Table S2. with altered expression in MCF7-T and MCF7-F cells Fold Change (vs. MCF7) 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- 1, zinc CAP2 NM_006366 -3.23 -6.03 CAP, adenylate cyclase-associated , 2 (yeast) CD24 NM_013230 -4.20 -3.89 CD24 antigen (small cell 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 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 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 J FOLR1 NM_016731 -4.56 -4.54 Folate 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 (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 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 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 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- , polypeptide 6 BRIP1 NM_032043 3.31 7.30 BRCA1 interacting -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/ 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 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- 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 , 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/ 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 subfamily 3, group C, member 1 () 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 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- 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 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- 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 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 ACSL4 NM_022977 21.15 - Acyl-CoA synthetase long-chain family member 4 ADAMTS19 NM_133638 5.74 2.06 A disintegrin-like and metalloprotease with thrombospondin type 1 motif, 19 ADCY1 NM_021116 3.59 - Adenylate cyclase 1 (brain) BASP1 NM_006317 5.08 -1.69 Brain abundant, membrane attached signal protein 1 BCMP11 NM_176813 4.47 - Breast cancer membrane protein 11 BOC NM_033254 3.06 1.91 Brother of CDO CDT1 NM_030928 3.16 - DNA replication factor CHST8 NM_022467 3.23 - Carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8 COL1A1 Hs.172928 12.09 - Collagen, type I, alpha 1 COLEC12 NM_130386 4.98 - Collectin sub-family member 12 CSPG2 NM_004385 3.92 - 2 () CSRP2 NM_001321 4.75 - Cysteine and glycine-rich protein 2 CTNNAL1 NM_003798 5.19 1.35 (cadherin-associated protein), alpha-like 1 CUTL2 Hs.407196 24.76 - cut-like 2 (Drosophila) DKFZP434B044 NM_031476 3.89 1.86 Cysteine-rich secretory protein LCCL domain containing 2 ELOVL6 NM_024090 5.75 2.53 ELOVL family member 6, elongation of long chain fatty acids ESPL1 NM_012291 3.09 1.52 Extra spindle poles like 1 (S. cerevisiae) FADS1 NM_013402 3.35 2.09 Fatty acid desaturase 1 FAT4 NM_024582 3.27 2.81 FAT tumor suppressor homolog 4 (Drosophila) FLJ38508 Hs.42572 3.38 - Aldehyde dehydrogenase 1 family, member L2 FUT4 NM_002033 3.00 1.21 4 (alpha (1,3) fucosyltransferase, myeloid-specific) FXYD6 NM_022003 8.73 -1.34 FXYD domain containing ion transport regulator 6 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase- GALNTL1 Hs.21035 6.44 -2.02 like 1 GPR30 NM_001505 4.16 2.71 -coupled receptor 30 HOP NM_139212 13.85 - Homeodomain-only protein HOXC6 NM_153693 3.27 - Homeo box C4 HPCA NM_002143 3.91 - Hippocalcin ID4 NM_001546 6.86 - Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein IQGAP3 NM_178229 3.02 - IQ motif containing GTPase activating protein 3 ISL1 NM_002202 7.13 - ISL1 transcription factor, LIM/homeodomain, (islet-1) ITGA7 NM_002206 4.91 - , alpha 7 KATNAL2 Hs.404137 5.69 - Katanin p60 subunit A-like 2 KCNJ8 NM_004982 5.74 -1.25 Potassium inwardly-rectifying channel, subfamily J, member 8 KCNMA1 NM_002247 4.77 2.15 Potassium large conductance calcium-activated channel, subfamily Mα1

3 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 MCF7-T, unchanged in MCF7-F KNTC2 NM_006101 3.32 1.24 Kinetochore associated 2 KSP37 NM_031950 34.39 - Ksp37 protein LCP1 NM_002298 3.09 1.65 Lymphocyte cytosolic protein 1 (L-plastin) LDHB NM_002300 14.91 - Lactate dehydrogenase B LTBP4 NM_003573 3.07 2.99 Latent transforming growth factor beta binding protein 4 MAP1B NM_032010 3.07 - Microtubule-associated protein 1B MGC46719 NM_153713 3.13 - Lix1 homolog (mouse) like MPRG NM_017705 3.16 - Progestin and adipoQ receptor family member V NAP1L3 NM_004538 4.99 - Nucleosome assembly protein 1-like 3 NOVA1 NM_006491 3.51 2.63 Neuro-oncological ventral antigen 1 NRM NM_007243 3.77 - Nurim ( membrane protein) NRXN3 NM_138970 3.87 1.99 Neurexin 3 NSE1 NM_145175 6.31 - NSE1 NUDT1 NM_198954 3.46 -1.79 Nudix (nucleoside diphosphate linked moiety X)-type motif 1 PCDH8 NM_032949 6.64 - Protocadherin 8 PCDHB16 NM_020957 3.29 2.08 Protocadherin beta 16 PCSK9 NM_174936 3.63 - Proprotein convertase subtilisin/kexin type 9 PDE3B NM_000922 4.73 - Phosphodiesterase 3B, cGMP-inhibited PDZK4 NM_032512 3.46 - PDZ domain containing 4 PEG10 NM_015068 44.60 -1.24 paternally expressed 10 PHGDH NM_006623 4.27 1.75 Phosphoglycerate dehydrogenase PLEKHH2 Hs.164162 3.00 1.66 Pleckstrin homology domain containing, family H,member 2 PLXNC1 NM_005761 3.32 - Plexin C1 PRCP NM_199418 3.56 - GCRG-P224 PROM1 NM_006017 3.37 - Prominin 1 PRTFDC1 NM_020200 3.96 2.61 Phosphoribosyl transferase domain containing 1 RAFTLIN NM_015150 3.81 - Raft-linking protein RAI2 NM_021785 3.08 - induced 2 RECK NM_021111 4.55 - Reversion-inducing-cysteine-rich protein with kazal motifs RGS3 NM_144489 3.35 1.33 Regulator of G-protein signalling 3 RODH NM_003725 3.13 2.83 Hydroxysteroid (17-beta) dehydrogenase 6 RPS6KA5 NM_182398 3.08 2.15 kinase, 90kDa, polypeptide 5 RRAGD NM_021244 3.07 - Ras-related GTP binding D SART2 NM_013352 3.26 2.99 Squamous cell carcinoma antigen recognized by T cells 2 SCNN1B NM_000336 4.36 - Sodium channel, nonvoltage-gated 1, beta (Liddle syndrome) SEMA6A NM_020796 3.99 1.35 Sema domain, transmembrane domain (TM), and cytoplasmic domain, 6A SEPT6 NM_145802 4.13 - Septin 6 SESN3 NM_144665 3.89 1.42 Sestrin 3 SGCB NM_000232 3.03 - Sarcoglycan, beta (43kDa -associated glycoprotein) SLC27A6 NM_014031 4.32 - Solute carrier family 27 (fatty acid transporter), member 6 SLC39A6 NM_012319 5.59 2.93 Solute carrier family 39 (zinc transporter), member 6 SLC7A5 NM_015923 3.25 2.97 solute carrier family 7 (cationic amino acid transporter, y+ system), member 5 SLCO4C1 NM_180991 4.14 -1.58 Solute carrier organic anion transporter family, member 4C1 SLIT2 NM_004787 3.87 1.37 Slit homolog 2 (Drosophila) SMAD2 NM_005901 3.00 -1.87 SMAD, mothers against DPP homolog 2 (Drosophila) SMAD9 NM_005905 5.85 - SMAD, mothers against DPP homolog 9 (Drosophila) NM_003106 12.58 -1.80 SRY (sex determining region Y)-box 2 STARD4 NM_139164 3.40 2.70 START domain containing 4, sterol regulated STATIP1 NM_018255 3.05 - Signal transducer and activator of transcription 3 interacting protein 1 TGFB1I1 NM_015927 3.28 1.27 Transforming growth factor beta 1 induced transcript 1 THBS4 NM_003248 4.25 1.26 Thrombospondin 4 TMSNB NM_021992 3.22 -2.18 Thymosin-like 8 TRG@ NG_001336 5.91 -2.14 (clone HGP06) receptor gamma-chain mRNA, V region TRGV9 Hs.407442 6.84 - Similar to T-cell receptor gamma chain C region PT-gamma-1/2 ZDHHC22 NM_174976 14.72 - Zinc finger, DHHC-type containing 22 ZNF284 Hs.445395 3.10 1.80 Zinc finger protein 284 ZNF492 Hs.232108 4.01 -2.02 Zinc finger protein 492 ZNF505 NM_031218 3.03 - Zinc finger protein 505 ZNF569 NM_152484 4.21 - Zinc finger protein 569

4 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 MCF7-T, downregulated in MCF7-F BFSP2 NM_003571 4.35 -9.81 Beaded filament structural protein 2, phakinin HSPA2 Hs.432648 3.70 -3.36 Heat shock 70kDa protein 2 LOC118430 NM_058173 4.55 -5.48 Small breast epithelial LOC340542 Hs.47209 3.30 -8.88 NGFRAP1-like 1 LRRN1 NM_020873 3.59 -4.50 Leucine rich repeat neuronal 1 MID1 NM_033291 3.53 -3.00 Midline 1 (Opitz/BBB syndrome) PRIMA1 NM_178013 3.48 -3.22 Proline rich membrane anchor 1 RHOF NM_019034 3.14 -3.04 Ras homolog gene family, member F (in filopodia) RLN2 NM_134441 4.21 -4.20 Relaxin 2

Downregulated in MCF7-T, unchanged in MCF7-F ABLIM3 Hs.282566 -4.12 -1.26 binding LIM , member 3 ALDH4A1 NM_170726 -3.81 1.43 Aldehyde dehydrogenase 4 family, member A1 AMIGO2 NM_181847 -7.03 2.67 Adhesion molecule with Ig-like domain 2 ANXA9 NM_003568 -3.52 2.11 Annexin A9 AP1S1 NM_057089 -3.37 -2.37 Adaptor-related protein complex 1, sigma 1 subunit AREG NM_001657 -6.44 -1.26 Amphiregulin (schwannoma-derived growth factor) ARHGDIB NM_001175 -4.02 -1.95 Rho GDP dissociation inhibitor (GDI) beta ATP8B1 NM_005603 -4.02 2.19 ATPase, Class I, type 8B, member 1 BLNK NM_013314 -5.43 - B-cell linker C1QTNF6 NM_182486 -15.71 -2.48 C1q and tumor necrosis factor related protein 6 C5R1 NM_001736 -3.04 2.31 Complement component 5 receptor 1 (C5a ligand) CaMKIINalpha NM_018584 -4.05 1.25 Calcium/calmodulin-dependent protein kinase II inhibitor 1 CAV1 NM_001753 -3.56 -1.59 Caveolin 1, caveolae protein, 22kDa CD97 NM_078481 -6.30 2.57 CD97 antigen CEACAM6 NM_002483 -6.55 -2.33 Carcinoembryonic antigen-related molecule 6 CLDN1 NM_021101 -6.42 1.73 Claudin 1 CLDN23 NM_194284 -4.69 - Claudin 23 CLSTN2 NM_022131 -18.80 2.13 Calsyntenin 2 CMKOR1 NM_020311 -3.94 -1.28 Chemokine orphan receptor 1 CXCL12 NM_199168 -4.22 1.28 Chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) CXXC5 NM_016463 -5.12 -1.62 CXXC finger 5 CYBA NM_000101 -3.55 2.27 Cytochrome b-245, alpha polypeptide DAPK1 NM_004938 -4.04 -1.32 Death-associated protein kinase 1 DOC1 NM_182909 -3.84 -2.27 Downregulated in 1 DUSP4 NM_057158 -4.39 1.23 Dual specificity 4 DUSP5 NM_004419 -3.66 -1.26 Dual specificity phosphatase 5 DYRK4 NM_003845 -17.18 -2.28 Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4 DYX1C1 NM_130810 -4.39 -1.37 Dyslexia susceptibility 1 candidate 1 EDG3 NM_182599 -4.42 1.69 endothelial differentiation, sphingolipid G-protein-coupled receptor, 3 EGR1 NM_001964 -3.03 -1.49 Early growth response 1 ELK3 NM_005230 -4.30 - ELK3, ETS-domain protein (SRF accessory protein 2) EMP1 NM_001423 -5.47 1.71 Epithelial membrane protein 1 ETV4 NM_001986 -3.61 2.25 Ets variant gene 4 (E1A enhancer binding protein, E1AF) FANK1 NM_145235 -3.22 1.73 Fibronectin type III and repeat domains 1 FECH NM_000140 -4.16 -1.37 Ferrochelatase (protoporphyria) FLJ23129 NM_024763 -28.21 -2.21 WD repeat domain 78 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase GALNT10 NM_198321 -3.18 - 10 (GalNAc-T10) GJB3 NM_024009 -3.77 - Gap junction protein, beta 3, 31kDa (connexin 31) H19 XR_000200 -7.90 -2.15 H19, imprinted maternally expressed untranslated mRNA HOMER3 NM_004838 -3.84 - Homer homolog 3 (Drosophila) HPGD NM_000860 -12.08 -1.94 Hydroxyprostaglandin dehydrogenase 15-(NAD) IMP-2 NM_006548 -4.37 - IGF-II mRNA-binding protein 2 INPP4B NM_003866 -3.24 -2.55 Inositol polyphosphate-4-phosphatase, type II, 105kDa KCTD11 Hs.440328 -3.01 -2.47 Potassium channel tetramerisation domain containing 11 LEMD1 Hs.104830 -4.06 -1.21 LEM domain containing 1 LFNG Hs.159142 -8.97 -1.33 Lunatic fringe homolog (Drosophila) LOC91316 Hs.272302 -3.49 1.93 similar to bK246H3.1 MFAP3L Hs.178121 -9.19 -2.03 Microfibrillar-associated protein 3-like

5 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 Downregulated in MCF7-T, unchanged in MCF7-F MGC42367 Hs.136732 -4.16 -2.93 similar to 2010300C02Rik protein MYO6 Hs.118483 -5.14 1.78 VI MGP NM_000900 -134.10 -2.70 Matrix Gla protein KRTHB6 NM_002284 -4.69 -2.67 , hair, basic, 6 (monilethrix) LIN7A NM_004664 -10.11 -2.55 Lin-7 homolog A (C. elegans) LOXL1 NM_005576 -3.24 - Lysyl oxidase-like 1 MMS19L NM_022362 -3.17 1.41 MMS19-like (MET18 homolog, S. cerevisiae) L1CAM NM_024003 -3.40 1.74 L1 cell adhesion molecule OPA1 NM_130837 -4.19 - Optic atrophy 1 (autosomal dominant) MAFB NM_152258 -3.11 2.20 V- musculoaponeurotic fibrosarcoma oncogene homolog B (avian) MAFF NM_152878 -4.43 1.22 V-maf musculoaponeurotic fibrosarcoma oncogene homolog F (avian) MUC1 NM_182741 -3.33 -1.76 Mucin 1, transmembrane OXTR NM_000916 -3.97 -1.45 Oxytocin receptor PCTP NM_021213 -3.23 1.24 Phosphatidylcholine transfer protein PDGFC NM_016205 -4.05 - Platelet derived growth factor C PDK4 NM_002612 -11.41 1.84 Pyruvate dehydrogenase kinase, isoenzyme 4 PHLDA2 NM_003311 -3.71 -1.36 Pleckstrin homology-like domain, family A, member 2 PIGN NM_176787 -6.15 2.43 Phosphatidylinositol glycan, class N PLAC2 NM_153375 -3.00 -1.72 Placenta-specific 2 PLCD3 NM_133373 -3.91 1.34 C, delta 3 PLK2 NM_006622 -5.84 - Polo-like kinase 2 (Drosophila) PPL NM_002705 -4.38 1.98 PRODH NM_016335 -3.26 -1.22 Proline dehydrogenase (oxidase) 1 PSCA NM_005672 -5.10 -1.28 Prostate stem cell antigen RAB27B NM_004163 -5.43 -1.92 RAB27B, member RAS oncogene family RAP1GA1 NM_002885 -3.09 -2.84 RAP1, GTPase activating protein 1 RASGRP1 NM_005739 -9.91 - RAS guanyl releasing protein 1 (calcium and DAG-regulated) RBPMS NM_006867 -3.55 - RNA binding protein with multiple splicing RDX NM_002906 -4.07 - Radixin RIN2 NM_018993 -3.46 -1.94 Ras and Rab interactor 2 RTKN NM_033046 -3.42 -1.44 Rhotekin SCUBE2 NM_020974 -9.30 -2.60 Signal peptide, CUB domain, EGF-like 2 SERPINA3 NM_001085 -3.42 1.25 Serine (or cysteine) proteinase inhibitor, clade A, member 3 SERPINE1 NM_000602 -5.50 2.77 Serine (or cysteine) proteinase inhibitor, clade E, member 1 SH3BGRL NM_003022 -4.73 -1.31 SH3 domain binding glutamic acid-rich protein like SLC41A2 NM_032148 -3.08 -1.65 Solute carrier family 41, member 2 SMPDL3A NM_006714 -3.14 -2.30 Sphingomyelin phosphodiesterase, acid-like 3A SOCS6 NM_004232 -3.03 1.28 Suppressor of cytokine signaling 6 SOX4 NM_003107 -3.31 -1.20 SRY (sex determining region Y)-box 4 SULF1 NM_015170 -8.11 -2.79 1 SUSD2 NM_019601 -8.59 -2.24 Sushi domain containing 2 TAGLN2 NM_003564 -3.01 -2.31 Transgelin 2 TGFA NM_003236 -5.94 2.47 Transforming growth factor, alpha TMEM8 NM_021259 -4.21 - Transmembrane protein 8 (five membrane-spanning domains) TNFRSF12A NM_016639 -3.38 2.02 Tumor necrosis factor receptor superfamily, member 12A TSPAN1 NM_005727 -9.00 1.20 Tetraspanin 1 ZADH2 Hs.408128 -3.06 - zinc binding alcohol dehydrogenase, domain containing 2 ZNF532 NM_018181 -3.59 2.97 Zinc finger protein 532

Downregulated in MCF7-T, upregulated in MCF7-F ABCC3 NM_020038 -12.48 6.50 ATP-binding cassette, sub-family C (CFTR/MRP), member 3 ALCAM NM_001627 -3.72 10.55 Activated leukocyte cell adhesion molecule ALDH1A3 NM_000693 -4.22 3.36 Aldehyde dehydrogenase 1 family, member A3 ALDH3B1 NM_000694 -4.72 4.66 Aldehyde dehydrogenase 3 family, member B1 ANXA1 NM_000700 -3.04 14.28 Annexin A1 CDKN2B NM_078487 -15.17 5.15 -dependent kinase inhibitor 2B (p15, inhibits CDK4) DNAPTP6 NM_015535 -4.42 4.07 DNA polymerase-transactivated protein 6 EFNB2 NM_004093 -4.11 8.50 Ephrin-B2 GPCR5A NM_003979 -6.37 3.19 G protein-coupled receptor, family C, group 5, member A HSPG2 NM_005529 -4.07 3.42 proteoglycan 2 ()

6 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 Downregulated in MCF7-T, upregulated in MCF7-F HSPH1 NM_006644 -3.08 9.03 Heat shock 105kDa/110kDa protein 1 IFI27 NM_005532 -3.41 12.45 Interferon, alpha-inducible protein 27 ITGB6 NM_000888 -16.35 63.88 Integrin, beta 6 KCNJ3 NM_002239 -4.00 4.11 Potassium inwardly-rectifying channel, subfamily J, member 3 LY6E NM_002346 -4.82 3.82 Lymphocyte antigen 6 complex, E LYPDC1 NM_144586 -5.25 5.62 LY6/PLAUR domain containing 1 MAN1A1 NM_005907 -15.72 4.60 Mannosidase, alpha, class 1A, member 1 MUC15 NM_145650 -5.52 3.26 Mucin 15 MUC20 NM_152673 -9.09 6.42 PHLDB2 NM_145753 -29.04 4.36 Pleckstrin homology-like domain, family B, member 2 PPARG NM_138712 -5.18 4.32 Peroxisome proliferative activated receptor, gamma S100P NM_005980 -4.18 3.40 S100 calcium binding protein P SE57-1 NM_025214 -7.31 3.26 CTCL tumor antigen se57-1 SESTD1 NM_178123 -3.87 3.34 SEC14 and domains 1 SOX9 NM_000346 -4.53 3.24 sex determining region Y-box 9 (campomelic dysplasia, autosomal sex-reversal) SP100 NM_003113 -11.33 5.54 Nuclear antigen Sp100 THBD NM_000361 -3.47 20.42 Thrombomodulin TM4SF1 NM_014220 -16.83 4.38 Transmembrane 4 L six family member 1 TNFRSF11B NM_002546 -8.70 4.38 Tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) TPM2 NM_003289 -6.87 4.36 2 (beta) VAV3 NM_006113 -8.69 6.68 Vav 3 oncogene VIPR1 NM_004624 -5.29 3.55 Vasoactive intestinal peptide receptor 1 WASL NM_003941 -4.62 3.23 Wiskott-Aldrich syndrome-like WNT6 NM_006522 -3.47 3.93 Wingless-type MMTV integration site family, member 6

Unchanged in MCF7-T, upregulated in MCF7-F AASS NM_005763 - 7.48 Aminoadipate-semialdehyde synthase ABCA1 NM_005502 2.45 16.13 ATP-binding cassette, sub-family A (ABC1), member 1 ABCA2 NM_001606 1.37 5.52 ATP-binding cassette, sub-family A (ABC1), member 2 ABCA5 NM_172232 1.61 7.95 ATP-binding cassette, sub-family A (ABC1), member 5 ABCC1 NM_019902 - 3.48 ATP-binding cassette, sub-family C (CFTR/MRP), member 1 ABCC4 NM_005845 - 3.29 ATP-binding cassette, sub-family C (CFTR/MRP), member 4 ABCD3 NM_002858 - 6.09 ATP-binding cassette, sub-family D (ALD), member 3 ABI1 NM_005470 - 9.77 Abl-interactor 1 ABI2 NM_005759 - 3.22 Abl interactor 2 ABP1 NM_001091 - 5.06 Amiloride binding protein 1 (amine oxidase (copper-containing)) ACHE NM_015831 - 23.26 (YT blood group) ACOXL NM_018308 - 21.15 Acyl-Coenzyme A oxidase-like ACPL2 NM_152282 1.33 4.53 -like 2 ACRC NM_052957 - 3.58 Acidic repeat containing ACSL3 NM_004457 - 7.39 Acyl-CoA synthetase long-chain family member 3 ACSL5 NM_016234 - 18.94 Acyl-CoA synthetase long-chain family member 5 ACTR2 NM_005722 - 3.11 ARP2 actin-related protein 2 homolog (yeast) ADAM10 NM_001110 - 12.89 A disintegrin and metalloproteinase domain 10 ADAM12 NM_021641 - 6.18 A disintegrin and metalloproteinase domain 12 (meltrin alpha) ADAM17 NM_021832 - 9.02 A disintegrin and metalloproteinase domain 17 ADAM22 NM_021723 1.57 3.53 A disintegrin and metalloproteinase domain 22 ADAM9 NM_003816 - 22.29 A disintegrin and metalloproteinase domain 9 (meltrin gamma) ADAMTS1 NM_006988 - 24.79 A disintegrin-like and metalloprotease with thrombospondin type 1 motif, 1 ADAMTS20 NM_175851 - 11.05 A disintegrin-like and metalloprotease with thrombospondin type 1 motif, 20 ADCK5 NM_174922 - 5.14 AarF domain containing kinase 5 ADCY5 Hs.9572 - 5.13 Adenylate cyclase 5 ADM NM_001124 1.30 3.40 Adrenomedullin ADNP Hs.293736 - 4.47 Activity-dependent neuroprotector ADPGK NM_031284 1.39 5.32 ADP-dependent glucokinase ADRBK1 NM_001619 - 11.13 Adrenergic, beta, receptor kinase 1 AF5Q31 NM_014423 1.33 3.78 AF4/FMR2 family, member 4 AFG3L2 NM_006796 1.34 3.77 AFG3 ATPase family gene 3-like 2 (yeast) AGPAT2 NM_006412 -1.22 3.59 1-acylglycerol-3-phosphate O-acyltransferase 2 AGPAT3 NM_031487 1.35 5.07 1-acylglycerol-3-phosphate O-acyltransferase 3

7 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 Unchanged in MCF7-T, upregulated in MCF7-F AGRN Hs.273330 1.46 5.26 Agrin AHI1 NM_017651 - 3.91 Abelson helper integration site AHR NM_001621 -1.23 3.21 Aryl hydrocarbon receptor AHSA2 NM_152392 1.33 4.74 AHA1, activator of heat shock 90kDa protein ATPase homolog 2 (yeast) AKAP1 NM_139275 1.83 6.15 A kinase (PRKA) anchor protein 1 AKAP10 NM_007202 1.23 4.92 A kinase (PRKA) anchor protein 10 AKAP11 NM_144490 1.67 3.21 A kinase (PRKA) anchor protein 11 AKAP8 NM_005858 1.62 3.28 A kinase (PRKA) anchor protein 8 AKAP8L NM_014371 - 6.86 A kinase (PRKA) anchor protein 8-like AKR1B10 NM_020299 - 11.42 Aldo-keto reductase family 1, member B10 (aldose reductase) AKR1C1 NM_001353 - 7.89 Aldo-keto reductase family 1, member C1 AKR1C2 NM_001354 2.14 14.98 Aldo-keto reductase family 1, member C2 AKR1C3 NM_003739 - 25.05 Aldo-keto reductase family 1, member C3 ALDH3A1 NM_000691 - 20.98 Aldehyde dehydrogenase 3 family, memberA1 ALDH3B2 NM_000695 - 17.13 Aldehyde dehydrogenase 3 family, member B2 ALOX12P2 Hs.378695 - 4.62 Arachidonate 12-lipoxygenase 2 ALOX5 NM_000698 - 6.95 Arachidonate 5-lipoxygenase ALPK1 NM_025144 - 7.67 Alpha-kinase 1 ALS2CL NM_182775 1.36 3.12 ALS2 C-terminal like ALS2CR3 NM_015049 1.50 3.23 Amyotrophic lateral sclerosis 2 (juvenile) region, candidate 3 ALS2CR8 NM_024744 - 3.41 Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8 AMSH-LP NM_020799 - 4.49 Associated molecule with the SH3 domain of STAM (AMSH) like protein AMY2A NM_000699 - 18.90 Amylase, alpha 2A; pancreatic ANAPC5 NM_016237 1.60 3.47 Anaphase promoting complex subunit 5 ANGPTL4 NM_139314 - 3.60 Angiopoietin-like 4 ANGPTL6 NM_031917 - 10.70 Angiopoietin-like 6 ANK3 NM_020987 1.30 5.18 Cancer susceptibility candidate 4 ANKFY1 NM_020740 - 7.53 Ankyrin repeat and FYVE domain containing 1 ANKH NM_054027 - 5.86 Ankylosis, progressive homolog (mouse) ANKHD1 NM_024668 1.58 8.04 Ankyrin repeat and KH domain containing 1 ANKMY2 Hs.157378 - 10.42 Ankyrin repeat and MYND domain containing 2 ANKRD10 NM_017664 1.81 5.33 Ankyrin repeat domain 10 ANKRD15 NM_153186 -1.26 4.11 Ankyrin repeat domain 15 ANKRD22 NM_144590 - 4.03 Ankyrin repeat domain 22 ANKRD23 NM_144994 - 6.56 Ankyrin repeat domain 23 ANKRD28 Hs.273104 - 5.13 ankyrin repeat domain 28 ANKRD29 NM_173505 - 4.63 Ankyrin repeat domain 29 ANKRD3 Hs.55565 - 33.66 ankyrin repeat domain 3 ANLN NM_018685 1.93 6.78 Anillin, actin binding protein (scraps homolog, Drosophila) ANTXR2 NM_058172 - 17.68 Anthrax toxin receptor 2 ANXA10 NM_007193 - 162.71 Annexin A10 AP1GBP1 Hs.101480 - 12.93 AP1 gamma subunit binding protein 1 APEH NM_001640 - 9.00 N-acylaminoacyl-peptide APG16L NM_198890 - 4.88 APG16 autophagy 16-like (S. cerevisiae) APH-1A NM_016022 - 4.94 Anterior pharynx defective 1 homolog A (C. elegans) API5 Hs.435771 - 4.49 inhibitor 5 APLP1 NM_005166 - 9.64 (A4) precursor-like protein 1 APLP2 NM_016160 1.72 5.59 amyloid beta (A4) precursor-like protein 2 APOL6 NM_030641 - 6.62 Apolipoprotein L, 6 APP NM_201414 - 4.14 Amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) APPBP2 NM_006380 1.83 3.57 Amyloid beta precursor protein (cytoplasmic tail) binding protein 2 APRIN NM_015928 1.38 4.91 Androgen-induced proliferation inhibitor ARF1 NM_001658 - 6.33 ADP-ribosylation factor 1 ARFGEF1 NM_006421 -1.27 3.67 ADP-ribosylation factor guanine nucleotide-exchange factor 1 ARFGEF2 NM_006420 - 3.92 ADP-ribosylation factor guanine nucleotide-exchange factor 2 ARFIP1 NM_014447 1.21 3.98 ADP-ribosylation factor interacting protein 1 (arfaptin 1) ARG99 NM_194311 - 13.56 ARG99 protein ARHE NM_005168 - 3.28 Rho family GTPase 3 ARHGAP26 NM_015071 1.52 3.28 Rho GTPase activating protein 26

