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Table S9: Summary of CN Loss Genes Identified by Fisher Test on ASCAT

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Table S9: Summary of CN Loss Genes Identified by Fisher Test on ASCAT Table S9: Summary of CN Loss Genes identified by Fisher Test on ASCAT Gene Symbol Chromosome Start End Length FIGF chrX 15363712 15402535 38824 PIR-FIGF chrX 15363712 15509432 145721 PIR chrX 15402923 15511711 108789 BMX chrX 15518899 15574652 55754 ACE2 chrX 15579155 15620192 41038 TMEM27 chrX 15645440 15683154 37715 CA5BP1 chrX 15693038 15721474 28437 CA5B chrX 15756411 15805748 49338 INE2 chrX 15803838 15805712 1875 ZRSR2 chrX 15808573 15841382 32810 AP1S2 chrX 15843928 15873100 29173 GRPR chrX 16141423 16171641 30219 SUPT20HL1 chrX 24380877 24383541 2665 PDK3 chrX 24483343 24568583 85241 PCYT1B chrX 24576203 24690979 114777 SSX9 chrX 48160984 48165614 4631 SSX3 chrX 48205862 48216142 10281 SSX4B chrX 48242956 48252785 9830 SSX4 chrX 48242967 48252785 9819 SSX4 chrX 48261523 48271344 9822 SSX4B chrX 48261523 48271355 9833 SLC38A5 chrX 48316926 48328644 11719 FTSJ1 chrX 48334548 48344752 10205 PORCN chrX 48367370 48379202 11833 EBP chrX 48380163 48387104 6942 TBC1D25 chrX 48398074 48420997 22924 RBM3 chrX 48432740 48439553 6814 WDR13 chrX 48455879 48463582 7704 WAS chrX 48542185 48549817 7633 SUV39H1 chrX 48555130 48567406 12277 GLOD5 chrX 48620153 48632064 11912 GATA1 chrX 48644981 48652717 7737 HDAC6 chrX 48660486 48683380 22895 ERAS chrX 48684922 48688279 3358 PCSK1N chrX 48689503 48694036 4534 TIMM17B chrX 48750729 48755426 4698 PQBP1 chrX 48755194 48760422 5229 SLC35A2 chrX 48760458 48769235 8778 PIM2 chrX 48770458 48776413 5956 OTUD5 chrX 48779302 48815648 36347 KCND1 chrX 48818638 48828251 9614 GRIPAP1 chrX 48830133 48858675 28543 TFE3 chrX 48886241 48900990 14750 CCDC120 chrX 48910960 48927510 16551 PRAF2 chrX 48928817 48931662 2846 WDR45 chrX 48932091 48958059 25969 GPKOW chrX 48969021 48980079 11059 MAGIX chrX 49019180 49023836 4657 PLP2 chrX 49028183 49031468 3286 PRICKLE3 chrX 49031905 49042776 10872 SYP chrX 49044264 49056661 12398 CACNA1F chrX 49061522 49089833 28312 IRAK1 chrX 153275956 153285342 9387 MIR718 chrX 153285370 153285440 71 MECP2 chrX 153287263 153363188 75926 OPN1LW chrX 153409724 153424507 14784 OPN1MW2 chrX 153448084 153461637 13554 OPN1MW chrX 153448084 153462352 14269 OPN1MW2 chrX 153485202 153498755 13554 OPN1MW chrX 153485202 153499470 14269 TEX28 chrX 153498929 153523564 24636 TKTL1 chrX 153524026 153558713 34688 FLNA chrX 153576899 153603006 26108 EMD chrX 153607596 153609883 2288 RPL10 chrX 153626570 153630680 4111 SNORA70 chrX 153628621 153628756 136 DNASE1L1 chrX 153629578 153640427 10850 TAZ chrX 153639876 153650063 10188 ATP6AP1 chrX 153656977 153664862 7886 GDI1 chrX 153665258 153671814 6557 FAM50A chrX 153672472 153679002 6531 PLXNA3 chrX 153686622 153701985 15364 LAGE3 chrX 153705240 153707596 2357 UBL4A chrX 153712055 153714932 2878 SLC10A3 chrX 153715649 153719002 3354 FAM3A chrX 153733326 153744566 11241 G6PD chrX 153759605 153775787 16183 IKBKG chrX 153770458 153793261 22804 FAM223A chrX 153799478 153800188 711 FAM223B chrX 153799478 153800188 711 CTAG1A chrX 153813417 153815075 1659 CTAG1B chrX 153813417 153815075 1659 CTAG1A chrX 153845864 153847522 1659 CTAG1B chrX 