Table S5-Correlation of cytogenetic changes with gene expression in MCF10CA1a FeatureNumCytoband GeneName Description logFC Fold change 28 4087 2p21 TACSTD1 Homo sapiens tumor-associated calcium signal transducer 1 (TACSTD1), mRNA-7.04966 [NM_002354]0.007548158 37 38952 20p12.2 JAG1 Homo sapiens jagged 1 (Alagille syndrome) (JAG1), mRNA [NM_000214] -6.44293 0.011494322 67 2569 20q13.33 COL9A3 Homo sapiens collagen, type IX, alpha 3 (COL9A3), mRNA [NM_001853] -6.04499 0.015145263 72 44151 2p23.3 KRTCAP3 Homo sapiens clone DNA129535 MRV222 (UNQ3066) mRNA, complete cds. [AY358993]-6.03013 0.015302019 105 40016 8q12.1 CA8 Homo sapiens carbonic anhydrase VIII (CA8), mRNA [NM_004056] 5.68101 51.30442111 129 34872 20q13.32 SYCP2 Homo sapiens synaptonemal complex protein 2 (SYCP2), mRNA [NM_014258]-5.21222 0.026975242 140 27988 2p11.2 THC2314643 Unknown -4.99538 0.031350145 149 12276 2p23.3 KRTCAP3 Homo sapiens keratinocyte associated protein 3 (KRTCAP3), mRNA [NM_173853]-4.97604 0.031773429 154 24734 2p11.2 THC2343678 Q6E5T4 (Q6E5T4) Claudin 2, partial (5%) [THC2343678] 5.08397 33.91774866 170 24047 20q13.33 TNFRSF6B Homo sapiens tumor necrosis factor receptor superfamily, member 6b, decoy (TNFRSF6B),-5.09816 0.029194423 transcript variant M68C, mRNA [NM_032945] 177 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.88156 [NM_000930]0.033923737 186 31003 20p11.23 OVOL2 Homo sapiens ovo-like 2 (Drosophila) (OVOL2), mRNA [NM_021220] -4.69868 0.038508469 200 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.78576 [NM_000930]0.036252773 209 9317 2p14 ARHGAP25 Homo sapiens Rho GTPase activating protein 25 (ARHGAP25), transcript variant-4.62265 1, mRNA0.040592167 [NM_001007231] 211 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA -4.7152[NM_000930]0.038070134 212 16979 2p13.1 MGC10955 Homo sapiens hypothetical protein MGC10955, mRNA (cDNA clone MGC:10955-4.70762 IMAGE:3632495),0.038270716 complete cds. [BC004960] 226 17873 2p13.3 TGFA Homo sapiens transforming growth factor, alpha (TGFA), mRNA [NM_003236]-4.80546 0.035761153 227 24069 8q13.3 SULF1 Homo sapiens sulfatase 1 (SULF1), mRNA [NM_015170] 4.79472 27.7558046 238 10756 20q13.31 BMP7 Homo sapiens bone morphogenetic protein 7 (osteogenic protein 1) (BMP7), mRNA-4.74443 [NM_001719]0.037306451 241 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.67472 [NM_000930]0.039153439 253 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.70373 [NM_000930]0.038374016 256 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.71094 [NM_000930]0.038182703 257 4244 20q13.33 SLCO4A1 Homo sapiens solute carrier organic anion transporter family, member 4A1 (SLCO4A1),-4.4338 mRNA0.046269366 [NM_016354] 258 10059 20q13.33 PTK6 Homo sapiens PTK6 protein tyrosine kinase 6 (PTK6), mRNA [NM_005975] -4.41726 0.04680276 261 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.66825 [NM_000930]0.039329442 265 37039 20q13.12 SLPI Homo sapiens secretory leukocyte peptidase inhibitor (SLPI), mRNA [NM_003064]-4.39728 0.047455435 268 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.69536 [NM_000930]0.038597278 277 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.64443 [NM_000930]0.039984186 288 39605 8p11.21 PLAT Homo sapiens plasminogen activator, tissue (PLAT), transcript variant 1, mRNA-4.65348 [NM_000930]0.039734012 291 32344 8q12.1 AK055621 Homo sapiens cDNA FLJ31059 fis, clone HSYRA2000832. [AK055621] 4.30573 19.77667175 296 5333 20q13.12 EYA2 Homo sapiens eyes absent homolog 2 (Drosophila) (EYA2), transcript variant 2,-4.29336 mRNA [NM_172113]0.051000101 304 30720 9p22.1 AK024898 Homo sapiens cDNA: FLJ21245 fis, clone COL01184. [AK024898] -4.26394 0.052050697 308 13188 20q13.33 STMN3 Homo sapiens stathmin-like 3 (STMN3), mRNA [NM_015894] -5.19578 0.027284363 311 20510 20q13.12 SLPI Homo sapiens secretory leukocyte peptidase inhibitor (SLPI), mRNA [NM_003064]-4.2296 0.05330455 324 24279 20p12.1 FLRT3 Homo sapiens fibronectin leucine rich transmembrane protein 3 (FLRT3), transcript-4.387 variant0.047794886 2, mRNA [NM_198391] 332 14493 20q13.12 JPH2 Homo sapiens junctophilin 2 (JPH2), transcript variant 1, mRNA [NM_020433] 4.20088 18.39034261 374 11143 2p14 C2orf32 Homo sapiens chromosome 2 open reading frame 32 (C2orf32), mRNA [NM_015463]4.64416 25.00534113 378 7410 2p24.2 VSNL1 Homo sapiens visinin-like 1 (VSNL1), mRNA [NM_003385] -4.52644 0.043391705 392 43642 20p13 SLC4A11 Homo sapiens solute carrier family 4, sodium bicarbonate transporter-like, member-4.0555 11 (SLC4A11),0.060141128 mRNA [NM_032034] 406 28657 20q13.12 PI3 Homo sapiens peptidase inhibitor 3, skin-derived (SKALP) (PI3), mRNA [NM_002638]-4.4964 0.044304471 412 27477 2p23.3 LOC339778 Homo sapiens cDNA FLJ34164 fis, clone FCBBF3014567. [AK091483] -4.7973 0.035964031 416 44593 8p23.1 ENST00000360178sWSS3420 Eric D. Green Homo sapiens STS cDNA clone 7B04E04, sequence-4.77852 tagged site.0.036435302 [G30702] 428 41456 20q11.23 C20orf102 Homo sapiens chromosome 20 open reading frame 102 (C20orf102), mRNA [NM_080607]3.89398 14.86640223 423 15662 8p23.1 C8orf13 Homo sapiens chromosome 8 open reading frame 13 (C8orf13), mRNA [NM_053279]4.68132 25.65771845 452 20927 20q13.32 SYCP2 Homo sapiens synaptonemal complex protein 2 (SYCP2), mRNA [NM_014258]-5.54167 0.021467958 470 21367 2p16.1 ENST00000233161Homo sapiens mRNA for KIAA1912 protein, partial cds. [AB067499] 4.21931 18.62688614 488 28361 20q13.12 WISP2 Homo sapiens WNT1 inducible signaling pathway protein 2 (WISP2), mRNA [NM_003881]3.72058 13.18272872 497 6733 2p11.2 TGOLN2 Homo sapiens trans-golgi network protein 2 (TGOLN2), mRNA [NM_006464] -4.04294 0.060666976 504 44651 8q13.2 C8orf34 Homo sapiens chromosome 8 open reading frame 34 (C8orf34), mRNA [NM_052958]3.72261 13.20133721 514 15821 20q13.13 KCNG1 Homo sapiens potassium voltage-gated channel, subfamily G, member 1 (KCNG1),-3.7499 transcript0.074330534 variant 1, mRNA [NM_002237] 526 19331 2p24.1 BI058698 BI058698 PM1-GN0499-060401-006-h10 GN0499 Homo sapiens cDNA, mRNA-3.66398 sequence0.078891898 [BI058698] 530 12678 20q13.12 SULF2 Homo sapiens sulfatase 2 (SULF2), transcript