8 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 Unchanged in MCF7-T, upregulated in MCF7-F ARHGAP5 NM_001173 1.96 5.83 Rho GTPase activating protein 5 ARHGEF10 NM_014629 - 3.04 Rho guanine nucleotide exchange factor (GEF) 10 ARHGEF7 NM_145735 1.30 3.40 Rho guanine nucleotide exchange factor (GEF) 7 ARIH2 NM_006321 1.30 3.04 Ariadne homolog 2 (Drosophila) ARL6IP2 NM_022374 - 3.03 ADP-ribosylation factor-like 6 interacting protein 2 ARL6IP5 NM_006407 1.43 4.74 ADP-ribosylation-like factor 6 interacting protein 5 ARNTL NM_001178 - 3.03 Aryl hydrocarbon receptor nuclear translocator-like ARPC1A Hs.124126 - 8.27 Actin related protein 2/3 complex, subunit 1A, 41kDa ARPC4 NM_005718 - 3.13 Actin related protein 2/3 complex, subunit 4, 20kDa ARS2 NM_182800 - 35.91 Arsenate resistance protein ARS2 ARSD NM_009589 - 3.38 Arylsulfatase D ARTS-1 NM_016442 1.21 4.18 Type 1 tumor necrosis factor receptor shedding aminopeptidase regulator ASAH1 NM_177924 - 6.19 N-acylsphingosine amidohydrolase (acid ceramidase) 1 ASCC3L1 NM_014014 1.52 3.10 Activating signal cointegrator 1 complex subunit 3-like 1 ASPH NM_032468 -2.21 4.03 Aspartate beta-hydroxylase ASXL1 NM_015338 - 4.22 Additional sex combs like 1 (Drosophila) ASXL2 NM_018263 - 8.18 Additional sex combs like 2 (Drosophila) ATF2 NM_001880 - 10.76 Activating transcription factor 2 ATP10D NM_020453 - 19.51 ATPase, Class V, type 10D ATP13A3 NM_024524 - 23.08 ATPase type 13A3 ATP2B1 NM_001682 - 7.83 ATPase, Ca++ transporting, plasma membrane 1 ATP2B4 NM_001684 1.61 11.41 ATPase, Ca++ transporting, plasma membrane 4 ATP5C1 NM_005174 1.83 7.43 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 ATP5J2 NM_004889 1.68 5.69 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit f, isoform 2 ATP6AP2 NM_005765 1.20 3.80 ATPase, H+ transporting, lysosomal accessory protein 2 ATP6V0A1 NM_005177 - 10.30 ATPase, H+ transporting, lysosomal V0 subunit a isoform 1 ATP6V1A NM_001690 1.38 3.67 ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A ATP6V1C1 NM_001695 - 3.29 ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1 ATP7A NM_000052 - 3.17 ATPase, Cu++ transporting, alpha polypeptide (Menkes syndrome) ATP9A Hs.406434 1.76 3.04 ATPase, Class II, type 9A ATR NM_001184 - 3.16 Ataxia telangiectasia and Rad3 related ATRX NM_138271 2.77 11.00 Alpha thalassemia/mental retardation syndrome X-linked AVIL NM_006576 -1.91 3.47 Advillin AZI2 NM_022461 - 4.48 5-azacytidine induced 2 B3GNT1 NM_033252 - 9.44 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1 B3GNT5 NM_032047 - 7.78 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5 B4GALT5 Hs.370487 - 6.44 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 B7-H4 NM_024626 - 7.18 V-set domain containing T cell activation inhibitor 1 BACE2 NM_138992 1.43 3.73 Beta-site APP-cleaving 2 BAGE4 Hs.512803 - 5.38 B melanoma antigen family, member 4 BAT1 NM_080598 - 12.18 HLA-B associated transcript 1 BBS1 NM_024649 - 5.35 Bardet-Biedl syndrome 1 BBX NM_020235 1.75 3.17 Bobby sox homolog (Drosophila) BCAP29 NM_018844 -1.45 3.29 B-cell receptor-associated protein 29 BCAR1 Hs.479747 - 7.22 Breast cancer anti-estrogen resistance 1 BCAS1 NM_003657 - 3.57 Breast carcinoma amplified sequence 1 BCL2L1 NM_138578 - 4.66 BCL2-like 1 BCL2L11 NM_138627 -1.24 3.06 BCL2-like 11 (apoptosis facilitator) BCLAF1 Hs.80338 - 3.39 BCL2-associated transcription factor 1 BCMSUNL Hs.499406 1.66 6.65 BCMS upstream neighbor-like BCOR NM_020926 1.31 3.01 BCL6 co- BDKRB2 NM_000623 - 3.91 Bradykinin receptor B2 BDP1 NM_018429 - 3.84 B double prime 1, subunit of RNA polymerase III transcription IIIB BENE NM_005434 - 10.20 BENE protein BHLHB3 NM_030762 -1.24 15.21 Basic helix-loop-helix domain containing, class B, 3 BMP1 NM_006132 - 5.66 Bone morphogenetic protein 1 BMPR2 NM_033346 - 3.92 Bone morphogenetic protein receptor, type II (serine/threonine kinase) BRAF NM_004333 - 3.62 V-raf murine sarcoma viral oncogene homolog B1 BRCA2 NM_000059 1.84 3.78 Breast cancer 2, early onset

9 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 Unchanged in MCF7-T, upregulated in MCF7-F BRD4 Hs.187763 1.34 4.09 Bromodomain containing 4 BRD9 NM_023924 - 4.74 Bromodomain containing 9 BSG NM_198591 - 5.36 Basigin (OK blood group) BST2 NM_004335 - 180.88 stromal cell antigen 2 BTN2A1 NM_078476 - 3.24 Butyrophilin, subfamily 2, member A1 BTN3A1 NM_194441 - 3.85 Butyrophilin, subfamily 3, member A1 BTN3A2 NM_007047 - 6.99 Butyrophilin, subfamily 3, member A2 BTN3A3 NM_197974 - 12.69 Butyrophilin, subfamily 3, member A3 BTNL9 NM_152547 - 4.05 Butyrophilin-like 9 BUB1 NM_004336 2.09 3.00 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB3 NM_004725 - 4.85 BUB3 budding uninhibited by benzimidazoles 3 homolog (yeast) C1orf8 NM_004872 - 21.61 Transmembrane protein 59 C1QDC1 NM_032156 1.35 6.09 C1q domain containing 1 C20orf119 Hs.411022 - 7.97 Similar to embryonic poly(A) binding protein C3 NM_000064 - 13.37 Complement component 3 C3F NM_005768 1.36 4.10 Putative protein similar to nessy (Drosophila) C6orf12 Hs.302037 1.59 3.33 HLA complex group 8 C6orf83 NM_145169 - 9.83 SFT2 domain containing 1 C7orf2 NM_022458 1.53 4.00 Limb region 1 homolog (mouse) C9orf60 Hs.147950 - 3.08 Zyg-11 homolog B (C. elegans)-like CA4 NM_000717 - 4.41 Carbonic anhydrase IV Cab45 NM_016547 - 3.48 Stromal cell derived factor 4 CACNG4 NM_032659 - 4.15 calcium channel, voltage-dependent, gamma subunit 4 CALD1 NM_033157 - 56.46 Caldesmon 1 CALM2 NM_001743 1.61 4.85 Calmodulin 2 ( kinase, delta) CALR NM_004343 1.30 3.56 Calreticulin CALU NM_001219 - 7.11 Calumenin CAMK2G NM_172173 1.49 3.81 Calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma CAMKK2 NM_172226 - 4.28 Calcium/calmodulin-dependent protein kinase kinase 2, beta CANT1 NM_138793 - 7.76 Calcium activated 1 CANX NM_001746 - 4.29 Calnexin CAPN13 NM_144575 - 4.62 Calpain 13 CAPNS2 NM_032330 - 13.63 Calpain, small subunit 2 CAPS NM_080590 1.27 5.80 Calcyphosine CAPZA2 NM_006136 - 13.38 Capping protein (actin filament) muscle Z-line, alpha 2 CARS NM_139273 - 7.03 Cysteinyl-tRNA synthetase CASK NM_003688 -1.29 6.27 Calcium/calmodulin-dependent serine protein kinase (MAGUK family) CASP8 NM_033358 1.20 3.09 Caspase 8, apoptosis-related cysteine protease CAT NM_001752 1.70 4.08 CBFA2T2 NM_175864 - 3.78 Core-binding factor, runt domain, alpha subunit 2; translocated to, 2 CBFB NM_022845 -1.65 3.29 Core-binding factor, beta subunit CBR4 NM_032783 - 4.89 Carbonic reductase 4 CBX3 NM_016587 1.36 8.19 Chromobox homolog 3 (HP1 gamma homolog, Drosophila) CCAR1 NM_018237 - 13.23 Cell division cycle and apoptosis regulator 1 CCNE2 NM_057749 1.34 3.80 Cyclin E2 CCNJ NM_019084 - 3.23 Cyclin J CCNL1 NM_020307 1.35 5.73 Cyclin L1 CCNL2 NM_030937 - 5.10 Cyclin L2 CD36 NM_000072 - 26.74 CD36 antigen (collagen type I receptor, thrombospondin receptor) CD44 NM_000610 2.35 9.37 CD44 antigen (homing function and Indian blood group system) CD47 NM_198793 - 3.12 CD47 antigen (Rh-related antigen, integrin-associated signal transducer) CD58 NM_001779 1.58 5.17 CD58 antigen, (lymphocyte function-associated antigen 3) CD99L2 NM_134446 - 4.61 CD99 antigen-like 2 CDA08 NM_030790 - 3.34 T-cell immunomodulatory protein CDC27 NM_001256 1.34 4.70 Cell division cycle 27 CDC2L1 NM_033493 - 3.28 Cell division cycle 2-like 1 (PITSLRE ) CDC2L2 NM_033621 - 6.67 cell division cycle 2-like 2 CDC2L5 NM_031267 - 3.96 Cell division cycle 2-like 5 (-related cell division controller) CDC2L6 NM_015076 - 3.84 Cell division cycle 2-like 6 (CDK8-like)

10 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 Unchanged in MCF7-T, upregulated in MCF7-F CDC42EP3 NM_006449 -2.81 3.87 CDC42 effector protein (Rho GTPase binding) 3 CDH1 NM_004360 - 30.77 Cadherin 1, type 1, E-cadherin (epithelial) CDH11 NM_033664 2.27 3.88 Cadherin 11, type 2, OB-cadherin (osteoblast) CDH2 NM_001792 - 72.57 Cadherin 2, type 1, N-cadherin (neuronal) CDK10 NM_052988 - 3.09 Cyclin-dependent kinase (CDC2-like) 10 CDK2 NM_052827 - 4.71 Cyclin-dependent kinase 2 CDK5RAP3 NM_176096 1.52 4.30 CDK5 regulatory subunit associated protein 3 CDKL3 NM_016508 1.44 3.95 Cyclin-dependent kinase-like 3 CDW92 NM_080546 1.63 3.38 CDW92 antigen CDYL NM_170752 - 3.45 Chromodomain protein, Y-like CEACAM1 NM_001712 - 69.50 Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) CEL NM_001807 - 17.93 Carboxyl ester lipase (bile salt-stimulated lipase) CENPJ NM_018451 2.18 3.13 Centromere protein J CENTD3 NM_022481 - 4.05 Centaurin, delta 3 Cep72 NM_018140 1.42 4.46 Centrosomal protein 72 kDa CFLAR NM_003879 1.37 3.47 CASP8 and FADD-like apoptosis regulator CGI-14 NM_015944 - 4.08 CGI-14 protein CGI-62 Hs.271876 - 12.10 CGI-62 protein CHD1L NM_024568 2.33 4.30 chromodomain helicase DNA binding protein 1-like CHD2 NM_001271 2.11 6.12 Chromodomain helicase DNA binding protein 2 CHD6 NM_032221 - 5.85 Chromodomain helicase DNA binding protein 6 CHD7 Hs.397426 - 4.69 chromodomain helicase DNA binding protein 7 CHD9 NM_025134 - 7.00 Chromodomain helicase DNA binding protein 9 CHES1 Hs.434286 - 4.38 Checkpoint suppressor 1 ChGn NM_018371 - 3.76 Chondroitin beta1,4 N-acetylgalactosaminyltransferase CHKA NM_001277 -1.26 4.24 alpha CHKB NM_152247 - 3.54 Choline kinase beta CHPT1 NM_020244 2.68 5.06 Choline phosphotransferase 1 CHRNA5 NM_000745 2.66 5.30 Cholinergic receptor, nicotinic, alpha polypeptide 5 CIRBP NM_001280 1.73 7.81 Cold inducible RNA binding protein CKLFSF3 NM_181555 - 3.15 Chemokine-like factor super family 3 CLCA2 NM_006536 - 9.51 Chloride channel, calcium activated, family member 2 CLCN3 NM_173872 - 4.40 Chloride channel 3 CLECSF12 NM_197954 - 3.72 C-type lectin domain family 7, member A CLECSF6 NM_194450 - 3.07 C-type lectin domain family 4, member A CLK1 NM_004071 -1.26 3.93 CDC-like kinase 1 CLK4 NM_020666 - 45.37 CDC-like kinase 4 CLN6 NM_017882 - 16.16 Ceroid-lipofuscinosis, neuronal 6, late infantile, variant CLTC NM_004859 - 4.61 Clathrin, heavy polypeptide (Hc) CNGA1 NM_000087 1.55 4.18 Putative anti-CNG alpha 1 cation channel product CNNM3 NM_199078 1.77 5.98 Cyclin M3 CNOT1 NM_016284 - 3.59 CCR4-NOT transcription complex, subunit 1 CNOT4 NM_013316 - 4.56 CCR4-NOT transcription complex, subunit 4 CNOT7 NM_054026 - 4.00 CCR4-NOT transcription complex, subunit 7 CNP Hs.273621 - 3.82 2',3'-cyclic nucleotide 3' phosphodiesterase CNR1 NM_033181 - 6.80 Cannabinoid receptor 1 (brain) COG2 NM_007357 - 9.30 Component of oligomeric golgi complex 2 COG3 NM_031431 - 8.99 Component of oligomeric golgi complex 3 COL12A1 NM_080645 - 14.30 Collagen, type XII, alpha 1 COL16A1 NM_001856 1.92 4.41 Collagen, type XVI, alpha 1 COL21A1 NM_030820 - 17.48 Collagen, type XXI, alpha 1 COL27A1 NM_032888 2.81 6.81 Collagen, type XXVII, alpha 1 COL4A5 NM_033381 - 346.03 Collagen, type IV, alpha 5 (Alport syndrome) COL4A6 NM_033641 - 7.20 Collagen, type IV, alpha 6 COL5A1 NM_000093 2.81 4.12 Collagen, type V, alpha 1 COL5A2 NM_000393 -1.33 3.03 Collagen, type V, alpha 2 COLM NM_181789 -1.22 5.90 Collomin COPA NM_004371 - 3.51 Coatomer protein complex, subunit alpha CP NM_000096 - 3.48 Ceruloplasmin (ferroxidase)

11 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 Unchanged in MCF7-T, upregulated in MCF7-F CPD NM_001304 1.42 3.14 Carboxypeptidase D CPEB4 NM_030627 - 3.87 Cytoplasmic polyadenylation element binding protein 4 CPSF6 NM_007007 1.52 3.99 Cleavage and polyadenylation specific factor 6, 68kDa CPZ NM_003652 - 5.68 Carboxypeptidase Z CRA NM_181873 1.55 5.22 Myotubularin related protein 11 CREBL1 NM_004381 2.34 6.84 CAMP responsive element binding protein-like 1 CRIM1 NM_016441 - 7.21 Cysteine rich transmembrane BMP regulator 1 (chordin-like) CRLF1 NM_004750 1.62 3.93 Cytokine receptor-like factor 1 CRLF3 NM_015986 1.43 3.67 Cytokine receptor-like factor 3 CROP NM_016424 1.93 6.91 Cisplatin resistance-associated overexpressed protein CRR9 NM_030782 - 5.52 Cisplatin resistance related protein CRR9p CRSP3 NM_015979 -1.34 5.12 required for Sp1 transcriptional activation, subunit 3, 130kDa CRYGS NM_017541 - 12.23 Crystallin, gamma S CRYZL1 NM_145858 1.68 3.42 Crystallin, zeta (quinone reductase)-like 1 CSE1L NM_177436 1.95 3.01 CSE1 chromosome segregation 1-like (yeast) CSNK1A1 Hs.442592 1.67 3.79 Casein kinase 1, alpha 1 CSPG6 NM_005445 - 4.30 Chondroitin sulfate proteoglycan 6 (bamacan) CSS3 Hs.165050 - 12.35 chondroitin sulfate synthase 3 CTBS NM_004388 1.26 3.84 Chitobiase, di-N-acetyl- CTGLF1 NM_133446 - 3.13 Centaurin, gamma-like family, member 1 CTL2 NM_020428 - 3.03 CTL2 protein CTNNA1 NM_001903 - 8.04 Catenin (cadherin-associated protein), alpha 1, 102kDa CTNNB1 NM_001904 2.93 4.89 Catenin (cadherin-associated protein), beta 1, 88kDa CTNND1 NM_001331 - 4.03 Catenin (cadherin-associated protein), delta 1 CTSB NM_147783 -2.26 5.03 Cathepsin B CTSC NM_148170 - 43.25 Cathepsin C CTSD NM_001909 1.32 3.87 Cathepsin D (lysosomal aspartyl protease) CUGBP1 NM_198700 - 3.55 CUG triplet repeat, RNA binding protein 1 CUL4B NM_003588 - 3.74 Cullin 4B CYB561 NM_001915 2.12 3.46 Cytochrome b-561 CYLN2 NM_032719 - 3.19 cytoplasmic linker 2 CYP19A1 NM_031226 - 21.38 Cytochrome P450, family 19, subfamily A, polypeptide 1 CYP24A1 NM_000782 - 8.31 Cytochrome P450, family 24, subfamily A, polypeptide 1 CYP2D6 NM_000106 2.08 6.77 Cytochrome P450, family 2, subfamily D, polypeptide 6 CYP2E1 Hs.75183 - 3.20 cytochrome P450, family 2, subfamily E, polypeptide 1 CYP2J2 NM_000775 2.10 6.49 Cytochrome P450, family 2, subfamily J, polypeptide 2 CYP3A43 NM_057096 - 3.57 Cytochrome P450, family 3, subfamily A, polypeptide 43 CYP3A5 NM_000777 - 8.92 Cytochrome P450, family 3, subfamily A, polypeptide 5 pseudogene 2 CYP4B1 NM_000779 -1.48 4.37 Cytochrome P450, family 4, subfamily B, polypeptide 1 CYP4F11 NM_021187 - 6.13 Cytochrome P450, family 4, subfamily F, polypeptide 11 CYP4F12 NM_023944 - 10.01 Cytochrome P450, family 4, subfamily F, polypeptide 12 CYP4F3 NM_000896 - 21.28 Cytochrome P450, family 4, subfamily F, polypeptide 3 CYP4F8 NM_007253 - 35.21 Cytochrome P450, family 4, subfamily F, polypeptide 8 CYP4Z1 NM_178134 - 74.02 Cytochrome P450 4Z2 pseudogene DAAM1 NM_014992 - 12.54 Dishevelled associated activator of morphogenesis 1 DATF1 Hs.438300 2.08 3.92 death associated transcription factor 1 DCAMKL1 Hs.21355 - 7.89 doublecortin and CaM kinase-like 1 DCBLD1 NM_173674 - 5.32 Discoidin, CUB and LCCL domain containing 1 DCBLD2 NM_080927 - 36.06 Discoidin, CUB and LCCL domain containing 2 DCLRE1C NM_022487 1.23 3.06 DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae) DDB2 NM_000107 - 6.80 LIM 3 DDEF1 Hs.386779 -1.87 3.98 development and differentiation enhancing factor 1 DDHD1 Hs.202641 - 6.93 DDHD domain containing 1 DDX11 NM_030655 - 10.57 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 DDX17 NM_030881 - 4.66 DEAD (Asp-Glu-Ala-Asp) box polypeptide 17 DDX3X NM_024005 - 5.55 DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked DDX42 NM_007372 1.47 20.40 DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 DDX50 NM_024045 1.97 4.08 DEAD (Asp-Glu-Ala-Asp) box polypeptide 50 DDX58 NM_014314 -1.40 9.18 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58

12 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 Unchanged in MCF7-T, upregulated in MCF7-F DEGS1 NM_144780 - 3.26 Degenerative spermatocyte homolog 1, lipid desaturase (Drosophila) DERA Hs.39429 - 6.18 2-deoxyribose-5-phosphate aldolase homolog (C. elegans) DGAT1 NM_012079 - 3.60 Diacylglycerol O-acyltransferase homolog 1 (mouse) DHCR7 NM_001360 2.43 3.19 7-dehydrocholesterol reductase DHRS2 NM_182908 -2.77 4.17 Dehydrogenase/reductase (SDR family) member 2 DHRS3 NM_004753 -2.07 7.86 Dehydrogenase/reductase (SDR family) member 3 DHRS6 NM_020139 2.52 4.00 Dehydrogenase/reductase (SDR family) member 6 DHX35 Hs.7174 - 7.19 DEAH (Asp-Glu-Ala-His) box polypeptide 35 DHX57 Hs.468226 1.66 3.33 DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57 DHX9 NM_030588 - 17.89 DEAH (Asp-Glu-Ala-His) box polypeptide 9 DIAPH1 NM_005219 -1.46 4.78 Diaphanous homolog 1 (Drosophila) DIO2 NM_013989 - 44.94 Deiodinase, iodothyronine, type II DISP1 NM_032890 1.90 3.14 Dispatched homolog 1 (Drosophila) DKFZP564D166 Hs.4996 - 7.02 putative ankyrin-repeat containing protein DKFZp762C186 Hs.438942 - 4.06 tangerin DKFZp762K222 Hs.21958 2.87 4.27 Storkhead box 2 DLEU2 NM_006021 1.83 5.11 Deleted in lymphocytic leukemia, 2 DLG1 NM_004087 - 6.84 Discs, large homolog 1 (Drosophila) DLX1 NM_178120 2.67 3.38 Distal-less homeo box 1 DLX2 NM_004405 2.23 3.63 Distal-less homeo box 2 DMXL2 NM_015263 - 6.41 Dmx-like 2 DNA2L Hs.194665 1.34 3.05 DNA2 DNA replication helicase 2-like (yeast) DNAJB4 NM_007034 - 10.40 DnaJ (Hsp40) homolog, subfamily B, member 4 DNAJC10 NM_018981 - 6.43 DnaJ (Hsp40) homolog, subfamily C, member 10 DNAJC11 NM_018198 - 3.51 DnaJ (Hsp40) homolog, subfamily C, member 11 DNAJC14 NM_032364 -1.43 3.77 DnaJ (Hsp40) homolog, subfamily C, member 14 DNAJC7 NM_003315 - 3.50 DnaJ (Hsp40) homolog, subfamily C, member 7 DNASE2 NM_001375 - 4.46 II, lysosomal DOCK4 NM_014705 - 4.87 Dedicator of cytokinesis 4 DOCK7 Hs.406156 - 3.18 Dedicator of cytokinesis 7 DPP7 NM_013379 1.22 3.02 Dipeptidylpeptidase 7 DPYD NM_000110 - 130.89 Dihydropyrimidine dehydrogenase DRF1 NM_145663 - 8.79 Dbf4-related factor 1 DSC2 NM_024422 -1.40 3.57 Desmocollin 2 DSG2 NM_001943 2.92 3.07 Desmoglein 2 DST NM_183380 2.40 3.17 DUSP6 NM_022652 -1.74 3.56 Dual specificity phosphatase 6 DYRK1A NM_130438 - 4.55 Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A DYRK2 NM_006482 -1.76 4.61 Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2 DZIP3 NM_014648 - 13.37 Zinc finger DAZ interacting protein 3 ECHDC1 NM_018479 - 5.22 Enoyl Coenzyme A hydratase domain containing 1 EDARADD NM_145861 - 7.75 EDAR-associated death domain EDG4 NM_004720 1.23 3.38 Endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4 EDIL3 NM_005711 - 60.02 EGF-like repeats and discoidin I-like domains 3 EDN2 NM_001956 1.89 3.18 Endothelin 2 EED NM_152991 1.89 9.31 Embryonic ectoderm development EFHC1 NM_018100 2.18 5.50 EF-hand domain (C-terminal) containing 1 EGFL5 Hs.236216 2.36 3.67 EGF-like-domain, multiple 5 EGFR NM_201284 1.29 3.24 Epidermal growth factor receptor EHBP1 NM_015252 - 5.95 EH domain binding protein 1 EHF NM_172233 1.22 5.54 ets homologous factor EIF2AK2 NM_002759 - 4.35 initiation factor 2-alpha kinase 2 EIF2C2 NM_012154 -2.02 3.33 Eukaryotic translation initiation factor 2C, 2 EIF2S3 NM_001415 - 4.94 Eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa EIF3S9 NM_182712 1.37 3.56 Eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa EIF4A2 NM_001967 - 33.15 Eukaryotic translation initiation factor 4A, isoform 2 EIF4G1 NM_198244 - 3.40 Eukaryotic translation initiation factor 4 gamma, 1 EIF4G3 NM_003760 - 6.42 Eukaryotic translation initiation factor 4 gamma, 3 ELL2 NM_012081 1.51 4.54 , RNA polymerase II, 2