153845864 153847522 1659 FAM223A chrX 153860738 153861448 711 FAM223B chrX 153860738 153861448 711 CTAG2 chrX 153880245 153881853 1609 GAB3 chrX 153903526 153979348 75823 SNORA36A chrX 153996802 153996932 131 MIR644B chrX 153996870 153996931 62 DKC1 chrX 153991030 154005964 14935 SNORA56 chrX 154003272 154003401 130 MPP1 chrX 154006958 154033802 26845 SMIM9 chrX 154051622 154062937 11316 H2AFB1 chrX 154113316 154113833 518 H2AFB3 chrX 154113316 154113833 518 F8A2 chrX 154114649 154115765 1117 F8A3 chrX 154114649 154115765 1117 F8A1 chrX 154114634 154116336 1703 MIR1184-1 chrX 154115634 154115733 100 MIR1184-2 chrX 154115634 154115733 100 MIR1184-3 chrX 154115634 154115733 100 F8 chrX 154064063 154250998 186936 FUNDC2 chrX 154255063 154285191 30129 CMC4 chrX 154289899 154299547 9649 MTCP1 chrX 154292308 154299547 7240 BRCC3 chrX 154299694 154351349 51656 VBP1 chrX 154444700 154468098 23399 RAB39B chrX 154487525 154493852 6328 CLIC2 chrX 154505499 154563986 58488 TMLHE-AS1 chrX 154576449 154603823 27375 H2AFB2 chrX 154610435 154610783 349 H2AFB1 chrX 154610427 154610944 518 H2AFB3 chrX 154610427 154610944 518 F8A2 chrX 154611763 154612879 1117 F8A3 chrX 154611763 154612879 1117 F8A1 chrX 154611748 154613450 1703 MIR1184-1 chrX 154612748 154612847 100 MIR1184-2 chrX 154612748 154612847 100 MIR1184-3 chrX 154612748 154612847 100 MIR1184-1 chrX 154687177 154687276 100 MIR1184-2 chrX 154687177 154687276 100 MIR1184-3 chrX 154687177 154687276 100 F8A1 chrX 154686574 154688276 1703 F8A2 chrX 154687145 154688261 1117 F8A3 chrX 154687145 154688261 1117 H2AFB1 chrX 154689079 154689596 518 H2AFB3 chrX 154689079 154689596 518 H2AFB2 chrX 154689240 154689588 349 TMLHE-AS1 chrX 154696200 154723771 27572 TMLHE chrX 154718672 154842622 123951 SPRY3 chrX 154997450 155012117 14668 VAMP7 chrX 155110942 155173433 62492 IL9R chrX 155227245 155240482 13238 Name c-fos iNduced growth factor (vascular eNdothelial growth factor D) PIR-FIGF readthrough piriN (iroN-biNdiNg Nuclear proteiN) BMX NoN-receptor tyrosiNe kiNase angioteNsiN I coNvertiNg eNzyme (peptidyl-dipeptidase A) 2 transmembrane proteiN 27 carboNic anhydrase VB pseudogeNe 1 carboNic anhydrase VB, mitochoNdrial iNactivatioN escape 2 (NoN-proteiN codiNg) ziNc fiNger (CCCH type), RNA-biNdiNg motif and seriNe/argiNiNe rich 2 adaptor-related proteiN complex 1, sigma 2 subuNiT gastriN-releasiNg peptide receptor suppressor of Ty 20 homolog (S. cerevisiae)-like 1 pyruvate dehydrogeNase kiNase, isozyme 3 phosphate cytidylyltransferase 1, choliNe, beta syNovial sarcoma, X breakpoiNt 9 syNovial sarcoma, X breakpoiNt 3 syNovial sarcoma, X breakpoiNt 4B syNovial sarcoma, X breakpoiNt 4 syNovial sarcoma, X breakpoiNt 4 syNovial sarcoma, X breakpoiNt 4B solute carrier family 38, member 5 FtsJ RNA methyltransferase homolog 1 (E. coli) porcupiNe homolog (Drosophila) emopamil biNdiNg proteiN (sterol isomerase) TBC1 domaiN family, member 25 RNA biNdiNg motif (RNP1, RRM) proteiN 3 WD repeat domaiN 13 Wiskott-Aldrich syNdrome suppressor of variegatioN 3-9 homolog 1 (Drosophila) glyoxalase domaiN coNtaiNiNg 5 GATA biNdiNg proteiN 1 (globiN transcriptioN factor 1) histoNe deacetylase 6 ES cell expressed Ras proproteiN coNvertase subtilisiN/kexiN type 1 iNhibitor translocase of iNNer mitochoNdrial membrane 17 homolog B (yeast) polyglutamiNe biNdiNg