SNP6 Copy number analysis (GISTIC2)
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C10000P1
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C10000P1
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.21 (Firehose task version: 127).

Summary

There were 28 tumor samples used in this analysis: 9 significant arm-level results, 7 significant focal amplifications, and 19 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 7 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
2p15 | 1.4081e-09 | 1.4081e-09 | chr2:60961583-61776974 | 12
Xq27.3 | 0.016447 | 0.016447 | chrX:144689696-144696094 | 0 [SLITRK2]
3q27.3 | 0.054088 | 0.054088 | chr3:187616647-187814476 | 0 [LPP-AS2]
1q31.1 | 0.20522 | 0.20522 | chr1:120522602-220400735 | 912
8q24.12 | 0.21233 | 0.21233 | chr8:113190838-146364022 | 225
12q13.12 | 0.21233 | 0.21233 | chr12:44497239-51015508 | 95
16p11.2 | 0.22191 | 0.22191 | chr16:30572436-30626628 | 3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p15.

Table S1. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
REL
PEX13
XPO1
USP34
PAPOLG
KIAA1841
AHSA2
PUS10
LOC339803
C2orf74
FLJ16341
SNORA70B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q31.1.

Table S2. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ABL2
ARNT
BCL9
ELK4
FCGR2B
MDM4
MUC1
NOTCH2
NTRK1
PBX1
PRCC
SDHC
TPM3
TPR
PDE4DIP
SLC45A3
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
ADORA1
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATF3
ATP1A2
ATP1A4
ATP1B1
ATP2B4
AVPR1B
BGLAP
C4BPA
C4BPB
CACNA1E
CACNA1S
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD34
CD48
CENPF
CHI3L1
CHIT1
CHRNB2
CKS1B
CLK2
COPA
CR1
CR1L
CR2
CRABP2
CRP
CSRP1
CTSE
CTSK
CTSS
CD55
DHX9
DPT
ECM1
EIF2D
EFNA1
EFNA3
EFNA4
ELF3
ENSA
EPRS
ESRRG
ETV3
F5
F13B
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GBA
GBAP1
GJA5
GJA8
GLUL
GPR25
HDGF
CFH
CFHR1
CFHR2
MR1
HSD11B1
HSPA6
HSPA7
IFI16
IL6R
IL10
ILF2
INSRR
IRF6
IVL
KCNH1
KCNJ9
KCNJ10
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LMNA
LMX1A
LOR
LY9
MCL1
CD46
SMCP
MEF2D
MGST3
MNDA
MPZ
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NEK2
NHLH1
NIT1
NPR1
DDR2
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPOX
PPP2R5A
PRELP
PRKAB2
PROX1
PSMB4
PSMD4
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PEX19
RAB13
RABIF
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
TROVE2
SSR2
XCL2
CNTN2
VPS72
TGFB2
THBS3
TCHH
TNNI1
TNNT2
TNR
TOP1P1
TRAF5
CCT3
TUFT1
TNFSF4
UCK2
USF1
USH2A
SLC30A1
DAP3
NPHS2
BTG2
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
DYRK3
RGS5
PPFIA4
ITGA10
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
RAB7L1
SELENBP1
TNFSF18
MPZL1
SH2D2A
ANGPTL1
TBX19
FCGR2C
PRPF3
ARHGEF2
DEDD
XPR1
FAIM3
MAPKAPK2
GPR37L1
GPR52
AIM2
RASAL2
ADAMTS4
SEC22B
CHD1L
SOX13
PRDX6
IKBKE
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SETDB1
ZC3H11A
SMG7
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
LPGAT1
KIF14
RBM8A
NR1I3
SCAMP3
ARPC5
PRG4
GPA33
STX6
SF3B4
BPNT1
PIAS3
TIMM17A
LRRN2
HAX1
C1orf61
SEMA6C
SLC19A2
POLR3C
IVNS1ABP
TXNIP
PMVK
FAM189B
NES
KDM5B
CFHR4
CFHR3
OCLM
JTB
MTMR11
MLLT11
SLC27A3
IL24
TDRKH
CD160
CELF3
PMF1
DUSP12
VPS45
PLEKHA6
KIAA0907
KIFAP3
ATF6
KIF21B
NMNAT2
NFASC
POGZ
GLT25D2
RGL1
SYT11
PRRC2C
RPRD2
CAMSAP2
SRGAP2
SMG5
NCSTN
CRB1
GPR161
ZNF281
SNAPIN
PHLDA3
RUSC1
CA14
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
BRP44
INTS7
OLFML2B
C1orf43
NSL1
DNM3
TOR1AIP1
CHTOP
LCE2B
OPTC
OR10J1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
RNU5F-1
USP21
DIEXF
CACYBP
SLC39A1
RNF115
KLHL20
LAMTOR2
FLVCR1
UBE2T
TMOD4
NME7
NENF
IL19
CERS2
CRNN
G0S2
IL20
DCAF8
F11R
RRP15
GLRX2
BOLA1
ZBTB7B
RRNAD1
ADIPOR1
APH1A
KCTD3
PLEKHO1
ACP6
IER5
UCHL5
C1orf9
GPR89B
HSD17B7
UFC1
DTL
METTL13
OAZ3
CYB5R1
CD244
DPM3
MRPS21
TMCO1
ADAMTSL4
CRCT1
SWT1
GON4L
GPATCH4
LAX1
DUSP23
C1orf27
C1orf56
RALGPS2
GPATCH2
MSTO1
DARS2
GOLPH3L
KLHDC8A
ETNK2
KIRREL
TMEM206
YY1AP1
YOD1
BATF3
SLC30A10
UBE2Q1
ITLN1
IARS2
IPO9
C1orf112
HHAT
RCOR3
C1orf106
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
SLC50A1
SERTAD4
SLAMF8
CDC42SE1
UBQLN4
SMYD2
LHX9
OTUD7B
RAB25
PGLYRP4
RHBG
SCYL3
CAMK1G
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
POGK
HCN3
KIAA1614
FAM5B
C1orf114
SLAMF7
CADM3
PRUNE
KLHL12
LGR6
HAPLN2
GAS5
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
TOR3A
RFWD2
RGS18
NUCKS1
MRPL9
INTS3
SCNM1
C1orf116
MGC4473
FCRL2
CDC73
MRPL24
TNFAIP8L2
C1orf54
VASH2
PAQR6
TRIM46
C1orf129
TARS2
EDEM3
FLAD1
TRAF3IP3
NPL
OR6N2
OR6K2
CFHR5
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
FCAMR
C1orf49
HORMAD1
TOMM40L
POLR3GL
TMEM79
ACBD6
ZBTB37
LCE3D
LINC00260
LINC00467
FCRLA
ANKRD36BP1
PPP1R15B
MAEL
RGS8
NAV1
SEC16B
AQP10
LHX4
SLAMF9
PYGO2
ANGEL2
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
PIGM
IGSF8
LEMD1
C1orf85
PGLYRP3
GNRHR2
SLAMF6
SLC26A9
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
AXDND1
HIST2H3C
LYPLAL1
ATP6V1G3
OR10J5
DCST2
ZNF648
TEDDM1
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
LIX1L
SPATA17
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ITLN2
C1orf74
CREB3L4
C1orf51
LOC148696
LOC148709
PTPRVP
HFE2
ANKRD35
FAM163A
MFSD4
PM20D1
LELP1
RC3H1
DCST1
METTL11B
FAM78B
SHISA4
BNIPL
LRRC71
PYHIN1
C1orf227
FAM71A
DENND1B
TDRD5
TOR1AIP2
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
FLJ23867
KRTCAP2
CRTC2
TMEM9
SLC41A1
LCE5A
SYT14
ARHGAP30
C1orf192
ASPM
TIPRL
RIIAD1
THEM5
SLC9A11
NBPF15
LINC00303
LOC284576
LOC284578
LOC284581
ANKRD34A
RUSC1-AS1
LOC284648
DKFZP564C196
C1orf204
C1orf111
LOC284688
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
ANKRD45
FAM5C
C1orf110
FAM58BP
RD3
OR10R2
FCRL6
KCNT2
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
ZBTB41
CYCSP52
LOC375010
PEAR1
SFT2D2
RPS10P7
ILDR2
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
LINC00272
C1orf53
TMEM81
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
C1orf220
NBPF9
LOC401980
APOBEC4
MIR181B1
MIR194-1
MIR199A2
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
MIR9-1
RGS21
HIST2H2BF
ETV3L
LRRC52
LOC440700
LOC440704
C1orf186
OR10J3
MIR135B
KPRP
LCE6A
SUMO1P3
C1orf98
HIST2H4B
C1orf133
PRR9
MIR488
SNORD74
RPL31P11
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
TMEM183B
FAM72B
PCP4L1
SCARNA3
SCARNA4
SNORA36B
SNORA42
SNORA77
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
LOC728463
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
FAM72A
LOC730102
LOC730159
LOC730227
PPIAL4E
PFN1P2
MIR765
MIR190B
MIR921
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131234
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
GM140
LOC100288079
LOC100289211
MIR1231
MIR1278
MIR1295A
MIR548F1
MIR664
LOC100302401
ZBED6
MIR3119-1
MIR3120
MIR4260
MIR3122
MIR4257
MIR3119-2
MIR4258
MIR3121
MIR3658
LOC100505633
LOC100505666
LOC100505795
PROX1-AS1
LOC100505918
LOC100506023
LOC100506046
KDM5B-AS1
PMF1-BGLAP
LOC100527964
TNFAIP8L2-SCNM1
MIR4424
MIR4735
MIR4654
DNM3OS
LINC00538

