 7 superfamily member 1 (upregulated in kidney) TNFRSF25 NM_148974 3.14 5.38 Tumor necrosis factor receptor superfamily, member 25 TYMS NM_001071 4.40 3.76 Thymidylate synthetase WASPIP NM_003387 5.07 3.86 Wiskott-Aldrich syndrome protein interacting protein WFDC2 NM_080736 4.88 3.06 WAP four-disulfide core domain 2 WNT5A NM_003392 11.59 12.91 Wingless-type MMTV integration site family, member 5A ZNF222 NM_013360 4.71 4.83 Zinc finger protein 222 ZNF230 NM_006300 3.29 13.36 Zinc finger protein 230 ZNF519 NM_145287 3.51 3.31 Zinc finger protein 519 ZNF537 NM_020856 10.49 5.36 Zinc finger protein 537 Upregulated in MCF7-T, unchanged in MCF7-F ACLY NM_198830 3.47 2.46 ATP citrate