Supplementary Table S1A Primers used for real-time RT-PCR gene regulation and their confirmation Gene Name Accession no Size Region Forward Primer Reverse Primer Efficiency% AKT1 v-akt oncogene homolog 1 NM_005163 174 2184-2358 GAA AAC TAT CCT GCG GGT TT CTG ACA GAG TGA GGG GAC AC 100.5 AKT2 v-akt oncogene homolog 2 NM_001626 230 1466-1695 GAGGTCATGGAGCACAGGTT CTGGCCGAGTAGGAGAACTG 98.0 AKT3 v-akt l oncogene homolog 3 NM_005465 213 2576-2788 CAA ACG CAG CTC CAA CTT AT TGG GGA TTT TCT CAT TTT CA 99.7 Adipocyte-specific adhesion NM_024769 187 1107-1293 98.8 ASAM molecule CTC TTG GTG TGG CTG CTA AT AGG CAC TAT TTG CTG TGG AG CGA Glycoprotein hormone, alpha NM_000735 184 32-215 AAATCCCTCTTCGGATCCAC TTCCTGTAGCGTGCATTCTG 98.4 CGNL1 Cingulin-like 1 NM_032866 196 870-1065 ACC CTG AAA CCA AGA AAA CC TCA TGA CGA TTG ACG TTG TC 100.1 CPE Carboxypeptidase E NM_001873 205 492-696 CCATCAGCAGGATTTACACG TCGTTCCCCTTCTGGTATTC 99.3 ESR1 Estrogen receptor 1 NM_000125 168 3211-3380 AGA GGG AAA GTA GGG CAG AA TGG GAA ATG AAG AAG AGC TG 96.8 GAL Galanin prepropeptide NM_015973 156 303-458 AAGGAAAAACGAGGCTGGAC GGACCTGTCAAAGCTTCCTG 101.1 Imprinted maternally BC053636 163 1121-1283 103.5 H19 expressed AGAAGCGGGTCTGTTTCTTT TGCAGCATATTCATTTCCAA Membrane metallo- NM_000902 144 99-242 98.0 MME endopeptidase TGA GGG GTC ACG ATT TTA GG ATG ATG GTG AGG AGC AGG AC PIM1 Pim-1 gene NM_002648 256 695-950 GGAGTGGTCCTGCTGAAGAA GGATGTTTTCGTCCTTGATG 100.2 Protein tyrosine phosphatase NM_002843 165 735-899 104.0 PTPRJ receptor J CTGTTTCCATCAGTCCAACC ATGAAGTCGCTGGACGTAAG RPL13A Ribosomal protein L13a NM_012423.2 126 487-612 CCTGGAGGAGAAGAGGAAAGAGA TTGAGGACCTCTGTGTATTTGTCAA 100.1 RRM2 Ribonucleotide reductase M2 NM_001165931 225 1474-1698 ACC AAC TAG CCA CAC CAT GA GGA CTG TTT AAT CCC GCT GT 100.1

Supplementary Table 1B Microarray data deposited into the Gene Expression Ominbus (GSE34291) using Agilent's platform GPL4133 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34291) Sample Array Abbreviation Description Number MC MC Self-Self GSM846848 MC ME Control vs Estrogen treated MCF-7 cells ME MC Dye-Swap GSM846849 MC MT Control vsTamoxifen treated MCF-7 cells MT MC Dye-Swap AC AC Self-Self GSM846850 MC AC Control treated MCF-7 cells vs Control treated Akt3 over-expressing MCF-7 cells AC MC Dye-Swap GSM846851 ME AE Estrogen treated MCF-7 cells vs Estrogen treated Akt3 over-expressing MCF-7 cells AE ME Dye-Swap GSM846852 MT AT Tamoxifen treated MCF-7 cells vs Tamoxifen treated Akt3 over-expressing MCF-7 AT MT Dye-Swap GSM846853 AC AE Control vs Estrogen treated Akt3 over-expressing MCF-7 cells AE AC Dye-Swap GSM846854 AC AT Control vs Tamoxifen treated Akt3 overr-expressing MCF-7 cells AT AC Dye-Swap