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.12.

Table S3. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
EXT1
MYC
RECQL4
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
ADCY8
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
POU5F1B
PTK2
PVT1
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRPS1
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
JRK
EIF3H
DGAT1
GPAA1
WISP1
FOXH1
LRRC14
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
COLEC10
KHDRBS3
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
MTBP
EIF2C2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
C8orf55
FAM49B
CHRAC1
EXOSC4
LY6K
TRMT12
WDYHV1
SLC39A4
GSDMC
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
GSDMD
ZNF696
ARHGAP39
ZNF34
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
MAF1
UTP23
PARP10
C8orf76
TIGD5
FAM83A
PPP1R16A
MED30
ZNF251
KIFC2
NAPRT1
WDR67
HPYR1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
TOP1MT
ZNF572
LYPD2
TMEM71
TMEM65
LOC157381
FAM84B
FAM91A1
SLC30A8
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
SPATC1
FLJ43860
MAFA
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
C8orf85
LRRC24
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
LINC00051
C8orf73
SCXB
RAD21-AS1
FER1L6
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR937
MIR939
LOC100128338
SCXA
LOC100130231
CCDC166
LOC100131726
LOC100133669
LOC100288181
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR2053
MIR1208
MIR3610
LOC100507117
ZHX1-C8ORF76
MIR4663
MIR4472-1
MIR4664
PCAT1
LINC00536

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.12.

Table S4. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MLL2
hsa-mir-1293
hsa-mir-1291
ACCN2
ADCY6
AQP2
AQP5
AQP6
ARF3
CACNB3
CCNT1
COL2A1
GPD1
LALBA
NELL2
PFKM
PRKAG1
PRPH
RNY5
SMARCD1
TMBIM6
VDR
WNT1
WNT10B
TUBA1A
ENDOU
SCAF11
DDX23
TROAP
TUBA1B
RAPGEF3
MCRS1
FAIM2
DDN
KCNH3
ANP32D
PRPF40B
RND1
RACGAP1
SENP1
DHH
PLEKHA8P1
FKBP11
LIMA1
HDAC7
SLC38A2
KANSL2
SLC38A4
SLC48A1
LMBR1L
DIP2B
NCKAP5L
SPATS2
TMEM106C
RPAP3
DNAJC22
SLC38A1
RACGAP1P
FAM186B
TMEM117
TUBA1C
C12orf62
CCDC65
FMNL3
CERS5
FAM113B
LARP4
FAM186A
RHEBL1
C12orf54
ZNF641
OR10AD1
ASB8
BCDIN3D
ANO6
ARID2
LOC255411
LOC283332
C1QL4
H1FNT
OR8S1
AMIGO2
C12orf68
LOC400027
DBX2
SNORA2A
SNORA2B
SNORA34
LOC100233209
LOC100286844
MIR1293
MIR1291
LOC100335030
MIR4701
MIR4698

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p11.2.

Table S5. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ZNF689
ZNF785
ZNF688

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 19 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 1.9824e-07 | 1.9824e-07 | chr9:21865498-22448737 | 4
6q23.3 | 0.00090582 | 0.0046839 | chr6:137814087-138410514 | 1
1q43 | 0.005622 | 0.005622 | chr1:240637663-245913707 | 28
15q21.1 | 0.00049172 | 0.005622 | chr15:44851245-45036916 | 3
10q23.31 | 0.0074196 | 0.0074196 | chr10:89574877-93668989 | 39
6q14.1 | 0.005622 | 0.014256 | chr6:76017227-111139036 | 139
17q24.1 | 0.01508 | 0.01508 | chr17:62970616-63134027 | 1
2q23.1 | 0.024457 | 0.025125 | chr2:133425861-164600454 | 92
1p13.1 | 0.052876 | 0.072627 | chr1:108107499-119946150 | 141
13q14.2 | 0.031642 | 0.079699 | chr13:43424188-73307526 | 107
7p21.1 | 0.10783 | 0.11053 | chr7:9667988-20260876 | 33
19p13.2 | 0.11053 | 0.11053 | chr19:2006286-10467501 | 252
8q12.1 | 0.13249 | 0.12824 | chr8:54623401-71525707 | 86
13q33.3 | 0.082511 | 0.12824 | chr13:99510088-115169878 | 87
8p23.1 | 0.22025 | 0.21969 | chr8:1-24783837 | 203
16q23.1 | 0.21211 | 0.21969 | chr16:78129058-79627770 | 1
15q15.1 | 0.012316 | 0.24209 | chr15:35837298-48066663 | 144
16p13.13 | 0.24209 | 0.24209 | chr16:8886383-12754094 | 31
1p22.1 | 0.10389 | 0.25808 | chr1:1-249250621 | 2410

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.3.

Table S6. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q23.3.