13 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 Unchanged in MCF7-T, upregulated in MCF7-F ELOVL5 NM_021814 2.41 9.44 ELOVL family member 5, elongation of long chain fatty acids ELYS NM_175865 - 30.17 AT hook containing transcription factor 1 EMCN NM_016242 - 3.67 Endomucin EML4 NM_019063 -1.22 5.36 Echinoderm microtubule associated protein like 4 EML5 NM_183387 2.03 3.34 Echinoderm microtubule associated protein like 5 EMR2 NM_152921 - 4.62 Egf-like module containing, mucin-like, -like 2 ENC1 NM_003633 -1.28 13.93 Ectodermal-neural cortex (with BTB-like domain) ENO1 NM_005945 - 17.66 enolase 1, (alpha) ENTH NM_014666 - 4.01 Enthoprotin ENTPD4 NM_004901 - 5.55 Ectonucleoside triphosphate diphosphohydrolase 4 EPAG Hs.522713 - 9.75 Early lymphoid activation protein EPAS1 NM_001430 -2.44 4.01 Endothelial PAS domain protein 1 EPB41 Hs.175437 - 3.92 Erythrocyte membrane protein band 4.1 (elliptocytosis 1, RH-linked) EPB41L1 NM_177996 - 3.28 Erythrocyte membrane protein band 4.1-like 1 EPB41L2 NM_001431 -1.37 3.71 Erythrocyte membrane protein band 4.1-like 2 EPHA2 NM_004431 - 5.83 EPH receptor A2 EPHA4 Hs.244624 -1.37 4.39 EphA4 EPHA7 NM_004440 - 23.64 EPH receptor A7 EPHB2 NM_017449 - 9.04 EPH receptor B2 EPHB3 NM_004443 1.23 3.21 EPH receptor B3 EPHB6 NM_004445 1.24 8.92 EPH receptor B6 EPHX1 NM_000120 1.53 8.95 Epoxide hydrolase 1, microsomal (xenobiotic) EPRS NM_004446 - 7.62 Glutamyl-prolyl-tRNA synthetase EPS8L2 NM_022772 - 7.57 EPS8-like 2 ERBB2 NM_004448 - 6.61 V-erb-b2 erythroblastic leukemia viral oncogene homolog 2 ERBB3 NM_001982 1.40 7.07 V-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) Excision repair cross-complementing rodent repair deficiency, complementation ERCC1 NM_001983 1.39 3.39 group 1 ERP70 NM_004911 1.50 5.84 Protein disulfide family A, member 4 ESCO1 NM_052911 - 4.41 Establishment of cohesion 1 homolog 1 (S. cerevisiae) ESD NM_001984 2.75 8.81 D/formylglutathione hydrolase ETAA16 NM_019002 - 3.46 ETAA16 protein ETFA Hs.39925 - 3.33 TYRO3P protein tyrosine kinase pseudogene ETS2 NM_005239 2.57 5.39 V-ets erythroblastosis virus E26 oncogene homolog 2 (avian) EVA1 NM_144765 - 3.66 Epithelial V-like antigen 1 EVI1 NM_005241 - 12.14 Ecotropic viral integration site 1 EWSR1 NM_013986 - 9.06 Ewing sarcoma breakpoint region 1 EXT1 NM_000127 -1.26 5.65 Exostoses (multiple) 1 EYA4 NM_172105 - 17.69 Eyes absent homolog 4 (Drosophila) F2R NM_001992 - 11.13 Coagulation factor II (thrombin) receptor F2RL1 NM_005242 -1.39 5.89 Coagulation factor II (thrombin) receptor-like 1 FANCA NM_000135 1.80 3.85 Fanconi anemia, complementation group A FARSLB NM_005687 - 6.08 Phenylalanine-tRNA synthetase-like, beta subunit FAS NM_152877 - 7.93 Fas (TNF receptor superfamily, member 6) FBLN1 NM_006487 1.83 8.57 Fibulin 1 FBXL20 NM_032875 - 3.46 F-box and leucine-rich repeat protein 20 FBXL3 NM_012158 - 3.54 F-box and leucine-rich repeat protein 3 FBXO28 NM_015176 - 5.73 F-box protein 28 FBXO38 NM_024862 - 30.00 F-box protein 38 FBXO9 NM_033481 1.39 12.76 F-box protein 9 FBXW11 NM_033645 - 3.38 F-box and WD-40 domain protein 11 FBXW2 NM_012164 - 7.59 F-box and WD-40 domain protein 2 FDFT1 NM_004462 2.74 4.69 Farnesyl-diphosphate farnesyltransferase 1 FER1L3 NM_133337 -2.61 3.03 Fer-1-like 3, myoferlin (C. elegans) FER1L4 NR_001442 -2.75 7.50 Fer-1-like 4 (C. elegans) FGD6 Hs.170623 - 3.40 FYVE, RhoGEF and PH domain containing 6 FGFR1OP2 NM_015633 - 5.35 FGFR1 oncogene partner 2 FGFR2 NM_023031 - 5.35 Fibroblast growth factor receptor 2 FGG NM_021870 -1.23 5.35 Fibrinogen gamma chain FIGNL1 NM_022116 1.39 3.40 Fidgetin-like 1

14 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 Unchanged in MCF7-T, upregulated in MCF7-F FKRP NM_024301 - 22.67 Fukutin related protein FLJ10052 NM_017982 1.31 4.13 Sushi domain containing 4 FLJ10330 NM_018061 1.42 3.41 PRP38 pre-mRNA processing factor 38 (yeast) domain containing B FLJ10407 NM_018087 1.38 3.70 Transmembrane protein 48 FLJ10539 NM_018130 - 120.84 SHQ1 homolog (S. cerevisiae) FLJ10618 NM_018155 - 5.73 Solute carrier family 25, member 36 FLJ10747 NM_018202 - 3.31 Transmembrane protein 57 FLJ11142 NM_018338 -1.77 4.28 WD repeat domain 52 FLJ11457 NM_024753 - 18.52 Tetratricopeptide repeat domain 21B FLJ12892 NM_022757 1.51 3.18 Coiled-coil domain containing 14 FLJ12895 NM_023926 2.15 3.31 Zinc finger protein 447 FLJ14281 NM_024920 -1.60 3.81 DnaJ (Hsp40) homolog, subfamily B, member 14 FLJ14494 NM_032795 - 5.07 RNA pseudouridylate synthase domain containing 4 FLJ22490 NM_024790 1.44 3.26 Centrosome spindle pole associated protein FLJ22595 NM_025047 - 77.79 ADP-ribosylation factor 7 FLJ23375 NM_024956 1.74 3.12 Transmembrane protein 62 FLJ23518 NM_024725 - 14.00 HSPC048 protein FLJ23598 NM_024783 - 6.44 ATP/GTP binding protein-like 2 FLJ32384 NM_144608 - 3.44 Hexamthylene bis-acetamide inducible 2 FLJ34389 NM_152649 1.21 8.05 Mixed lineage kinase domain-like FLJ38507 NM_016206 - 5.22 Vestigial-like 3 FLJ38736 NM_182758 1.44 9.72 WD repeat domain 72 FLOT1 NM_005803 - 8.01 Flotillin 1 FLRT3 NM_198391 -1.47 16.20 Fibronectin leucine rich transmembrane protein 3 FLT3LG NM_001459 - 4.15 Fms-related tyrosine kinase 3 ligand FLVCR Hs.7055 1.40 3.87 Feline leukemia virus subgroup C cellular receptor FNBP1 NM_015033 - 8.29 Formin binding protein 1 FNBP1L Hs.134060 - 3.88 Formin binding protein 1-like FNBP3 Hs.298735 1.40 4.25 Formin binding protein 3 FNBP4 NM_015308 1.36 3.81 Formin binding protein 4 FNDC3A NM_014923 - 8.48 Fibronectin type III domain containing 3A FNDC3B NM_022763 - 3.05 Fibronectin type III domain containing 3B FOXF1 NM_001451 - 22.79 Forkhead box F1 FOXO1A NM_002015 - 4.60 Forkhead box O1A (rhabdomyosarcoma) FOXO3A NM_001455 - 14.52 Forkhead box O3A FOXP1 NM_032682 - 3.53 Forkhead box P1 FOXQ1 NM_033260 -1.72 11.24 Forkhead box Q1 FRMD4A NM_018027 - 6.28 FERM domain containing 4A FSTL4 Hs.123420 - 58.71 follistatin-like 4 FUBP1 NM_003902 1.24 5.20 Far upstream element (FUSE) binding protein 1 FUBP3 Hs.98751 2.21 6.06 Far upstream element (FUSE) binding protein 3 FYN NM_153048 1.57 3.45 FYN oncogene related to SRC, FGR, YES G1P2 NM_005101 -1.74 23.42 Interferon, alpha-inducible protein (clone IFI-15K) G1P3 NM_022873 -1.63 77.77 Interferon, alpha-inducible protein (clone IFI-6-16) G3BP Hs.3353 - 11.59 Ras-GTPase-activating protein SH3-domain-binding protein GABPA NM_002040 - 3.38 GA binding protein transcription factor, alpha subunit 60kDa GABPB2 NM_181427 - 4.03 GA binding protein transcription factor, beta subunit 2 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase GALNT1 NM_020474 1.43 3.73 1 (GalNAc-T1) UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase GALNT2 NM_004481 - 5.02 2 (GalNAc-T2) GALT NM_147132 - 5.94 Galactose-1-phosphate uridylyltransferase GARNL1 Hs.113150 - 5.78 GTPase activating Rap/RanGAP domain-like 1 GARNL3 NM_032293 - 3.02 GTPase activating Rap/RanGAP domain-like 3 GART NM_175085 1.73 7.38 Phosphoribosylglycinamide formyltransferase GAS6 NM_000820 - 5.45 Growth arrest-specific 6 GASP Hs.113082 -1.28 3.99 G protein-coupled receptor-associated sorting protein GATA5 NM_080473 - 15.19 GATA binding protein 5 GBP1 NM_002053 - 56.60 Guanylate binding protein 1, interferon-inducible, 67kDa

15 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 Unchanged in MCF7-T, upregulated in MCF7-F GBP2 NM_004120 - 3.85 Guanylate binding protein 2, interferon-inducible GBP3 NM_018284 - 33.58 Guanylate binding protein 3 GCC2 NM_181453 1.63 8.33 GRIP and coiled-coil domain containing 2 GDAP2 NM_017686 1.22 7.70 Ganglioside induced differentiation associated protein 2 GDF15 NM_004864 -1.86 4.86 Growth differentiation factor 15 GDPD1 NM_182569 -1.20 3.58 Glycerophosphodiester phosphodiesterase domain containing 1 GEM NM_181702 - 3.79 GTP binding protein overexpressed in skeletal muscle GFM1 NM_024996 - 3.24 G elongation factor, mitochondrial 1 GGA1 NM_013365 1.32 4.09 Golgi associated, gamma adaptin ear containing, ARF binding protein 1 GGA2 NM_138640 - 20.52 Golgi associated, gamma adaptin ear containing, ARF binding protein 2 GGTL3 NM_178026 - 9.26 Gamma-glutamyltransferase-like 3 GIT2 NM_139201 - 6.06 G protein-coupled receptor kinase interactor 2 GJB2 NM_004004 - 10.61 Gap junction protein, beta 2, 26kDa (connexin 26) GJB5 NM_005268 - 12.59 Gap junction protein, beta 5 (connexin 31.1) GK001 NM_020198 2.92 3.63 GK001 protein GLE1L NM_001499 -1.33 4.34 GLE1 RNA export mediator-like (yeast) GLG1 NM_012201 1.37 3.41 Golgi apparatus protein 1 GLMN NM_053274 - 5.20 Glomulin, FKBP associated protein GLS NM_014905 - 9.52 Glutaminase GLT25D1 NM_024656 - 4.04 25 domain containing 1 GM2A NM_000405 - 4.72 GM2 ganglioside activator GNA13 NM_006572 - 11.11 Guanine nucleotide binding protein (G protein), alpha 13 GNAI1 NM_002069 - 14.96 G protein, alpha inhibiting activity polypeptide 1 GNAS NM_080426 2.06 5.96 GNAS complex locus GNB2L1 NM_006098 1.58 6.68 Guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 GNG12 NM_018841 - 7.47 Guanine nucleotide binding protein (G protein), gamma 12 GNG12 NM_018841 1.29 3.39 Guanine nucleotide binding protein (G protein), gamma 12 GNS NM_002076 - 9.55 Glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID) GOLGA1 NM_002077 1.28 3.19 Golgi autoantigen, golgin subfamily a, 1 GOLGA2 NM_004486 - 4.15 Golgi autoantigen, golgin subfamily a, 2 GOLGIN-67 NM_181077 - 6.84 88-kDa golgi protein GOLPH2 NM_177937 1.23 3.39 Golgi phosphoprotein 2 GOLPH4 NM_014498 - 3.41 Golgi phosphoprotein 4 GOPC NM_020399 -1.74 4.39 Golgi associated PDZ and coiled-coil motif containing GOSR2 NM_054022 1.25 3.13 Golgi SNAP receptor complex member 2 GPAM NM_020918 - 3.05 Glycerol-3-phosphate acyltransferase, mitochondrial GPATC2 NM_018040 1.49 8.94 G patch domain containing 2 GPLD1 NM_177483 - 3.68 Glycosylphosphatidylinositol specific GPNMB NM_002510 - 4.65 Glycoprotein (transmembrane) nmb GPR110 NM_153840 - 25.32 G protein-coupled receptor 110 GPR115 NM_153838 - 3.90 G protein-coupled receptor 115 GPR172A NM_024531 -1.86 3.20 G protein-coupled receptor 172A GPR39 NM_001508 - 28.07 G protein-coupled receptor 39 GPR51 NM_005458 2.69 3.53 G protein-coupled receptor 51 GPR56 NM_201525 - 8.78 G protein-coupled receptor 56 GPR75 Hs.21691 - 8.92 G protein-coupled receptor 75 GPR87 NM_023915 - 41.56 G protein-coupled receptor 87 GRB10 Hs.512118 - 9.21 growth factor receptor-bound protein 10 GSDML NM_018530 - 4.50 Gasdermin-like GSPT1 NM_002094 1.85 3.63 G1 to S phase transition 1 GTF2F1 NM_002096 - 3.52 General transcription factor IIF, polypeptide 1, 74kDa GTF2H2 NM_001515 2.32 5.14 General transcription factor IIH, polypeptide 2, 44kDa GTF2I NM_033003 1.25 11.00 general transcription factor II, i GTF2IRD2 NM_173537 1.23 5.16 GTF2I repeat domain containing 2 GTF3A NM_002097 1.29 3.01 General transcription factor IIIA GTF3C3 NM_012086 - 4.83 General transcription factor IIIC, polypeptide 3, 102kDa GTPBP2 NM_019096 1.55 3.97 GTP binding protein 2 GTPBP5 NM_015666 - 13.91 GTP binding protein 5 (putative) GULP1 NM_016315 - 8.63 GULP, engulfment adaptor PTB domain containing 1

16 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 Unchanged in MCF7-T, upregulated in MCF7-F H2AFY NM_138610 1.60 5.06 H2A histone family, member Y HADHA NM_000182 - 4.31 Hydroxyacyl-Coenzyme A dehydrogenase HAS3 NM_138612 - 21.84 Decreased expression in renal and prostate HBP1 NM_012257 - 5.88 HMG-box transcription factor 1 HBS1L NM_006620 - 5.81 HBS1-like (S. cerevisiae) HCRP1 Hs.306802 1.62 3.98 hepatocellular carcinoma-related HCRP1 HDCMA18P NM_016648 1.58 3.29 HDCMA18P protein HECA NM_016217 - 4.41 Headcase homolog (Drosophila) HECTD1 NM_015382 - 18.47 HECT domain containing 1 HEG Hs.433452 - 18.75 HEG homolog HELLS NM_018063 - 3.00 Helicase, lymphoid-specific HERC5 NM_016323 2.12 23.76 Hect domain and RLD 5 HERC6 Hs.435365 1.23 12.46 hect domain and RLD 6 HEXA NM_000520 - 8.32 Hexosaminidase A (alpha polypeptide) HIAT1 Hs.124156 1.48 3.60 Hippocampus abundant transcript 1 HIATL2 NM_032318 1.49 7.11 Hippocampus abundant gene transcript-like 2 HIC NM_199072 - 5.93 MyoD family inhibitor domain containing HIP1 NM_005338 - 3.07 Huntingtin interacting protein 1 HIPK1 NM_198269 - 3.81 Homeodomain interacting protein kinase 1 HIPK3 NM_005734 - 3.62 Homeodomain interacting protein kinase 3 HIS1 NM_006460 - 4.75 Hexamethylene bis-acetamide inducible 1 HKR3 NM_005341 - 4.78 GLI-Kruppel family member HKR3 HLA-B NM_005514 2.01 16.67 Major histocompatibility complex, class I, B HLA-DOB NM_002120 - 7.11 Major histocompatibility complex, class II, DO beta HLA-E NM_005516 - 5.91 Major histocompatibility complex, class I, E HLA-G NM_002127 2.92 11.13 HLA-G histocompatibility antigen, class I, G HM13 Hs.373741 - 4.85 Histocompatibility (minor) 13 HMGA2 NM_003483 - 7.80 High mobility group AT-hook 2 HMGCS1 NM_002130 2.58 4.27 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) HNRPA1 NM_031157 2.03 5.54 Heterogeneous nuclear ribonucleoprotein A1 HNRPA2B1 NM_031243 1.52 6.40 Heterogeneous nuclear ribonucleoprotein A2/B1 HNRPA3 NM_194247 - 8.37 Heterogeneous nuclear ribonucleoprotein A3 HNRPD NM_031370 1.96 12.20 Heterogeneous nuclear ribonucleoprotein D HNRPDL NM_031372 2.12 4.23 Heterogeneous nuclear ribonucleoprotein D-like HNRPH1 NM_005520 - 7.73 Heterogeneous nuclear ribonucleoprotein H1 (H) HNRPL NM_001533 1.78 4.43 Heterogeneous nuclear ribonucleoprotein L HNRPM NM_031203 - 3.19 Heterogeneous nuclear ribonucleoprotein M HNRPU NM_031844 1.79 8.67 Heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) HP1-BP74 NM_016287 1.37 3.43 Heterochromatin protein 1, binding protein 3 HRB NM_004504 - 5.44 HIV-1 Rev binding protein HRIHFB2122 NM_138632 - 5.88 Tara-like protein HRMT1L1 NM_001535 - 6.15 HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae) HS3ST1 NM_005114 - 7.26 Heparan sulfate (glucosamine) 3-O-sulfotransferase 1 HS6ST2 NM_147175 2.14 8.89 Heparan sulfate 6-O-sulfotransferase 2 HSH2D NM_032855 - 3.04 Hematopoietic SH2 domain containing HSMPP8 NM_017520 1.34 3.52 M-phase phosphoprotein, mpp8 HSPC072 NM_014162 - 3.34 HSPC072 protein HSPC121 NM_016395 - 4.65 Butyrate-induced transcript 1 HSPCB NM_007355 -1.70 9.48 Heat shock 90kDa protein 1, beta HSRTSBETA NM_017512 1.98 4.22 Enolase superfamily member 1 HSXIAPAF1 NM_199139 - 11.85 XIAP associated factor-1 HTATSF1 NM_014500 - 3.58 HIV TAT specific factor 1 HTR2C NM_000868 - 7.32 5-hydroxytryptamine (serotonin) receptor 2C HYPB NM_014159 - 4.36 Huntingtin interacting protein B IARS Hs.445403 1.72 3.46 Isoleucine-tRNA synthetase IDH1 NM_005896 2.56 7.00 Isocitrate dehydrogenase 1 (NADP+), soluble IDS NM_006123 - 8.23 Iduronate 2-sulfatase (Hunter syndrome) IFI16 NM_005531 - 7.85 Interferon, gamma-inducible protein 16 IFI30 NM_006332 -1.48 3.27 Interferon, gamma-inducible protein 30

17 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 Unchanged in MCF7-T, upregulated in MCF7-F IFI35 NM_005533 - 14.87 Interferon-induced protein 35 IFI44 NM_006417 - 212.67 Interferon-induced protein 44 IFI44L NM_006820 - 842.24 Interferon-induced protein 44-like IFIH1 NM_022168 - 10.58 Interferon induced with helicase C domain 1 IFIT1 NM_001548 - 147.60 Interferon-induced protein with tetratricopeptide repeats 1 IFIT2 NM_001547 - 7.04 Interferon-induced protein with tetratricopeptide repeats 2 IFIT3 NM_001549 - 24.68 Interferon-induced protein with tetratricopeptide repeats 3 IFIT5 NM_012420 - 4.98 Interferon-induced protein with tetratricopeptide repeats 5 IFITM1 NM_003641 - 9.33 Interferon induced transmembrane protein 1 (9-27) IFNGR1 NM_000416 - 4.50 receptor 1 IGF2R NM_000876 - 4.39 Insulin-like growth factor 2 receptor IGFBP3 NM_000598 - 96.08 Insulin-like growth factor binding protein 3 IGFBP7 NM_001553 - 22.94 Insulin-like growth factor binding protein 7 IGSF1 NM_001555 -1.37 3.09 Immunoglobulin superfamily, member 1 IGSF4 NM_014333 1.54 3.95 Immunoglobulin superfamily, member 4 IKBKB NM_001556 - 3.16 Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta IL11RA NM_147162 - 3.48 Interleukin 11 receptor, alpha IL13RA1 NM_001560 -1.28 4.16 Interleukin 13 receptor, alpha 1 IL1A NM_000575 - 3.82 Interleukin 1, alpha IL1RAP NM_134470 - 10.37 Interleukin 1 receptor accessory protein IL20RA NM_014432 - 14.69 Interleukin 20 receptor, alpha IL6ST NM_175767 1.54 3.67 Interleukin 6 signal transducer (gp130, oncostatin M receptor) IL8 NM_000584 - 3.31 Interleukin 8 ILF3 NM_153464 - 17.18 Interleukin enhancer binding factor 3, 90kDa INADL NM_176878 - 3.93 InaD-like (Drosophila) ING5 NM_032329 - 11.72 Inhibitor of growth family, member 5 INSIG1 NM_198337 2.97 3.13 Insulin induced gene 1 IQGAP1 NM_003870 - 4.48 IQ motif containing GTPase activating protein 1 IREB2 NM_004136 - 4.51 Iron-responsive element binding protein 2 IRF2BP2 NM_182972 1.29 3.74 Interferon regulatory factor 2 binding protein 2 IRF6 NM_006147 - 14.09 Interferon regulatory factor 6 IRF7 NM_004031 1.25 8.87 Interferon regulatory factor 7 IRS1 NM_005544 -1.43 4.80 Insulin receptor substrate 1 IRX2 NM_033267 -1.97 6.27 Iroquois homeobox protein 2 ISGF3G NM_006084 - 13.25 Interferon-stimulated transcription factor 3, gamma 48kDa ISYNA1 NM_016368 1.61 3.43 Myo-inositol 1-phosphate synthase A1 ITGA2 NM_002203 -1.71 7.18 Integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) ITGA3 NM_005501 - 4.91 Integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor) ITGA6 NM_000210 2.14 14.18 Integrin, alpha 6 ITGB1 NM_133376 -1.45 8.15 Integrin, beta 1 (fibronectin receptor, beta polypeptide) ITGB4 NM_000213 - 4.56 Integrin, beta 4 ITGB5 NM_002213 2.29 3.34 Integrin, beta 5 ITGBL1 NM_004791 - 30.27 Integrin, beta-like 1 (with EGF-like repeat domains) ITM1 NM_152713 - 3.64 Integral membrane protein 1 ITM2C NM_030926 1.45 6.09 Integral membrane protein 2C ITPKB Hs.119065 - 7.30 Inositol 1,4,5-trisphosphate 3-kinase B ITPR1 NM_002222 1.48 8.17 Inositol 1,4,5-triphosphate receptor, type 1 JAG1 NM_000214 1.48 5.97 Jagged 1 (Alagille syndrome) JAK1 NM_002227 -1.26 4.46 Janus kinase 1 (a protein tyrosine kinase) JMJD1C NM_004241 2.19 4.32 Jumonji domain containing 1C JMJD2C Hs.157106 - 4.47 Jumonji domain containing 2C JRK NM_003724 - 4.28 Jerky homolog (mouse) KAL1 NM_000216 - 4.33 Kallmann syndrome 1 sequence KAT3 NM_019610 - 3.52 RNA binding motif protein, X-linked-like 1 KBTBD2 Hs.20237 - 6.08 kelch repeat and BTB (POZ) domain containing 2 KCNJ13 NM_002242 - 3.66 Potassium inwardly-rectifying channel, subfamily J, member 13 KCNK1 NM_002245 -1.22 4.14 Potassium channel, subfamily K, member 1 KCNK2 NM_014217 - 15.13 Potassium channel, subfamily K, member 2 KCNN4 NM_002250 - 7.86 Potassium intermediate/small conductance calcium-activated channel, N4

18 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 Unchanged in MCF7-T, upregulated in MCF7-F KCTD5 NM_018992 - 3.20 Potassium channel tetramerisation domain containing 5 KCTD7 NM_153033 2.18 3.65 Potassium channel tetramerisation domain containing 7 KDELR1 NM_006801 - 4.18 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1 KDELR2 NM_006854 1.41 3.39 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 KIAA0459 Hs.374987 1.60 3.31 OTU domain containing 3 KIAA0650 Hs.8118 1.75 3.65 Structural maintenance of flexible hinge domain containing 1 KIAA0792 Hs.119387 - 6.96 Transmembrane protein 63A KIAA0877 Hs.408623 1.65 3.19 Dpy-19-like 1 (C. elegans) KIAA0992 NM_016081 - 3.90 Palladin KIAA1363 NM_020792 -1.46 4.60 Arylacetamide deacetylase-like 1 KIAA1559 Hs.35524 - 3.29 Mouse zinc finger protein 14-like KIAA1573 NM_020925 2.37 12.93 Von Willebrand factor type A and cache domain containing 1 KIAA1726 Hs.376289 - 27.57 Zinc finger CCCH-type containing 12C KIDINS220 Hs.9873 - 4.52 Kinase D-interacting substance of 220 kDa KIF13A NM_022113 - 3.34 family member 13A KIF24 NM_018278 - 4.45 Kinesin family member 24 KIFC2 NM_145754 - 3.12 Kinesin family member C2 KITLG NM_003994 - 5.74 KIT ligand KLF11 NM_003597 - 5.16 Kruppel-like factor 11 KLF12 NM_016285 - 10.47 Kruppel-like factor 12 KLF6 Hs.4055 1.65 8.55 Kruppel-like factor 6 KLHL21 Hs.7764 1.48 3.92 Kelch-like 21 (Drosophila) KLK5 Hs.50915 - 3.45 Kallikrein 5 KLK6 NM_002774 -2.02 7.27 Kallikrein 6 (neurosin, zyme) KLRA1 NM_006611 - 9.43 Killer cell lectin-like receptor subfamily A, member 1 KNS2 NM_182923 - 38.00 Kinesin 2 60/70kDa KNTC1 NM_014708 2.15 3.87 Kinetochore associated 1 KRT1 NM_006121 - 8.94 (epidermolytic hyperkeratosis) KRT13 NM_153490 - 18.70 KRT15 NM_002275 - 13.47 KRT16 NM_005557 - 6.57 (focal non-epidermolytic palmoplantar keratoderma) KRT4 NM_002272 - 11.80 KRT5 NM_000424 - 55.11 L3MBTL NM_032107 - 3.38 L(3)mbt-like (Drosophila) LACTB NM_171846 1.54 3.29 Lactamase, beta LAMA3 NM_198129 - 55.74 Laminin, alpha 3 LAMA5 NM_005560 1.67 3.41 Laminin, alpha 5 LAMB1 NM_002291 - 3.72 Laminin, beta 1 LAMB3 NM_000228 - 30.81 Laminin, beta 3 LAMC1 NM_002293 2.60 5.20 Laminin, gamma 1 (formerly LAMB2) LAMC2 NM_018891 - 17.22 Laminin, gamma 2 LAMP1 NM_005561 - 5.62 Lysosomal-associated membrane protein 1 LAMP3 NM_014398 1.69 24.02 Lysosomal-associated membrane protein 3 LAP1B NM_015602 1.44 8.95 Torsin A interacting protein 1 LAPTM5 NM_006762 - 7.14 Lysosomal associated multispanning membrane protein 5 LARS NM_020117 - 6.53 Leucyl-tRNA synthetase LASS5 Hs.270525 - 3.82 LAG1 longevity assurance homolog 5 (S. cerevisiae) LASS6 Hs.387400 - 4.64 LAG1 longevity assurance homolog 6 (S. cerevisiae) LBR NM_194442 2.10 4.01 B receptor LCHN Hs.521240 1.58 6.24 LCHN protein LCN2 NM_005564 -2.22 3.39 Lipocalin 2 (oncogene 24p3) LENG4 NM_024298 - 3.24 Leukocyte receptor cluster (LRC) member 4 LENG8 NM_052925 1.46 3.96 Leukocyte receptor cluster (LRC) member 8 LEPR NM_002303 - 3.74 Leptin receptor LEPREL1 NM_018192 - 48.75 Leprecan-like 1 LETMD1 NM_015416 1.82 5.57 LETM1 domain containing 1 LGALS3BP NM_005567 - 13.92 Lectin, galactoside-binding, soluble, 3 binding protein LHFPL2 NM_005779 - 4.13 Lipoma HMGIC fusion partner-like 2 LIFR NM_002310 - 13.72 Leukemia inhibitory factor receptor