Supplementary Table S2 Genes modified upon hormonal treatment in MCF-7 and Akt3 overexpressing cells ACCESSION SYMBOL MT AT MC ME MC MT MC AC ME AE AC AT AC AE NUMBER Cell Proliferation NM_015973 GAL* 6.90 3.54 NM_001034 RRM2* 5.09 2.50 NR_002196 H19 3.29 2.92 NM_002220 ITPKA 2.77 2.35 NM_080656 MGC13017 2.45 2.43 NM_005672 PSCA* 2.25 -4.87 NM_176072 P2RY2 2.14 2.29 NM_014326 DAPK2 -2.01 -2.47 NG_012209.1 PTPRJ -2.10 -2.02 -2.10 NM_022783 DEPDC6 -2.11 3.69 -3.47 NM_002648 PIM1 -3.03 -2.06 NM_021785 RAI2 -4.39 -4.04 -2.66 NM_014668 GREB1** 8.53 -12.83 NM_001080416 MYBL1** 6.58 -2.35 4.42 NM_002776 KLK10** 5.51 -3.01 NM_003225 TFF1** 4.76 -3.39 NM_001657 AREG 16.88 6.38 NM_003714 STC2 -2.01 -2.17 2.25 Cell motility NM_005554 KRT6A 8.37 2.15 NM_003064 SLPI 5.88 5.03 NM_005532 IFI27* 4.47 6.06 NM_012337 CCDC19 4.37 5.29 NM_001032281 TFPI 2.53 3.43 NM_006000 TUBA4A 2.50 3.65 3.90 NM_001070 TUBG1 2.44 2.01 NM_015262 FAM21C -2.35 -2.34 NM_001008707 EML1 -2.60 -3.03 NM_001005404 YPEL2 -2.86 -2.18 -2.28 NM_000095 COMP -2.97 -3.34 NM_032866 CGNL1 -3.20 -2.39 NM_000304 PMP22 -5.08 -5.07 NM_007289 MME* -7.31 -2.82 NM_003793 CTSF 8.23 8.72 NM_006818 MLLT11 3.42 3.12 NM_024769 ASAM -2.59 -2.22 Different aspects of cellular metabolism and transporters NM_001873 CPE 10.58 8.70 NM_014848 SV2B 10.41 8.28 6.48 NM_000849 GSTM3 6.90 7.16 NM_146421 GSTM1 3.91 3.10 3.66 NM_001353 AKR1C1 3.71 4.30 NM_152313 SLC36A4 3.47 2.65 NM_000454 SOD1 2.87 2.51 NM_022445 TPK1 2.75 2.69 -2.07 NM_003748 ALDH4A1 2.63 -2.02 U18197 ACLY 2.24 2.03 NM_004969 IDE 2.01 2.03 NM_001218 CA12 -2.12 -2.03 -3.90 NM_000146 FTL -2.42 -2.82 -2.31 NM_000792 DIO1 -2.60 -2.54 NM_007231 SLC6A14 -4.23 -5.02 NM_019036 HMGCLL1 -4.48 -4.16 NM_032385 C5orf4 -6.70 -6.62 -4.35 NM_182751 MCM10 2.78 2.34 NM_003740 KCNK5 2.24 -2.04 -2.68 NM_014747 RIMS3 4.51 3.49 NM_016529 ATP8A2 2.79 3.69 NM_000101 CYBA 2.30 2.16 NM_001072 UGT1A6 2.01 2.32 NM_018043 TMEM16A -3.09 2.37 NM_000817 GAD1 -3.68 2.66 Transcription and translation, signal transduction NM_000735 CGA 10.27 6.02 16.81 NM_019845 RPRM 4.22 5.15 NM_012168 FBXO2 2.38 2.02 NM_001039577 CCNL2 2.27 2.02 NM_022464 SIL1 2.20 2.26 NM_018193 FANCI 2.08 2.47 NM_002154 HSPA4 2.03 2.02 NM_005855 RAMP1 -2.27 -2.23 NM_004024 ATF3 -3.60 -2.56 NM_012435 SHC2 -3.64 -2.51 NM_015668 RGS22 -3.86 -3.44 NM_014622 LOH11CR2A -5.59 -2.94 NM_000599 IGFBP5 6.18 3.21 NM_022873 IFI6* 2.53 5.46 5.03 NM_031942 CDCA7 3.25 -2.10 2.21 NM_004091 E2F2* -2.14 2.14 7.65 NM_002467 MYC* -2.71 6.22 ENST00000373093 GRIK3 -3.02 7.65 NM_003485 GPR68 -3.49 5.43 Miscellaneous THC2650372 7.50 5.84 AF088062 FLJ33630 3.08 3.46 A_24_P161733 2.51 2.11 NM_173624 FLJ40504 2.51 2.03 THC2638238 2.34 2.05 THC2514800 2.24 2.27 THC2657781 -2.03 -2.39 XM_934188 LOC653801 -2.38 -2.73 -2.50 CR624517 -2.41 -2.43 -2.17 ENST00000329809 -3.13 -3.04 BC064586 LOC145837 3.04 -2.22 * Genes showed up under cellular proliferation and cell motility ** Estrogen regulated genes Supplementary Table S3 Ingenuity database gene networks associated with hormonal treatment and Akt over-expression Focus ID Genes in Network Score Top Functions Genes MT AT Ap1, ATF3↓, CA12↓, CCNL2, CGA↑, CGB, CMTM2A, CPE ↑, Creb, DIO1↓, ERK1/2, FSH, GAL↑, GALR1, GALR3, GSTM1↑, GSTM3↑, H19↑, Histone h3, HSPA4, IDE↑, Lh, NFkB (complex), Cell proliferation 1 35 18 P2RY2↑, PDGF BB, PIM1↓, PRLH, PTPN21, PTPRJ↓, RNA polymerase II, RPRM↑, SLPI↑, and growth SOD1↑, TFPI↑