Table S7. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TNFAIP3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

Table S8. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FH
hsa-mir-3123
ADSS
CHML
HNRNPU
RGS7
KMO
EXO1
CEP170
AKT3
ZNF238
SDCCAG8
OPN3
PPPDE1
KIF26B
GREM2
EFCAB2
FAM36A
WDR64
PLD5
C1orf100
C1orf101
HNRNPU-AS1
LOC339529
MAP1LC3C
LOC731275
MIR3123
MIR4677

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

Table S9. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
B2M
SPG11
PATL2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.31.

Table S10. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PTEN
hsa-mir-107
ACTA2
FAS
HTR7
IFIT2
IFIT1
IFIT3
LIPA
PPP1R3C
LIPF
CH25H
KIF20B
RPP30
IFIT5
ANKRD1
PANK1
RNLS
STAMBPL1
TNKS2
PCGF5
ANKRD22
NUDT9P1
LIPJ
CFL1P1
HECTD2
FLJ37201
LIPM
SLC16A12
MIR107
IFIT1B
LIPK
LIPN
LOC643529
KLLN
LOC100188947
FAS-AS1
MIR4679-1
MIR4679-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.1.

Table S11. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
AIM1
BCKDHB
CCNC
CGA
CNR1
EPHA7
FOXO3
GABRR1
GABRR2
GPR6
GRIK2
HTR1B
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
CDK19
MDN1
UFL1
ORC3
PNISR
IBTK
SENP6
FBXL4
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
CYB5R4
C6orf203
CDC40
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
FAM46A
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
MANEA
GPR63
SPACA1
SH3BGRL2
ARMC2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
MRAP2
RWDD2A
KLHL32
RIPPLY2
IRAK1BP1
PM20D2
SRSF12
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
LACE1
MMS22L
SCML4
CEP57L1
PPIL6
GJB7
SNHG5
LINC00222
LIN28B
TSG1
SNORD50B
LOC728012
C6orf186
LOC100130890
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.1.

Table S12. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GNA13

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q23.1.

Table S13. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
hsa-mir-128-1
ACVR1
ACVR2A
RND3
CACNB4
CCNT2
DARS
DPP4
FAP
GCG
GPD2
HNMT
ITGB6
KCNJ3
KIF5C
LCT
LY75
MCM6
MGAT5
NEB
NR4A2
ORC4
RBMS1
TNFAIP6
CXCR4
PKP4
KYNU
NMI
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
TBR1
GALNT5
NXPH2
PLA2R1
RAB3GAP1
UBXN4
R3HDM1
GCA
EPC2
ARL5A
MMADHC
BAZ2B
LRP1B
FIGN
RIF1
PRPF40A
MBD5
ARHGAP15
RPRM
SLC4A10
ERMN
IFIH1
MARCH7
GTDC1
YSK4
THSD7B
TMEM163
ZRANB3
TANC1
KCNH7
DAPL1
FMNL2
GALNT13
ACMSD
ACVR1C
LYPD6
LYPD6B
CCDC148
ARL6IP6
WDSUB1
UPP2
SPOPL
NCKAP5
RBM43
DKFZp686O1327
MIR128-1
LOC554201
LOC647012
PABPC1P2
LOC100129961
LOC100144595
ZEB2-AS1
MIR3679
LOC100507600
LY75-CD302
MIR4785
MIR4773-1
MIR4773-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.1.

Table S14. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
NRAS
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
ADORA3
ALX3
AMPD1
AMPD2
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CSF1
CELSR2
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
WNT2B
CSDE1
TTF2
SLC16A4
CD101
LRIG2
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
DDX20
WDR47
CLCC1
PTPN22
CHIA
GPSM2
SLC25A24
HAO2
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
SLC22A15
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
PROK1
PSRC1
ATP1A1OS
FAM40A
HENMT1
MAB21L3
ATXN7L2
C1orf194
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
RP11-165H20.1
DENND2C
FNDC7
UBL4B
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
PPM1J
MYBPHL
SLC6A17
MIR197
LOC440600
BCL2L15
PGCP1
SRG7
CYMP
LOC643441
NBPF6
SCARNA2
MIR942
LOC100129269
LOC100287722
MIR320B1
MIR4256
LOC100506343

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

Table S15. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LCP1
RB1
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
ATP7B
RCBTB2
CPB2
DACH1
ESD
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
NEK3
PCDH8
PCDH9
ATXN8OS
TPT1
SUCLA2
DLEU2
TSC22D1
ITM2B
UTP14C
LPAR6
TRIM13
DLEU1
OLFM4
SUGT1
LECT1
FNDC3A
ZC3H13
LRCH1
INTS6
CKAP2
NUFIP1
PCDH17
MED4
DNAJC15
VPS36
PHF11
ENOX1
RCBTB1
NUDT15
KIAA1704
THSD1
CYSLTR2
SPRYD7
KLHL1
PCDH20
RNASEH2B
DHRS12
KIAA0226L
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
EBPL
EPSTI1
ARL11
WDFY2
LINC00284
PRR20A
LACC1
LINC00330
HNRNPA1L2
ST13P4
CCDC122
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
OR7E156P
SIAH3
KCNRG
LINC00282
LINC00550
NEK5
THSD1P1
KCTD4
SERP2
MIR15A
MIR16-1
ALG11
MZT1
TSC22D1-AS1
SERPINE3
SNORA31
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR759
MIR3169
MIR3613
LOC100509894
MIR4703

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p21.1.

Table S16. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ETV1
hsa-mir-3146
hsa-mir-1302-6
AHR
DGKB
MEOX2
NDUFA4
TWIST1
PHF14
HDAC9
ARL4A
AGR2
SNX13
SOSTDC1
TSPAN13
BZW2
TMEM106B
ANKMY2
SCIN
AGR3
PER4
VWDE
PRPS1L1
TWISTNB
THSD7A
FERD3L
TMEM196
MACC1
AGMO
ISPD
MIR3146
LOC100506025
LRRC72

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.2.

