Table 2 : Comparison of GISTIC results with the TCGA data on breast cancer.


A -Overlapping GISTIC - DCIS

Amplification Deletion

Cytoband Genes Cytoband Genes

8p11.23 No overlapping genes 3p21.31 C3orf18, C3orf45, CACNA2D2, CYB561D2, GNAI2, GNAT1, HEMK1, hsa-mir-566, HYAL1, HYAL2, HYAL3, IFRD2, NAT6, RASSF1, SEMA3B, SEMA3F, SLC38A3, TMEM115, TUSC2, ZMYND10
11q13.3 No overlapping genes 4p16.3 ATP5I, CPLX1, DGKQ, FGFRL1, GAK, hsa-mir-571, IDUA, MFSD7, MYL5, PCGF3, PDE6B, PIGG, RNF212, SLC26A1, SPON2, TMEM175, ZNF141, ZNF595, ZNF718, ZNF721
16q12.1 No overlapping genes 7p22.3 C7orf50, COX19, CYP2W1, FAM20C, GPER, GPR146, HEATR2, hsa-mir-339, INTS1, MAD1L1, MAFK, MICALL2, PDGFA, PRKAR1B, PSMG3, TMEM184A, UNCX, ZFAND2A
17q12 ERBB2 8p23.2 CSMD1
    8q24.3 ADCK5, BOP1, C8orf73, CPSF1, CYC1, CYHR1, DGAT1, EEF1D, EPPK1, EXOSC4, FAM83H, FBXL6, FOXH1, GLI4, GPAA1, GPIHBP1, GPR172A, GPT, GRINA, hsa-mir-661, hsa-mir-939, HSF1, KIFC2, LRRC14, LRRC24, LY6H, MAF1
    9p13.1 ANKRD20A3, CNTNAP3, FAM74A3, FAM75A2, FAM75A3, FAM75A5, FOXD4L2, ZNF658
    11p15.5 B4GALNT4, C11orf35, HRAS, hsa-mir-210, IRF7, LRRC56, PKP3, PTDSS2, RASSF7, RNH1, SCT, SIGIRR
    11q13.1 No overlapping genes
    12q24.33 GALNT9
    15q11.2 OR4N4, OR4M2
    19p13.3 ATP5D, C19orf23, C19orf24, C19orf26, CIRBP, EFNA2, GPX4, MIDN, MUM1, SBNO2, STK11

B - Overlapping GISTIC - T1

Amplification Deletion

Cytoband Genes Cytoband Genes

1q21.3 No overlapping genes 2q37.3 AGXT, ANKMY1, AQP12A, AQP12B, ATG4B, BOK, C2orf54, CAPN10, D2HGDH, DTYMK, DUSP28, FARP2, GAL3ST2, GPC1, GPR35, HDLBP, hsa-mir-149, ING5, KIF1A, MTERFD2, NEU4, PASK, PDCD1, PPP1R7, RNPEPL1
1q44 OR2T27, PGBD2, SH3BP5L, ZNF672, ZNF692 3p12.3 C3orf38, CADM2, CGGBP1, CHMP2B, GBE1, HTR1F, POU1F1, ROBO1, ROBO2, VGLL3, ZNF654
8p11.23 ZNF703 3p21.31 C3orf45, CACNA2D2, CYB561D2, GNAI2, HYAL1, HYAL2, HYAL3, IFRD2, NAT6, RASSF1, SEMA3B, SLC38A3, TMEM115, TUSC2, ZMYND10
8q24.21 MYC 4p16.3 PDE6B
11q14.1 C11orf67, CLNS1A, RSF1 7p22.3 C7orf50, COX19, FAM20C, CYP2W1, GPER, GPR146, HEATR2, hsa-mir-339, INTS1, MAD1L1, MAFK, MICALL2, PDGFA, PRKAR1B, PSMG3, TMEM184A, UNCX, ZFAND2A
12q15 CPM, MDM2, CPSF6 8p21.2 ADAM7, ADAM28, ADAMDEC1, STC1
17q12 ERBB2 10q23.31 PTEN
17q23.1 TUBD1, RPS6KB1 10q26.3 ADAM8, GPR123, hsa-mir-202, KNDC1, TUBGCP2, UTF1, VENTX
20q13.2 ZNF217 11p15.5 AP2A2, ATHL1, B4GALNT4, BET1L, BRSK2, C11orf35, CD151, CEND1, CHID1, DEAF1, DRD4, EFCAB4A, EPS8L2, HRAS, hsa-mir-210, IFITM1, IFITM2, IFITM3, IFITM5, IRF7, LRDD, LRRC56, MUC2, MUC5B, MUC6, NLRP6, ODF3, PDDC1, PKP3, PNPLA2, POLR2L, PSMD13, PTDSS2, RASSF7, RIC8A, RNH1, RPLP2, SCGB1C1, SCT, SIGIRR, SIRT3, SLC25A22, TALDO1, TMEM80, TOLLIP, TSPAN4
    12q24.33 GALNT9
    15q11.2 OR4M2
    17p12 hsa-mir-744, MAP2K4
    19p13.3 ATP5D, C19orf23, C19orf24, C19orf26, CIRBP, EFNA2, GPX4, MIDN, MUM1, SBNO2, STK11