19 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 Unchanged in MCF7-T, upregulated in MCF7-F LIG4 NM_002312 - 5.16 Ligase IV, DNA, ATP-dependent LIPA NM_000235 1.35 4.95 Lipase A, lysosomal acid, cholesterol esterase (Wolman disease) LISCH7 NM_015925 1.38 4.25 Liver-specific bHLH-Zip transcription factor LMAN1 NM_005570 - 14.59 Lectin, mannose-binding, 1 LMLN NM_033029 -1.28 3.05 Leishmanolysin-like (metallopeptidase M8 family) LMO7 NM_005358 - 3.13 LIM domain 7 LNPEP NM_005575 - 5.88 Leucyl/cystinyl aminopeptidase LOC115294 NM_052937 1.49 3.06 Similar to hypothetical protein FLJ10883 LOC132671 NM_145263 1.28 3.35 Spermatogenesis associated 18 homolog (rat) LOC134492 NM_145266 - 7.49 NudC domain containing 2 LOC153222 NM_153607 -1.20 3.77 Adult retina protein LOC201176 Hs.60659 - 55.64 similar to Rho GTPase activating protein 12 LOC221955 NM_139179 1.53 3.14 KCCR13L LOC254531 NM_153613 - 3.85 PLSC domain containing protein LOC338692 Hs.438673 - 5.35 Ankyrin repeat domain 13 family, member D LOC51136 NM_016125 -2.29 3.56 PTD016 protein LOC51336 NM_016646 - 3.93 mesenchymal stem cell protein DSCD28 LOC55971 NM_018842 1.43 3.33 BAI1-associated protein 2-like 1 LOC80298 NM_025198 1.67 3.04 MTERF domain containing 3 LOC91120 Hs.306298 - 5.00 Zinc finger protein 682 LOXL2 NM_002318 - 8.45 Lysyl oxidase-like 2 LRAP NM_022350 - 29.67 Leukocyte-derived arginine aminopeptidase LRCH3 NM_032773 1.37 3.94 Leucine-rich repeats and calponin homology (CH) domain containing 3 LRDD NM_145887 - 5.42 Leucine-rich repeats and death domain containing LRIG2 Hs.448972 - 3.08 Leucine-rich repeats and immunoglobulin-like domains 2 LRP6 NM_002336 - 6.76 Low density lipoprotein receptor-related protein 6 LRPAP1 NM_002337 2.09 3.15 Low density lipoprotein receptor-related protein associated protein 1 LRPPRC NM_133259 1.72 5.35 Leucine-rich PPR-motif containing LRRC14 Hs.155650 - 6.36 leucine rich repeat containing 14 LRRC17 NM_005824 - 5.12 Leucine rich repeat containing 17 LRRC8 NM_019594 - 3.48 Leucine rich repeat containing 8 family, member A LRRIQ2 NM_024548 - 3.72 Leucine-rich repeats and IQ motif containing 2 LRSAM1 NM_138361 - 3.54 Leucine rich repeat and sterile alpha motif containing 1 LTB4R Hs.445013 - 4.04 leukotriene B4 receptor LTBP1 NM_000627 - 4.86 Latent transforming growth factor beta binding protein 1 LUC7L NM_201412 -1.34 3.06 LUC7-like (S. cerevisiae) LXN NM_020169 1.66 3.16 Latexin LY6G5B NM_021221 1.44 4.19 Lymphocyte antigen 6 complex, locus G5B LYPLAL1 Hs.125291 1.20 8.85 -like 1 LYST NM_000081 - 3.37 Lysosomal trafficking regulator M17S2 NM_031862 - 3.78 Neighbor of BRCA1 gene 1 M6PR NM_002355 -1.34 12.69 Mannose-6-phosphate receptor (cation dependent) MAF NM_005360 - 8.12 V-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) MAK NM_005906 - 9.64 Male germ cell-associated kinase MALAT1 Hs.187199 -1.31 4.60 Metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) MAML2 NM_032427 - 4.90 Mastermind-like 2 (Drosophila) MAN1A2 NM_006699 - 3.74 Mannosidase, alpha, class 1A, member 2 MAN2A1 NM_002372 1.20 4.46 Mannosidase, alpha, class 2A, member 1 MAN2C1 NM_006715 1.46 3.56 Mannosidase, alpha, class 2C, member 1 MANEA NM_024641 1.54 3.04 Mannosidase, endo-alpha MAOA NM_000240 1.75 5.11 Monoamine oxidase A MAP1D NM_199227 - 8.61 Methionine aminopeptidase 1D MAP2 NM_031847 - 6.54 Microtubule-associated protein 2 MAP2K5 Hs.114198 - 12.47 Mitogen-activated protein kinase kinase 5 MAP3K1 Hs.170610 - 14.11 mitogen-activated protein kinase kinase kinase 1 MAP3K14 NM_003954 -1.34 3.10 Mitogen-activated protein kinase kinase kinase 14 MAP3K2 NM_006609 - 7.88 Mitogen-activated protein kinase kinase kinase 2 MAP3K5 NM_005923 - 3.60 Mitogen-activated protein kinase kinase kinase 5 MAP3K7 NM_145333 - 4.18 Mitogen-activated protein kinase kinase kinase 7

20 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 Unchanged in MCF7-T, upregulated in MCF7-F MAP3K8 NM_005204 2.10 8.33 Mitogen-activated protein kinase kinase kinase 8 MAP4K4 NM_145687 - 3.05 Mitogen-activated protein kinase kinase kinase kinase 4 MAP4K5 NM_198794 - 6.16 Mitogen-activated protein kinase kinase kinase kinase 5 MAPK14 NM_139014 - 4.16 Mitogen-activated protein kinase 14 MARCH-VI NM_005885 - 6.82 Membrane-associated ring finger (C3HC4) 6 MARCKS NM_002356 1.46 4.65 Myristoylated alanine-rich protein kinase C substrate MARS NM_004990 2.17 3.90 Methionine-tRNA synthetase MASP2 NM_139208 1.33 4.63 Mannan-binding lectin serine protease 2 MAST2 NM_015112 - 3.08 Microtubule associated serine/threonine kinase 2 MATR3 NM_018834 - 7.32 Matrin 3 MBD4 NM_003925 2.00 7.89 Methyl-CpG binding domain protein 4 MBNL1 NM_021038 1.60 6.24 Muscleblind-like (Drosophila) MBNL2 NM_144778 -2.00 7.79 Muscleblind-like 2 (Drosophila) MBTD1 NM_017643 1.30 3.13 Mbt domain containing 1 MCCC2 NM_022132 - 4.79 Methylcrotonoyl-Coenzyme A carboxylase 2 (beta) MCL1 NM_182763 - 5.96 Myeloid cell leukemia sequence 1 (BCL2-related) MCLC NM_015127 1.67 3.47 Mid-1-related chloride channel 1 MCMDC1 NM_153255 - 3.63 Minichromosome maintenance deficient domain containing 1 MCOLN3 NM_018298 1.67 8.49 Mucolipin 3 MCP NM_172361 1.37 11.69 Membrane cofactor protein MDH1 NM_005917 2.01 4.20 Malate dehydrogenase 1, NAD (soluble) MDH1B Hs.147816 - 6.08 Malate dehydrogenase 1B, NAD (soluble) MDM4 NM_002393 1.49 3.91 Mdm4, transformed 3T3 cell double minute 4, binding protein (mouse) MDN1 NM_014611 - 4.82 MDN1, midasin homolog (yeast) MDS009 NM_020234 1.29 7.64 DTW domain containing 1 ME1 Hs.21160 - 5.16 Malic enzyme 1, NADP(+)-dependent, cytosolic MED31 NM_016060 - 10.61 Mediator of RNA polymerase II transcription, subunit 31 homolog (yeast) MERTK NM_006343 -1.62 3.65 C-mer proto-oncogene tyrosine kinase MET NM_000245 1.28 7.41 Met proto-oncogene (hepatocyte growth factor receptor) METAP2 NM_006838 1.59 5.65 Methionyl aminopeptidase 2 METTL4 NM_022840 1.93 3.26 Methyltransferase like 4 MFI2 NM_033316 - 3.08 Antigen p97 (melanoma associated) MFN1 NM_033540 1.41 3.08 Mitofusin 1 MGC14816 NM_144620 - 5.69 Leucine rich repeat containing 39 MGC27466 NM_152373 - 4.30 Zinc finger protein 684 MGC3222 NM_024334 - 4.56 Transmembrane protein 43 MGC3262 NM_024029 - 3.60 Yip1 domain family, member 2 MGC39558 NM_152490 - 4.27 UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2 MGC40405 NM_152789 1.52 6.50 Similar to RIKEN cDNA 5830415L20 MGC40489 Hs.405627 - 9.33 Similar to adapter protein 162 (LOC400615), mRNA MGC43690 NM_182552 - 4.01 WD repeat domain 27 MGC45564 Hs.136901 - 3.93 GTPase activating Rap/RanGAP domain-like 1 MGC5395 NM_024060 - 6.54 AHNAK nucleoprotein (desmoyokin) MGC72104 Hs.446528 - 6.45 similar to FRG1 protein (FSHD region gene 1 protein) MGEA5 NM_012215 - 3.31 Meningioma expressed antigen 5 (hyaluronidase) MGST1 NM_145792 2.35 8.65 Microsomal glutathione S-transferase 1 MIB1 Hs.140903 - 4.29 Mindbomb homolog 1 (Drosophila) MKLN1 NM_013255 - 5.20 Muskelin 1, intracellular mediator containing kelch motifs MKNK1 NM_198973 - 6.99 MAP kinase interacting serine/threonine kinase 1 MLL Hs.258855 - 6.72 Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) MLL5 NM_182931 -1.74 3.81 Myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila) MMP1 NM_002421 - 22.19 Matrix metalloproteinase 1 (interstitial collagenase) MMP13 NM_002427 - 3.03 Matrix metalloproteinase 13 (collagenase 3) MMP28 NM_032950 - 6.59 Matrix metalloproteinase 28 MN7 Hs.458334 1.56 4.59 D15F37 gene MOBK1B NM_018221 - 4.35 MOB1, Mps One Binder kinase activator-like 1B (yeast) MORF4L2 NM_012286 - 6.69 Mortality factor 4 like 2 MOV10 NM_020963 - 6.17 Mov10, Moloney leukemia virus 10, homolog (mouse) MPDZ NM_003829 - 6.51 Multiple PDZ domain protein

21 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 Unchanged in MCF7-T, upregulated in MCF7-F MPHOSPH9 NM_022782 1.21 3.52 M-phase phosphoprotein 9 MPPE1 NM_138608 2.55 4.20 Metallophosphoesterase 1 MR1 NM_001531 1.83 3.43 Major histocompatibility complex, class I-related MRC2 NM_006039 1.45 3.03 Mannose receptor, C type 2 MRCL3 Hs.190086 1.81 7.65 Myosin regulatory light chain MRCL3 MRPS30 NM_016640 - 4.48 Mitochondrial ribosomal protein S30 MRPS31 NM_005830 - 10.35 Mitochondrial ribosomal protein S31 MRPS5 NM_031902 - 3.29 Mitochondrial ribosomal protein S5 MSCP NM_018579 - 18.19 Solute carrier family 25, member 37 MSH5 NM_172166 1.38 4.70 MutS homolog 5 (E. coli) MSI2 NM_170721 - 3.47 Musashi homolog 2 (Drosophila) MST4 NM_016542 2.89 9.51 Mst3 and SOK1-related kinase MTAP NM_002451 2.19 3.82 Methylthioadenosine phosphorylase MTBP NM_022045 - 7.40 Mdm2, transformed 3T3 cell double minute 2 MTMR1 NM_176789 - 13.00 Myotubularin related protein 1 MTRR NM_024010 - 3.88 5-methyltetrahydrofolate-homocysteine methyltransferase reductase MUC5B Hs.103707 - 15.83 mucin 5, subtype B, tracheobronchial MUM1 NM_032853 -1.32 3.91 Melanoma associated antigen (mutated) 1 MX1 NM_002462 - 3.18 Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) MX2 NM_002463 - 7.18 Myxovirus (influenza virus) resistance 2 (mouse) MYH10 Hs.16355 - 14.35 Myosin, heavy polypeptide 10, non-muscle MYL6 NM_079425 1.28 5.19 Myosin, light polypeptide 6, alkali, smooth muscle and non-muscle MYLIP NM_013262 2.07 4.79 Myosin regulatory light chain interacting protein NAALADL2 Hs.416922 - 13.88 N-acetylated alpha-linked acidic dipeptidase 2 NAB1 NM_005966 1.20 4.30 NGFI-A binding protein 1 (EGR1 binding protein 1) NACA NM_005594 2.38 3.74 Nascent-polypeptide-associated complex alpha polypeptide NAPB Hs.12600 - 3.32 N-ethylmaleimide-sensitive factor attachment protein, beta NAPE-PLD NM_198990 1.68 8.74 N-acyl-phosphatidylethanolamine-hydrolyzing NARG2 NM_024611 - 6.12 NMDA receptor regulated 2 NASP NM_172164 - 7.72 Nuclear autoantigenic sperm protein (histone-binding) NAV1 NM_020443 2.48 3.15 navigator 1 NAV2 NM_182964 -1.86 3.52 Neuron navigator 2 NAV3 NM_014903 - 60.78 Ribosomal protein S16 family protein NBEAL1 NM_198945 - 5.18 Neurobeachin-like 1 NCBP1 NM_002486 - 6.47 Nuclear cap binding protein subunit 1, 80kDa NCOA3 NM_181659 -1.42 3.69 Nuclear receptor coactivator 3 NDUFB4 NM_004547 - 4.14 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa NEB NM_004543 1.59 3.37 Nebulin NEDD1 NM_152905 - 3.13 Neural precursor cell expressed, developmentally down-regulated 1 NF1 NM_000267 1.53 6.03 (neurofibromatosis) Nuclear factor of activated T-cells, cytoplasmic, -dependent 2 interacting NFATC2IP NM_032815 - 5.88 protein NFE2L3 NM_004289 1.25 3.32 Nuclear factor (erythroid-derived 2)-like 3 NFX1 NM_147134 -1.23 3.05 Nuclear transcription factor, X-box binding 1 NFYA NM_021705 - 3.06 Nuclear transcription factor Y, alpha NGLY1 NM_018297 - 3.35 N-glycanase 1 NHS NM_198270 -1.51 3.92 Nance-Horan syndrome (congenital cataracts and dental anomalies) NICAL NM_022765 - 5.04 Microtubule associated monoxygenase, calponin and LIM domain containing 1 NIPBL NM_133433 - 4.09 Nipped-B homolog (Drosophila) NKTR NM_005385 1.39 4.02 Natural killer-tumor recognition sequence NMI NM_004688 -2.68 5.37 N- (and STAT) interactor NNT NM_182977 1.23 4.47 Nicotinamide nucleotide transhydrogenase NOD27 NM_032206 - 9.66 Nucleotide-binding oligomerization domains 27 NOG NM_005450 - 10.36 Noggin NOTCH2 NM_024408 - 3.39 Notch homolog 2 (Drosophila) NOTCH2NL Hs.502564 - 6.00 Notch homolog 2 (Drosophila) N-terminal like NOV NM_002514 -2.25 5.00 Nephroblastoma overexpressed gene NPC-A-5 Hs.510543 - 12.04 Nasopharyngeal carcinoma-associated antigen NPC-A-5 NPEPL1 NM_024663 - 3.80 Aminopeptidase-like 1

22 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 Unchanged in MCF7-T, upregulated in MCF7-F NPEPPS NM_006310 - 4.01 Aminopeptidase puromycin sensitive NPFF NM_003717 1.72 3.41 Neuropeptide FF-amide peptide precursor NPL NM_030769 - 7.38 N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) NR2C1 NM_003297 - 3.15 Nuclear receptor subfamily 2, group C, member 1 NR2C2 NM_003298 - 5.88 Nuclear receptor subfamily 2, group C, member 2 NR2F1 NM_005654 1.21 3.89 Nuclear receptor subfamily 2, group F, member 1 NRBP2 NM_178564 1.31 3.80 Nuclear receptor binding protein 2 NRD1 NM_002525 - 3.93 Nardilysin (N-arginine dibasic convertase) NRF1 NM_005011 - 7.30 Nuclear respiratory factor 1 NRK NM_198465 - 5.30 Nik related kinase NRP1 NM_003873 - 3.19 Neuropilin 1 NSMAF NM_003580 - 3.15 Neutral sphingomyelinase (N-SMase) activation associated factor NSUN6 NM_182543 - 3.71 NOL1/NOP2/Sun domain family, member 6 NT5C2 Hs.158209 - 5.80 5'-nucleotidase, cytosolic II NTN4 NM_021229 - 99.53 Netrin 4 NUCB1 NM_006184 1.47 4.20 Nucleobindin 1 NUDT9 Hs.149500 - 5.73 Nudix (nucleoside diphosphate linked moiety X)-type motif 9 NUMA1 NM_006185 - 8.65 Nuclear mitotic apparatus protein 1 NUP210 NM_024923 1.44 3.58 210kDa NUSAP1 NM_018454 2.58 4.72 Nucleolar and spindle associated protein 1 NYREN18 NM_016118 - 16.89 NEDD8 ultimate buster-1 OAS1 NM_016816 - 120.76 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS2 NM_016817 - 6.60 2'-5'-oligoadenylate synthetase 2, 69/71kDa OAS3 NM_006187 1.23 20.79 2'-5'-oligoadenylate synthetase 3, 100kDa OASL NM_198213 1.35 8.97 2'-5'-oligoadenylate synthetase-like OCIAD1 NM_017830 - 7.78 OCIA domain containing 1 OCIL NM_013269 -1.81 6.38 C-type lectin superfamily 2, member D ODAG NM_021167 - 4.41 GATA zinc finger domain containing 1 ODZ4 Hs.5028 - 20.11 odz, odd Oz/ten-m homolog 4 (Drosophila) OFD1 NM_003611 1.34 4.14 Oral-facial-digital syndrome 1 OGDH NM_002541 - 6.13 Oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) OGFR NM_007346 - 8.78 Opioid growth factor receptor OGT NM_181673 1.21 5.34 GlcNAc transferase ORMDL1 NM_016467 1.29 10.41 ORM1-like 1 (S. cerevisiae) OSBP NM_002556 1.30 3.01 Oxysterol binding protein OSGEPL1 NM_022353 - 3.69 O- endopeptidase-like 1 OVOS2 NM_173498 2.54 4.28 ovostatin 2 OXR1 NM_181354 - 4.08 Oxidation resistance 1 P2RY2 NM_176072 - 3.21 Purinergic receptor P2Y, G-protein coupled, 2 p44S10 Hs.152536 - 6.54 Proteasome (prosome, macropain) 26S subunit, non-ATPase, 6 P4HB NM_000918 - 15.54 Procollagen-proline, 2-oxoglutarate 4-dioxygenase, beta polypeptide PADI3 NM_016233 - 4.44 Peptidyl arginine deiminase, type III PAFAH1B1 NM_000430 1.28 5.11 Platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa PAN3 Hs.369984 - 6.97 PABP1-dependent poly A-specific subunit PAN3 PAPD4 NM_173797 - 3.71 PAP associated domain containing 4 PAPLN Hs.458428 - 3.20 Papilin, proteoglycan-like sulfated glycoprotein PAPSS2 NM_004670 -2.16 4.46 3'-phosphoadenosine 5'-phosphosulfate synthase 2 PAQR6 NM_198406 - 4.04 Progestin and adipoQ receptor family member VI PARP10 NM_032789 - 12.76 Poly (ADP-ribose) polymerase family, member 10 PARP9 NM_031458 - 16.25 Poly (ADP-ribose) polymerase family, member 9 PB1 NM_181042 - 10.90 Polybromo 1 PBEF1 NM_182790 1.25 5.73 Pre-B-cell colony enhancing factor 1 PBX4 NM_025245 2.55 6.08 Pre-B-cell leukemia transcription factor 4 PBXIP1 NM_020524 - 5.64 Pre-B-cell leukemia transcription factor interacting protein 1 PCAF NM_003884 - 6.91 P300/CBP-associated factor PCDH7 NM_032457 - 26.14 BH-protocadherin (brain-heart) PCDHB10 NM_018930 2.29 3.06 Protocadherin beta 10 PCDHB13 NM_018933 - 10.79 Protocadherin beta 13 PCDHB8 NM_019120 2.24 3.04 Protocadherin beta 8

23 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 Unchanged in MCF7-T, upregulated in MCF7-F PCDHGC3 NM_032403 1.47 5.91 Protocadherin gamma subfamily A, 12 PCF11 NM_015885 - 5.76 Pre-mRNA cleavage complex II protein Pcf11 PCGF5 Hs.500512 2.14 5.11 Polycomb group ring finger 5 PCSK7 NM_004716 1.96 3.86 Proprotein convertase subtilisin/kexin type 7 PCTK2 NM_002595 - 6.03 PCTAIRE protein kinase 2 PCYOX1 NM_016297 -1.46 6.20 Prenylcysteine oxidase 1 PCYT1A NM_005017 - 3.10 Phosphate cytidylyltransferase 1, choline, alpha isoform PDCD5 NM_004708 2.61 6.18 Programmed cell death 5 PDCD6 NM_013232 - 5.04 Aryl-hydrocarbon receptor repressor PDE4DIP NM_014644 1.27 3.89 Phosphodiesterase 4D interacting protein (myomegalin) PDE7A NM_002604 - 8.65 Phosphodiesterase 7A PDLIM5 NM_006457 - 3.08 PDZ and LIM domain 5 PDZK8 NM_173791 1.24 3.07 PDZ domain containing 8 PELI1 NM_020651 - 11.53 Pellino homolog 1 (Drosophila) PELI2 NM_021255 - 4.65 Pellino homolog 2 (Drosophila) PEX1 NM_000466 - 3.85 Peroxisome biogenesis factor 1 PGK1 NM_000291 - 9.52 Phosphoglycerate kinase 1 PGM2L1 NM_173582 1.21 4.17 Phosphoglucomutase 2-like 1 PGRMC1 NM_006667 2.51 3.60 membrane component 1 PGS1 NM_024419 - 4.70 Phosphatidylglycerophosphate synthase PHC3 NM_024947 1.62 3.34 Polyhomeotic like 3 (Drosophila) PHF11 NM_016119 - 4.66 PHD finger protein 11 PHF15 NM_015288 - 15.00 PHD finger protein 15 PHF20L1 NM_198513 - 3.46 PHD finger protein 20-like 1 PHGDHL1 Hs.508545 - 4.49 Phosphoglycerate dehydrogenase like 1 PHLDA1 NM_007350 -1.26 8.13 Pleckstrin homology-like domain, family A, member 1 PHTF2 Hs.128653 - 11.13 putative homeodomain transcription factor 2 PIB5PA NM_014422 - 8.66 Phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A PICALM NM_007166 -1.27 3.11 Phosphatidylinositol binding clathrin assembly protein PIG8 Hs.101014 1.79 3.30 Translokin PIGB NM_004855 - 3.56 Phosphatidylinositol glycan, class B PIGL NM_004278 - 3.39 Phosphatidylinositol glycan, class L PIK3C2A NM_002645 - 6.07 Phosphoinositide-3-kinase, class 2, alpha polypeptide PIK3CB NM_006219 - 5.38 Phosphoinositide-3-kinase, catalytic, beta polypeptide PIK3R1 NM_181524 2.89 3.92 Phosphoinositide-3-kinase, regulatory subunit 1 (p85 alpha) PILRB NM_178238 1.41 4.05 Paired immunoglobin-like type 2 receptor beta PIP5K1A NM_003557 - 9.98 Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha PIP5K3 NM_015040 1.27 3.56 Phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III PITPNB NM_012399 1.22 5.78 Phosphatidylinositol transfer protein, beta PITRM1 NM_014889 - 3.43 Pitrilysin metalloproteinase 1 PKD1 Hs.75813 - 13.78 Polycystic kidney disease 1 (autosomal dominant) PKD2 NM_000297 1.48 4.64 Polycystic kidney disease 2 (autosomal dominant) PKM2 NM_182471 1.65 4.02 Pyruvate kinase, muscle PLAG1 NM_002655 - 7.42 Pleiomorphic adenoma gene 1 PLAUR NM_002659 1.74 5.80 Plasminogen activator, urokinase receptor PLCXD3 Hs.145404 - 34.13 Phosphatidylinositol-specific , X domain containing 3 PLD1 NM_002662 - 4.37 Phospholipase D1, phophatidylcholine-specific PLEC1 NM_201384 - 7.76 1, binding protein 500kDa PLEKHA5 Hs.188614 - 3.04 Pleckstrin homology domain containing, family A member 5 PLGL NM_002665 - 3.90 Plasminogen-like B1 PLOD2 NM_182943 - 7.76 Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 PLRG1 NM_002669 - 5.19 Pleiotropic regulator 1 (PRL1 homolog, Arabidopsis) PLSCR1 NM_021105 - 8.77 scramblase 1 PLSCR4 NM_020353 - 7.40 Phospholipid scramblase 4 PLXNA1 NM_032242 - 4.02 Plexin A1 PLXNA2 NM_153014 - 9.02 Plexin A2 PLXNA3 NM_017514 -1.34 3.22 Plexin A3 PLXNB1 NM_002673 - 5.03 Plexin B1 PML NM_033250 - 9.94 Promyelocytic leukemia

24 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 Unchanged in MCF7-T, upregulated in MCF7-F PNN NM_002687 2.33 3.11 Pinin, desmosome associated protein PNPT1 NM_033109 - 5.13 Polyribonucleotide nucleotidyltransferase 1 POGZ NM_145796 1.50 4.87 Pogo transposable element with ZNF domain POLR2B Hs.149353 - 4.21 polymerase (RNA) II (DNA directed) polypeptide B, 140kDa POLR2J2 NM_145325 - 4.41 DNA directed RNA polymerase II polypeptide J-related gene POLS NM_006999 1.59 4.91 Polymerase (DNA directed) sigma POM121 NM_172020 - 4.03 POM121 membrane glycoprotein (rat) PON2 NM_000305 1.29 4.90 2 PPAP2A NM_176895 - 3.20 Phosphatidic acid phosphatase type 2A PPFIA1 NM_177423 - 3.15 Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF) PPFIBP1 NM_177444 - 4.90 PTPRF interacting protein, binding protein 1 (liprin beta 1) PPIA NM_021130 - 10.16 Peptidylprolyl isomerase A ( A) PPIB NM_000942 - 3.09 Peptidylprolyl isomerase B (cyclophilin B) PPP2R2A NM_002717 1.54 3.16 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform PPP2R2B NM_181678 - 12.51 (formerly 2A), regulatory subunit B (PR 52), beta isoform PPP4R1L Hs.278224 - 6.17 protein phosphatase 4, regulatory subunit 1-like PPT2 NM_138934 1.55 3.16 Palmitoyl-protein 2 PRIC285 NM_033405 -1.40 6.85 Peroxisomal proliferator-activated receptor A interacting complex 285 PRICKLE1 NM_153026 -1.22 3.26 Prickle-like 1 (Drosophila) PRKAA1 NM_006251 1.29 4.71 Protein kinase, AMP-activated, alpha 1 catalytic subunit PRKACA NM_002730 - 5.09 Protein kinase, cAMP-dependent, catalytic, alpha PRKAR1A NM_002734 1.39 3.05 Protein kinase, cAMP-dependent, regulatory, type I, alpha PRKCA NM_002737 1.49 3.25 Protein kinase C, alpha PRKCBP1 NM_183048 1.36 4.13 Protein kinase C binding protein 1 PRKCI NM_002740 - 3.28 Protein kinase C, iota PRKCSH NM_002743 1.30 4.18 Protein kinase C substrate 80K-H PRKD3 NM_005813 1.60 3.40 Protein kinase D3 PRKDC NM_006904 - 4.87 Protein kinase, DNA-activated, catalytic polypeptide PRKRA NM_003690 - 5.19 Protein kinase, interferon-inducible double stranded RNA dependent activator PRKRIP1 NM_024653 - 4.08 PRKR interacting protein 1 (IL11 inducible) PRNP NM_183079 - 4.43 Prion protein (p27-30) (Creutzfeld-Jakob disease) PROM2 NM_144707 -2.39 4.46 Prominin 2 PRPF4B NM_176800 1.69 4.76 PRP4 pre-mRNA processing factor 4 homolog B (yeast) PRPSAP1 NM_002766 2.48 9.07 Phosphoribosyl pyrophosphate synthetase-associated protein 1 PRR3 NM_025263 - 3.97 Proline rich 3 PRR6 NM_181716 2.12 3.14 Proline rich 6 PRRG1 NM_000950 - 14.39 Proline rich Gla (G-carboxyglutamic acid) 1 PRSS2 NM_002770 - 6.49 Protease, serine, 2 (trypsin 2) PSAP NM_002778 1.32 6.00 Prosaposin (variant Gaucher disease and variant metachromatic leukodystrophy) PSCD2 NM_017457 - 3.86 Pleckstrin homology, Sec7 and coiled-coil domains 2 (cytohesin-2) PSEN1 NM_007319 1.33 7.06 Presenilin 1 (Alzheimer disease 3) PSIP1 NM_033222 - 4.12 PC4 and SFRS1 interacting protein 1 PSMB7 NM_002799 - 21.09 Proteasome (prosome, macropain) subunit, beta type, 7 PSMB9 NM_148954 1.78 4.99 Proteasome (prosome, macropain) subunit, beta type, 9 PSMD7 NM_002811 - 36.14 Proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 PSME4 NM_014614 - 4.41 Proteasome (prosome, macropain) activator subunit 4 PSPC1 NM_018282 - 3.30 component 1 PTAR1 Hs.220677 - 3.75 protein prenyltransferase alpha subunit repeat containing 1 PTBP1 NM_175847 - 6.52 Polypyrimidine tract binding protein 1 PTBP2 NM_021190 - 5.61 Polypyrimidine tract binding protein 2 PTCD2 NM_024754 - 7.92 Pentatricopeptide repeat domain 2 PTEN NM_000314 - 10.62 Phosphatase and tensin homolog (mutated in multiple advanced 1) PTGES NM_198797 - 6.39 Prostaglandin E synthase PTGFRN NM_020440 1.40 3.00 Prostaglandin F2 receptor negative regulator PTK2 NM_153831 -1.82 3.50 PTK2 protein tyrosine kinase 2 PTPDC1 NM_177995 - 5.33 Protein tyrosine phosphatase domain containing 1 PTPLB NM_198402 - 10.17 Protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b PTPN11 NM_032904 - 3.32 protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) PTPN12 NM_002835 - 18.80 Protein tyrosine phosphatase, non-receptor type 12