Table S17. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GNA11
MLLT1
SH3GL1
hsa-mir-4322
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
AES
AMH
C3
CAPS
CD70
DAPK3
DNMT1
EEF2
ELAVL1
EMR1
FCER2
FUT3
FUT5
FUT6
GNA15
GNG7
MKNK2
GTF2F1
ICAM1
ICAM3
ICAM4
INSR
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NRTN
OAZ1
P2RY11
PIN1
MAP2K2
MAP2K7
PSPN
PTPRS
RFX2
RPS28
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
THOP1
ICAM5
TLE2
VAV1
ZNF121
ZNF177
SF3A2
CLPP
RANBP3
KHSRP
EIF3G
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
S1PR2
TRIP10
LONP1
APBA3
SAFB2
CHAF1A
SH2D3A
EBI3
PLIN3
CLEC4M
HMG20B
TUBB4A
TIMM44
SEMA6B
ZNF266
PNPLA6
KDM4B
ZFR2
ARHGEF18
PIP5K1C
RPL36
TIMM13
OR7E24
SNORD37
TJP3
ITGB1BP3
UHRF1
SLC39A3
CD209
COL5A3
RDH8
MRPL4
ANGPTL4
MARCH2
CD320
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
ZNF562
FBXL12
PLEKHJ1
C19orf66
FEM1A
STAP2
CCDC94
C19orf10
PPAN
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
MCOLN1
CAMSAP3
ZNF317
ZNF77
C19orf29
UBL5
CELF5
SLC25A23
ZNF426
FSD1
ZNF557
CERS4
TLE6
DENND1C
ZNF556
LRRC8E
FLJ22184
UBXN6
ACSBG2
ADAMTS10
DOHH
ANGPTL6
PRAM1
ALKBH7
ZNF414
DOT1L
FBN3
ZNF559
CREB3L3
HDGFRP2
LMNB2
RAX2
MPND
ATCAY
MBD3L1
DPP9
CRB3
PEX11G
ZNF561
OLFM2
MUC16
FDX1L
IZUMO4
ZNF554
EVI5L
MRPL54
LRG1
RAVER1
OR7D4
OR7G1
OR1M1
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
NDUFA11
ZNF358
ZNF560
TICAM1
ZNRF4
ZNF558
DIRAS1
ZNF555
ZNF846
OR7D2
PRR22
ANKRD24
C19orf59
KANK3
PLAC2
TMEM146
ACTL9
OR2Z1
LOC284385
C19orf77
MIR7-3HG
SLC25A41
MBD3L5
EMR4P
CLEC4G
TMPRSS9
C19orf35
HSD11B1L
C19orf45
ZNF699
LOC388499
C3P1
OR7G2
OR7G3
VMAC
CTXN1
C19orf29-AS1
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
LINGO3
ARRDC5
MBD3L4
MBD3L3
SNORD105
PPAN-P2RY11
MIR637
PLIN4
ZNF812
SNORD105B
ZGLP1
C19orf71
LOC100128573
LOC100131094
C19orf79
MIR1227
MIR4322
MIR4321
MIR3940
LOC100507567
LOC100507588
ZNF559-ZNF177
MIR4747
MIR4746

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q12.1.

Table S18. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PLAG1
TCEA1
NCOA2
CHCHD7
hsa-mir-124-2
ASPH
CA8
CRH
CYP7A1
LYN
MOS
MYBL1
PDE7A
PENK
RAB2A
RP1
RPS20
SDCBP
TTPA
NSMAF
RGS20
GGH
CYP7B1
MTFR1
TOX
LYPLA1
ARFGEF1
COPS5
RRS1
SULF1
TRAM1
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
PRDM14
SOX17
CSPP1
VCPIP1
PREX2
SLCO5A1
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
C8orf34
TMEM68
ADHFE1
UBXN2B
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC401463
MIR124-2
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q33.3.

Table S19. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
ATP4B
COL4A1
COL4A2
GPR183
EFNB2
F7
F10
FGF14
GAS6
GPR18
ING1
LAMP1
LIG4
PCCA
GRK1
SLC10A2
SOX1
TFDP1
TPP2
ZIC2
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
ITGBL1
TM9SF2
TUBGCP3
TNFSF13B
RASA3
MYO16
ATP11A
MCF2L
DOCK9
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
TEX29
METTL21CP1
SPACA7
CLYBL
METTL21C
NALCN
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
UBAC2
FAM70B
C13orf35
FLJ44054
CCDC168
FLJ41484
MIR623
LINC00460
FAM155A
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR4306
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4705

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.1.

Table S20. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PCM1
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
NAT1
NAT2
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
EGR3
EPB49
CLN8
FDFT1
FGL1
GATA4
GFRA2
LOXL2
LPL
MSR1
MSRA
NEFM
NKX3-1
PDGFRL
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
ADAM28
LZTS1
XPO7
RHOBTB2
PSD3
SLC39A14
FBXO25
FGF20
ADAMDEC1
CNOT7
ZDHHC2
SLC25A37
PINX1
PIWIL2
INTS10
AGPAT5
CSGALNACT1
HR
DEFB103B
BIN3
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
FAM160B2
MTMR9
MCPH1
PPP1R3B
NUDT18
FLJ14107
REEP4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
NKX2-6
SGCZ
DEFB104A
LOC157273
SGK223
PEBP4
LOC157627
C8orf42
ERICH1
TDH
C8orf48
ZNF596
DEFT1P
R3HCC1
PRSS55
C8orf74
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
FLJ10661
XKR6
LOC286059
LOC286083
EFHA2
LOC286114
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC389641
LOC392196
MIR124-1
MIR320A
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
MIR383
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
DEFB135
DEFB136
DEFB134
DEFB109P1B
RPL23AP53
FAM90A14
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
DEFA1B
FAM90A20
FAM90A19
ZNF705D
FAM66B
LOC100128993
ZNF705G
FAM66E
LOC100132396
FAM66D
FAM66A
LOC100133267
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR3926-2
MIR3926-1
LOC100506990
LOC100507156
MIR4659A
MIR4660
MIR4659B
LOC100652791

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

Table S21. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

Table S22. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BUB1B
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
B2M
CAPN3
CKMT1B
EPB42
GANC
GATM
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
RAD51
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
SLC28A2
TGM5
PPIP5K1
LCMT2
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
MAPKBP1
RTF1
MGA
VPS39
CCNDBP1
C15orf63
TMEM87A
RPAP1
PLDN
RPUSD2
TUBGCP4
EHD4
DUOX2
NDUFAF1
NUSAP1
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
PPP1R14D
HAUS2
FAM82A2
DNAJC17
PAK6
CASC5
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
SPRED1
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
PLA2G4F
LRRC57
HMGN2P46
FAM98B
PLA2G4D
MRPL42P5
C15orf52
C15orf53
C15orf54
DUOXA2
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
MIR626
MIR627
LOC728758
OIP5-AS1
MIR147B
LOC100131089
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4310
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4510

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.13.

Table S23. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TNFRSF17
CIITA
SOCS1
hsa-mir-548h-2
EMP2
GRIN2A
GSPT1
NUBP1
PMM2
PRM1
PRM2
TNP2
USP7
SNN
LITAF
CLEC16A
CARHSP1
TMEM186
RSL1D1
DEXI
C16orf72
ZC3H7A
TXNDC11
PRM3
ATF7IP2
SNX29
RMI2
TEKT5
BCAR4
FAM18A
MIR548X

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p22.1.