proteiN 1 solute carrier family 35 (UDP-galactose transporter), member A2 pim-2 oncogene OTU domaiN coNtaiNiNg 5 potassium voltage-gated chanNel, Shal-related subfamily, member 1 GRIP1 associated proteiN 1 transcriptioN factor biNdiNg to IGHM eNhancer 3 coiled-coil domaiN coNtaiNiNg 120 PRA1 domaiN family, member 2 WD repeat domaiN 45 G patch domaiN and KOW motifs MAGI family member, X-liNked proteolipid proteiN 2 (coloNic epithelium-eNriched) prickle homolog 3 (Drosophila) syNaptophysiN calcium chanNel, voltage-depeNdeNt, L type, alpha 1F subuNiT iNterleukiN-1 receptor-associated kiNase 1 microRNA 718 methyl CpG biNdiNg proteiN 2 (Rett syNdrome) opsiN 1 (coNe pigmeNts), loNg-wave-seNsitive opsiN 1 (coNe pigmeNts), medium-wave-seNsitive 2 opsiN 1 (coNe pigmeNts), medium-wave-seNsitive opsiN 1 (coNe pigmeNts), medium-wave-seNsitive 2 opsiN 1 (coNe pigmeNts), medium-wave-seNsitive testis expressed 28 transketolase-like 1 filamiN A, alpha emeriN ribosomal proteiN L10 small Nucleolar RNA, H/ACA box 70 deoxyriboNuclease I-like 1 tafazziN ATPase, H+ transportiNg, lysosomal accessory proteiN 1 GDP dissociatioN iNhibitor 1 family with sequeNce similarity 50, member A plexin A3 L antigeN family, member 3 ubiquitiN-like 4A solute carrier family 10 (sodium/bile acid cotransporter family), member 3 family with sequeNce similarity 3, member A glucose-6-phosphate dehydrogeNase iNhibitor of kappa light polypeptide geNe eNhancer iN B-cells, kiNase gamma family with sequeNce similarity 223, member A (NoN-proteiN codiNg) family with sequeNce similarity 223, member B (NoN-proteiN codiNg) cancer/testis antigeN 1A cancer/testis antigeN 1B cancer/testis antigeN 1A cancer/testis antigeN 1B family with sequeNce similarity 223, member A (NoN-proteiN codiNg) family with sequeNce similarity 223, member B (NoN-proteiN codiNg) cancer/testis antigeN 2 GRB2-associated biNdiNg proteiN 3 small Nucleolar RNA, H/ACA box 36A microRNA 644b dyskeratosis coNgeNita 1, dyskeriN small Nucleolar RNA, H/ACA box 56 membrane proteiN, palmitoylated 1, 55kDa small iNtegral membrane proteiN 9 H2A histoNe family, member B1 H2A histoNe family, member B3 coagulatioN factor VIII-associated 2 coagulatioN factor VIII-associated 3 coagulatioN factor VIII-associated 1 microRNA 1184-1 microRNA 1184-2 microRNA 1184-3 coagulatioN factor VIII, procoagulant compoNeNT FUN14 domaiN coNtaiNiNg 2 C-x(9)-C motif coNtaiNiNg 4 homolog (S. cerevisiae) mature T-cell proliferatioN 1 BRCA1/BRCA2-coNtaiNiNg complex, subuNit 3 voN Hippel-LiNdau biNdiNg proteiN 1 RAB39B, member RAS oNcogeNe family chloride iNtracellular chanNel 2 TMLHE antiseNse RNA 1 H2A histoNe family, member B2 H2A histoNe family, member B1 H2A histoNe family, member B3 coagulatioN factor VIII-associated 2 coagulatioN factor VIII-associated 3 coagulatioN factor VIII-associated 1 microRNA 1184-1 microRNA 1184-2 microRNA 1184-3 microRNA 1184-1 microRNA 1184-2 microRNA 1184-3 coagulatioN factor VIII-associated 1 coagulatioN factor VIII-associated 2 coagulatioN factor VIII-associated 3 H2A histoNe family, member B1 H2A histoNe family, member B3 H2A histoNe family, member B2 TMLHE antiseNse RNA 1 trimethyllysiNe hydroxylase, epsiloN sprouty homolog 3 (Drosophila) vesicle-associated membrane proteiN 7 iNterleukiN 9 receptor.
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