Table S1. ShRNA sequences used in the present study* shRNA mature sequence ERBB2 CCCTGGCCGTGCTAGACAA NR1D1 GGCATGGTGTTACTGTGTA PBP CCGAGTTCCTCTTATCCTA MAP2K6 CAGATGACCTGGAGCCTAT SPINT1 CTGTGTAGTTTGTGCTGTA PFN2 AGCATTACGCCAATAGAAA MKI67 GCTACAAACTCCTAAGGAA TPD52 CTGTGAGATTCCTACCTTT BNIP3L AGCAGCAATGGCAATGATA LASP1 GGACCAGATCAGTAATATA CA9 CTTTGAATGGGCGAGTGAT FADS2 CCCATAGGGAGCTGATCGT ERBB3 CTACCAGTTGGAACACTTA GRB7 CTCGCCATCTGCATCCATC STARD3 AGGAGATCATCCAGTACAA FASN CTGGCCCAGGCTGAAGTTT ACLY GGGAGGAAGCTGATGAATA ACACA CACATGACCTTAAGATTAT MDH1 CGAGCTAAAGCTAAATTG ME1 GGCTTTATCCTCCTTTGAA *all shRNA sequences used in the present study can be retrieved in http://codex.cshl.edu

Table S2. Primer pairs used for qRT-PCR in the present study forward primer reverse primer ERBB2 5’-AGACACGTTTGAGTCCATGCC-3’ 5’-ATCCCACGTCCGTAGAAAGGT-3’ NR1D1 5’-CCGTGACCTTTCTCAGCATGA-3’ 5’-CACTGTCTGGTCCTTCACGTTG-3’ PBP 5’-GGCAACAACCCAATGAGTGGT-3’ 5’-ATGCCGATCTTTGATGCTCATG-3’ FASN 5’-GAACTCCTTGGCGGAAGAGAA-3’ 5’-GCGAGAAGTCAACACGAGCTT-3’ ACLY 5’-AAGATCTCGTGGCCAATGGA-3’ 5’-AGGTTTGCGGATCAAACCAA-3’ ACACA 5’-CTTTGTGCCCACGGTTATCA-3’ 5’-AGTGGTCCCTGTTTGTCTCCA-3’ MDH1 5’-TGCAAGGAAAGGAAGTTGGTG-3’ 5’-TTCGAGCCTTGATGACAGCAG-3’ FADS2 5’ TGGTCATTGACCGCAAGGTT-3’ 5’-AGGCATCCGTTGCATCTTCTC-3’ ME1 5’-GCCATTGTGGTGACTGATGGA-3’ 5’-TCATCCCTCCGCAAGCTGTAT-3’ aP2 5’-GCATGGCCAAACCTAACATGAT-3’ 5’-CCTGGCCCAGTATGAAGGAAA-3’ -actin 5’-CTGTCCACCTTCCAGCAGATGT-3’ 5’-CCTGGCCCAGTATGAAGGAAA-3’ Table S3. The RNAi screen on overexpressed in ERBB2-positive breast cancer Accession # Symbol Description Reference shRNA-1* shRNA-2 shRNA-3 % control** ***s.d. z-score % control s.d. z-score % control s.d. z-score NM_006408 AGR2 anterior gradient homolog 2 (Xenopus laevis) 6 65.11 24.59 -1.09 NM_003220 AP2A factor AP-2 alpha (activating enhancer binding 2 alpha) 56 63.64 25.82 -1.15 NM_003222 AP-2 transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) 56 120.44 13.24 1.43 NM_024320 ATAD4 ATPase family, AAA domain containing 4 6 80.99 10.22 -0.36 NM_005765 ATP6AP2 ATPase, H+ transporting, lysosomal accessory protein 2 6 101.38 20.56 0.56 111.66 45.63 1.03 NM_004888 ATP6V1G1 ATPase, H+ transporting, lysosomal (vacuolar proton pump), member J 6 79.34 8.16 -0.44 88.00 8.47 -0.05 91.86 17.35 0.13 NM_004281 BAG3 BCL2-associated athanogene 3 6 123.59 50.76 1.57 NM_004331 BNIP3L BCL2/adenovirus E1B 19kDa interacting protein 3-like 6 54.62 9.66 -1.61 NM_032937 C9orf37 9 open reading frame 37 6 73.97 14.26 -0.68 75.96 4.18 -0.59 NM_001216 CA9 carbonic anhydrase CA IX 57 54.00 15.87 -1.59 113.45 21.59 1.11 NM_053056 CCND1 cyclin D1 CCND1 58 103.82 36.74 0.67 111.71 17.78 1.03 112.12 12.80 1.05 NM_013230 