Table S24. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ABL2
ARNT
BCL9
CDKN2C
ELK4
EPS15
FCGR2B
FH
JAK1
JUN
LCK
MDM4
MPL
MUC1
MUTYH
MYCL1
NOTCH2
NRAS
NTRK1
PAX7
PBX1
PRCC
RPL22
SDHB
SDHC
SFPQ
TAL1
TPM3
TPR
ARID1A
TNFRSF14
BCL10
PDE4DIP
THRAP3
TRIM33
PRDM16
RBM15
SLC45A3
MDS2
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
hsa-mir-761
hsa-mir-30c-1
hsa-mir-4255
hsa-mir-552
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ABCA4
ACADM
ACTA1
ACTN2
ADAR
ADORA1
ADORA3
PARP1
ADSS
AGL
AGT
AK2
AK4
ALDH9A1
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
ARF1
RHOC
ASTN1
SERPINC1
ATF3
RERE
ATP1A1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
ATP5F1
ATP6V0B
AVPR1B
BAI2
BGLAP
BMP8B
BRDT
C1QA
C1QB
C1QC
C4BPA
C4BPB
C8A
C8B
CA6
CACNA1E
CACNA1S
CAPN2
CAPZA1
CAPZB
CASP9
CASQ1
CASQ2
RUNX3
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
TNFRSF8
CD34
CD48
CD53
CD58
CDA
CDK11B
CDC20
CDC42
CD52
CENPF
RCC1
CHI3L1
CHI3L2
CHIT1
CHML
LYST
CHRM3
CHRNB2
CKS1B
CLCA1
CLCN6
CLCNKA
CLCNKB
CLK2
PLK3
CNN3
CNR2
COL8A2
COL9A2
COL11A1
COL16A1
COPA
CORT
CPT2
CR1
CR1L
CR2
CRABP2
CRP
CRYZ
CSF1
CSF3R
CSRP1
CTBS
CTH
CTPS
CTSE
CTSK
CTSS
CYP2J2
CYP4A11
CYP4B1
DAB1
CD55
DBT
GADD45A
DDOST
DHX9
DFFA
DFFB
DHCR24
DIO1
DPH2
DPT
DPYD
DR1
DVL1
E2F2
ECE1
ECM1
S1PR1
EDN2
PHC2
EIF2D
EFNA1
EFNA3
EFNA4
CELSR2
MEGF6
EPHA2
ELAVL4
ELF3
ENO1
ENSA
EPB41
EPHA8
EPHB2
EPHX1
EPRS
ESRRG
ETV3
EXTL1
EXTL2
EYA3
F3
F5
F13B
FAAH
FABP3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FGR
FHL3
FOXE3
FOXD2
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
MTOR
NR5A2
FUCA1
DARC
IFI6
GABRD
GALE
GALNT2
GBA
GBAP1
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GLUL
GNAI3
GNAT2
GNB1
GNG4
GNG5
SFN
GPR3
GPR25
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
GUK1
H3F3A
HCRTR1
HDAC1
HDGF
CFH
CFHR1
CFHR2
ZBTB48
MR1
HLX
HMGN2
HMGCL
HMGCS2
HNRNPU
HPCA
HSD3B1
HSD3B2
HSD11B1
HSPA6
HSPA7
IGSF3
HSPG2
HTR1D
HTR6
ID3
IFI16
CYR61
IL6R
IL10
IL12RB2
TNFRSF9
ILF2
INPP5B
INSRR
IPP
IRF6
ITPKB
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNH1
KCNJ9
KCNJ10
KCNK1
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
STMN1
LBR
LEPR
LGALS8
LMNA
LMX1A
LOR
LY9
TACSTD2
MAGOH
MARK1
MATN1
MCL1
CD46
SMCP
MEF2D
MFAP2
MGST3
MNDA
MOV10
MPZ
MSH4
MTF1
MTHFR
MTR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NASP
NBL1
NCF2
NDUFS2
NDUFS5
NEK2
NFIA
NFYC
NGF
NHLH1
NHLH2
NID1
NIT1
NPPA
NPPB
NPR1
NRD1
YBX1
ROR1
DDR2
NVL
OPRD1
ORC1
OVGP1
PAFAH2
PRDX1
CDK18
PDC
PDE4B
PDZK1
PEX10
PEX14
PFDN2
PFKFB2
PGD
PGM1
PIGC
PIGR
PIK3C2B
PIK3CD
PI4KB
PIN1P1
PKLR
PKP1
PLA2G2A
PLA2G4A
PLA2G5
PLOD1
PLXNA2
EXOSC10
PRRX1
POU2F1
POU3F1
PPOX
PPP1R8
PPP2R5A
PPT1
PRELP
PRKAA2
PRKAB2
PRKACB
PKN2
PRKCZ
PROX1
PSEN2
PSMA5
PSMB2
PSMB4
PSMD4
PTAFR
PTGER3
PTGFR
PTGFRN
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PTPRF
PEX19
ABCD3
RAB3B
RAB4A
RAB13
RABGGTB
RABIF
RAP1A
RAP1GAP
RBBP4
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RHCE
RHD
RIT1
RLF
RNASEL
RNF2
RNPEP
SNORD21
RORC
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RPS27
RSC1A1
RXRG
RYR2
S100A1
SORT1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SARS
SCNN1D
SCP2
XCL1
SELE
SELL
SELP
SRSF4
SHC1
ST3GAL3
STIL
SKI
SLAMF1
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SLC16A1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SRM
SRP9
TROVE2
SSR2
AURKAPS1
STXBP3
XCL2
SYCP1
TAF12
TAF13
TARBP1
CNTN2
TBCE
TBX15
TCEA3
TCEB3
VPS72
TGFB2
LEFTY2
TGFBR3
THBS3
TCHH
TIE1
TLR5
GPR137B
TNFRSF1B
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TP73
TRAF5
CCT3
TSHB
TSNAX
TTC4
TUFT1
TNFSF4
TNFRSF4
UCK2
UQCRH
UROD
USF1
USP1
USH2A
VCAM1
WNT2B
WNT9A
ZSCAN20
ZNF124
ZBTB17
SLC30A1
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
DAP3
NPHS2
BTG2
PTP4A2
HIST3H3
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
SNHG3
NR0B2
RAD54L
GNPAT
DYRK3
TTF2
CDC42BPA
RGS5
PPFIA4
PIK3R3
MMP23B
MMP23A
KCNAB2
ITGA10
LMO4
FCN3
BLZF1
CDC14A
DEGS1
KMO
YARS
MKNK1
AKR7A2
PPAP2B
RTCD1
PTCH2
ALDH4A1
EIF3I
EIF4G3
VAMP4
PEA15
B4GALT3
B4GALT2
B3GALT2
TNFRSF25
ADAM15
PABPC4
TNFRSF18
FPGT
PEX11B
CREG1
CD84
PER3
FUBP1
EIF2B3
RAB7L1
SELENBP1
TNFSF18
TAF1A
MPZL1
SH2D2A
ARTN
MAP3K6
ANGPTL1
DIRAS3
TBX19
FCGR2C
SLC16A4
PRPF3
KCNQ4
EXO1
ARHGEF2
DEDD
ZMYM4
ZMYM6
XPR1
FAIM3
DHRS3
MAPKAPK2
GPR37L1
GPR52
SRSF11
VAMP3