ABCG2, AKR1C1, ALDH4A1↑, CGNL1↓, COMP↓, CYP19A1, DAPK2, FANCI↑, GAL↑, IFI27, IGF1, IGFBP1↑, IL6, KLK2, KRT15, KRT17, KRT6A↑, MATN4, MME↓, MPZ, NR3C1, NTS, 2 36 14 Cell Motility NUPR1, PBSN, PMP22↑, RPRM↑, RRM2↑, RRM2B, SLC6A14↑, SLPI↑, SMARCA4, SV2B↑, TP53, ZEB1

ABL1, ACTN2, AKT3, BAIAP2, BDNF,CGA↑, CPE↑, F Actin, FANCI↑, FBXO2↑, FES, GAL↑, GRIN1, GRIN2B, Hsp90, ITPKA, KIF23, LIMK1, MARK4, MBP, MLLT11↑, MME ↓, NDEL1, Neuropepetide 3 35 14 NUMA1, P2RY2↑,PARK2, PMP22 ↓, RAB8B, RASSF1,SHC2 ↓,SLPI↑, SV2B↑, TUBA1A, signaling TUBA4A↑,TUBG1↑ MC ME AChR, BCAS3, C14ORF156, CASP1, E2F2↓, ERCC2, ERK1/2, ESR1, Esr1-Estrogen-Fos-Jun, FAM110B, FLII, GAL↑, GREB1↑, H19↑, HEXIM1, HMGN1, HTR1A, KLK10↑, LIN37, MCM10↑, Cell proliferation 1 36 12 MME↓, MYBL1↑, NCOA4, NFATC4, NR2C2, OTUB1, Pkc(s), PSCA ↓, PTPRJ↑, RRM2↑, SAFB, and growth SMOC2, TFDP2, TFF1↓, TGFB1, WWC1