variant 1, mRNA [NM_018837] -3.92152 0.065994033 544 33261 20q12 MAFB Homo sapiens v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian)3.74947 (MAFB),13.44940682 mRNA [NM_005461] 550 33475 8q12.3 A_24_P247205Unknown 3.62918 12.37345333 561 12530 8p11.23 TACC1 Homo sapiens transforming, acidic coiled-coil containing protein 1 (TACC1), mRNA3.72957 [NM_006283]13.26515625 615 36804 20q13.12 EYA2 Homo sapiens eyes absent homolog 2 (Drosophila) (EYA2), transcript variant 2,-3.45369 mRNA [NM_172113]0.091271608 632 828 20q13.13 CD521096 CD521096 AGENCOURT_14355292 NIH_MGC_191 Homo sapiens cDNA clone-3.41836 IMAGE:304108150.093534412 5', mRNA sequence [CD521096] 633 3535 20q13.13 B4GALT5 Homo sapiens UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide-3.41584 5 (B4GALT5),0.093697831 mRNA [NM_004776] 640 23593 9p13.1 CNTNAP3 Homo sapiens contactin associated protein-like 3 (CNTNAP3), mRNA [NM_033655]-3.40789 0.094215736 659 7516 9p24.2 VLDLR Homo sapiens very low density lipoprotein receptor (VLDLR), transcript variant -3.520161, mRNA [NM_003383]0.087162109 666 33255 9p13.3 AQP3 Homo sapiens aquaporin 3 (Gill blood group) (AQP3), mRNA [NM_004925] -3.85854 0.068938626 676 12567 2p23.1 GALNT14 Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase3.66894 12.71920927 14 (GalNAc-T14) (GALNT14), mRNA [NM_024572] 702 42931 2p23.3 CGREF1 Homo sapiens cell growth regulator with EF-hand domain 1 (CGREF1), mRNA -3.36409[NM_006569]0.097119723 698 33432 20p13 TRIB3 Homo sapiens tribbles homolog 3 (Drosophila) (TRIB3), mRNA [NM_021158] -3.31312 0.100612116 743 8193 9p13.1 RP11-138L21.1Homo sapiens cDNA FLJ30083 fis, clone BGGI12001097, weakly similar to Homo-3.24132 sapiens0.105746456 contactin associated protein (Caspr) mRNA. [AK054645] 781 40097 9p13.3 AQP3 Homo sapiens aquaporin 3 (Gill blood group) (AQP3), mRNA [NM_004925] -3.31398 0.100552233 797 23893 8q21.11 RDH10 Homo sapiens retinol dehydrogenase 10 (all-trans) (RDH10), mRNA [NM_172037]-3.63066 0.080735154 803 20306 2p13.1 HK2 Homo sapiens hexokinase 2 (HK2), mRNA [NM_000189] -3.47097 0.090185227 839 44377 9p13.1 CNTNAP3 Homo sapiens contactin associated protein-like 3 (CNTNAP3), mRNA [NM_033655]-3.10109 0.116541211 849 6490 2p22.2 CYP1B1 Homo sapiens cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1),3.32189 mRNA [NM_000104]9.999709112 854 42256 8q12.3 BC040678 Homo sapiens cDNA clone IMAGE:4817707. [BC040678] 3.07738 8.440823164 855 5798 2p22.3 LTBP1 Homo sapiens latent transforming growth factor beta binding protein 1 (LTBP1),3.34948 transcript variant10.19280661 1, mRNA [NM_206943] 871 27596 20q11.22 PROCR Homo sapiens protein C receptor, endothelial (EPCR) (PROCR), mRNA [NM_006404]-3.17936 0.110386936 878 21008 8p21.2 DPYSL2 Homo sapiens dihydropyrimidinase-like 2 (DPYSL2), mRNA [NM_001386] 3.22224 9.332324875 886 496 8q12.1 C8orf72 Homo sapiens chromosome 8 open reading frame 72 (C8orf72), mRNA [NM_147189]3.09399 8.538516277 902 27757 2p23.1 XDH Homo sapiens xanthine dehydrogenase (XDH), mRNA [NM_000379] -3.4198 0.093440847