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
AIM2
GGPS1
RASAL2
C1orf38
ADAMTS4
TMEM59
SEC22B
CHD1L
H6PD
SOX13
PRDX6
CLCA3P
CLCA2
ISG15
IKBKE
PLCH2
HS2ST1
IPO13
SDC3
SLC25A44
KIAA0040
KDM4A
CROCC
PUM1
NOS1AP
TMEM63A
CEP104
RIMS3
TOMM20
KIAA0494
URB2
ARHGEF11
DNAJC6
CEP350
CEP170
LRIG2
SETDB1
ZC3H11A
SMG7
LPPR4
UBAP2L
SV2A
KLHL21
SLC35E2
DENND4B
RABGAP1L
TMCC2
FAM20B
ZBTB40
LPGAT1
MFN2
KIF14
RBM8A
NR1I3
AKT3
INSL5
PIGK
SCAMP3
PTPRU
ARPC5
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
PRG4
ANGPTL7
GPA33
STX6
HNRNPR
SRRM1
CNKSR1
SF3B4
ZMPSTE24
UBE4B
BCAS2
AKR1A1
WARS2
BPNT1
CEPT1
PIAS3
TESK2
TIMM17A
LRRN2
PPIE
VAV3
HAX1
MAD2L2
PPIH
ZNF238
C1orf61
CAP1
LRRC41
SEMA6C
HBXIP
SLC19A2
IFI44
POLR3C
IVNS1ABP
TXNIP
PDPN
LEFTY1
SPHAR
PMVK
KHDRBS1
GMEB1
FAM189B
AP4B1
NUDC
PHTF1
MASP2
CAPN9
NES
KDM5B
AHCYL1
SRSF10
SDCCAG8
CFHR4
CFHR3
WDR3
OCLM
JTB
MTMR11
MAN1A2
UTS2
SF3A3
MLLT11
IFI44L
EBNA1BP2
SLC27A3
KIF2C
IL24
TDRKH
RER1
DNAJB4
ADAM30
RCAN3
FAF1
CD160
GLMN
HHLA3
CELF3
MST1P2
DDX20
DUSP10
MST1P9
PADI2
PMF1
DUSP12
VPS45
LYPLA2
PARK7
CTRC
ACOT7
COG2
CLCA4
MTF2
DNAJC8
NTNG1
PLEKHA6
CLSTN1
FOXJ3
KIAA0907
WDR47
KIFAP3
ATF6
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
RBM34
USP33
WDTC1
KIF21B
NMNAT2
KIAA0090
KIF1B
NFASC
POGZ
GLT25D2
MAST2
NCDN
CLCC1
SLC35D1
RGL1
PLEKHM2
SYT11
PRRC2C
FBXO28
RPRD2
OTUD3
KAZN
CAMTA1
LPHN2
CAMSAP2
KIAA1107
ZCCHC11
SZT2
DNAJC16
UBR4
USP24
SRGAP2
SMG5
NCSTN
ATP13A2
CRB1
ITGB3BP
GPR161
TARDBP
CELA3B
SLC35A3
ABCB10
ICMT
MACF1
LRRC8B
ZNF281
SNAPIN
LPAR3
PADI4
DDAH1
TMEM50A
OPN3
PHLDA3
RUSC1
CA14
KPNA6
SSBP3
STX12
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
BRP44
TRIM58
INTS7
OLFML2B
AHCTF1
C1orf43
CLIC4
NSL1
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
CHD5
DNM3
TOR1AIP1
CHTOP
C1orf144
LDLRAP1
SERBP1
NOC2L
OR1C1
PTPN22
PHGDH
FBXO2
LCE2B
OR2M4
OR2L2
OR2L1P
OPTC
FBXO6
PLA2G2D
AK5
MYCBP
OR10J1
HEYL
EIF2C1
OR4F3
OR2T1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORA66
SNORD47
SNORD45B
SNORD45A
SNORD44
SNORD55
RNU11
RNU5F-1
RNF11
USP21
FOXD3
DIEXF
TRAPPC3
TAF5L
CACYBP
HSPB7
CHIA
SLC39A1
DISC2
DISC1
ARHGEF16
AHDC1
RNF115
KLHL20
TEKT2
SMPDL3B
ANGPTL3
LAMTOR2
FLVCR1
PRO0611
UBE2T
LINC00339
CNIH4
SSU72
TMOD4
GNL2
GPSM2
UBIAD1
PYCR2
NME7
ALG6
NENF
PADI1
IL19
CERS2
SLC25A24
PLA2G2E
DNTTIP2
WRAP73
CRNN
G0S2
IL20
SLC45A1
DCAF8
HP1BP3
F11R
TMED5
RRP15
GLRX2
BOLA1
PPPDE1
CELA2B
ZNF593
ZBTB7B
ZNF691
TXNDC12
TNNI3K
RRNAD1
ADIPOR1
SCCPDH
SH3GLB1
MECR
APH1A
UTP11L
TRIM17
KCTD3
SDF4
MRTO4
PLEKHO1
HAO2
ACP6
TMEM69
MRPL37
IER5
HOOK1
SNX7
UCHL5
C1orf9
HPCAL4
YTHDF2
GPR89B
HSD17B7
UFC1
DTL
ZCCHC17
METTL13
DPH5
HSPB11
OAZ3
PADI3
CYB5R1
CMPK1
ARID4B
CD244
GPR88
ERRFI1
DPM3
WNT4
YIPF1
FBXO42
MRPS21
CCDC76
TMCO1
ADAMTSL4
CRCT1
RNF186
SPATA6
EGLN1
MXRA8
L1TD1
HES2
KIAA1383
RSBN1
ZNHIT6
GPN2
LEPROT
FBLIM1
MED18
TRIT1
GIPC2
SWT1
GDAP2
FAM46C
GON4L
GPATCH4
PALMD
FNBP1L
ST7L
PQLC2
CASZ1
LAX1
RHBDL2
DUSP23
ADPRHL2
TRNAU1AP
C1orf27
C1orf109
C1orf56
CPSF3L
C1orf123
C1orf159
MARC2
AURKAIP1
TTC22
MRPL20
AIM1L
SUSD4
KIF26B
TMEM51
RALGPS2
GPATCH2
BSDC1
XKR8
TMEM39B
PRPF38B
HEATR1
CDCA8
LRRC8D
MSTO1
DARS2
ARHGEF10L
PRMT6
RNF220
VPS13D
FAM176B
GOLPH3L
ATAD3A
TMEM57
KLHDC8A
TRIM62
ETNK2
RAVER2
PANK4
KIRREL
TMEM206
YY1AP1
ECHDC2
FGGY
MCOLN3
SLC22A15
YOD1
CAMK2N1
BATF3
SLC30A10
UBE2Q1
RNPC3
ITLN1
ASAP3
POMGNT1
PNRC2
LRRC40
DEPDC1
PIGV
ZNF692
NBPF1
IARS2
MAP7D1
IPO9
TMEM48
NECAP2
IQCC
C1orf112
HHAT
DNAJC11
ENAH
NUP133
RCOR3
C1orf106
LRIF1
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
RCC2
FAM212B
DMAP1
AJAP1
GNG12
SLC50A1
TMEM234
FAM54B
SERTAD4
CCBL2
ERO1LB
FMN2
SLAMF8
CDC42SE1
UBQLN4
TMEM167B
OLFML3
SMYD2
LHX9
OTUD7B
ADCK3
CTNNBIP1
C1orf63
AGTRAP
PITHD1
RAB25
PGLYRP4
ZNF695
RHBG
MAN1C1
SCYL3
GJC2
CAMK1G
NIPAL3
SEPN1
ATP8B2
TP73-AS1
VANGL2
FAM91A2
PBXIP1
S100A14
PLEKHG5
GATAD2B
AMIGO1
LRRC47
ODF2L
CGN
KIAA1324
PTCHD2
IGSF9
LRRC7
SIPA1L2
KIF17
ZNF687
ZSWIM5
POGK
KIAA1522
HCN3
CACHD1
MIER1
KIAA1614
FAM5B
HES4
C1orf114
GRHL3
SLAMF7
ZP4
CADM3
PTBP2
RHOU
PRUNE
DNASE2B
DLGAP3
IL22RA1
HIVEP3
KLHL12
LGR6
GPBP1L1
HAPLN2
MIIP
GAS5
PAPPA2
CELA2A
BCAN
GPATCH3
TNN
MRPS14
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ELTD1
TINAGL1
LEPRE1
TFB2M
SEMA4A
TOR3A
RFWD2
GREM2
RGS18
PLA2G2F
HIAT1
NUCKS1
SMAP2
ACBD3
SMYD3
ATPAF1
MARC1
S100PBP
MEAF6
DEM1
CEP85
ARV1
NMNAT1
ELOVL1