ALDH4A1↓, BCAS3, beta-estradiol, CDC6, CDC45, CDCA7↑, DDX17, ESR2, FANCI↑, GHR, GRP, Gene Expression, GTF2B, HOXC6, HSPB1, KAT2B, MCM3, MCM7, MED1, MED14, MME↓, MSN, MYBL1↑, 2 35 5 Recombination, and MYBL2, MYC, NDRG1, NPPB, PGR, POLR2A, RBL2, SET, SMARCA2, SMARCE1, SP3, SUCLA2, Repair SYP MC MT

BCAS3, BRCA1, CA12↑, CASP1, CDCA7↑, Ck2, DCLK1, DDX11, DLEU1, DLEU2, E2F2↑, ERF, 1 GM10155, GPR68↓, GREB1↓, HCG, IFI6↑, KLK10↓, MFAP1, MIR193B, MYBL1↓, MYC↓, NARS, 33 11 Cell Death Nc2, NOP56, PERP, PTGS2, RNA polymerase II, SPRR3, SSBP2, STC2↓, TFF1↓, TMEM126A

MC AC ACO1, beta-estradiol, CA12↑, Cbp/p300-Maf-Nfe2l2, CEBPB, CHI3L1, CSPG4, CTNNB1, CTSS, CYBA, Cyba-Ncf1c-Ncf2-Nox-Ncf4, FTL, GSTM1↑, GSTM3↑, HRAS, IFI6↑, IFI27↑, IRF9, MPZ, Cell Cycle 1 35 10 MYC, nitric oxide, NUPR1, PMP22↓, SKI, SPRR1A, STC2↓, TGFB1, TM4SF1, Top2, TUBA4A↑, progression TUBG1↑, TXN2, UGT1A1, UGT1A6↑

Actin, ADAM12, AHSG, AKT1, ASAM↓, ATP8A2, BCL2, C1S, CARHSP1, CCNL2, CGA↑ CHI3L1, CSPG4, CTSF↑, CTSL2, CTSS, DYRK2, FAM110B, FBXO2↑, GRN, HNF4A, Igf, ITGB1, 2 36 10 Cell Motility ITPKA↑, LGALS3, Mapk, NRTN, PNO1, POLR3F, PRSS1 , PRSS3, PTPRJ↓, RAI2↑, RAMP1↓, SKI, STC2↓, TGFB1↓, TLR6

ABL1, ACTN2, AKT3, ASAM↓, BAIAP2, BDNF,CGA↑, F Actin, FBXO2↑, FES, GAD1↓, GAL↑, GPR155↑, GRIN1, GRIN2B, Hsp90, IFI6↑, ITPKA, KCNK5↓, KIF23, MARK4, MBP, MLLT11↑, Neuropepetide 3 35 15 NDEL1, NUMA1, P2RY2↑,PARK2, PMP22 ↓, RAB8B, RASSF1,RHOBTB3↑, TUBA1A, signaling TUBA4A↑,TUBG1↑, VIM↑ ME AE ADAM17, ADAMTS1, ATF3↓, C1R, CDKN2AIPNL, CYBA, Cyba-Ncf1c-Ncf2-Nox-Ncf4, EML1, GSK3B, HNF4A, HSPA5, IFI6↑, IFNG, IL1B, MAP2K1, ONECUT1, PRKCZ, RAI2↓, Rap1-gp91- 1 33 6 Signal Tranduction p22 phox-p40 phox-p47 phox-p67 phox, RBM23, RGS22↓, RPL12, Rsk, SIL1↓, SLC3A1, SOCS7, STAR, TG, TNFAIP6, TUBA4A↑ Tubulin, UGT1A1, VWA5A