25 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 Unchanged in MCF7-T, upregulated in MCF7-F PTPN2 NM_080423 2.51 5.82 Protein tyrosine phosphatase, non-receptor type 2 PTPN21 NM_007039 - 10.43 Protein tyrosine phosphatase, non-receptor type 21 PTPN9 NM_002833 - 4.16 Protein tyrosine phosphatase, non-receptor type 9 PTPRA NM_080841 - 6.38 Protein tyrosine phosphatase, receptor type, A PTPRF NM_130440 - 5.54 Protein tyrosine phosphatase, receptor type, F PTPRK NM_002844 -1.47 3.59 Protein tyrosine phosphatase, receptor type, K PTPRS NM_130855 - 15.61 Protein tyrosine phosphatase, receptor type, S PVR NM_006505 - 4.73 Poliovirus receptor PVT1 Hs.459222 - 4.75 Pvt1 oncogene homolog, MYC activator (mouse) PXMP3 NM_000318 - 16.13 Peroxisomal membrane protein 3, 35kDa (Zellweger syndrome) QPCT NM_012413 - 3.81 Glutaminyl-peptide cyclotransferase (glutaminyl cyclase) RAB12 Hs.270074 1.29 3.33 RAB12, member RAS oncogene family RAB18 NM_021252 - 5.90 RAB18, member RAS oncogene family RAB23 NM_183227 - 3.10 RAB23, member RAS oncogene family RAB3-GAP150 NM_012414 - 6.08 Rab3 GTPase-activating protein, non-catalytic subunit (150kD) RAB7B NM_177403 - 9.40 RAB7B, member RAS oncogene family RAB8B NM_016530 - 3.31 RAB8B, member RAS oncogene family RAD21 NM_006265 -1.34 3.48 RAD21 homolog (S. pombe) RAD52 NM_134424 - 3.70 RAD52 homolog (S. cerevisiae) RAF1 Hs.159130 - 6.22 V-raf-1 murine leukemia viral oncogene homolog 1 RANBP2 NM_006267 - 11.24 RAN binding protein 2 RANBP2L1 NM_032260 - 4.09 RAN binding protein 2-like 1 RAP1GDS1 NM_021159 - 3.70 RAP1, GTP-GDP dissociation stimulator 1 RAPGEF2 Hs.373588 - 4.36 Rap guanine nucleotide exchange factor (GEF) 2 RAPGEFL1 NM_016339 - 5.39 Rap guanine nucleotide exchange factor (GEF)-like 1 RASA1 NM_022650 - 5.81 RAS p21 protein activator (GTPase activating protein) 1 RASA2 NM_006506 1.23 3.95 RAS p21 protein activator 2 RASEF NM_152573 - 9.53 RAS and EF-hand domain containing RASGEF1A NM_145313 - 9.72 RasGEF domain family, member 1A RB1 NM_000321 - 8.75 Retinoblastoma 1 (including osteosarcoma) RB1CC1 Hs.196102 - 6.53 RB1-inducible coiled-coil 1 RBBP6 NM_032626 1.44 3.20 Retinoblastoma binding protein 6 RBL2 NM_005611 - 17.95 Retinoblastoma-like 2 (p130) RBM11 NM_144770 - 9.11 RNA binding motif protein 11 RBM14 NM_006328 - 5.74 RNA binding motif protein 14 RBM22 NM_018047 -1.20 3.34 RNA binding motif protein 22 RBM25 Hs.197184 1.67 3.76 RNA binding motif protein 25 RBM30 NM_031492 1.65 4.07 RNA binding motif protein 30 RBM5 NM_005778 - 4.94 RNA binding motif protein 5 RBM6 NM_005777 2.60 3.95 RNA binding motif protein 6 RBMX NM_002139 1.64 4.07 RNA binding motif protein, X-linked RBP1 NM_002899 - 4.00 binding protein 1, cellular RCBTB1 NM_018191 - 3.15 Regulator of chromosome condensation and BTB domain containing protein 1 RCN1 NM_002901 - 21.92 Reticulocalbin 1, EF-hand calcium binding domain RCN2 NM_002902 1.23 3.58 Reticulocalbin 2, EF-hand calcium binding domain RCOR3 NM_018254 1.31 3.33 REST corepressor 3 REC14 NM_025234 - 9.92 WD repeat domain 61 REC8L1 NM_005132 - 7.68 REC8-like 1 (yeast) RENT1 NM_002911 - 3.25 Regulator of nonsense transcripts 1 REPIN1 NM_014374 - 8.76 Replication initiator 1 REPS1 NM_031922 1.67 7.26 RALBP1 associated Eps domain containing 1 RERE NM_012102 - 4.47 Arginine-glutamic acid dipeptide (RE) repeats REV1L NM_016316 - 3.27 REV1-like (yeast) RFP2 NM_052811 - 7.51 Ret finger protein 2 RGL1 NM_015149 2.23 3.48 Ral guanine nucleotide dissociation stimulator-like 1 RGMB NM_173670 - 9.81 RGM domain family, member B RHBDL7 NM_020684 - 3.31 Rhomboid, veinlet-like 7 (Drosophila) RHOB Hs.406064 - 7.60 ras homolog gene family, member B RHOBTB3 NM_014899 - 3.56 Rho-related BTB domain containing 3

26 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 Unchanged in MCF7-T, upregulated in MCF7-F RHOT1 NM_018307 - 5.20 Ras homolog gene family, member T1 Rif1 Hs.19150 - 3.62 telomere-associated protein RIF1 homolog RIOK3 NM_145906 1.46 4.19 RIO kinase 3 (yeast) RIP NM_032308 1.69 6.21 RPA interacting protein RIPK1 NM_003804 -1.48 3.66 Receptor (TNFRSF)-interacting serine-threonine kinase 1 RIPK4 NM_020639 - 3.31 Receptor-interacting serine-threonine kinase 4 RIPX NM_014961 - 5.50 Rap2 interacting protein x RIS1 NM_015444 - 8.00 Ras-induced senescence 1 RNASE4 NM_194431 2.26 3.24 Ribonuclease, RNase A family, 4 RNASEL NM_021133 -1.46 3.68 Ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent) RNF111 Hs.404423 - 9.56 Ring finger protein 111 RNF128 NM_194463 - 80.76 Ring finger protein 128 RNF130 NM_018434 1.30 3.06 Ring finger protein 130 RNF19 Hs.292882 - 5.13 Ring finger protein 19 RNF3 NM_153250 - 3.42 ring finger protein 3 RNGTT NM_003800 - 3.69 RNA guanylyltransferase and 5'-phosphatase RNP NM_017619 - 6.05 RNA-binding region (RNP1, RRM) containing 3 RNP24 NM_006815 -1.33 5.18 Coated vesicle membrane protein RNPC2 NM_184244 -1.35 4.98 RNA-binding region (RNP1, RRM) containing 2 ROR1 NM_005012 - 14.84 Receptor tyrosine kinase-like orphan receptor 1 RPL10 NM_032241 2.56 4.83 Ribosomal protein L10 RPL23 NM_000978 - 3.15 Ribosomal protein L23 RPL29 NM_000992 - 8.56 Ribosomal protein L29 RPL37A NM_000998 1.27 3.69 Ribosomal protein L37a RPN2 NM_002951 - 4.18 Ribophorin II RPS14 NM_005617 - 5.35 Ribosomal protein S14 RPS15A NM_001019 1.52 4.04 Ribosomal protein S15a RPS24 NM_033022 1.48 7.32 Ribosomal protein S24 RPS6 NM_001010 - 4.88 Ribosomal protein S6 RPS6KA6 NM_014496 - 20.71 Ribosomal protein S6 kinase, 90kDa, polypeptide 6 RRBP1 NM_004587 - 6.73 binding protein 1 homolog 180kDa (dog) RSAD2 NM_080657 - 23.35 Radical S-adenosyl methionine domain containing 2 RSAFD1 NM_018264 1.29 3.01 Radical S-adenosyl methionine and flavodoxin domains 1 RSN NM_198240 - 21.94 Restin (Reed-Steinberg cell-expressed intermediate filament-associated protein) RTN4 Hs.429581 1.67 4.81 Reticulon 4 RUFY2 NM_017987 - 4.80 RUN and FYVE domain containing 2 RUNDC1 NM_173079 - 3.40 RUN domain containing 1 RUVBL1 NM_003707 1.31 3.06 RuvB-like 1 (E. coli) RXRB NM_021976 - 11.29 , beta RYK NM_002958 - 3.35 RYK receptor-like tyrosine kinase RYR3 NM_001036 - 6.22 3 S100A10 NM_002966 - 4.68 S100 calcium binding protein A10 (annexin II ligand, calpactin I) S100A2 NM_005978 1.30 14.72 S100 calcium binding protein A2 S100A8 NM_002964 - 51.48 S100 calcium binding protein A8 (calgranulin A) S100A9 NM_002965 - 30.28 S100 calcium binding protein A9 (calgranulin B) SAFB NM_002967 - 4.71 Scaffold attachment factor B SAMD9 NM_017654 - 139.84 Sterile alpha motif domain containing 9 SAMHD1 NM_015474 - 5.48 SAM domain and HD domain 1 SART3 NM_014706 -1.54 3.46 Squamous cell carcinoma antigen recognised by T cells 3 SATB1 NM_002971 - 6.25 Special AT-rich sequence binding protein 1 SBF2 NM_030962 - 4.59 SET binding factor 2 SC5DL NM_006918 - 8.89 Sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, fungal)-like SCAMP1 NM_052822 - 4.33 Secretory carrier membrane protein 1 SCARB2 Hs.349656 -1.27 8.21 Scavenger receptor class B, member 2 SCD4 NM_024906 - 3.51 Stearoyl-CoA desaturase 5 SCNN1A NM_001038 -2.80 6.86 Sodium channel, nonvoltage-gated 1 alpha SCNN1G NM_001039 - 23.19 Sodium channel, nonvoltage-gated 1, gamma SCOTIN NM_016479 -1.50 3.23 Scotin SCPEP1 NM_021626 2.53 7.79 Serine carboxypeptidase 1

27 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 Unchanged in MCF7-T, upregulated in MCF7-F SCYE1 NM_004757 - 5.48 Small inducible cytokine subfamily E, member 1 SCYL2 NM_017988 - 12.58 SCY1-like 2 (S. cerevisiae) SDC1 NM_002997 1.57 4.32 Syndecan 1 SDC2 NM_002998 2.73 6.90 Syndecan 2 (heparan sulfate proteoglycan 1, fibroglycan) SDCBP NM_005625 1.31 3.02 Syndecan binding protein (syntenin) SDCCAG8 NM_006642 - 8.82 Serologically defined colon cancer antigen 8 SDK1 NM_152744 1.85 3.77 Sidekick homolog 1 (chicken) SEC10L1 NM_006544 - 4.47 SEC10-like 1 (S. cerevisiae) SEC23IP NM_007190 -1.49 4.29 SEC23 interacting protein SEC31L1 NM_016211 1.22 4.49 SEC31-like 1 (S. cerevisiae) SEC61A1 NM_015968 1.39 16.99 Sec61 alpha 1 subunit (S. cerevisiae) SEC61A2 NM_018144 1.57 3.05 Sec61 alpha 2 subunit (S. cerevisiae) SEC6L1 NM_007277 - 8.85 SEC6-like 1 (S. cerevisiae) SEC8L1 NM_021807 - 27.50 SEC8-like 1 (S. cerevisiae) SEL1L NM_005065 1.71 3.08 Sel-1 suppressor of lin-12-like (C. elegans) SELO NM_031454 - 3.96 Selenoprotein O SEMA3C Hs.269109 - 3.07 Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, 3C SEMA3F NM_004186 -1.22 3.37 Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, 3F SEMA4B NM_198925 -1.34 4.26 Sema domain, Ig, TM and short cytoplasmic domain, secreted, 4B Sema domain, seven thrombospondin repeats, TM and shoct basic domain, secreted SEMA5A NM_003966 - 24.24 5A SEN54L Hs.378501 1.30 3.26 TRNA splicing 54 homolog (SEN54, S. cerevisiae) SENP6 NM_015571 1.43 8.28 SUMO1/sentrin specific protease 6 SENP7 NM_020654 - 7.26 SUMO1/sentrin specific protease 7 SEPP1 NM_005410 - 380.95 Selenoprotein P, plasma, 1 SEPT10 NM_178584 1.82 3.42 Septin 10 SEPT2 NM_004404 1.33 4.86 Septin 2 SEPT8 Hs.307944 - 15.65 septin 8 SERPINB5 NM_002639 - 33.63 Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5 SERPINE2 NM_006216 - 10.43 Serine (or cysteine) proteinase inhibitor, clade E SERPINF1 NM_002615 - 5.70 Serine (or cysteine) proteinase inhibitor, clade F SF3B1 NM_012433 - 5.68 Splicing factor 3b, subunit 1, 155kDa SFPQ NM_005066 1.40 5.68 Splicing factor proline/glutamine-rich SFRS1 NM_006924 1.52 5.59 Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) SFRS11 NM_004768 - 3.39 Splicing factor, arginine/serine-rich 11 SFRS15 NM_020706 1.24 3.11 Splicing factor, arginine/serine-rich 15 SFRS2IP NM_004719 1.46 3.36 Splicing factor, arginine/serine-rich 2, interacting protein SFRS5 NM_006925 - 8.60 Splicing factor, arginine/serine-rich 5 SFRS6 NM_006275 - 5.79 Splicing factor, arginine/serine-rich 6 SFRS7 NM_006276 - 7.31 Splicing factor, arginine/serine-rich 7, 35kDa SFXN1 NM_022754 - 10.34 Sideroflexin 1 SFXN3 NM_030971 - 3.69 Sideroflexin 3 SGPL1 NM_003901 - 5.17 Sphingosine-1-phosphate lyase 1 SH3BP2 NM_003023 - 4.49 SH3-domain binding protein 2 SH3GLB2 NM_020145 -1.36 5.06 SH3-domain GRB2-like endophilin B2 SIAH1 NM_003031 - 5.79 Seven in absentia homolog 1 (Drosophila) SIMP NM_178862 - 4.45 Source of immunodominant MHC-associated peptides SIPA1L1 Hs.208846 2.42 3.18 Signal-induced proliferation-associated 1 like 1 SKP2 NM_032637 - 8.03 S-phase kinase-associated protein 2 (p45) SLC12A9 NM_020246 - 8.75 Solute carrier family 12 (potassium/chloride transporters), member 9 SLC16A1 NM_003051 -1.60 14.99 AKR7 family pseudogene SLC16A7 NM_004731 - 6.02 Solute carrier family 16 (monocarboxylic acid transporters), member 7 SLC1A3 NM_004172 - 37.58 Solute carrier family 1 (glial high affinity glutamate transporter), member 3 SLC20A1 NM_005415 1.69 3.73 Solute carrier family 20 (phosphate transporter), member 1 SLC23A2 NM_005116 - 3.61 Solute carrier family 23 (nucleobase transporters), member 2 SLC24A3 NM_020689 - 12.77 Solute carrier family 24 (sodium/potassium/calcium exchanger), member 3 SLC24A6 NM_024959 - 8.66 Solute carrier family 24 (sodium/potassium/calcium exchanger), member 6 SLC25A13 NM_014251 -1.74 3.88 Solute carrier family 25, member 13 () SLC25A27 NM_004277 - 9.54 Solute carrier family 25, member 27

28 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 Unchanged in MCF7-T, upregulated in MCF7-F SLC25A28 NM_031212 1.51 3.39 Solute carrier family 25, member 28 SLC25A29 Hs.497598 - 10.65 Solute carrier family 25, member 29 SLC26A7 NM_134266 - 11.66 Solute carrier family 26, member 7 SLC29A1 NM_004955 1.22 4.96 Solute carrier family 29 (nucleoside transporters), member 1 SLC2A12 NM_145176 2.30 4.56 Solute carrier family 2 (facilitated glucose transporter), member 12 SLC30A1 NM_021194 1.27 3.13 Solute carrier family 30 (zinc transporter), member 1 SLC30A5 NM_024055 - 3.03 Solute carrier family 30 (zinc transporter), member 5 SLC30A7 NM_133496 -1.24 3.07 Solute carrier family 30 (zinc transporter), member 7 SLC31A2 NM_001860 - 8.46 Solute carrier family 31 (copper transporters), member 2 SLC33A1 NM_004733 - 4.09 Solute carrier family 33 (acetyl-CoA transporter), member 1 SLC35D1 NM_015139 - 4.29 Solute carrier family 35, member D1 SLC35D2 Hs.386278 - 3.84 solute carrier family 35, member D2 SLC37A4 Hs.132760 - 4.37 Solute carrier family 37 (glycerol-6-phosphate transporter), member 4 SLC39A10 Hs.32793 - 8.81 solute carrier family 39 (zinc transporter), member 10 SLC39A8 NM_022154 1.73 3.01 Solute carrier family 39 (zinc transporter), member 8 SLC3A2 NM_002394 1.71 3.47 Solute carrier family 3, member 2 SLC4A4 NM_003759 - 17.47 Solute carrier family 4, sodium bicarbonate cotransporter, member 4 SLC4A7 NM_003615 - 9.82 Solute carrier family 4, sodium bicarbonate cotransporter, member 7 SLC6A16 NM_014037 - 4.67 Solute carrier family 6, member 16 SLC6A6 NM_003043 - 9.40 Solute carrier family 6 (neurotransmitter transporter, taurine), member 6 SLC7A1 NM_003045 1.97 3.11 Solute carrier family 7 (cationic amino acid transporter, y+ system), member 1 SLC7A11 NM_014331 2.77 12.84 Solute carrier family 7, (cationic amino acid transporter, y+ system) member 11 SLC7A6 Hs.441169 - 3.03 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 SLC8A1 NM_021097 - 3.06 Solute carrier family 8 (sodium/calcium exchanger), member 1 SLC9A2 NM_003048 - 11.28 Solute carrier family 9 (sodium/hydrogen exchanger), isoform 2 SLCO3A1 NM_013272 - 4.59 Solute carrier organic anion transporter family, member 3A1 SLCO4A1 NM_016354 1.76 3.45 Solute carrier organic anion transporter family, member 4A1 SLIT3 NM_003062 - 5.52 Slit homolog 3 (Drosophila) SLPI NM_003064 -1.32 19.97 Secretory leukocyte protease inhibitor (antileukoproteinase) SMA3 NM_006780 1.45 4.12 SMA3 SMA5 Hs.166361 1.66 4.73 SMA5 SMAD1 NM_005900 - 3.23 SMAD, mothers against DPP homolog 1 (Drosophila) SMAD3 NM_005902 -1.70 5.75 SMAD, mothers against DPP homolog 3 (Drosophila) SMAD4 NM_005359 - 3.91 SMAD, mothers against DPP homolog 4 (Drosophila) SMAP NM_014267 2.13 8.60 Small acidic protein SWI/SNF related, matrix associated, actin dependent regulator of , SMARCA2 NM_139045 - 4.42 subfamily a, member 2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, SMARCA4 NM_003072 - 3.22 subfamily a, member 4 SMC4L1 NM_005496 1.99 3.85 SMC4 structural maintenance of chromosomes 4-like 1 (yeast) SMC6L1 NM_024624 - 28.48 SMC6 structural maintenance of chromosomes 6-like 1 (yeast) SMG1 NM_015092 - 5.32 PI-3-kinase-related kinase SMG-1 SMU1 Hs.174021 1.24 5.27 Smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) SMYD2 NM_020197 - 4.93 SET and MYND domain containing 2 SNAI2 NM_003068 - 14.84 Snail homolog 2 (Drosophila) SNAP23 NM_130798 - 3.17 Synaptosomal-associated protein, 23kDa SNAPC3 NM_003084 - 3.08 Small nuclear RNA activating complex, polypeptide 3, 50kDa SNRP70 NM_003089 - 8.55 Small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) SNRPA1 NM_003090 1.71 5.98 Small nuclear ribonucleoprotein polypeptide A' SNX1 NM_152826 1.90 3.95 Sorting nexin 1 SNX13 NM_015132 - 3.80 Sorting nexin 13 SNX19 Hs.409862 - 3.33 sorting nexin 19 SNX27 Hs.192326 - 5.29 Sorting nexin family member 27 SNX5 NM_152227 - 8.07 Sorting nexin 5 SOAT1 NM_003101 - 3.00 Sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1 SORCS2 NM_020777 - 3.10 Sortilin-related VPS10 domain containing receptor 2 SORT1 NM_002959 - 10.36 Sortilin 1 SOS1 NM_005633 - 3.07 homolog 1 (Drosophila) SOS2 NM_006939 1.84 5.88 Son of sevenless homolog 2 (Drosophila)

29 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 Unchanged in MCF7-T, upregulated in MCF7-F SP1 NM_138473 - 3.85 SP110 NM_080424 -1.40 4.69 SP110 nuclear body protein SP192 NM_021639 1.45 9.10 GC-rich promoter binding protein 1-like 1 SP6 Hs.253603 1.35 3.66 Sp6 transcription factor SPATA13 NM_153023 - 10.48 Spermatogenesis associated 13 SPATA5L1 NM_024063 - 5.33 Spermatogenesis associated 5-like 1 SPFH1 NM_006459 - 5.54 SPFH domain family, member 1 SPG4 NM_199436 - 3.59 Spastin SPG7 NM_199367 - 5.79 Spastic paraplegia 7, paraplegin (pure and complicated autosomal recessive) SPINK5 NM_006846 1.20 3.42 Serine protease inhibitor, Kazal type 5 SPIRE1 Hs.16758 - 3.49 spire homolog 1 (Drosophila) SPOCD1 NM_144569 - 13.04 SPOC domain containing 1 SPOCK NM_004598 - 18.08 Sparc/, cwcv and kazal-like domains proteoglycan () SPTAN1 NM_003127 1.26 3.16 Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) SPTBN1 NM_178313 - 4.05 Spectrin, beta, non-erythrocytic 1 SPTLC1 NM_178324 - 5.18 Serine palmitoyltransferase, long chain base subunit 1 SQLE NM_003129 2.62 3.38 Squalene epoxidase SQSTM1 NM_003900 - 4.33 Sequestosome 1 SR140 Hs.370907 - 4.90 U2-associated SR140 protein SRGAP1 Hs.408259 - 5.08 SLIT-ROBO Rho GTPase activating protein 1 SRP54 Hs.167535 1.61 3.59 Signal recognition particle 54kDa SRPR NM_003139 - 11.65 Signal recognition particle receptor ('docking protein') SRPX NM_006307 1.29 3.56 Sushi-repeat-containing protein, X-linked SRRM1 NM_005839 - 3.34 Serine/arginine repetitive matrix 1 SSR1 NM_003144 - 3.56 Signal sequence receptor, alpha (translocon-associated protein alpha) STARD7 NM_139267 1.60 3.07 START domain containing 7 STAT1 NM_139266 -2.07 10.88 Signal transducer and activator of transcription 1, 91kDa STAT2 NM_005419 - 4.51 Signal transducer and activator of transcription 2, 113kDa STC1 NM_003155 - 5.10 Stanniocalcin 1 STIM2 NM_020860 - 3.66 Stromal interaction molecule 2 STK11IP NM_052902 - 3.55 Serine/threonine kinase 11 interacting protein STK38 NM_007271 1.31 3.81 Serine/threonine kinase 38 STK4 NM_006282 - 5.36 Serine/threonine kinase 4 STN2 NM_033104 2.04 3.15 Stonin 2 SUCLG1 NM_003849 - 11.49 Succinate-CoA ligase, GDP-forming, alpha subunit SUI1 NM_005801 - 18.41 Putative translation initiation factor SULF2 NM_198596 1.31 3.59 Sulfatase 2 SUPT16H NM_007192 - 39.66 Suppressor of Ty 16 homolog (S. cerevisiae) SURF4 NM_033161 - 3.79 Surfeit 4 SUV39H2 NM_024670 1.27 3.58 Suppressor of variegation 3-9 homolog 2 (Drosophila) SUV420H1 NM_017635 -1.27 3.46 Suppressor of variegation 4-20 homolog 1 (Drosophila) SUZ12 NM_015355 2.18 6.34 Suppressor of zeste 12 homolog (Drosophila) SYCP2 NM_014258 1.25 3.74 Synaptonemal complex protein 2 SYK NM_003177 - 14.92 tyrosine kinase NM_030786 - 4.07 Syncoilin, intermediate filament 1 SYT1 NM_005639 - 7.73 Synaptotagmin I TAF11 NM_005643 - 5.21 TAF11 RNA polymerase II, TBP-associated factor, 28kDa TAF15 NM_139215 - 8.10 TAF15 RNA polymerase II, TBP-associated factor, 68kDa TAF1C NM_139353 1.81 3.58 TBP-associated factor, RNA polymerase I, C, 110kDa TAF5L Hs.270621 - 6.44 TAF5-like RNA polymerase II, p300/CBP-associated factor-associated factor TAF9L NM_015975 - 7.89 TAF9-like RNA polymerase II, TBP-associated factor TAP1 NM_000593 1.28 8.42 Transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) TAP2 NM_018833 1.64 26.40 Transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) TAPBP NM_172209 1.20 4.18 TAP binding protein (tapasin) TARBP1 NM_005646 1.37 5.19 TAR (HIV) RNA binding protein 1 TARDBP NM_031214 - 4.35 TAR DNA binding protein TAS2R10 NM_023921 - 7.39 Taste receptor, type 2, member 10 TAS2R5 NM_018980 - 9.68 Taste receptor, type 2, member 5 TAZ NM_181314 - 3.75 (cardiomyopathy, endocardial fibroelastosis 2; Barth syndrome)