AIDA
VWA1
DCLRE1B
MRPS15
MRPL9
PINK1
JMJD4
MARCKSL1
PRAMEF1
PRAMEF2
INTS3
NADK
ZNF643
SELRC1
PHACTR4
C1orf135
SCNM1
ERI3
C1orf50
WDR77
C1orf116
MGC4473
CCDC28B
C1orf35
EFHD2
MMEL1
RSG1
FCRL2
DLEU2L
OR4F5
NKAIN1
TTC13
EPS8L3
CDC73
MRPL24
MUL1
PGBD5
TNFAIP8L2
C1orf54
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
NOL9
PPCS
LIN28A
SH3D21
TTLL7
SNIP1
C1orf115
HHIPL2
VASH2
AGMAT
WDR78
ZMYM1
LINC00115
ZNF669
RPAP2
ZNF672
MORN1
FAM110D
KIAA0319L
DHDDS
PAQR6
DENND2D
WLS
PCNXL2
GPR157
TRIM46
C1orf129
RPF1
SIKE1
ZC3H12A
SPSB1
TARS2
WDR26
TRIM45
EDEM3
FLAD1
TRAF3IP3
GLTPD1
ZNF436
TAS1R2
TAS1R1
SH3BP5L
NPL
GJA9
OR4F16
OR6N2
OR6K2
OR2G3
OR2G2
OR2C3
SYNC
CFHR5
TRIM11
C1orf21
ACTL8
ANKRD13C
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
TSSK3
CCNL2
NUAK2
VANGL1
ST6GALNAC5
ISG20L2
HYI
FCRL5
FCRL4
SH3BGRL3
DDX59
NUF2
RASSF5
SESN2
ESPN
TAS1R3
ATAD3B
HMCN1
GPR61
MIXL1
STK40
C1orf124
TM2D1
FCAMR
REG4
OBSCN
TMEM222
C1orf49
PLEKHN1
HORMAD1
TOMM40L
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
SLC25A33
TMEM79
NTPCR
EFCAB2
DDI2
ACBD6
LZIC
PROK1
KIAA1804
EFCAB7
ZBTB37
NT5C1A
LCE3D
TRIM63
LINC00260
PSRC1
FAM167B
LINC00467
MGC12982
C1orf170
CROCCP2
FCRLA
ANKRD36BP1
ZNF496
HPDL
ATP1A1OS
AGBL4
MFSD2A
C1orf198
PPP1R15B
ATG4C
MAEL
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
DISP1
SNHG12
FAM40A
RGS8
DOCK7
KIAA1751
WNT3A
NAV1
SEC16B
AQP10
LHX4
SLAMF9
KIAA2013
THAP3
C1orf201
PYGO2
ANGEL2
SPOCD1
ZNF697
IGFN1
NUP210L
BTF3L4
UBXN11
NEXN
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
HIST3H2A
PIGM
IGSF8
C1orf158
LEMD1
ZNF670
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
DNAJA1P5
C1orf85
MED8
KTI12
C1orf212
ADC
TMEM54
HENMT1
TOE1
NLRP3
ERMAP
PGLYRP3
CSMD2
MYSM1
GNRHR2
CROCCP3
FHAD1
SLAMF6
OSBPL9
SLC26A9
LOC115110
OMA1
RAB42
FCRL1
FCRL3
LRRC42
GBP4
GBP5
FAM46B
FMO9P
FAM36A
RBP7
TSEN15
FAM129A
SNAP47
ACAP3
TADA1
THEM4
SH2D1B
SSX2IP
UBE2J2
OLFM3
GABPB2
TCHHL1
RPTN
CCDC163P
TDRD10
SHE
C1orf172
C1orf96
LRRC38
AADACL3
PUSL1
B3GALT6
WDR63
KLHDC9
AXDND1
MAB21L3
IFFO2
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
ASB17
TYW3
C1orf173
LRRIQ3
TPRG1L
FAM213B
MYOM3
DMBX1
OR10J5
TMCO2
ZNF684
TCEANC2
PODN
LRRC39
GJB4
HMGB4
RNF19B
DCST2
DNAH14
OR2B11
ZNF648
TEDDM1
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
LIX1L
HSD3BP4
SPATA17
EDARADD
KLF17
TMEM125
C1orf182
IQGAP3
APOA1BP
ARHGEF19
MRPL55
HIST3H2BB
DRAM2
C1orf88
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ACTRT2
MIB2
ITLN2
SYT6
C1orf74
CREB3L4
C1orf127
BROX
SAMD11
LOC148413
SAMD13
C1orf52
PHF13
C1orf51
TMEM56
NBPF4
UBE2U
SLC35F3
LOC148696
LOC148709
PTPRVP
HFE2
ANKRD35
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
SLC30A7
CCDC27
C1orf213
KNCN
MOB3C
GLIS1
LELP1
RC3H1
MGC27382
DCDC2B
ZNF362
LOC149086
DCST1
CNIH3
LOC149134
MANEAL
IL23R
METTL11B
FAM78B
SHISA4
EXOC8
PDIK1L
BNIPL
CLDN19
WDR65
C1orf210
CCDC24
BTBD19
CCDC17
LRRC71
C1orf64
RNF187
RP11-165H20.1
PYHIN1
C1orf227
FAM71A
SLC2A7
DENND2C
GBP6
LPPR5
FNDC7
DENND1B
TDRD5
TOR1AIP2
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
SPRR4
KANK4
SASS6
C1orf55
CNST
FAM43B
PPIAL4A
HFM1
PAQR7
TTC24
C1orf65
UBL4B
PDIA3P
EIF2C3
EIF2C4
LCE4A
ALG14
FAM76A
LINC00466
C1orf168
TMEM201
TMEM61
CYP4Z1
C1orf86
CDCP2
SLC5A9
CC2D1B
NBPF11
NUDT17
FLJ23867
TXLNA
TCTEX1D1
PLD5
C1orf100
SPAG17
SLFNL1
KRTCAP2
CRTC2
C1orf126
IBA57
HIPK1
SLC44A5
ATAD3C
AKR7L
AKR7A2P1
TMEM9
FNDC5
EPHX4
LOC254099
TTLL10
AKNAD1
SLC41A1
OR2T6
LCE5A
TMCO4
MCOLN2
COL24A1
LOC255654
PCSK9
SYT14
ST6GALNAC3
C1orf101
ZNF683
ARHGAP30
C1orf192
NEGR1
ASPM
CYP4X1
MAGI3
TIPRL
NPHP4
BEST4
PGBD2
FAM19A3
RIIAD1
THEM5
OR2L13
SLC9A11
OR14A16
CYP4A22
C1orf185
LOC284551
NBPF15
LINC00303
LOC284576
LOC284578
LOC284581
FAM41C
FAM102B
SYPL2
CYB561D1
ANKRD34A
RUSC1-AS1
LOC284632
LOC284648
DKFZP564C196
RSPO1
EPHA10
LOC284661
C1orf204
C1orf111
LOC284688
ZNF326
BTBD8
HNRNPU-AS1
RIMKLA
SLC25A34
ESPNP
LIN9
VN1R5
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
FAM151A
S100A7A
LINGO4
RXFP4
ANKRD45
LOC339442
C1orf174
KLHL17
TMEM240
TMEM52
FAM5C
MTMR9LP
ZBTB8OS
TFAP2E
ZNF678
PRSS38
LOC339505
C1orf110
FAM58BP
LOC339524
LOC339529
LOC339535
C1orf228
ZNF642
RD3
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
CCDC18
OR6F1
OR2W3
OR2T8
OR2T3
MYBPHL
OR10R2
FCRL6
KCNT2
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