Endocrine System AKR1C1, AREG↑, ATP8A2, beta-estradiol, CGA↑, CGB, CMTM2A, COMP↓, CPE↑, Creb, CTSF↑, Development and 2 DAPK2↓, FSH, FSHB, FTL, GSTM1↑, GSTM3↑, hCG, Histone h3, HSPA4↑, IGF1, IGFBP5↑, IL6, 33 16 Function, Molecular Lh, Mapk, MYC, PIM1↓, RPRM↑, SHC2↓, SLC6A14↓, SV2B↑, TGFBR1, UGT1A6↓ Transport AC AT ACTN2, ASAM↓, BDNF, CAMK2A,CENPJ, Ck2,F Actin, FBXO2↑, MARK4, MBP, RAB8B, 1 17 4 Cell Motility RASSF1,SUSD4↓, UBA1A, TUBA4A, TUBB, TUBG1 AC AE ANO1, AREG↑, ATAD2, ATPIF1, BCAS3, beta-estradiol, c-Myc/N-Myc, CDCA7, CEBPB, Ck2, CRISP3, CSTB, DCLK1, DIO1↓, EGFR ligand, ERK1/2, FSH, GAD1↑, GM10155, GPR68, HCG 1 28 7 Signal Tranduction 1787519, KRT6A↑, MIR193B, MIRLET7B, MYBL1↑, MYC↑, NARS, NFkB (complex), NOP56, PTGS2, SPRR3, SQRDL, SSBP2, STC2↑, XIST

ACLY, AKT1, AR, ARHGAP32, BAG4, C15ORF29, CDKN2AIPNL, CTSL2, DEPDC6↑, FTL, Gene Expression, GSK3B, HNF4A, HSPA5, HSPA1B, HSPB2, KNG1, MME↓, MTOR, ONECUT1, PARK7, PPP2R5B, 2 35 7 Recombination, and PRKAA1, PSCA↓, Ptk, RAI2↓, RAMP1, RBM23, RGS22↓, SHC2↓, SIL1↑, SRC, SUCLA2, SYP, Repair UGT1A1, VWA5A

Supplementary Table S4 Comparison of Fold change of selected genes by microarray analysis and RT-qPCR

Cell line CGA CPE GAL H19 RRM2 ASAM CGNL1 MME PIM1 PTPRJ MT AT Akt3 10.27 10.58 6.90 3.29 5.09 -3.20 -7.31 -3.03 -2.10 Microarray* Akt3 11.44 8.46 9.67 2.66 5.34 -3.89 -7.14 -2.56 -2.20

Akt1 7.79 9.62 8.48 2.60 5.58 -3.53 -8.33 -2.27 -2.32

MDA-MB-468 8.25 8.94 7.62 2.52 8.99 -6.57 -12.07 -2.57 -2.50

RT-qPCR** ZR-75-1 4.91 14.87 3.58 5.10 2.27 -5.36 -13.50 -3.17 -3.12

MDA-MB-231 5.13 10.42 4.42 2.74 5.91 -5.92 -11.69 -2.45 -3.69 ME AE Akt3 16.81 8.70 -2.06 Microarray* Akt3 11.44 6.73 -2.48

Akt1 8.42 6.89 -2.47

MDA-MB-468 5.17 12.56 -2.78

RT-qPCR** ZR-75-1 6.12 4.93 -3.50

MDA-MB-231 5.01 4.99 -3.39 MC AC Akt3 6.02 -2.59 -2.39 -2.10 Microarray* Akt3 7.76 -3.39 -2.65 -3.37

Akt1 7.43 -2.89 -2.52 -2.00

MDA-MB-468 4.25 -1.97 -2.00 -2.20

RT-qPCR* ZR-75-1 5.98 -2.47 -1.92 -2.28

MDA-MB-231 6.52 -3.06 -2.48 -3.08 AC AT Akt3 -2.22 Microarray* Akt3 -2.43

Akt1 -2.06

MDA-MB-468 -1.80

ZR-75-1 -1.99 RT-qPCR** MDA-MB-231 -1.50

MC ME MCF-7 3.54 2.92 2.50 -2.82 -2.02 Microarray* RT-qPCR** MCF-7 4.22 2.63 1.99 -2.57 -2.04