CD24 CD24 6 95.47 31.12 0.29 NM_004933 CDH15 15, M-cadherin (myotubule) CDH15 7 76.98 7.42 -0.55 NM_001793 CDH3 cadherin 3, type 1, P-cadherin (placental) 6 117.26 22.75 1.28 NM_003159 CDLK5 cyclin-dependent kinase-like 5 (CDKL5) 7 79.47 17.01 -0.43 100.02 2.94 0.50 100.25 3.83 0.51 NM_001803 CDW52 CDW52 (CAMPATH-1 antigen) 6 108.56 18.74 0.89 NM_001408 CELSR2 cadherin, EGF LAG seven-pass G-type receptor 2 CELSR2 7 67.39 28.09 -0.98 99.12 9.85 0.46 NM_003909 CPNE3 Copine III 6 68.27 8.09 -0.94 97.32 24.84 0.38 101.69 3.20 0.58 NM_001311 CRIP1 Cysteine-rich protein 1, intestinal 6 109.82 4.13 0.95 NM_024223 CRIP2 cysteine-rich protein 2 6 89.35 24.35 0.02 NM_003651 CSDA Cold shock domain protein A 6 58.04 20.17 -1.41 89.02 3.76 0.00 104.97 13.45 0.73 NM_005213 CSTA cystatin A (stefin A) CSTA 7 72.87 30.71 -0.73 86.53 4.23 -0.11 88.76 3.12 -0.01 NM_005930 CTAGE5 CTAGE family, member 5 (CTAGE5), transcript variant 1 6 107.75 11.03 0.85 NM_001903 CTNNA1 1-Catenin 6 70.10 7.78 -0.86 NM_015462 DKFZP586L0724 DKFZP586L0724 protein 59 97.09 13.30 0.37 99.84 5.44 0.49 100.78 2.70 0.54 NM_004747 DLG5 Discs (Drosophila), large homolog 5 6 97.94 25.44 0.41 NM_005494 DNAJB6 DnaJ (Hsp40) homolog, subfamily B, member 6 6 106.38 6.13 0.79 NM_022365 DNAJC1 DnaJ (Hsp40) homolog, subfamily C, member 1 6 101.86 12.65 0.58 NM_021800 DNAJC12 DnaJ (Hsp40) homolog, subfamily C, member 12 6 87.18 6.46 -0.08 106.17 15.44 0.78 114.95 14.81 1.18 NM_001405 EFNA2 ETS-related transcription factor Elf-1/ephrin-A2 (EFNA2) 60 98.62 19.66 0.44 NM_005228 EGFR epidermal growth factor receptor EGFR 61 67.06 3.17 -1.00 71.46 24.89 -0.80 98.80 20.91 0.45 NM_024757 EHMT1 euchromatic histone-lysine N-methyltransferase 1 (EHMT1) 6 95.40 17.28 0.29 109.08 17.33 0.91 NM_012843 EMP1 epithelial 1 6 95.63 37.20 0.30 NM_004901 ENTPD4 ectonucleoside triphosphate diphosphohydrolase 4 (ENTPD4) 6 98.04 2.46 0.41 NM_001429 EP300 ER81 coactivator p300 62 73.43 1.30 -0.71 NM_004448 ERBB2 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 (avian) 5,6,7 27.03 6.30 -2.82 42.18 6.62 -2.13 48.74 8.93 -1.83 NM_001006600 ERBB2IP erbb2 interacting protein 5 94.51 20.92 0.25 120.82 19.67 1.45 BC082992 ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) 65 69.33 16.86 -0.89 72.18 20.51 -0.76 72.34 0.93 -0.76 NM_000125 ESR1 estrogen receptor 1 ESR1 5, 7 62.29 23.24 -1.21 88.15 15.99 -0.04 91.71 19.06 0.12 NM_004956 ETV1 ETS transcription factor ER81/ets variant gene 1 (ETV1) 62 73.96 4.61 -0.68 92.26 11.39 0.15 105.00 9.21 0.73 NM_178516 EXOC3L exocyst complex component 3-like (loc283849) 7 80.71 1.90 -0.38 81.61 4.20 -0.34 97.27 2.06 0.38 NM_004265 FADS2 fatty acid