30 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 Unchanged in MCF7-T, upregulated in MCF7-F TBC1D3 NM_032258 - 5.77 TBC1 domain family, member 3 TBC1D8 NM_007063 - 3.61 TBC1 domain family, member 8 (with GRAM domain) TBRG1 NM_032811 1.41 5.43 Transforming growth factor beta regulator 1 TBX3 NM_016569 2.30 5.26 T-box 3 (ulnar mammary syndrome) TCERG1 NM_006706 - 14.06 Transcription elongation regulator 1 TCF7L2 NM_030756 2.24 3.32 Transcription factor 7-like 2 (T-cell specific, HMG-box) TCIRG1 NM_006053 - 5.06 T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein 3 TCN1 NM_001062 - 7.02 Transcobalamin I (vitamin B12 binding protein, R binder family) TCTE3 NM_174910 1.27 3.17 T-complex-associated-testis-expressed 3 TDE1 NM_198941 -1.21 4.02 Tumor differentially expressed 1 TDRD7 NM_014290 - 4.24 Tudor domain containing 7 TFCP2L2 NM_198182 - 3.17 Grainyhead-like 1 (Drosophila) TFG NM_006070 - 5.07 TRK-fused gene TFPI NM_006287 -2.38 10.98 Tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) TFPI2 NM_006528 - 11.27 Tissue factor pathway inhibitor 2 TFRC NM_003234 - 65.31 (p90, CD71) TGDS NM_014305 - 3.50 TDP-glucose 4,6-dehydratase TGFB1I4 NM_183422 1.61 4.05 TSC22 domain family, member 1 TGFBI NM_000358 - 11.59 Transforming growth factor, beta-induced, 68kDa TGFBR2 NM_003242 -2.00 4.31 Transforming growth factor, beta receptor II (70/80kDa) TGOLN2 NM_006464 1.98 6.35 Trans-golgi network protein 2 THADA NM_198554 - 3.60 Thyroid adenoma associated THBS1 NM_003246 1.85 11.62 Thrombospondin 1 THEA NM_147161 - 11.21 Thioesterase, adipose associated THOC2 Hs.81376 - 3.08 THO complex 2 THRB NM_000461 1.30 6.53 , beta TIA1 NM_022173 - 10.34 TIA1 cytotoxic granule-associated RNA binding protein TIP120A NM_018448 - 8.26 Cullin-associated and neddylation-dissociated 1 TJP2 NM_004817 2.23 9.36 Tight junction protein 2 (zona occludens 2) TLE4 NM_007005 - 8.13 Transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) TLR2 NM_003264 - 4.11 Toll-like receptor 2 TLR3 NM_003265 - 11.69 Toll-like receptor 3 TM4SF12 NM_012338 - 12.45 Tetraspanin 12 TM4SF9 NM_005723 2.67 4.47 Tetraspanin 5 TM9SF4 NM_014742 - 4.15 Transmembrane 9 superfamily protein member 4 TMCC1 NM_015008 - 9.33 Transmembrane and coiled-coil domain family 1 TMED7 NM_181836 - 3.98 Transmembrane emp24 protein transport domain containing 7 TMEM1 NM_003274 1.23 4.66 Transmembrane protein 1 TMEM30A NM_018247 - 10.88 Transmembrane protein 30A TMEM37 NM_183240 - 17.40 Transmembrane protein 37 TMEM38A NM_024074 -1.68 3.21 Transmembrane protein 38A TMF1 NM_007114 - 3.23 TATA element modulatory factor 1 TMOD2 NM_014548 1.97 3.13 2 (neuronal) TMPRSS2 NM_005656 -2.04 4.75 Transmembrane protease, serine 2 TMPRSS4 NM_183247 - 5.23 Transmembrane protease, serine 4 TNC NM_002160 - 6.51 Tenascin C (hexabrachion) TNFAIP2 NM_006291 1.27 3.89 Tumor necrosis factor, alpha-induced protein 2 TNFAIP8 NM_014350 - 3.09 Tumor necrosis factor, alpha-induced protein 8 TNFRSF10B NM_147187 1.31 5.04 Tumor necrosis factor receptor superfamily, member 10b TNFRSF1A NM_001065 - 4.67 Tumor necrosis factor receptor superfamily, member 1A TNFRSF21 NM_016629 -2.97 8.53 tumor necrosis factor receptor superfamily, member 21 TNFSF10 NM_003810 - 11.22 Tumor necrosis factor (ligand) superfamily, member 10 TNIK Hs.252550 - 4.06 TRAF2 and NCK interacting kinase TNKS2 NM_025235 -1.23 5.56 Tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2 TNPO2 NM_013433 - 9.05 Transportin 2 ( 3, karyopherin beta 2b) TOM1L1 NM_005486 1.39 3.95 Target of myb1-like 1 (chicken) TOP1 NM_003286 -1.35 3.54 Topoisomerase (DNA) I TOP2A NM_001067 2.74 3.09 Topoisomerase (DNA) II alpha 170kDa TP73L NM_003722 - 3.86 Tumor protein -like

31 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 Unchanged in MCF7-T, upregulated in MCF7-F TPARL NM_018475 - 4.93 TPA regulated locus TPCN2 Hs.387396 1.45 3.01 Two pore segment channel 2 TPM1 NM_000366 - 5.32 Tropomyosin 1 (alpha) TPM4 NM_003290 1.53 3.62 Tropomyosin 4 TPP1 NM_000391 - 3.18 Tripeptidyl peptidase I TPPP NM_007030 - 8.01 Brain-specific protein p25 alpha TPR NM_003292 - 7.45 Translocated promoter region (to activated MET oncogene) TPST2 NM_003595 -1.67 3.24 Tyrosylprotein sulfotransferase 2 TPTE NM_199261 - 3.76 Transmembrane phosphatase with tensin homology TRA1 NM_003299 1.40 11.87 Tumor rejection antigen (gp96) 1 TRA2A NM_013293 1.34 4.80 Transformer-2 alpha TRAM1 NM_014294 - 9.66 Translocation associated membrane protein 1 TRG Hs.489751 - 6.72 Testin-related protein TRG mRNA, complete cds TRIB2 NM_021643 - 21.62 Tribbles homolog 2 (Drosophila) TRIM16 NM_006470 1.48 3.25 Tripartite motif-containing 16 TRIM2 NM_015271 - 7.61 Tripartite motif-containing 2 TRIM21 NM_003141 - 4.20 Tripartite motif-containing 21 TRIM22 NM_006074 - 60.43 Tripartite motif-containing 22 TRIM23 NM_033228 - 5.94 Tripartite motif-containing 23 TRIM25 NM_005082 - 3.47 Tripartite motif-containing 25 TRIM26 NM_003449 - 4.34 Tripartite motif-containing 26 TRIM33 NM_033020 1.35 3.64 Tripartite motif-containing 33 TRIM50C NM_198853 1.24 5.58 Tripartite motif-containing 50C TRIM52 NM_032765 - 4.35 Tripartite motif-containing 52 TRIO NM_007118 - 3.27 Triple functional domain (PTPRF interacting) TRIP12 Hs.388373 1.36 3.63 thyroid hormone receptor interactor 12 TRIP13 NM_004237 1.42 3.73 Thyroid hormone receptor interactor 13 TRPC1 Hs.250687 - 7.67 Transient receptor potential cation channel, subfamily C, member 1 TRPM4 NM_017636 2.74 5.86 Transient receptor potential cation channel, subfamily M, member 4 TRPM7 NM_017672 1.28 6.77 Transient receptor potential cation channel, subfamily M, member 7 TRRAP NM_003496 - 5.79 Transformation/transcription domain-associated protein TSAP6 NM_182915 -2.27 3.09 STEAP family member 3 TSPAN2 NM_005725 - 45.57 Tetraspanin 2 TTC13 NM_024525 - 4.47 Tetratricopeptide repeat domain 13 TTC14 NM_133462 1.32 3.74 Tetratricopeptide repeat domain 14 TTC18 NM_145170 - 4.20 Tetratricopeptide repeat domain 18 TTC3 NM_003316 - 45.35 Tetratricopeptide repeat domain 3 TTLL4 NM_014640 - 3.87 tyrosine ligase-like family, member 4 TUBE1 NM_016262 - 4.32 Tubulin, epsilon 1 TUBGCP2 NM_006659 2.71 3.53 Tubulin, gamma complex associated protein 2 TUBGCP6 NM_020461 - 11.36 Tubulin, gamma complex associated protein 6 TUSC3 NM_178234 - 4.91 Tumor suppressor candidate 3 TUWD12 NM_172240 - 16.89 WD repeat domain 51B TXNDC NM_030755 1.51 6.24 Thioredoxin domain containing TXNDC7 NM_005742 - 3.01 Protein disulfide isomerase family A, member 6 TXNIP NM_006472 -1.28 5.68 Thioredoxin interacting protein TXNL1 NM_004786 - 7.16 Thioredoxin-like 1 TXNRD2 NM_145748 - 8.91 Thioredoxin reductase 2 TYRP1 NM_000550 - 3.00 Tyrosinase-related protein 1 U2AF1 NM_006758 1.49 4.66 U2(RNU2) small nuclear RNA auxiliary factor 1 U2AF1L2 NM_005089 1.24 3.56 U2(RNU2) small nuclear RNA auxiliary factor 1-like 2 UBE1L NM_003335 - 8.87 Ubiquitin-activating enzyme E1-like UBE2D3 NM_181893 - 7.13 Threonine synthase, UBE2G2 NM_182688 - 3.13 Ubiquitin-conjugating enzyme E2G 2 (UBC7 homolog, yeast) UBE2J1 NM_016021 - 3.55 Ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast) UBE2L6 NM_198183 - 4.77 Ubiquitin-conjugating enzyme E2L 6 UBE3B NM_183415 - 4.04 Ubiquitin protein ligase E3B UBE3C Hs.155287 - 3.33 ubiquitin protein ligase E3C UBE4B NM_006048 - 10.70 Ubiquitination factor E4B (UFD2 homolog, yeast)

32 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 Unchanged in MCF7-T, upregulated in MCF7-F UBXD2 NM_014607 1.29 7.93 UBX domain containing 2 UCC1 NM_017549 - 5.77 Ependymin related protein 1 (zebrafish) UCN NM_003353 - 7.30 Urocortin Ufm1 NM_016617 - 5.06 Ubiquitin-fold modifier 1 UGCG NM_003358 - 3.47 UDP-glucose ceramide UGCGL1 NM_020120 1.68 3.65 UDP-glucose ceramide glucosyltransferase-like 1 UGCGL2 NM_020121 - 4.25 UDP-glucose ceramide glucosyltransferase-like 2 UGP2 NM_006759 - 3.08 UDP-glucose pyrophosphorylase 2 UGT1A6 NM_019075 1.82 4.34 UDP 1 family, polypeptide A9 ULK3 NM_015518 1.40 3.07 Unc-51-like kinase 3 (C. elegans) UNC50 NM_014044 - 6.05 Unc-50 homolog (C. elegans) UNC84B NM_015374 - 3.63 Unc-84 homolog B (C. elegans) UNC93B1 NM_030930 -1.34 7.40 Unc-93 homolog B1 (C. elegans) UPF3A NM_080687 - 8.44 UPF3 regulator of nonsense transcripts homolog A (yeast) UPK1A NM_032896 1.36 5.94 Uroplakin 1A UPK3A NM_006953 - 17.22 Uroplakin 3A UPK3B NM_182684 -1.45 4.34 Uroplakin 3B UQCRC2 NM_003366 - 10.12 Ubiquinol-cytochrome c reductase core protein II URG4 NM_017920 2.05 3.03 Up-regulated gene 4 UROD NM_000374 - 5.26 Uroporphyrinogen decarboxylase USP10 NM_005153 1.36 7.65 Ubiquitin specific protease 10 USP18 NM_017414 - 3.80 Ubiquitin specific protease 18 USP25 NM_013396 - 3.89 Ubiquitin specific protease 25 USP31 NM_020718 -1.32 4.56 Ubiquitin specific protease 31 USP32 NM_032582 1.42 9.03 Ubiquitin specific protease 32 USP34 NM_014709 - 4.01 Ubiquitin specific protease 34 USP47 NM_017944 - 5.70 Ubiquitin specific protease 47 USP48 NM_032759 - 7.74 ubiquitin specific protease 48 UTRN NM_007124 - 4.07 (homologous to dystrophin) UTX NM_021140 - 3.96 Ubiquitously transcribed tetratricopeptide repeat, VAMP3 NM_004781 -1.21 3.44 Vesicle-associated membrane protein 3 (cellubrevin) VAPA NM_194434 1.72 6.93 VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa VAPB NM_004738 - 10.75 VAMP (vesicle-associated membrane protein)-associated protein B and C VDP Hs.292689 1.45 4.67 Vesicle docking protein p115 VEGF NM_003376 1.20 3.05 Vascular endothelial growth factor VIL2 NM_003379 -1.33 4.10 Villin 2 (ezrin) VKORC1L1 NM_173517 - 3.35 Vitamin K epoxide reductase complex, subunit 1-like 1 VLDLR NM_003383 2.41 5.66 Very low density lipoprotein receptor VMP1 NM_030938 1.30 7.43 Transmembrane protein 49 VPS13C NM_017684 - 5.63 Vacuolar protein sorting 13C (yeast) VPS35 NM_018206 -1.20 4.15 Vacuolar protein sorting 35 (yeast) WBSCR19 NM_175064 - 3.12 Williams Beuren syndrome chromosome region 19 WBSCR20C NM_149379 1.32 4.20 Williams Beuren syndrome chromosome region 20C WDFY1 NM_178350 - 5.56 WD repeat and FYVE domain containing 1 WDFY2 NM_052950 1.71 4.73 WD repeat and FYVE domain containing 2 WDR1 NM_017491 - 3.57 WD repeat domain 1 WDR11 NM_018117 1.48 3.49 Bromodomain and WD repeat domain containing 2 WDR26 NM_025160 - 3.69 WD repeat domain 26 WDR32 Hs.118394 - 6.81 WD repeat domain 32 WDR42A NM_015726 - 7.79 WD repeat domain 42A WDR5 NM_052821 - 3.42 WD repeat domain 5 WDR6 NM_052826 - 23.09 WD repeat domain 6 WDR9 NM_033656 - 3.70 Bromodomain and WD repeat domain containing 1 WEE1 NM_003390 1.21 4.15 WEE1 homolog (S. pombe) WFS1 NM_006005 - 5.90 Wolfram syndrome 1 (wolframin) WHSC1 NM_133336 1.91 6.23 Wolf-Hirschhorn syndrome candidate 1 WINS1 NM_181740 1.32 3.16 Lines homolog 1 (Drosophila) WIZ Hs.442138 - 4.88 Widely-interspaced zinc finger motifs WNT11 NM_004626 - 12.64 Wingless-type MMTV integration site family, member 11

33 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 Unchanged in MCF7-T, upregulated in MCF7-F WSB1 NM_134265 1.32 9.03 WD repeat and SOCS box-containing 1 XK NM_021083 1.93 3.65 Kell blood group precursor (McLeod phenotype) XPO1 NM_003400 1.20 5.06 Exportin 1 (CRM1 homolog, yeast) XPO5 NM_020750 2.33 5.83 Exportin 5 XPO7 NM_015024 - 3.02 Exportin 7 XRCC5 NM_021141 - 6.20 X-ray repair complementing defective repair in Chinese hamster cells 5 XRN1 NM_019001 - 3.71 5'-3' 1 YARS NM_003680 1.38 4.31 Tyrosyl-tRNA synthetase YME1L1 NM_139313 - 3.76 YME1-like 1 (S. cerevisiae) YPEL2 Hs.368672 - 4.55 yippee-like 2 (Drosophila) YT521 NM_133370 - 15.37 Splicing factor YT521-B YTHDC2 NM_022828 - 6.27 YTH domain containing 2 YTHDF3 NM_152758 - 4.27 YTH domain family, member 3 ZA20D2 NM_006007 - 3.49 Zinc finger, A20 domain containing 2 ZBED4 Hs.13604 - 3.31 zinc finger, BED domain containing 4 ZBTB11 NM_014415 - 13.95 Zinc finger and BTB domain containing 11 ZBTB20 NM_015642 - 5.37 Zinc finger and BTB domain containing 20 ZC3HDC1 NM_022750 - 6.86 Poly (ADP-ribose) polymerase family, member 12 ZC3HDC7 NM_014153 - 3.80 Zinc finger CCCH-type containing 7A ZCCHC6 Hs.12742 - 6.11 zinc finger, CCHC domain containing 6 ZCSL3 NM_181706 - 6.99 Zinc finger, CSL-type containing 3 ZDHHC11 NM_024786 - 6.60 Zinc finger, DHHC-type containing 11 ZDHHC13 NM_019028 - 4.23 Zinc finger, DHHC-type containing 13 ZDHHC17 NM_015336 - 25.89 Zinc finger, DHHC-type containing 17 ZDHHC21 NM_178566 - 6.63 Zinc finger, DHHC-type containing 21 ZDHHC5 NM_015457 - 3.43 Zinc finger, DHHC-type containing 5 ZF NM_021212 1.40 3.11 HCF-binding transcription factor Zhangfei ZFOC1 NM_152437 2.78 6.66 Zinc finger protein 664 ZFP36L2 NM_006887 - 5.67 Zinc finger protein 36, C3H type-like 2 ZFR NM_016107 - 3.84 Zinc finger RNA binding protein ZFYVE16 NM_014733 - 4.92 Zinc finger, FYVE domain containing 16 ZMYND11 NM_006624 - 18.45 Zinc finger, MYND domain containing 11 ZMYND17 NM_178451 - 7.64 Zinc finger, MYND domain containing 17 ZNF10 NM_015394 2.33 4.22 Zinc finger protein 10 ZNF117 Hs.250693 - 3.70 Zinc finger protein 117 (HPF9) ZNF12 NM_016265 - 3.06 Zinc finger protein 12 ZNF131 Hs.97845 2.21 7.17 Zinc finger protein 131 (clone pHZ-10) ZNF137 NM_003438 1.23 3.02 Zinc finger protein 137 (clone pHZ-30) ZNF160 NM_198893 1.38 4.98 Zinc finger protein 160 ZNF175 NM_007147 - 5.53 Zinc finger protein 175 ZNF195 NM_007152 - 4.53 Zinc finger protein 195 ZNF198 NM_197968 - 7.72 Zinc finger protein 198 ZNF207 NM_003457 - 9.66 Zinc finger protein 207 ZNF224 NM_013398 2.04 4.47 Zinc finger protein 224 ZNF226 NM_016444 2.01 3.86 Zinc finger protein 226 ZNF229 Hs.285574 - 3.82 Zinc finger protein 229 ZNF236 NM_007345 1.44 3.30 Zinc finger protein 236 ZNF238 NM_006352 -1.27 4.87 Zinc finger protein 238 ZNF24 NM_006965 - 4.24 Zinc finger protein 24 (KOX 17) ZNF251 Hs.133250 -2.63 3.71 Similar to zinc finger protein 517 ZNF265 NM_005455 - 3.20 Zinc finger protein 265 ZNF277 NM_021994 1.25 3.36 Zinc finger protein 277 ZNF317 NM_020933 - 3.21 Zinc finger protein 317 ZNF335 NM_022095 1.86 4.00 Zinc finger protein 335 ZNF404 Hs.76561 - 4.28 Zinc finger protein 404 ZNF41 NM_153380 - 3.74 Zinc finger protein 41 ZNF42 Hs.458361 - 4.13 zinc finger protein 42 (myeloid-specific retinoic acid-responsive) ZNF431 NM_133473 1.58 3.17 Zinc finger protein 431 ZNF451 NM_015555 1.84 3.69 Zinc finger protein 451

34 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 Unchanged in MCF7-T, upregulated in MCF7-F ZNF493 NM_145326 2.01 5.19 Zinc finger protein 493 ZNF512 NM_032434 - 3.21 Zinc finger protein 512 ZNF518 Hs.29878 1.45 4.45 zinc finger protein 518 ZNF548 NM_152909 - 3.89 Zinc finger protein 548 ZNF567 NM_152603 - 3.88 Zinc finger protein 567 ZNF585A NM_199126 - 3.70 Zinc finger protein 585A ZNF587 Hs.288995 - 3.52 Zinc finger protein 587 ZNF600 NM_198457 1.31 3.37 Zinc finger protein 600 ZNF638 NM_014497 - 3.79 Zinc finger protein 638 ZNF75 NM_007131 - 5.04 Zinc finger protein 75 (D8C6) ZNF83 NM_018300 1.27 3.84 Zinc finger protein 83 (HPF1) ZRANB3 Hs.306327 - 3.03 RAB3 GTPase-activating protein

Unchanged in MCF7-T, downregulated in MCF7-F A1BG NM_130786 -1.87 -3.34 Alpha-1-B glycoprotein ABCC5 NM_005688 - -3.66 ATP-binding cassette, sub-family C (CFTR/MRP), member 5 ACAA2 NM_006111 -1.87 -3.58 Acetyl-Coenzyme A acyltransferase 2 ACTL6A NM_178042 -1.26 -3.05 Actin-like 6A AD023 NM_020679 -1.56 -4.51 AD023 protein ADK NM_006721 -1.20 -7.49 Adenosine kinase ADMP NM_145035 -2.72 -3.30 Likely ortholog of androgen down regulated gene expressed in mouse prostate AHSA1 NM_012111 - -4.03 AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast) AIP NM_003977 - -3.64 Aryl hydrocarbon receptor interacting protein AK7 NM_152327 - -28.73 Adenylate kinase 7 AKT1 NM_005163 1.28 -3.19 V-akt murine thymoma viral oncogene homolog 1 ALDH6A1 NM_005589 1.67 -4.27 Aldehyde dehydrogenase 6 family, member A1 AMOTL1 NM_130847 - -3.61 Angiomotin like 1 ANAPC10 NM_014885 - -3.32 Anaphase promoting complex subunit 10 ANAPC11 NM_016476 - -5.69 APC11 anaphase promoting complex subunit 11 homolog (yeast) ANAPC13 NM_015391 -1.37 -4.76 Anaphase promoting complex subunit 13 ANK2 NM_001029 - -3.27 Ankyrin 2, neuronal ANXA6 NM_004033 -2.28 -18.63 Annexin A6 AOX1 NM_001159 -1.80 -3.53 Aldehyde oxidase 1 AP4S1 Hs.293411 1.23 -4.04 Adaptor-related protein complex 4, sigma 1 subunit APG3L NM_022488 - -3.02 APG3 autophagy 3-like (S. cerevisiae) ARF3 NM_001659 - -3.44 ADP-ribosylation factor 3 ARF6 NM_001663 - -4.15 ADP-ribosylation factor 6 ARID2 Hs.317304 - -3.70 AT rich interactive domain 2 (ARID, RFX-like) ARL10B NM_138795 - -3.66 ADP-ribosylation factor-like 10B ARL4A NM_005738 -1.73 -5.24 ADP-ribosylation factor-like 4 ARPC3 NM_005719 -1.24 -4.11 Actin related protein 2/3 complex, subunit 3, 21kDa ARX NM_139058 - -3.58 Aristaless related homeobox ATF7 NM_006856 - -7.31 Activating transcription factor 7 ATF7IP2 NM_024997 1.50 -3.27 Activating transcription factor 7 interacting protein 2 ATOX1 NM_004045 -1.65 -6.43 ATX1 antioxidant protein 1 homolog (yeast) ATP5G2 NM_005176 - -4.84 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c2 ATP5H NM_006356 - -4.97 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d ATP5I NM_007100 -1.20 -7.04 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit e ATP5J NM_001685 -1.25 -5.87 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6 ATP5L NM_006476 - -3.20 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g ATP5O NM_001697 - -4.01 ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit ATP5S NM_015684 1.65 -3.92 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B) ATP6V1C2 NM_144583 -1.63 -4.43 ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2 ATP6V1D NM_015994 1.25 -3.84 ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D ATP6V1F NM_004231 -1.50 -3.91 ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F ATP6V1G1 NM_004888 -1.23 -3.30 ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 1 ATP8B2 NM_020452 -1.63 -12.49 ATPase, Class I, type 8B, member 2 ATPAF1 NM_022745 -1.34 -3.67 ATP synthase mitochondrial F1 complex assembly factor 1 ATPIF1 NM_178191 - -3.01 ATPase inhibitory factor 1 ATXN3 NM_030660 1.43 -3.48 Ataxin 3

35 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 Unchanged in MCF7-T, downregulated in MCF7-F AYP1 NM_032193 - -5.58 AYP1 protein B7 NM_006992 -2.83 -3.04 B7 gene BAG3 NM_004281 -2.52 -3.55 BCL2-associated athanogene 3 BATF NM_006399 1.23 -4.96 Basic transcription factor, ATF-like BCAS3 NM_017679 - -3.43 Breast carcinoma amplified sequence 3 BCCIP NM_078469 -1.39 -4.59 BRCA2 and CDKN1A interacting protein BCL7C NM_004765 - -3.51 B-cell CLL/lymphoma 7C BET1L NM_016526 -1.20 -3.03 Blocked early in transport 1 homolog (S. cerevisiae) like BIK NM_001197 -1.59 -3.14 BCL2-interacting killer (apoptosis-inducing) BIRC5 NM_001168 2.08 -3.46 Effector cell protease receptor 1 BLOC1S1 NM_001487 - -3.60 Biogenesis of lysosome-related complex-1, subunit 1 BLOC1S2 NM_173809 - -3.14 Biogenesis of lysosome-related organelles complex-1, subunit 2 BLVRA NM_000712 - -4.07 Biliverdin reductase A BLVRB NM_000713 - -3.28 Biliverdin reductase B (flavin reductase (NADPH)) BM039 NM_018455 2.19 -3.48 Uncharacterized bone marrow protein BM039 BNIP1 NM_013980 - -3.01 BCL2/adenovirus E1B 19kDa interacting protein 1 BRUNOL5 NM_021938 1.37 -3.15 Bruno-like 5, RNA binding protein (Drosophila) C14orf123 NM_014169 - -7.85 Chromatin modifying protein 4A C20orf178 NM_176812 -2.82 -3.29 Chromatin modifying protein 4B CA8 NM_004056 - -7.08 Carbonic anhydrase VIII CABLES1 NM_138375 -1.53 -3.11 Cdk5 and Abl enzyme substrate 1 CACNA2D2 NM_006030 - -3.59 Calcium channel, voltage-dependent, alpha 2/delta subunit 2 CACYBP NM_014412 -1.35 -3.94 Calcyclin binding protein CADPS2 NM_017954 -2.03 -3.70 Ca2+-dependent activator protein for secretion 2 CALM1 NM_006888 2.18 -3.64 Calmodulin 1 (phosphorylase kinase, delta) CALM3 NM_005184 - -3.26 Calmodulin 3 (phosphorylase kinase, delta) CALML5 NM_017422 -2.08 -5.34 Calmodulin-like 5 CAMK2D NM_172128 - -3.05 Calcium/calmodulin-dependent protein kinase (CaM kinase) II delta CAMTA1 Hs.253254 - -5.57 calmodulin binding transcription activator 1 CARHSP1 NM_014316 - -4.80 Calcium regulated heat stable protein 1, 24kDa CBX1 NM_006807 1.20 -3.01 Chromobox homolog 1 (HP1 beta homolog Drosophila ) CBX5 NM_012117 1.35 -4.98 Chromobox homolog 5 (HP1 alpha homolog, Drosophila) CCNB1IP1 NM_182852 1.60 -3.75 Cyclin B1 interacting protein 1 CCRN4L NM_012118 -1.42 -3.37 CCR4 carbon catabolite repression 4-like (S. cerevisiae) CDC26 NM_139286 - -5.42 Cell division cycle 26 CDC42SE2 NM_020240 1.37 -3.59 CDC42 small effector 2 CDK4 NM_032913 - -3.00 Cyclin-dependent kinase 4 CDKN1C NM_000076 -1.35 -3.21 Cyclin-dependent kinase inhibitor 1C (p57, Kip2) CDKN3 NM_005192 2.65 -4.16 Cyclin-dependent kinase inhibitor 3 CDV1 NM_031473 1.20 -3.05 Carnitine deficiency-associated, expressed in ventricle 1 CETN3 NM_004365 - -3.51 Centrin, EF-hand protein, 3 (CDC31 homolog, yeast) CFL2 NM_138638 1.26 -5.78 Cofilin 2 (muscle) CGI-111 NM_016048 1.47 -3.47 Isochorismatase domain containing 1 CGI-115 NM_016052 -1.27 -3.15 CGI-115 protein CGI-116 NM_016053 - -3.49 CGI-116 protein CGI-128 NM_016062 -1.22 -3.66 CGI-128 protein CGI-30 NM_015958 - -3.13 CGI-30 protein CGI-90 NM_016033 - -3.45 CGI-90 protein CHC1 NM_001269 -1.46 -3.03 Regulator of chromosome condensation 1 CHDH NM_018397 -1.47 -3.09 Choline dehydrogenase CHGA NM_001275 -2.24 -5.94 Chromogranin A (parathyroid secretory protein 1) CHURC1 NM_145165 -1.23 -4.14 Churchill domain containing 1 CIB3 NM_054113 -2.34 -4.28 Calcium and integrin binding family member 3 CINP NM_032630 1.27 -3.12 Cyclin-dependent kinase 2-interacting protein CIP29 NM_033082 - -3.67 Cytokine induced protein 29 kDa CIZ1 NM_012127 - -3.22 CDKN1A interacting zinc finger protein 1 CKB NM_001823 -1.78 -3.00 Creatine kinase, brain CKS1B NM_001826 1.76 -3.58 CDC28 protein kinase regulatory subunit 1B CLIC5 NM_016929 1.22 -3.64 Chloride intracellular channel 5