 C - Overlapping GISTIC - T2

Amplification Deletion

Cytoband Genes Cytoband Genes

1q44 LOC646627, OR2T27, PGBD2, SH3BP5L, ZNF672, ZNF692 2q37.3 AGXT, ANKMY1, AQP12A, AQP12B, ASB1, ATG4B, BOK, C2orf54, CAPN10, D2HGDH, DTYMK, DUSP28, ESPNL, FARP2, GAL3ST2, GPC1, GPR35, HDAC4, HDLBP, HES6, hsa-mir-149, ILKAP, ING5, KIF1A, KLHL30, MTERFD2
20q13.2 ZNF217 3p12.3 GBE1, ROBO1, ROBO2
7p11.2 EGFR, LANCL2 6q27 C6orf124, DACT2, FRMD1, KIF25;MLLT4, SMOC2
8p11.21 No overlapping genes 8p21.2 ADAM28, ADAM7, ADAMDEC1, NKX3-1, STC1
8p11.23 No overlapping genes 8p23.2 CSMD1
8q24.21 MYC 9p21.3 CDKN2A, CDKN2B, MTAP
11p13 C11orf41, CCDC73, CD59, CSTF3, DEPDC7, EIF3M, FBXO3, HIPK3, PRRG4, QSER1, TCP11L1, WIT1, WT1 9p24.1 PTPRD
11q14.1 C11orf67, INTS4, RSF1 10q23.31 PTEN
12p13.33 IQSEC3, SLC6A12, SLC6A13 13q14.2 RB1, LPAR6
12q15 CPSF6, FRS2, LYZ, YEATS4 15q11.2 OR4M2
17q12 ERBB2 17p12 hsa-mir-744, MAP2K4
17q23.1 TUBD1, RPS6KB1 19p13.3 No overlapping genes
19q12 CCNE1    

 D - Overlapping GISTIC - T3

Amplification Deletion

Cytoband Genes Cytoband Genes

1q44 LOC646627, OR2T27, PGBD2, SH3BP5L, 3p21.31 ABHD14A, ABHD14B, ACY1, ALAS1, AMIGO3, AMT, APEH, ARIH2, ATRIP, BAP1, BSN, C3orf18,
C3orf45, C3orf54, C3orf62, CACNA2D2, CAMKV, CAMP, CCDC36, CCDC51, CCDC71, CCDC72, CDC25A, CELSR3, CISH, COL7A1, CYB561D2, DAG1, DALRD3, DCP1A, DNAH1, DOCK3, DUSP7, FBXW12, GLT8D1, GLYCTK, GMPPB, GNAI2, GNAT1, GNL3, GPR62, GPX1, GRM2, HEMK1, hsa-let-7g, hsa-mir-135a-1, hsa-mir-191, hsa-mir-566, HYAL1, HYAL2, HYAL3, IFRD2, IMPDH2, IQCF1, IQCF2, IQCF3, ITIH1, ITIH3, ITIH4, KLHDC8B, LAMB2, LOC646498, MAPKAPK3, MON1A, MST1, MST1R, MUSTN1, NAT6, NCKIPSD, NEK4, NICN1, NISCH, NME6, NT5DC2, PARP3, PBRM1, PCBP4, PFKFB4, PHF7, PLXNB1, PPM1M, PRKAR2A, PRKCD, QARS, QRICH1, RAD54L2, RASSF1, RBM15B, RBM5, RBM6, RFT1, RHOA, RNF123, RPL29, RRP9, SEMA3B, SEMA3F, SEMA3G, SFMBT1, SLC25A20, SLC26A6, SLC38A3, SPCS1, SPINK8, STAB1, TCTA, TEX264, TKT, TLR9, TMEM110, TMEM115, TMEM89, TNNC1, TRAIP, TREX1, TUSC2, TWF2, UBA7, UCN2, UQCRC1, USP19, USP4, WDR6, WDR82, VPRBP, ZMYND10
6q21 hsa-mir-587   FOXO3, ARMC2, LACE1
8p11.23 No overlapping genes   C6orf124, DACT2, FRMD1, GPR31, KIF25, MLLT4, SMOC2, TCP10, TTLL2, UNC93A
8q24.21 MYC   CSMD1
10q22.3 No overlapping genes   ADAM8, BNIP3, C10orf125, C10orf91, C10orf93, CALY, CLRN3, CYP2E1, DPYSL4, EBF3, ECHS1, FOXI2, FRG2B, GLRX3, GPR123, hsa-mir-202, INPP5A, JAKMIP3, KNDC1, LRRC27, MGMT, MKI67, MTG1, NKX6-2, NPS, PAOX, PPP2R2D, PRAP1, PTPRE, PWWP2B, SPRN, STK32C, SYCE1, TCERG1L, TUBGCP2, UTF1, VENTX, ZNF511
11p13 CCDC73, PRRG4   hsa-mir-744, MAP2K4
11q14.1 C11orf67, INTS4, RSF1    
12p13.33 IQSEC3, SLC6A12, SLC6A13    
17q12 ERBB2    

Solvang et al.Journal of Medical Statistics and Informatics  2014 2:10DOI : 10.7243/2053-7662-2-10