desaturase 2 FADS2 7 63.55 27.33 -1.16 78.63 4.92 -0.47 86.03 4.08 -0.13 NM_004104 FASN fatty acid synthase FAS 66 75.41 4.15 -0.62 92.39 31.86 0.15 101.57 16.69 0.57 NM_002014 FKBP4 FK506-binding protein 4 6 54.62 4.51 -1.56 91.47 3.12 0.11 106.06 18.86 0.78 NM_004496 FOXA1 Homo sapiens forkhead box A1 (FOXA1) (Hepatocyte nuclear factor 3a) 5 82.08 29.60 -0.31 91.33 1.08 0.11 100.23 22.37 0.51 NM_004483 GCSH glycine cleavage system protein H (aminomethyl carrier) (GCSH) 6 87.16 1.40 -0.08 91.24 23.76 0.10 NM_005310 GRB7 growth factor receptor-bound protein 7 GRB7 5, 59 71.41 0.77 -0.80 76.58 9.95 -0.56 NM_004893 H2AFY H2A histone family, member Y 6 50.47 3.18 -1.75 68.85 19.60 -0.92 NM_005324 H3F3B H3 histone family, 3B 6 70.57 28.50 -0.84 100.91 3.12 0.54 106.72 1.61 0.81 NM_017802 HEATR2 HEAT repeat containing 2 (FLJ20397) 6 62.61 16.34 -1.20 NM_005345 HSPA1A heat shock 70kDa protein 1A 6 75.68 0.97 -0.61 101.02 6.07 0.55 110.94 10.28 1.00 NM_005346 HSPA1B heat shock 70kDa protein 1B 6 107.16 6.13 0.83 NM_005527 HSPA1L heat shock 70kDa protein 1-like 6 95.13 10.70 0.28 NM_002155 HSPA6 heat shock 70kDa protein 6 (HSP70B') (HSPA6) 6 48.23 5.95 -1.85 68.85 22.11 -0.92 70.58 10.38 -0.84 NM_024610 HSPBAP1 HSPB (heat shock 27kDa) associated protein 1 6 87.43 4.73 -0.07 113.28 6.85 1.10 135.30 6.72 2.10 NM_001017963 HSPCA heat shock protein 90kDa alpha (cytosolic), class A member 1 67 94.55 5.29 0.25 NM_007355 HSPCB heat shock protein 90kDa alpha (cytosolic), class B member 1 67 75.67 4.15 -0.61 89.26 1.29 0.01 92.41 5.85 0.16 NM_002203 ITGA2 , alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) ITGA2 7 65.74 31.78 -1.06 80.44 13.43 -0.39 99.28 2.97 0.47 NM_000419 ITGA2B integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B) 7 91.97 11.60 0.13 NM_000212 ITGB3 integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) ITGB3 7 89.68 10.76 0.03 93.79 14.41 0.22 102.73 24.09 0.62 NM_015202 KIAA0556 KIAA0556 protein 6 79.85 13.40 -0.42 114.45 4.26 1.16 NM_002266 KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) 6 78.63 6.77 -0.47 88.94 12.43 0.00 NM_000224 KRT18 Keratin 18 6 89.42 4.25 0.02 126.94 6.36 1.72 NM_005556 KRT7 Keratin 7 5 68.17 2.54 -0.95 NM_006148 LASP1 LIM and SH3 protein 1 59 37.54 15.30 -2.34 43.28 19.44 -2.08 NM_006498 LGALS1 lectin, galactoside-binding, soluble, 2 6 78.79 4.66 -0.46 NM_005570 LMAN1 lectin, mannose-binding, 1 6 86.64 16.09 -0.11 88.32 5.16 -0.03 100.50 6.82 0.52 NM_005574 LMO2 LIM domain only 2 66 67.25 4.93 -0.99 92.05 4.51 0.14 92.99 20.68 0.18 NM_006769 LMO4 LIM domain only 4 LMO4 66 91.97 1.74 0.13 111.19 5.08 1.01 121.30 21.70 1.47 NM_002317 LOX lysyl oxidase LOX 