36 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 Unchanged in MCF7-T, downregulated in MCF7-F CLMN NM_024734 1.85 -3.57 Calmin (calponin-like, transmembrane) CLNS1A NM_001293 - -3.54 Chloride channel, nucleotide-sensitive, 1A CML66 NM_032869 -1.39 -3.44 NudC domain containing 1 COBL NM_015198 -1.80 -3.89 Cordon-bleu homolog (mouse) COCH NM_004086 - -3.05 Coagulation factor C homolog, cochlin (Limulus polyphemus) COL9A3 NM_001853 1.44 -11.75 Collagen, type IX, alpha 3 COMMD10 NM_016144 -1.34 -3.43 COMM domain containing 10 COMMD2 NM_016094 - -4.45 COMM domain containing 2 COMMD6 Hs.356605 - -4.86 COMM domain containing 6 COMMD9 NM_014186 -1.39 -3.83 COMM domain containing 9 COQ4 NM_016035 1.54 -3.09 Coenzyme Q4 homolog (yeast) COX7A2L NM_004718 - -3.04 Cytochrome c oxidase subunit VIIa polypeptide 2 like COX7C NM_001867 - -4.56 Cytochrome c oxidase subunit VIIc COX8A NM_004074 - -3.22 Cytochrome c oxidase subunit 8A (ubiquitous) CPSF5 NM_007006 - -3.28 Nudix (nucleoside diphosphate linked moiety X)-type motif 21 CPT1A NM_001876 -1.88 -3.78 Carnitine palmitoyltransferase 1A (liver) CPT2 NM_000098 -1.67 -3.42 Carnitine palmitoyltransferase II CRABP1 NM_004378 -1.89 -7.02 Cellular retinoic acid binding protein 1 CREB3L4 NM_130898 -1.34 -3.58 CAMP responsive element binding protein 3-like 4 CRI1 NM_014335 - -6.01 CREBBP/EP300 inhibitor 1 CRIPT NM_014171 -1.28 -3.70 Postsynaptic protein CRIPT CRYL1 NM_015974 - -3.24 Crystallin, lambda 1 CSRP2BP NM_177926 -1.71 -7.84 CSRP2 binding protein CSTA NM_005213 -2.25 -14.30 Cystatin A (stefin A) CTTN NM_138565 -1.49 -5.09 Cortactin CYB5 NM_148923 -2.26 -4.37 Cytochrome b-5 CYP26B1 NM_019885 - -4.11 Cytochrome P450, family 26, subfamily B, polypeptide 1 DAP13 NM_018838 - -3.15 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12 DAZAP2 NM_014764 - -3.55 DAZ associated protein 2 DC13 NM_020188 - -4.21 DC13 protein DC36 NM_020667 -1.34 -3.43 COBW-like placental protein DCDC2 NM_016356 -1.52 -9.27 Doublecortin domain containing 2 DCTN6 NM_006571 - -3.08 6 DCXR NM_016286 - -3.33 Dicarbonyl/L-xylulose reductase DDAH1 NM_012137 - -3.34 Dimethylarginine dimethylaminohydrolase 1 DDX6 NM_004397 - -3.45 DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 DECR1 NM_001359 -1.35 -3.42 2,4-dienoyl CoA reductase 1, mitochondrial DESR1 Hs.517832 -1.36 -5.35 DESR1 protein DGCR6 NM_005675 -1.38 -3.88 DiGeorge syndrome critical region gene 6 DHX30 NM_138615 - -4.62 DEAH (Asp-Glu-Ala-His) box polypeptide 30 DKFZP564B167 NM_015415 1.55 -5.39 Brain protein 44 DKFZP564J0123 NM_199417 -1.27 -3.87 E3-3 DKFZP564O0463 NM_015420 -1.37 -3.07 WD repeats and SOF1 domain containing DKFZp761A132 NM_032296 -1.45 -3.09 FLYWCH-type zinc finger 1 Dlc2 Hs.356832 - -3.98 light chain 2 DLEU1 NM_005887 1.79 -4.88 Deleted in lymphocytic leukemia, 1 DNCL1 NM_003746 -1.31 -5.89 Dynein, cytoplasmic, light polypeptide 1 DNCL2A NM_177954 -1.87 -5.30 Dynein, cytoplasmic, light polypeptide 2A DNCL2B NM_130897 -2.10 -3.22 Dynein, cytoplasmic, light polypeptide 2B DSC96 Hs.61426 -1.29 -5.19 Mesenchymal stem cell protein DSC96 DSIPI NM_198057 1.21 -4.39 TSC22 domain family, member 3 DUSP23 NM_017823 -1.76 -6.17 Dual specificity phosphatase 23 DXS9879E NM_006014 - -4.84 DNA segment on chromosome X (unique) 9879 expressed sequence e(y)2 NM_020189 -1.33 -3.64 Enhancer of yellow 2 homolog (Drosophila) E2IG2 NM_016565 - -3.37 E2IG2 protein ECE2 NM_032331 -1.95 -3.49 Endothelin converting enzyme 2 EEF1G NM_017812 - -3.70 Eukaryotic translation elongation factor 1 gamma EFCBP1 NM_022351 1.34 -9.05 EF-hand calcium binding protein 1 EFHD1 NM_025202 - -3.10 EF-hand domain family, member D1

37 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 Unchanged in MCF7-T, downregulated in MCF7-F EGR3 NM_004430 -2.64 -3.99 Early growth response 3 EHD3 NM_014600 -2.22 -5.04 EH-domain containing 3 EIF1AX NM_001412 - -3.18 Eukaryotic translation initiation factor 1A, X-linked EIF2S1 NM_004094 1.35 -3.28 Eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa EIF3S6 NM_001568 - -3.63 Eukaryotic translation initiation factor 3, subunit 6 48kDa EIF4B NM_001417 1.29 -3.80 Eukaryotic translation initiation factor 4B EIF4E2 NM_004846 -1.43 -3.18 Eukaryotic translation initiation factor 4E member 2 EIF4EBP1 NM_004095 -1.35 -3.47 Eukaryotic translation initiation factor 4E binding protein 1 EIF5A NM_001970 -1.21 -3.24 Eukaryotic translation initiation factor 5A EIF5B NM_015904 -1.63 -3.74 Eukaryotic translation initiation factor 5B ELK1 NM_005229 -1.46 -3.59 ELK1, member of ETS oncogene family EML1 NM_004434 1.64 -6.27 Echinoderm microtubule associated protein like 1 EN2 NM_001427 - -4.30 homolog 2 ENPP1 NM_006208 - -5.46 Ectonucleotide pyrophosphatase/phosphodiesterase 1 ENSA NM_004436 -1.26 -4.38 Endosulfine alpha ERH NM_004450 1.23 -3.33 Enhancer of rudimentary homolog (Drosophila) ESCO2 Hs.99480 1.53 -3.52 Establishment of cohesion 1 homolog 2 (S. cerevisiae) ESR1 NM_000125 -2.19 -25.89 1 EXOSC3 NM_016042 -1.95 -3.55 Exosome component 3 F11R NM_144504 1.45 -4.39 F11 receptor F8 NM_019863 -1.79 -3.78 Coagulation factor VIII, procoagulant component (hemophilia A) FAHD1 NM_031208 -2.29 -3.13 Fumarylacetoacetate hydrolase domain containing 1 FAIM NM_018147 -1.37 -3.35 Fas apoptotic inhibitory molecule FBXL16 NM_153350 -1.88 -4.05 F-box and leucine-rich repeat protein 16 FGD4 NM_139241 -1.48 -3.23 FYVE, RhoGEF and PH domain containing 4 FGF13 NM_033642 -1.73 -29.30 Fibroblast growth factor 13 FGFR4 NM_022963 -1.89 -3.82 Fibroblast growth factor receptor 4 FIBL-6 NM_031935 -1.46 -11.06 Hemicentin 1 FIGN Hs.170999 -1.88 -5.26 Fidgetin FKBP1B NM_054033 1.56 -3.64 FK506 binding protein 1B, 12.6 kDa FKBP3 NM_002013 - -3.12 FK506 binding protein 3, 25kDa FKSG2 NM_021631 1.35 -3.54 Apoptosis inhibitor FLJ10116 NM_018000 - -3.62 Dilute suppressor FLJ11196 NM_197958 - -3.82 La ribonucleoprotein domain family, member 6 FLJ20625 NM_017907 - -4.43 Leucine rich repeat containing 51 FLJ33977 NM_173666 -1.20 -3.59 DTW domain containing 2 FOXA1 NM_004496 - -6.56 Forkhead box A1 FRAT2 NM_012083 - -3.16 Frequently rearranged in advanced T-cell lymphomas 2 FRK NM_002031 -2.68 -3.21 Fyn-related kinase FTH1 NM_002032 - -3.07 Ferritin, heavy polypeptide 1 FUNDC1 NM_173794 -1.43 -4.38 FUN14 domain containing 1 FUNDC2 NM_023934 -1.20 -5.65 FUN14 domain containing 2 G10 NM_003910 -1.30 -3.14 Maternal G10 transcript GA17 NM_006360 -1.27 -3.04 Dendritic cell protein GALM NM_138801 - -3.75 Galactose mutarotase (aldose 1-epimerase) GAN NM_022041 -1.75 -3.15 Giant axonal neuropathy () GEMIN6 NM_024775 - -3.58 Gem (nuclear ) associated protein 6 GFRA1 NM_145793 -2.63 -21.43 GDNF family receptor alpha 1 GGCX NM_000821 - -5.42 Gamma-glutamyl carboxylase GLRX NM_002064 -1.20 -3.96 Glutaredoxin (thioltransferase) GLRX2 NM_197962 -1.83 -3.39 Glutaredoxin 2 GLT28D1 NM_018466 - -4.39 Glycosyltransferase 28 domain containing 1 GLTP NM_016433 - -3.05 Glycolipid transfer protein GMPR2 NM_016576 - -4.25 Guanosine monophosphate reductase 2 GNA12 NM_007353 - -3.46 Guanine nucleotide binding protein (G protein) alpha 12 GNPNAT1 NM_198066 - -5.19 Glucosamine-phosphate N-acetyltransferase 1 GPR68 Hs.8882 -1.31 -3.73 G protein-coupled receptor 68 GRCC10 NM_138425 - -3.51 Likely ortholog of mouse gene rich cluster, C10 gene GRHPR NM_012203 -1.98 -3.07 Glyoxylate reductase/hydroxypyruvate reductase

38 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 Unchanged in MCF7-T, downregulated in MCF7-F GSTM3 NM_000849 -1.50 -8.26 Glutathione S-transferase M3 (brain) GSTO2 NM_183239 - -3.45 Glutathione S-transferase omega 2 GSTZ1 NM_145871 1.61 -6.99 Glutathione transferase zeta 1 (maleylacetoacetate isomerase) GTF2H3 NM_001516 - -3.22 General transcription factor IIH, polypeptide 3, 34kDa GTF2H5 Hs.356224 -1.55 -7.70 General transcription factor IIH, polypeptide 5 H2AFV NM_201517 - -5.13 H2A histone family, member V HAX1 NM_006118 - -3.29 HCLS1 associated protein X-1 HBA2 NM_000517 -1.26 -5.62 Hemoglobin, alpha 2 HBLD1 NM_194279 1.51 -4.88 HESB like domain containing 1 HBXIP NM_006402 -1.32 -4.26 Hepatitis B virus x interacting protein HCFC1R1 NM_017885 -1.94 -8.11 Host cell factor C1 regulator 1 (XPO1 dependant) HDGF NM_004494 - -3.10 Hepatoma-derived growth factor (high-mobility group protein 1-like) HES6 NM_018645 1.52 -3.40 Hairy and enhancer of split 6 (Drosophila) HIG2 NM_013332 -2.23 -7.84 Hypoxia-inducible protein 2 HINT1 NM_005340 1.25 -3.73 Histidine triad nucleotide binding protein 1 HINT2 NM_032593 -1.25 -3.29 Histidine triad nucleotide binding protein 2 HINT3 NM_138571 - -5.26 Histidine triad nucleotide binding protein 3 HIPK2 NM_022740 1.36 -6.01 Homeodomain interacting protein kinase 2 HIRIP5 NM_015700 - -3.23 HIRA interacting protein 5 HIST1H2BC NM_003526 -1.62 -5.40 Histone 1, H2bc HIST1H2BK NM_080593 - -3.19 Histone 1, H2bk HIST1H4F NM_003540 1.74 -3.59 Histone 1, H4f HIVEP1 NM_002114 - -3.10 Human immunodeficiency virus type I enhancer binding protein 1 HK2 NM_000189 -1.44 -4.80 Hexokinase 2 HMG4L Hs.472525 - -4.76 high-mobility group (nonhistone chromosomal) protein 4-like HMGB3 NM_005342 - -3.82 High-mobility group box 3 HNMT NM_006895 -1.68 -4.15 Histamine N-methyltransferase HNRPA0 NM_006805 - -3.14 Heterogeneous nuclear ribonucleoprotein A0 HNRPUL1 NM_144734 1.25 -4.73 Heterogeneous nuclear ribonucleoprotein U-like 1 HPS3 NM_032383 1.22 -3.69 Hermansky-Pudlak syndrome 3 HRB2 NM_007043 - -3.52 HIV-1 rev binding protein 2 HRSP12 NM_005836 -1.38 -6.07 Heat-responsive protein 12 HSBP1 NM_001537 - -3.95 binding protein 1 HSC20 Hs.182898 -1.57 -3.29 J-type co-chaperone HSC20 HSPB1 NM_001540 -1.57 -3.02 Heat shock 27kDa protein 1 HSPB8 NM_014365 -1.86 -7.27 Heat shock 22kDa protein 8 HSPC051 NM_013387 - -4.04 Ubiquinol-cytochrome c reductase complex (7.2 kD) HSPC128 NM_014167 - -3.64 HSPC128 protein HSPC132 NM_016399 - -3.86 P53-inducible cell-survival factor HSPC133 NM_014168 -1.35 -3.51 Methyltransferase like 5 HSPC182 NM_014188 -1.62 -3.79 Ssu72 RNA polymerase II CTD phosphatase homolog (yeast) HSPE1 NM_002157 -1.46 -4.51 Heat shock 10kDa protein 1 (chaperonin 10) HSU79274 NM_013300 -1.28 -3.38 Protein predicted by clone 23733 HUMPPA NM_014603 -1.27 -3.27 Paraneoplastic antigen IBRDC2 NM_182757 -1.50 -3.42 IBR domain containing 2 ICT1 NM_001545 -1.50 -3.45 Immature colon carcinoma transcript 1 IGBP1 NM_001551 - -3.39 Immunoglobulin (CD79A) binding protein 1 IGSF3 NM_001542 -1.72 -3.68 Immunoglobulin superfamily, member 3 IL17D NM_138284 - -3.20 Interleukin 17D IL1R1 NM_000877 -1.80 -3.44 Interleukin 1 receptor, type I ING1L NM_001564 - -4.88 Inhibitor of growth family, member 2 IRX3 NM_024336 1.53 -5.94 Iroquois homeobox protein 3 ITPK1 NM_014216 1.57 -3.09 Inositol 1,3,4-triphosphate 5/6 kinase K5B NM_173352 1.22 -3.32 Keratin 5b KCNK15 NM_022358 -1.53 -3.41 Potassium channel, subfamily K, member 15 KCTD12 NM_138444 - -3.44 Potassium channel tetramerisation domain containing 12 KCTD2 Hs.4935 -1.29 -3.18 potassium channel tetramerisation domain containing 2 KIF26A Hs.134970 1.37 -3.68 Kinesin family member 26A KLHL5 NM_199039 -1.62 -3.97 Kelch-like 5 (Drosophila)

39 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 Unchanged in MCF7-T, downregulated in MCF7-F KRAS2 NM_033360 -1.21 -3.30 V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog KRT10 NM_000421 - -3.69 (epidermolytic hyperkeratosis; keratosis palmaris et plantaris) KRT7 NM_005556 -1.52 -5.14 KRTAP8-1 NM_175857 - -3.01 Keratin associated protein 8-1 LDOC1 NM_012317 -2.17 -3.33 Leucine zipper, down-regulated in cancer 1 LITAF NM_004862 - -4.24 Lipopolysaccharide-induced TNF factor LMCD1 NM_014583 - -5.91 LIM and cysteine-rich domains 1 LOC116211 NM_152773 -1.26 -3.10 Transmembrane 4 L six family member 19 LOC124220 NM_145252 -2.55 -8.32 Similar to common salivary protein 1 LOC134147 NM_138809 - -3.44 Similar to mouse 2310016A09Rik gene LOC150678 NM_138336 - -4.90 Myeloma overexpressed 2 LOC163590 Hs.435773 -1.32 -3.81 Torsin A interacting protein 2 LOC200895 NM_176815 -1.36 -3.11 Dihydrofolate reductase-like 1 LOC220074 NM_145309 -1.32 -3.03 Leucine rich repeat containing 51 LOC255743 NM_198278 -1.27 -5.13 Likely ortholog of mouse nephronectin LOC284615 Hs.331667 2.09 -3.10 Ankyrin repeat domain 34 LOC388962 Hs.61472 1.47 -5.17 BolA-like 3 (E. coli) LOC401152 Hs.173705 -1.55 -5.10 HCV F-transactivated protein 1 LOC51123 Hs.374485 - -4.05 HSPC038 protein LOC56902 NM_020143 -1.70 -3.32 Putatative 28 kDa protein LOC84661 NM_032574 - -3.67 Dpy-30-like protein LOC91942 NM_174889 -1.27 -4.96 Myc-induced mitochondria protein LSM10 NM_032881 -1.28 -3.32 LSM10, U7 small nuclear RNA associated LSM5 NM_012322 - -3.94 LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM6 NM_007080 -1.22 -3.94 LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM7 NM_016199 -1.24 -3.41 LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM8 NM_016200 - -3.24 LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae) LY6G5C NM_025262 - -4.58 Lymphocyte antigen 6 complex, locus G5C LZIC NM_032368 - -3.04 Leucine zipper and CTNNBIP1 domain containing MADP-1 NM_033114 - -7.29 MADP-1 protein MAGEA12 NM_005367 -2.33 -4.60 CSAG family, member 4 MAGEE1 NM_020932 1.46 -4.51 Melanoma antigen family E, 1 MAGEF1 NM_022149 -1.46 -5.10 Melanoma antigen family F, 1 MAGOH NM_002370 -1.29 -4.89 Mago-nashi homolog, proliferation-associated (Drosophila) MAL NM_022440 -1.77 -4.48 Mal, T-cell differentiation protein MAP3K11 NM_002419 - -3.89 Mitogen-activated protein kinase kinase kinase 11 MAP3K12 NM_006301 - -4.23 Mitogen-activated protein kinase kinase kinase 12 MAP3K4 NM_006724 1.83 -3.58 Mitogen-activated protein kinase kinase kinase 4 MAP3K7IP2 NM_145342 -1.91 -3.07 Mitogen-activated protein kinase kinase kinase 7 interacting protein 2 MAPBPIP NM_014017 -1.44 -3.85 Mitogen-activated protein-binding protein-interacting protein MAPKAP1 NM_024117 - -3.08 Mitogen-activated protein kinase associated protein 1 MAPKAPK2 NM_032960 - -3.02 Mitogen-activated protein kinase-activated protein kinase 2 MAX NM_197957 1.39 -4.65 MYC associated factor X MB NM_005368 -2.79 -4.81 Myoglobin MCTS1 NM_014060 -1.33 -4.36 Malignant T cell amplified sequence 1 ME3 NM_006680 - -3.12 Malic enzyme 3, NADP(+)-dependent, mitochondrial MEA NM_014623 - -4.31 Male-enhanced antigen 1 MED28 NM_025205 - -4.44 Mediator of RNA polymerase II transcription, subunit 28 homolog (yeast) MED4 NM_014166 -1.33 -3.32 Mediator of RNA polymerase II transcription, subunit 4 homolog (yeast) MEG3 XR_000167 -1.44 -3.85 Maternally expressed 3 MELL1 NM_033467 -1.43 -3.35 Mel transforming oncogene-like 1 MESP1 NM_018670 -2.41 -34.32 Mesoderm posterior 1 METTL1 NM_023033 - -3.07 Methyltransferase like 1 MGC10561 NM_032647 - -3.04 Chromobox homolog 2 (Pc class homolog, Drosophila) MGC12458 NM_032328 1.31 -5.04 EF-hand calcium binding domain 2 MGC13379 NM_016499 - -3.07 HSPC244 MGC14798 Hs.149176 1.32 -3.45 similar to RIKEN cDNA 5730421E18 gene MGC20460 NM_053043 - -3.32 Proline rich 8 MGC23908 Hs.429839 - -3.97 Basic transcription factor 3-like 4

40 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 Unchanged in MCF7-T, downregulated in MCF7-F MGC23918 NM_144716 -1.21 -3.31 Coiled-coil domain containing 12 MGC29784 NM_173659 - -3.57 RNA pseudouridylate synthase domain containing 3 MGC3200 NM_032305 1.55 -5.07 Ankyrin repeat domain 34 MGC4549 NM_032377 - -3.03 Elongation factor 1 homolog (ELF1, S. cerevisiae) MGC88387 Hs.513885 -1.33 -3.89 Similar to HSPC296 MKKS NM_170784 - -7.45 McKusick-Kaufman syndrome MLC1SA NM_002475 1.32 -4.01 1 slow a MMRP19 NM_015957 - -3.74 Likely ortholog of mouse monocyte macrophage 19 MNAT1 NM_002431 1.54 -3.27 Menage a trois 1 (CAK assembly factor) MOAP1 NM_022151 1.47 -3.15 Modulator of apoptosis 1 MOCS2 NM_183418 -1.39 -3.78 Molybdenum cofactor synthesis 2 MOPT NM_194270 -2.01 -5.24 Protein containing single MORN motif in testis MPP7 NM_173496 -1.26 -4.89 Membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7) MRP63 NM_024026 - -3.83 Mitochondrial ribosomal protein 63 MRPL12 NM_002949 -1.30 -3.32 Mitochondrial ribosomal protein L12 MRPL14 NM_032111 -1.22 -3.95 Mitochondrial ribosomal protein L14 MRPL16 NM_017840 - -3.20 Mitochondrial ribosomal protein L16 MRPL18 NM_014161 - -5.27 Mitochondrial ribosomal protein L18 MRPL19 NM_014763 -1.97 -3.11 Mitochondrial ribosomal protein L19 MRPL20 NM_017971 -1.20 -4.27 Mitochondrial ribosomal protein L20 MRPL21 NM_181515 - -3.25 Mitochondrial ribosomal protein L21 MRPL23 NM_021134 -1.54 -3.43 Mitochondrial ribosomal protein L23 MRPL24 NM_145729 - -4.12 Mitochondrial ribosomal protein L24 MRPL27 NM_148571 - -3.39 Mitochondrial ribosomal protein L27 MRPL30 NM_145213 - -3.42 Mitochondrial ribosomal protein L30 MRPL33 NM_145330 1.21 -3.13 Mitochondrial ribosomal protein L33 MRPL34 NM_023937 -1.20 -3.97 Mitochondrial ribosomal protein L34 MRPL40 NM_003776 -1.30 -4.15 Mitochondrial ribosomal protein L40 MRPL42 NM_172178 - -3.04 Mitochondrial ribosomal protein L42 MRPL43 NM_176794 - -3.71 Mitochondrial ribosomal protein L43 MRPL47 NM_177988 -1.20 -5.18 Mitochondrial ribosomal protein L47 MRPL48 NM_016055 - -5.98 Mitochondrial ribosomal protein L48 MRPL49 NM_004927 -1.20 -4.05 Mitochondrial ribosomal protein L49 MRPL50 NM_019051 -1.20 -4.11 Mitochondrial ribosomal protein L50 MRPL51 NM_016497 -1.49 -4.06 Mitochondrial ribosomal protein L51 MRPL52 NM_181307 -1.20 -5.98 Mitochondrial ribosomal protein L52 MRPL53 NM_053050 - -4.67 Mitochondrial ribosomal protein L53 MRPS14 NM_022100 - -3.71 Mitochondrial ribosomal protein S14 MRPS16 NM_016065 - -4.14 Mitochondrial ribosomal protein S16 MRPS17 NM_015969 -1.41 -3.82 Mitochondrial ribosomal protein S17 MRPS18C NM_016067 - -3.16 Mitochondrial ribosomal protein S18C MRPS22 NM_020191 - -3.24 Mitochondrial ribosomal protein S22 MRPS23 NM_016070 - -3.04 Mitochondrial ribosomal protein S23 MRPS24 NM_032014 - -4.02 Mitochondrial ribosomal protein S24 MRPS28 NM_014018 -1.72 -4.22 Mitochondrial ribosomal protein S28 MRPS33 NM_053035 1.48 -4.49 Mitochondrial ribosomal protein S33 MRPS36 NM_033281 - -4.42 Mitochondrial ribosomal protein S36 MSMB NM_138634 -1.25 -26.45 Microseminoprotein, beta- MSRB2 NM_016064 -1.34 -4.03 Methionine sulfoxide reductase B2 MT1F Hs.438737 -2.57 -4.35 metallothionein 1F (functional) MT1G NM_032699 -2.06 -3.10 Metallothionein 1G MT1H NM_005951 -2.56 -5.25 Metallothionein 1H MT2A NM_005953 -2.98 -3.91 Metallothionein 2A MTIF3 NM_152912 -1.64 -4.95 Mitochondrial translational initiation factor 3 MTL5 NM_004923 -1.61 -3.07 Metallothionein-like 5, testis-specific (tesmin) MTRF1L NM_019041 -1.33 -3.03 Mitochondrial translational 1-like MTX1 NM_198883 - -3.41 Metaxin 1 MUC4 NM_138299 -1.47 -3.38 , tracheobronchial MYCBP NM_012333 -1.57 -3.80 C-myc binding protein

41 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 Unchanged in MCF7-T, downregulated in MCF7-F MYO1D Hs.39871 - -3.05 myosin ID MYPN NM_032578 -1.73 -7.97 Myopalladin NALP1 NM_033007 1.90 -3.33 NACHT, leucine rich repeat and PYD (pyrin domain) containing 1 NALP5 NM_153447 -1.43 -11.74 NACHT, leucine rich repeat and PYD containing 5 NANOS1 Hs.351851 - -3.18 Nanos homolog 1 (Drosophila) NAP1L1 NM_139207 - -3.06 (RPL6A) NDUFA2 NM_002488 - -3.08 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa NDUFA3 NM_004542 - -3.85 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9kDa NDUFA6 NM_002490 - -4.01 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa NDUFB1 NM_004545 1.39 -3.29 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa NDUFB10 NM_004548 -1.47 -3.63 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa NDUFB2 NM_004546 - -6.99 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa NDUFB3 NM_002491 - -3.01 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa NDUFB5 NM_002492 - -4.04 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa NDUFB6 NM_182739 -1.39 -3.52 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa NDUFB8 NM_005004 - -3.60 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa NDUFC1 NM_002494 -1.26 -6.79 NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 1, 6kDa NDUFS4 NM_002495 - -3.70 NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa NDUFS5 NM_004552 -1.20 -4.24 NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa NDUFV3 NM_021075 - -3.01 NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa NEDD8 NM_006156 - -10.26 Neural precursor cell expressed, developmentally down-regulated 8 NEK9 NM_033116 -1.98 -3.11 NIMA (never in mitosis gene a)- related kinase 9 NFIB NM_005596 -1.57 -4.36 /B NFIX NM_002501 2.02 -4.23 Nuclear factor I/X (CCAAT-binding transcription factor) NHP2L1 NM_005008 -1.22 -3.88 NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae) NINJ1 NM_004148 -1.53 -3.38 Ninjurin 1 NKAP NM_024528 - -3.29 NF-kappaB activating protein NME7 NM_197972 - -6.15 Non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase) NMT2 NM_004808 1.40 -3.14 N-myristoyltransferase 2 NOL7 NM_016167 - -3.23 Nucleolar protein 7, 27kDa NOLA1 NM_032993 -1.49 -3.72 Nucleolar protein family A, member 1 (H/ACA small nucleolar RNPs) NOLA3 NM_018648 - -3.73 Nucleolar protein family A, member 3 (H/ACA small nucleolar RNPs) NPM3 NM_006993 - -6.23 Nucleophosmin/nucleoplasmin, 3 NR2F2 NM_021005 -2.12 -3.42 Nuclear receptor subfamily 2, group F, member 2 NUBP1 NM_002484 - -3.16 Nucleotide binding protein 1 (MinD homolog, E. coli) NUCKS NM_022731 - -3.52 Nuclear casein kinase and cyclin-dependent kinase substrate 1 NUDT14 NM_177533 1.90 -4.09 Nudix (nucleoside diphosphate linked moiety X)-type motif 14 NUDT15 NM_018283 -1.23 -5.29 Nudix (nucleoside diphosphate linked moiety X)-type motif 15 NUDT2 NM_147173 -1.40 -3.73 Nudix (nucleoside diphosphate linked moiety X)-type motif 2 NUDT4 NM_199040 - -3.09 Nudix (nucleoside diphosphate linked moiety X)-type motif 4 pseudogene 2 NUP160 Hs.22559 - -4.30 nucleoporin 160kDa NXT2 NM_018698 - -3.59 Nuclear transport factor 2-like export factor 2 NY-REN-41 NM_080654 -1.32 -3.42 NY-REN-41 antigen OAZ3 Hs.407882 -1.87 -3.58 Ornithine decarboxylase antizyme 3 OAZIN NM_148174 - -3.95 Antizyme inhibitor 1 ODC1 NM_002539 -1.22 -3.68 Ornithine decarboxylase 1 OGFRL1 NM_024576 - -8.14 Opioid growth factor receptor-like 1 OPN5 NM_181744 - -3.72 Opsin 5 OSBPL10 NM_017784 -1.63 -4.92 Oxysterol binding protein-like 10 OSR2 NM_053001 -1.23 -4.18 Odd-skipped related 2 (Drosophila) PABPN1 NM_004643 - -3.14 Poly(A) binding protein, nuclear 1 PAICS NM_006452 - -3.38 Phosphoribosylaminoimidazole carboxylase PAIP2 NM_016480 - -3.45 Poly(A) binding protein interacting protein 2 PAK4 NM_005884 -1.29 -3.23 P21(CDKN1A)-activated kinase 4 PBP NM_002567 - -3.03 Prostatic binding protein PBX1 NM_002585 -1.97 -3.46 Pre-B-cell leukemia transcription factor 1 PBX2 NM_002586 - -3.13 Pre-B-cell leukemia transcription factor 2 PC4 NM_006713 - -4.32 Activated RNA polymerase II transcription cofactor 4 PCBD NM_000281 -1.45 -4.56 6-pyruvoyl-tetrahydropterin synthase