7 77.60 30.62 -0.52 88.35 8.63 -0.03 NM_006726 LRBA LPS-responsive vesicle trafficking, beach and anchor containing LRBA 67 90.99 3.94 0.09 NM_052886 MAL2 T-cell differentiation protein 2 (MAL2) 6 80.80 2.03 -0.37 NM_002758 MAP2K6 mitogen-activated protein kinase kinase 6 MAP2K6 7 37.23 11.97 -2.35 57.00 22.55 -1.45 68.63 3.69 -0.93 NM_005885 MARCH6 membrane-associated ring finger (C3HC4) 6 (MARCH6) 6 54.36 11.40 -1.57 71.29 6.58 -0.80 79.82 4.62 -0.42 NM_032315 MGC4399 Mitochondrial carrier protein 6 99.60 9.64 0.48 96.02 12.64 0.32 NM_033418 MGC9084 chromosome 1 open reading frame 156 (C1orf156) - MGC9084 6 85.82 9.36 -0.14 NM_020300 MGST1 Microsomal glutathione S-transferase 1 6 88.54 0.84 -0.02 110.86 19.34 0.99 NM_002417 MKI67 antigen identified by monoclonal antibody Ki-67 MKI67 7 32.99 5.78 -2.55 61.34 23.85 -1.26 NM_024101 MLPH melanophilin (MLPH) 6 70.55 9.71 -0.84 NM_002421 MMP1 matrix metallopeptidase 1 68 75.25 2.90 -0.62 80.41 8.00 -0.39 NM_033546 MRLC2 Myosin, light polypeptide, regulatory, non-sarcomeric MRLC2 6 81.66 27.47 -0.33 117.07 8.72 1.28 NM_018728 MYO5C myosin VC (MYO5C) 6 84.59 6.56 -0.20 NM_007067 MYST2 MYST histone acetyltransferase 2 (MYST2) 6 99.22 6.64 0.46 103.09 7.75 0.64 120.04 24.70 1.41 NM_000662 NAT1 N-acetyltransferase 1 (arylamine N-acetyltransferase) NAT1 7 138.19 23.72 2.24 NM_001135242 NDRG1 N-myc downstream regulated 1 6 53.95 8.69 -1.59 NM_005005 NDUFB9 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa (NDUFB9) 6 71.44 0.12 -0.80 NM_006169 NNMT nicotinamide N-methyltransferase 6 60.75 18.84 -1.28 122.17 5.25 1.51 NM_010928 NOTCH2 Notch gene homolog 2 70 95.47 5.65 0.29 107.53 26.55 0.84 109.97 8.28 0.95 NM_006432 NPC2 Niemann-Pick disease, type C2 (NPC2) 6 75.11 4.93 -0.63 75.25 12.98 -0.63 AY391444 NR1D1 nuclear receptor subfamily 1, group D, member 1 NR1D1 7 35.83 18.15 -2.42 49.74 2.00 -1.78 57.71 12.98 -1.42 NM_012229 NT5C2 5'-nucleotidase, cytosolic II (NT5C2) 6 73.98 6.41 -0.68 55.56 3.89 -1.52 93.81 18.01 0.22 NM_021980 OPTN optineurin (OPTN), transcript variant 2; TNF- inducible cellular protein 6 94.10 14.96 0.23 109.36 2.63 0.93 AJ001981 OXA1L Oxidase (cytochrome c) assembly-like 1 6 62.90 15.27 -1.19 88.31 13.39 -0.03 NM_001017973 P4HA2 procollagen-proline, 2-oxoglutarate 4-dioxygenase, alpha polypeptide II 6 68.27 7.02 -0.94 78.46 21.92 -0.48 NM_004643 PABPN1 poly(A) binding protein, nuclear 1 6 90.82 5.35 0.08 95.36 8.77 0.29 NM_005746 PBEF1 pre-B-cell colony enhancing factor 1 (PBEF1) 7 106.31 5.74 0.79 115.21 0.17 1.19 126.79 15.00 1.72 NM_004774 PBP PPAR binding protein PPARBP 7, 59 37.08 19.04 -2.36 59.69 5.99 -1.33 60.94 6.09 -1.28 NM_002585 PBX1 Homo sapiens pre-B-cell leukemia transcription factor 1 (PBX1) 6 100.60 16.93 0.53 89.29 9.62 0.01 NM_000442 PECAM1 platelet/endothelial molecule (CD31 antigen) PECAM1 7 62.53 15.20 -1.20 89.95 21.90 0.04 120.98 12.35 1.45 NM_033419 PERLD1 per1-like domain containing 1 (PERLD1) 6 100.59 23.56 0.53 112.26 13.13 1.06 NM_000287 PEX6 peroxisomal biogenesis factor 6 (PEX6) 6 90.71 16.72 0.08 118.94 14.70 1.36 NM_004566 PFKFB3 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 6 78.38 21.75 -0.48 98.45 19.23 0.43 115.55 15.48 1.21 NM_053024 PFN2 Homo sapiens profilin 2 (PFN2)s transcript variant 1, mRNA. 6 41.06 21.15 -2.18 56.45 14.58 -1.48 NM_004203 PKMYT1 Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase 6 110.19 7.97 0.96 NM_005030 PLK1 polo-like kinase 1 PLK1 70 78.29 31.41 -0.49 88.97 7.24 0.00 91.58 4.96 0.12 NM_006254 PRKCD protein kinase C, delta 71 93.71 5.55 0.21 121.42 8.52 1.47 NM_018979 PRKWNK1 Homo sapiens WNK lysine deficient protein kinase 1 (KIAA0344) 6 83.22 11.12 -0.26 86.02 19.22 -0.14 93.16 8.81 0.19 NM_002791 PSMA6 proteasome (prosome, macropain) subunit, alpha type, 6 (PSMA6) 6 105.57 28.72 0.75 NM_002795 PSMB3 proteasome (prosome, macropain) subunit, beta type, 3 PSMB3 7 78.28 19.55 -0.49 85.08 17.28 -0.18 NM_000963. PTGS2 prostaglandin-endoperoxide synthase 2 (PTGS2)/cyclooxygenase 2 COX-2 72 114.37 9.12 1.15 119.86 3.04 1.40 NM_006265 RAD21 RAD21 6 75.62 3.24 -0.61 121.12 15.21 1.46 123.12 3.11 1.55 NM_213589 RAPH1 Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 (RAPH1) 7 76.78 5.48 -0.56 118.17 9.88 1.33 NM_032308 RIP RPA interacting protein (RPAIN) 6 90.43 3.15 0.06 91.56 14.47 0.12 NM_000985 RPL17 Ribosomal protein L17 6 69.57 14.65 -0.88 NM_000981 RPL19 Ribosomal protein L19 7 95.48 9.43 0.29 124.84 5.35 1.63 NM_001026 RPS24 Ribosomal protein S24 6 84.98 18.64 -0.18 128.36 5.25 1.79 NM_001012 RPS8 Ribosomal protein S8 6 87.69 0.67 -0.06 108.87 9.48 0.90 111.65 11.99 1.03 NM_002411 SCGB2A2 secretoglobin, family 2A, member 2 6 82.54 14.45 -0.29 NM_020974 SCUBE2 signal peptide, CUB domain, EGF-like 2 SCUBE2 7 79.17 14.46 -0.45 80.36 10.96 -0.39 116.11 6.51 1.23 NM_004593 SFRS10 splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila) 6 98.62 3.17 0.44 NM_006276 SFRS7 splicing factor, arginine/serine-rich 7, 35kDa (SFRS7) 6 53.87 17.78 -1.60 72.75 14.01 -0.74 128.09 12.27 1.78 NM_006278 SIAT4C Homo sapiens sialyltransferase 4C (beta-galactoside ST3GAL4 6 53.30 23.70 -1.62 NM_005071 SLC1A6 solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6 6 96.03 12.20 0.32 NM_013272 SLCO3A1 solute carrier organic anion transporter family, member 3A1 (SLCO3A1) 6 94.28 10.77 0.24 