42 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 Unchanged in MCF7-T, downregulated in MCF7-F PCGF2 NM_007144 - -3.06 Polycomb group ring finger 2 PDAP1 NM_014891 -1.45 -3.07 PDGFA associated protein 1 PDCD4 NM_145341 -1.95 -4.32 Programmed cell death 4 (neoplastic transformation inhibitor) PDE4A NM_006202 - -3.97 Phosphodiesterase 4A, cAMP-specific PDHB NM_000925 -1.24 -3.22 Pyruvate dehydrogenase (lipoamide) beta PDZK11 NM_016484 - -3.36 PDZ domain containing 11 PEA15 NM_013287 -1.40 -4.64 phosphoprotein enriched in astrocytes 15 PEX13 NM_002618 1.30 -4.10 Peroxisome biogenesis factor 13 PEX26 NM_017929 -1.38 -3.38 Peroxisome biogenesis factor 26 PEX7 NM_000288 -2.07 -3.40 Peroxisomal biogenesis factor 7 PFDN2 NM_012394 -1.35 -5.39 Prefoldin 2 PGGT1B NM_005023 - -3.20 Protein geranylgeranyltransferase type I, beta subunit PGM5 NM_021965 - -6.73 Phosphoglucomutase 5 PGR1 NM_033296 - -3.14 Mof4 family associated protein 1 PHACTR2 Hs.102471 - -4.06 Phosphatase and actin regulator 2 PHF20 NM_016436 -1.62 -8.81 PHD finger protein 20 PHF5A NM_032758 - -3.02 PHD finger protein 5A PHIP Hs.511817 -1.51 -3.37 Pleckstrin homology domain interacting protein PIN1 NM_006221 -1.24 -3.57 Protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1 PKIA NM_181839 - -3.74 Protein kinase (cAMP-dependent, catalytic) inhibitor alpha PKIG NM_181805 -2.80 -3.20 Protein kinase (cAMP-dependent, catalytic) inhibitor gamma PLCB4 NM_182797 -1.26 -13.30 Phospholipase C, beta 4 PLEKHB1 NM_021200 -1.65 -6.00 Pleckstrin homology domain containing, family B (evectins) member 1 PLEKHF2 NM_024613 -2.21 -3.55 Pleckstrin homology domain containing, family F (with FYVE domain) member 2 PLEKHG2 Hs.111217 -2.16 -3.37 Pleckstrin homology domain containing, family G,member 2 PLSCR3 NM_020360 - -3.68 Phospholipid scramblase 3 PMP22 NM_153322 -1.57 -12.91 Peripheral myelin protein 22 PMVK NM_006556 -1.24 -3.60 Phosphomevalonate kinase POF1B NM_024921 -1.23 -8.03 Premature ovarian failure, 1B POLB NM_002690 - -3.66 Polymerase (DNA directed), beta POLE4 NM_019896 - -7.15 Polymerase (DNA-directed), epsilon 4 (p12 subunit) POLR2E NM_002695 -1.38 -3.77 Polymerase (RNA) II (DNA directed) polypeptide E, 25kDa POLR2F NM_021974 -1.44 -3.42 Polymerase (RNA) II (DNA directed) polypeptide F POLR2I NM_006233 - -3.38 Polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa POLR2K NM_005034 -1.38 -4.02 Polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa POLR2L NM_021128 - -6.48 Polymerase (RNA) II (DNA directed) polypeptide L, 7.6kDa POLR3K NM_016310 -1.34 -4.86 Polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa PP NM_021129 - -3.15 Pyrophosphatase (inorganic) PPA2 NM_176869 -1.41 -3.13 Inorganic pyrophosphatase 2 PPARGC1A NM_013261 1.25 -9.08 Peroxisome proliferative activated receptor, gamma, coactivator 1, alpha PPIL1 NM_016059 - -4.07 Peptidylprolyl isomerase (cyclophilin)-like 1 PPM1H Hs.21894 -2.06 -6.03 protein phosphatase 1H (PP2C domain containing) PPP1CB NM_002709 - -3.04 , catalytic subunit, beta isoform PPP1R11 NM_170781 -1.42 -3.25 Protein phosphatase 1, regulatory (inhibitor) subunit 11 PPP1R15B NM_032833 - -3.12 Protein phosphatase 1, regulatory (inhibitor) subunit 15B PPP2R5C NM_178588 1.91 -3.26 Protein phosphatase 2, regulatory subunit B (B56), gamma isoform PPP2R5E NM_006246 1.47 -3.01 Protein phosphatase 2, regulatory subunit B (B56), epsilon isoform PREI3 NM_199482 -1.42 -3.48 Preimplantation protein 3 PREX1 NM_020820 1.30 -40.65 Phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1 PRKAR2A NM_004157 -1.41 -3.93 Protein kinase, cAMP-dependent, regulatory, type II, alpha PRKCH NM_024064 - -4.76 protein kinase C, eta PRO0149 NM_014117 -1.52 -3.33 PRO0149 protein PRP19 NM_014502 - -5.24 PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae) PRPH NM_006262 2.07 -5.19 PRPS1 NM_002764 - -3.27 Phosphoribosyl pyrophosphate synthetase 1 PSMA2 NM_002787 - -3.31 Proteasome (prosome, macropain) subunit, alpha type, 2 PSMA4 NM_002789 - -3.09 Proteasome (prosome, macropain) subunit, alpha type, 4 PSMB5 NM_002797 -1.23 -4.21 Proteasome (prosome, macropain) subunit, beta type, 5 PSMB6 NM_002798 - -3.18 Proteasome (prosome, macropain) subunit, beta type, 6

43 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 Unchanged in MCF7-T, downregulated in MCF7-F PSMD10 NM_170750 - -3.25 Proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 PSMD9 NM_002813 - -4.41 Proteasome (prosome, macropain) 26S subunit, non-ATPase, 9 PTD015 NM_024684 1.46 -3.24 PTD015 protein PTE2B NM_152331 - -13.27 Peroxisomal acyl-CoA thioesterase 2B PTMA NM_002823 - -3.21 Prothymosin, alpha (gene sequence 28) PTP4A1 NM_003463 - -5.24 Protein tyrosine phosphatase type IVA, member 1 PTP4A2 Hs.82911 -1.26 -3.23 protein tyrosine phosphatase type IVA, member 2 PTS NM_000317 - -3.19 6-pyruvoyltetrahydropterin synthase PURB NM_033224 -1.20 -3.30 Purine-rich element binding protein B PWWP1 NM_138574 1.21 -3.15 Hepatoma derived growth factor-like 1 PXMP2 NM_018663 1.27 -4.27 Peroxisomal membrane protein 2, 22kDa PYCARD NM_145183 -1.94 -3.04 PYD and CARD domain containing PYCR1 NM_153824 -1.58 -3.39 Pyrroline-5-carboxylate reductase 1 PYM NM_032345 1.32 -5.85 Within bgcn homolog (Drosophila) QKI Hs.153355 -1.37 -18.02 quaking homolog, KH domain RNA binding (mouse) RAB21 NM_014999 -1.35 -3.32 RAB21, member RAS oncogene family RAB25 NM_020387 -1.27 -3.56 RAB25, member RAS oncogene family RAB31 NM_006868 - -3.69 RAB31, member RAS oncogene family RAB39B NM_171998 2.63 -14.05 RAB39B, member RAS oncogene family RAB3D Hs.464254 -1.28 -3.49 RAB3D, member RAS oncogene family RAB5C NM_201434 - -4.03 RAB5C, member RAS oncogene family RAB9A NM_004251 -1.74 -3.04 RAB9A, member RAS oncogene family RAB9P40 NM_005833 -1.33 -3.48 Rab9 effector protein with kelch motifs RABIF NM_002871 - -3.52 RAB interacting factor RAC3 NM_005052 -1.37 -7.14 Ras-related C3 botulinum toxin substrate 3 RAD51C NM_058217 1.30 -4.04 RAD51 homolog C (S. cerevisiae) RAD51L1 NM_133510 1.80 -3.20 RAD51-like 1 (S. cerevisiae) RALA NM_005402 -1.48 -3.86 V-ral simian leukemia viral oncogene homolog A (ras related) RALBP1 NM_006788 1.26 -3.94 RalA binding protein 1 RaLP Hs.207589 1.57 -16.71 Rai-like protein RAP2B NM_002886 - -3.42 RAP2B, member of RAS oncogene family RAP2C NM_021183 1.56 -6.69 RAP2C, member of RAS oncogene family RAPGEF1 NM_198679 - -3.01 Rap guanine nucleotide exchange factor (GEF) 1 RASGEF1B NM_152545 1.55 -6.74 RasGEF domain family, member 1B RBM24 NM_153020 -1.43 -42.24 RNA binding motif protein 24 RBM8A NM_021618 - -3.84 RNA binding motif protein 8A RBX1 NM_014248 - -3.50 Ring-box 1 RGS10 NM_002925 1.96 -3.81 Regulator of G-protein signalling 10 RHEB NM_005614 - -3.01 Ras homolog enriched in brain RHPN2 NM_033103 -1.33 -4.68 Rhophilin, Rho GTPase binding protein 2 RIPK2 NM_003821 - -3.41 Receptor-interacting serine-threonine kinase 2 RKHD2 NM_016626 -2.57 -3.54 Ring finger and KH domain containing 2 RNF135 NM_197939 -1.25 -3.59 Ring finger protein 135 RNF5 NM_006913 - -3.96 Ring finger protein 5 RNF7 NM_183237 -1.32 -3.94 Ring finger protein 7 RNUT1 NM_005701 - -3.33 RNA, U transporter 1 RP2 NM_006915 -1.24 -3.32 Retinitis pigmentosa 2 (X-linked recessive) RP42 NM_020640 -1.45 -3.22 RP42 homolog RPL10L NM_080746 - -16.46 Ribosomal protein L10-like RPL14 NM_003973 - -3.45 Ribosomal protein L14 RPL18 NM_000979 - -3.37 Ribosomal protein L18 RPL22 NM_000983 - -3.22 Ribosomal protein L22 RPL31 NM_000993 -1.84 -4.36 Ribosomal protein L31 RPL36 NM_033643 - -3.26 Ribosomal protein L36 RPL36AL NM_001001 1.27 -5.09 Ribosomal protein L36a-like RPL38 NM_000999 1.46 -4.06 Ribosomal protein L38 RPL4 Hs.432898 1.40 -4.12 Mitogen-activated protein kinase kinase kinase 13 RPL5 NM_000969 - -3.16 Ribosomal protein L5 RPP25 NM_017793 - -4.02 25kDa subunit

44 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 Unchanged in MCF7-T, downregulated in MCF7-F RPS2 Hs.498569 - -3.06 RNA, U64 small nucleolar RPS21 NM_001024 - -4.62 Ribosomal protein S21 RWDD1 NM_015952 - -4.54 RWD domain containing 1 SALL2 Hs.416358 - -4.43 Sal-like 2 (Drosophila) SAP18 NM_005870 - -3.02 Sin3-associated polypeptide, 18kDa SAP30 NM_003864 - -3.69 Sin3-associated polypeptide, 30kDa SAV1 NM_021818 1.33 -3.00 Salvador homolog 1 (Drosophila) SBK1 Hs.97837 -1.31 -4.14 SH3-binding domain kinase 1 SCIN NM_033128 1.25 -15.72 Scinderin SCIRP10 NM_013349 1.24 -3.22 SCIRP10-related protein SDCCAG33 NM_005786 -2.06 -3.24 Serologically defined colon cancer antigen 33 SDHB NM_003000 -1.79 -3.15 Succinate dehydrogenase complex, subunit B, iron sulfur (Ip) SDHC NM_003001 - -3.94 Succinate dehydrogenase complex, subunit C, integral membrane protein SDK2 NM_019064 -1.27 -5.91 Sidekick homolog 2 (chicken) SEC14L1 NM_003003 -1.62 -4.48 SEC14-like 1 (S. cerevisiae) SEC22L1 NM_004892 -1.24 -3.38 SEC22 vesicle trafficking protein-like 1 (S. cerevisiae) SEC61B NM_006808 -1.21 -4.39 Sec61 beta subunit SEC61G NM_014302 - -4.31 Sec61 gamma subunit SELENBP1 NM_003944 2.06 -3.81 Selenium binding protein 1 SEPT9 NM_006640 -1.42 -3.73 Septin 9 SEPX1 NM_016332 -1.50 -3.38 Selenoprotein X, 1 SERF1A NM_021967 - -5.42 Small EDRK-rich factor 1A (telomeric) SERF2 NM_005770 - -4.62 Small EDRK-rich factor 2 SERP1 NM_014445 - -3.88 Stress-associated endoplasmic reticulum protein 1 SET8 NM_020382 1.37 -3.05 PR/SET domain containing protein 8 SF3B5 NM_031287 - -4.91 Splicing factor 3b, subunit 5, 10kDa SH3BGRL2 NM_031469 - -3.06 SH3 domain binding glutamic acid-rich protein like 2 SHANK2 NM_133266 -1.80 -4.70 SH3 and multiple ankyrin repeat domains 2 SHFM1 NM_006304 - -3.85 Split hand/foot malformation (ectrodactyly) type 1 SHINC-4 Hs.506977 - -3.27 Shinc-4 mRNA, partial sequence SIAH2 NM_005067 -1.62 -3.21 Seven in absentia homolog 2 (Drosophila) SIP1 NM_003616 2.11 -3.30 protein interacting protein 1 SIVA NM_021709 2.33 -4.85 CD27-binding (Siva) protein SIX1 NM_005982 - -4.84 Sine oculis homeobox homolog 1 (Drosophila) SIX2 NM_016932 1.33 -3.32 Sine oculis homeobox homolog 2 (Drosophila) SKB1 NM_006109 - -3.06 SKB1 homolog (S. pombe) SKI NM_003036 - -4.67 V-ski sarcoma viral oncogene homolog (avian) SLC17A4 NM_005495 -1.20 -4.06 Solute carrier family 17 (sodium phosphate), member 4 SLC1A2 NM_004171 -2.45 -15.59 Solute carrier family 1 (glial high affinity glutamate transporter), member 2 SLC25A21 NM_030631 -1.57 -5.65 Solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21 SLC25A3 NM_005888 -1.34 -3.05 Solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 SLC25A4 NM_001151 - -3.71 Solute carrier family 25 SLC35F1 Hs.379705 - -3.89 solute carrier family 35, member F1 SLC39A4 NM_130849 -1.75 -3.45 Solute carrier family 39 (zinc transporter), member 4 SLC7A8 NM_182728 -2.91 -3.33 Solute carrier family 7 (cationic amino acid transporter, y+ system), member 8 SLC9A3R1 NM_004252 -1.68 -3.42 Solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 1 SLIT1 NM_003061 - -4.71 Slit homolog 1 (Drosophila) SNAPAP NM_012437 -1.26 -3.49 SNAP-associated protein SNAPC5 NM_006049 -1.23 -3.69 Small nuclear RNA activating complex, polypeptide 5, 19kDa SNRPB2 NM_198220 -1.40 -3.12 Small nuclear ribonucleoprotein polypeptide B'' SNRPC NM_003093 - -3.15 Small nuclear ribonucleoprotein polypeptide C SNRPD1 NM_006938 1.30 -5.27 Small nuclear ribonucleoprotein D1 polypeptide 16kDa SNRPD3 NM_004175 - -4.49 Small nuclear ribonucleoprotein D3 polypeptide 18kDa SNRPE NM_003094 - -3.12 Small nuclear ribonucleoprotein polypeptide E SOCS2 NM_003877 - -3.60 Suppressor of cytokine signaling 2 SOCS3 NM_003955 - -3.42 Suppressor of cytokine signaling 3 SOD2 NM_000636 1.27 -3.41 Superoxide dismutase 2, mitochondrial SORD NM_003104 1.32 -4.84 Sorbitol dehydrogenase SPA17 NM_017425 -1.54 -4.46 Sperm autoantigenic protein 17

45 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 Unchanged in MCF7-T, downregulated in MCF7-F SPAG7 NM_004890 - -3.01 Sperm associated antigen 7 SPATA11 NM_032306 - -3.02 Spermatogenesis associated 11 SPATS2 NM_023071 - -3.95 Spermatogenesis associated, serine-rich 2 SPDEF NM_012391 - -15.48 SAM pointed domain containing ets transcription factor SRA1 XR_000132 -1.64 -3.06 Steroid receptor RNA activator 1 SRP14 NM_003134 -1.21 -3.87 Signal recognition particle 14kDa (homologous Alu RNA binding protein) SRP46 NM_032102 - -3.47 Splicing factor, arginine/serine-rich, 46kD SRRM2 NM_016333 -1.91 -3.19 Serine/arginine repetitive matrix 2 SS18L2 NM_016305 - -3.22 Synovial sarcoma translocation gene on chromosome 18-like 2 SSNA1 NM_003731 - -3.79 Sjogren's syndrome nuclear autoantigen 1 SSTK-IP NM_144627 -1.26 -3.41 SSTK-interacting protein STARD10 NM_006645 -2.25 -11.93 START domain containing 10 STAT6 NM_003153 -1.35 -4.28 Signal transducer and activator of transcription 6, interleukin-4 induced STOM NM_198194 - -3.20 Stomatin STRA13 NM_144998 - -6.84 Stimulated by retinoic acid 13 homolog (mouse) STYX NM_145251 1.28 -3.87 Serine/threonine/tyrosine interacting protein SULT2B1 NM_177973 -1.52 -4.70 Sulfotransferase family, cytosolic, 2B, member 1 SUMO2 NM_006937 - -4.67 SMT3 suppressor of mif two 3 homolog 2 (yeast) SUPT4H1 NM_003168 - -4.87 Suppressor of Ty 4 homolog 1 (S. cerevisiae) TADA3L NM_133481 -1.70 -3.22 Transcriptional adaptor 3 (NGG1 homolog, yeast)-like TAF9 NM_016283 -1.20 -3.99 TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor TAS2R14 NM_023922 -1.84 -4.45 Taste receptor, type 2, member 14 TATDN1 NM_032026 -1.20 -5.50 TatD DNase domain containing 1 TBCA NM_004607 - -3.21 Tubulin-specific chaperone a TCEAL3 NM_032926 - -3.59 Transcription elongation factor A (SII)-like 3 TCEAL4 NM_024863 - -3.04 Transcription elongation factor A (SII)-like 4 TCEB1 NM_005648 -1.20 -3.47 Transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) TCEB2 NM_007108 -1.25 -3.44 Transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B) TCTEL1 NM_006519 -1.27 -3.86 T-complex-associated-testis-expressed 1-like 1 TEAD4 NM_003213 -1.73 -4.94 TEA domain family member 4 TENC1 NM_198316 -1.40 -9.63 Tensin like C1 domain containing phosphatase (tensin 2) TFDP1 NM_007111 1.75 -3.67 Transcription factor Dp-1 TFF1 NM_003225 1.26 -7.56 Trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in) TGFB2 NM_003238 -1.41 -3.45 Transforming growth factor, beta 2 THAP1 NM_199003 -1.21 -3.67 THAP domain containing, apoptosis associated protein 1 THAP11 NM_020457 - -4.60 THAP domain containing 11 THEM2 NM_018473 - -4.46 Thioesterase superfamily member 2 THNSL1 NM_024838 -1.69 -5.41 Threonine synthase-like 1 (bacterial) THRAP6 NM_080651 -1.55 -3.27 Thyroid hormone receptor associated protein 6 TIGA1 NM_053000 - -3.79 TIGA1 TIM14 NM_201261 - -3.72 Homolog of yeast TIM14 TIMM10 NM_012456 1.22 -3.27 of inner mitochondrial membrane 10 homolog (yeast) TIMM17B NM_005834 -1.27 -3.12 Translocase of inner mitochondrial membrane 17 homolog B (yeast) TIMM8A NM_004085 -1.27 -6.21 Translocase of inner mitochondrial membrane 8 homolog A (yeast) TIMM8B NM_012459 - -3.34 Translocase of inner mitochondrial membrane 8 homolog B (yeast) TIMM9 NM_012460 1.30 -4.03 Translocase of inner mitochondrial membrane 9 homolog (yeast) TINF2 NM_012461 - -3.36 TERF1 (TRF1)-interacting nuclear factor 2 TINP1 NM_014886 - -3.75 TGF beta-inducible nuclear protein 1 TMEM14B NM_030969 - -3.53 Transmembrane protein 14B TMEPAI NM_199171 -2.13 -3.38 Transmembrane, prostate androgen induced RNA TMPRSS3 NM_032405 -2.21 -3.13 Transmembrane protease, serine 3 TNNT1 NM_003283 1.38 -8.89 T1, skeletal, slow TOB1 NM_005749 1.29 -5.03 Transducer of ERBB2, 1 TOB2 NM_016272 -1.34 -3.98 Transducer of ERBB2, 2 TOMM7 NM_019059 - -4.50 Translocase of outer mitochondrial membrane 7 homolog (yeast) TP53RK NM_033550 -2.26 -3.76 TP53 regulating kinase TPD52L1 NM_003287 -1.49 -4.55 Tumor protein D52-like 1 TPK1 NM_022445 1.53 -3.01 Thiamin pyrophosphokinase 1 TRAPPC1 NM_021210 - -3.92 Trafficking protein particle complex 1

46 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 Unchanged in MCF7-T, downregulated in MCF7-F TRAPPC3 NM_014408 -1.49 -3.19 Trafficking protein particle complex 3 TRAPPC4 NM_016146 - -3.37 Trafficking protein particle complex 4 TRIM36 NM_018700 -1.61 -4.81 Tripartite motif-containing 36 TRIM59 NM_173084 1.22 -4.16 Tripartite motif-containing 59 TRIP3 NM_004773 -1.27 -3.45 Thyroid hormone receptor interactor 3 TRIP6 NM_003302 -1.68 -3.89 Thyroid hormone receptor interactor 6 TSHB NM_000549 -2.18 -3.01 Thyroid stimulating hormone, beta TTC9 Hs.79170 - -6.10 Tetratricopeptide repeat domain 9 TUBB2 NM_006088 - -3.68 Tubulin, beta, 2 TUSC4 NM_006545 -1.36 -3.02 Tumor suppressor candidate 4 TXNL4A NM_006701 -2.30 -3.13 Thioredoxin-like 4A TXNL4B NM_017853 -1.29 -3.41 Thioredoxin-like 4B UBE2D2 NM_181838 - -3.17 Ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast) UBE2E1 NM_182666 -1.29 -3.15 Ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homolog, yeast) UBE2L3 NM_198157 -1.25 -3.83 Ubiquitin-conjugating enzyme E2L 3 UBE2R2 NM_017811 -1.75 -3.65 Ubiquitin-conjugating enzyme E2R 2 UBL3 NM_007106 - -3.09 Ubiquitin-like 3 UBL5 NM_024292 - -4.71 Ubiquitin-like 5 UBP1 NM_014517 -1.50 -3.33 Upstream binding protein 1 (LBP-1a) UCK2 NM_012474 -1.24 -3.15 Uridine-cytidine kinase 2 UCP2 NM_003355 1.42 -3.09 Uncoupling protein 2 (mitochondrial, proton carrier) Ufc1 NM_016406 -1.54 -4.48 Ubiquitin-fold modifier conjugating enzyme 1 UGDH NM_003359 -2.00 -7.48 UDP-glucose dehydrogenase UGT2B15 NM_001076 - -5.10 UDP glucuronosyltransferase 2 family, polypeptide B15 UQCR NM_006830 - -3.13 Ubiquinol-cytochrome c reductase, 6.4kDa subunit UQCRB NM_006294 - -5.68 Ubiquinol-cytochrome c reductase binding protein UROS NM_000375 -1.81 -3.49 Uroporphyrinogen III synthase (congenital erythropoietic porphyria) USP15 NM_006313 -1.24 -3.43 Ubiquitin specific protease 15 USP45 Hs.512802 - -5.37 ubiquitin specific protease 45 USP6NL Hs.278526 1.29 -3.12 USP6 N-terminal like UTP14C Hs.190389 -1.78 -3.29 UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast) UXT NM_153477 - -3.37 Ubiquitously-expressed transcript VAV1 NM_005428 1.81 -3.13 Vav 1 oncogene VBP1 NM_003372 - -3.08 Von Hippel-Lindau binding protein 1 VDAC3 NM_005662 - -4.19 Voltage-dependent anion channel 3 VPS37C Hs.523715 - -3.62 Vacuolar protein sorting 37C (yeast) VTI1B NM_006370 1.49 -5.71 Vesicle transport through interaction with t-SNAREs homolog 1B (yeast) WDR23 NM_181357 -1.24 -3.76 WD repeat domain 23 WTAP NM_152858 - -3.00 Wilms tumor 1 associated protein XLHSRF-1 Hs.9740 1.21 -4.12 Dynein, axonemal, heavy polypeptide 1 XRCC4 NM_022550 -1.53 -3.27 X-ray repair complementing defective repair in Chinese hamster cells 4 YEATS4 NM_006530 - -3.49 YEATS domain containing 4 YWHAE NM_006761 - -3.00 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein ZAP128 NM_006821 1.68 -4.73 Peroxisomal long-chain acyl-coA thioesterase ZBTB10 NM_023929 -1.67 -3.49 Zinc finger and BTB domain containing 10 ZBTB2 NM_020861 - -3.11 Zinc finger and BTB domain containing 2 ZHX1 NM_007222 - -3.23 Zinc fingers and 1 ZHX2 NM_014943 -1.40 -3.73 Zinc fingers and homeoboxes 2 ZMYND12 NM_032257 -1.61 -3.78 Zinc finger, MYND-type containing 12 ZNF183 NM_006978 - -4.81 Ring finger protein 113A ZNF219 NM_016423 1.38 -3.01 Zinc finger protein 219 ZNF22 NM_006963 - -4.25 Zinc finger protein 22 (KOX 15) ZNF278 NM_032052 - -3.15 Zinc finger protein 278 ZNF462 NM_021224 1.31 -4.59 Zinc finger protein 462 ZNF511 NM_145806 -1.34 -4.35 Zinc finger protein 511 ZNF593 NM_015871 -2.70 -3.05 Zinc finger protein 593 ZNF6 NM_021998 2.31 -4.14 Zinc finger protein 6 (CMPX1) ZNRD1 NM_170783 - -3.43 Zinc ribbon domain containing, 1 ZRANB1 NM_017580 -1.29 -4.37 Zinc finger, RAN-binding domain containing 1

47