106.67 6.24 0.80 132.41 1.18 1.97 NM_003064 SLPI Secretory leukocyte protease inhibitor (antileukoproteinase) 6 38.65 6.13 -2.29 NG_001056 SNRPFP1 small nuclear ribonucleoprotein polypeptide F 1 6 103.62 29.16 0.66 NM_003710 SPINT1 Serine protease inhibitor, Kunitz type I 6 42.88 18.59 -2.10 NM_003129 SQLE squalene epoxidase 6 67.20 30.85 -0.99 NM_006804 STARD3 StAR-related lipid transfer (START) domain containing 3 59 66.88 9.93 -1.01 70.04 9.30 -0.86 106.19 10.66 0.78 NM_006819 STIP1 stress-induced-phosphoprotein 1 (/Hsp90-organizing protein) 6 103.66 36.03 0.67 104.33 29.51 0.70 114.00 11.84 1.14 NM_015894 STMN3 stathmin-like 3 6 58.96 12.81 -1.37 75.92 22.17 -0.59 NM_002353 TACSTD2 tumor-associated calcium signal transducer 2 6 74.98 19.93 -0.64 97.00 33.40 0.36 NM_000359 TGM1 transglutaminase 1 6 103.74 10.22 0.67 BC092442 TIF2 nuclear receptor coactivator 2, mRNA (TIF2) 75 106.87 11.88 0.81 111.28 7.47 1.01 117.91 4.70 1.31 NM_014399 TM4SF13 TSPAN13 tetraspanin 13 6 92.01 10.50 0.14 101.73 12.66 0.58 NM_003810 TNFSF10 TNF superfamily, member 10 (TNFSF10) 6 70.08 13.10 -0.86 104.86 10.82 0.72 118.69 14.84 1.35 NM_005079 TPD52 Tumor protein D52 6 46.50 23.29 -1.93 82.02 17.87 -0.32 96.08 38.50 0.32 NM_003376 VEGF vascular endothelial growth factor VEGF 76 71.24 20.17 -0.81 90.90 15.64 0.09 NM_003380 VIM vimentin 6 78.35 10.11 -0.48 87.87 23.69 -0.05 NM_012082 ZFPM2 Zinc finger protein, multitype 2 6 80.48 12.97 -0.39 93.72 10.99 0.21 120.95 4.68 1.45 BC094693 ZMYND17 zinc finger, MYND-type containing 17 (ZMYND17) 6 91.78 5.16 0.13 131.75 6.55 1.94 * at least three shRNAs are shown, where available ** average % proliferation (alamarBlue) of control shRNA and *** standard deviation from 9 parallel cultures Table S4. AlamarBlue results* of the best shRNAs from the screen transfected in various cell lines BT474 MDA-MB-361 SK-BR-3 MCF-7 MDA-MB-453 MDA-MB-468 HMEC HEK 293 Genes avg** stDev*** avg stDev avg stDev avg stDev avg stDev avg stDev avg stDev avg stDev SPINT1 42.87 18.59 103.07 23.76 79.28 10.19 97.20 0.56 87.07 7.58 109.04 6.68 97.42 13.11 107.80 9.89 RPL19 55.24 9.92 106.23 28.21 70.47 9.02 102.42 0.59 34.42 2.69 47.89 2.89 88.15 14.68 68.25 16.68 BNIP3L 54.62 9.66 48.45 42.97 79.57 10.12 89.22 0.99 76.22 7.85 75.09 3.81 78.91 17.14 ND ND PBP 37.08 19.04 37.71 35.51 46.02 1.12 120.29 3.05 103.26 3.46 90.11 3.16 101.65 1.97 90.96 3.34 NR1D1 35.83 18.15 50.36 5.11 0.93 6.29 103.15 1.61 116.13 5.24 98.25 7.38 101.69 1.86 104.22 10.95 PFN2 41.06 21.15 60.21 32.69 73.81 3.03 106.06 1.72 113.72 1.67 100.26 4.95 88.76 17.37 107.01 3.81 LASP1 43.27 19.44 39.36 29.50 4.42 4.33 7.94 1.12 59.44 9.07 90.24 6.35 57.76 2.19 104.50 9.30 SLPI 38.65 6.13 55.41 65.16 62.39 10.88 138.44 1.21 57.48 4.92 90.73 11.95 99.00 14.72 85.11 10.97 H2AFY 50.46 3.18 25.01 22.73 79.34 7.24 71.39 3.95 91.78 1.86 115.38 1.87 78.57 1.44 112.22 5.20 MAP2K6 37.23 11.97 96.05 6.51 91.87 1.70 79.97 0.52 96.81 4.79 99.13 11.75 99.18 6.67 106.69 6.85 SIAT4C 53.30 23.70 67.41 20.77 72.35 0.61 141.15 0.10 55.25 6.37 55.40 11.21 101.17 13.10 66.65 8.91 CA9 54.01 15.87 71.58 56.40 63.91 6.38 90.16 1.00 43.11 10.93 65.89 12.78 71.73 6.10 90.55 6.18 TPD52 46.50 23.29 58.00 35.90 63.69 11.65 91.71 0.88 49.05 9.20 55.93 10.00 78.06 13.44 ND ND MKI67 33.00 5.78 57.32 43.14 21.63 4.38 26.19 0.36 60.95 2.67 97.30 7.04 73.60 4.67 106.26 6.01 ERBB2 27.03 6.30 53.40 32.18 74.37 6.11 108.69 2.47 98.80 5.93 83.35 3.17 102.71 10.19 99.20 4.26 SFRS7 53.87 17.78 125.03 34.33 20.62 7.21 20.18 1.66 77.72 1.30 122.80 7.40 45.96 22.41 102.39 8.63 * shown as % of control (luciferase) shRNA; ** average; *** standard deviation Table S5. Microarray expression data showing correlation of NR1D1 and PBP to fat metabolism genes

ERBB2 ACLY Study: NR1D1 0.792 0.474 Title: Progression-specific genes identified by expression profiling of matched ductal carcinomas in situ and invasive breast tumors, combining laser capture microdissection and oligonucleotide microarray analysis. Author(s): Schuetz CS, Bonin M, Clare SE, Nieselt K, Sotlar K, Walter M, Fehm T, Solomayer E, Riess O, Wallwiener D, Kurek R, Neubauer HJ Reference: Cancer Res 2006/05/15 Measured 12,427 genes, 22,283 reporters. Experiment Type: mRNA Data Link(s): http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3893

ERBB2 ACACA Study: PBP 0.705 0.412 Title: Prognosis and profiling of 20q13-amplified breast cancers. [PubMed]

Author(s): Ginestier C, Cervera N, Finetti P, Esteyries S, Esterni B, Adelaide J, Xerri L, Viens P, Jacquemier J, Charafe-Jauffret E, Chaffanet M, Birnbaum D, Bertucci F Reference: Clin Cancer Res 2006/08/01 Measured 19,079 genes, 54,675 reporters. Experiment Type: mRNA

ERBB2 ACACA Study: PBP 0.657 0.239 Title: Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial. a substudy of the EORTC 10994/BIG 00-01 clinical trial. Author(s): Bonnefoi H, Potti A, Delorenzi M, Mauriac L, Campone M, Tubiana-Hulin M, Petit T, Rouanet P, Jassem J, Blot E, Becette V, Farmer P, Andre S, Acharya CR, Mukherjee S, Cameron D, Bergh J, Nevins JR, Iggo RD Reference: Lancet Oncol 2007/12/01 Measured 19,120 genes, 61,348 reporters. Experiment Type: mRNA Data Link(s): http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6861

Supplementary References (36-54)

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