OR2T29
SERINC2
FAM159A
FAM131C
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PADI6
RGSL1
BMP8A
IRF2BP2
ZBTB41
CYCSP52
C1orf187
SPATA21
CCDC23
ATPAF1-AS1
HEATR8
FAM73A
LOC375010
PEAR1
SFT2D2
MIA3
C1orf95
FAM89A
AGRN
RPS10P7
APITD1
CATSPER4
NSUN4
GPR153
ILDR2
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LOC388630
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
LINC00272
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
UOX
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
C1orf141
GBP1P1
FLJ27354
MIR137HG
C1orf226
LOC400794
C1orf220
C1orf140
NBPF9
FAM177B
RNF223
PRAMEF3
LDLRAD2
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
LOC402779
OR2T27
OR2T35
APOBEC4
MIR101-1
MIR137
MIR181B1
MIR186
MIR194-1
MIR197
MIR199A2
MIR200A
MIR200B
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
MIR30C1
MIR30E
MIR34A
MIR9-1
RGS21
LHX8
C1orf180
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
FLJ32224
FAM183A
ZYG11A
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
ETV3L
LRRC52
LOC440700
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
ANKRD65
PRAMEF7
PGCP1
OR10J3
OR2W5
OR13G1
MIR135B
KPRP
LCE6A
SUMO1P3
GEMIN8P4
RBMXL1
LURAP1
PEF1
MIR429
C1orf98
HIST2H4B
DUSP5P
C1orf133
PRR9
MIR488
CYB5RL
SNORD74
RPL31P11
LOC641515
FAM138F
MIR205HG
SRG7
FLVCR1-AS1
CYMP
KIAA0754
LOC643441
LOC643723
LOC643837
TMEM88B
C1orf233
LOC644242
PPIAL4G
LOC644961
C1orf200
PPIAL4D
LOC645166
SNRPD2P2
PRAMEF19
PRAMEF20
FAM138A
LOC645676
POU5F1P4
RPS7P5
S100A7L2
LOC646268
LOC646471
LOC646626
LOC646627
EMBP1
SRGAP2P2
LOC648740
LOC649330
ZBTB8A
NBPF6
LOC653160
PPIAL4B
LOC653513
GPR89A
LOC653566
PPIAL4C
HIST2H3D
PRAMEF22
PRAMEF15
WASH7P
TMEM183B
FAM72B
PRAMEF16
PCP4L1
SCARNA3
SCARNA2
SCARNA4
SCARNA1
SNORA14B
SNORA36B
SNORA42
SNORA44
SNORA55
SNORA61
SNORA77
SNORA59B
SNORA59A
SNORA16A
SNORD45C
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR548D1
MIR551A
MIR553
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
ZBTB8B
LOC728431
PPIEL
LOC728463
CCDC30
CDK11A
SLC35E2B
LOC728716
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
RPS15AP10
LOC728989
LOC729041
LOC729059
HSD52
PRAMEF14
FAM72A
FLJ37453
LOC729737
OR4F29
LOC729970
LOC729987
LOC730102
LOC730159
LOC730227
PPIAL4E
LOC731275
PFN1P2
MIR765
MIR942
MIR190B
MIR760
MIR921
LOC100128071
LOC100128787
LOC100129046
LOC100129138
LOC100129196
LOC100129269
C1orf68
MSTO2P
LOC100129534
LOC100129620
LOC100129924
LOC100130000
LOC100130093
LOC100130197
LOC100130331
LOC100130417
LOC100130557
LOC100131060
TSTD1
LOC100131234
LOC100131564
LOC100131825
LOC100132062
LOC100132111
LOC100132287
NBPF10
FCGR1C
ZRANB2-AS1
LOC100132774
LOC100133331
LOC100133445
LOC100133612
C2CD4D
LOC100286793
DDX11L1
LOC100287722
LOC100287814
TTC34
LGALS8-AS1
GM140
LOC100288069
LOC100288079
LOC100289178
LOC100289211
MIR320B1
MIR1182
MIR1537
MIR1231
MIR1278
MIR1295A
MIR1976
MIR548F1
MIR664
MIR1262
LOC100302401
LINC00184
TSNAX-DISC1
MIR320B2
MIR761
NPPA-AS1
ZBED6
MIR3119-1
MIR3123
MIR3115
MIR3117
MIR3124
MIR3120
MIR4260
MIR4255
MIR4253
MIR3122
MIR4251
MIR4252
MIR4256
MIR4257
MIR3119-2
MIR4258
MIR4254
MIR3121
MIR3659
MIR3917
MIR3620
MIR3658
MIR3916
MIR3605
MIR3671
MIR548AA1
MIR3675
LOC100505633
LOC100505666
LOC100505768
LOC100505795
PROX1-AS1
LOC100505918
ENO1-AS1
LOC100506023
LOC100506046
ZMYM6NB
LOC100506343
KDM5B-AS1
LOC100506730
LOC100506795
LOC100506801
LOC100506810
LOC100506963
LOC100507178
LOC100507423
LOC100507564
LOC100507634
APITD1-CORT
FPGT-TNNI3K
GJA9-MYCBP
HEATR8-TTC4
PMF1-BGLAP
LOC100527964
TMEM56-RWDD3
C1orf151-NBL1
ZNF670-ZNF695
TNFAIP8L2-SCNM1
MIR4695
MIR4420
MIR4753
MIR4422
MIR4666A
MIR4781
MIR4424
MIR4794
MIR4677
MIR4735
MIR4671
MIR4654
MIR4427
MIR4684
MIR4711
MIR4689
MIR4632
MIR2682
MIR4742
MIR4423
MIR4417
MIR378F
DNM3OS
RCAN3AS
NEGR1-IT1
ZRANB2-AS2
LINC00538

Arm-level results

Table 3. Get Full Table Arm-level significance table - 9 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.04 | -0.535 | 0.871 | 0.11 | 0.926 | 0.944
1q | 1955 | 0.15 | 1.63 | 0.227 | 0.04 | -0.523 | 0.944
2p | 924 | 0.08 | -0.0732 | 0.854 | 0.08 | -0.0732 | 0.944
2q | 1556 | 0.08 | 0.0697 | 0.854 | 0.08 | 0.0697 | 0.944
3p | 1062 | 0.18 | 1.95 | 0.157 | 0.00 | -1.41 | 0.944
3q | 1139 | 0.21 | 2.68 | 0.0369 | 0.00 | -1.37 | 0.944
4p | 489 | 0.00 | -1.59 | 0.944 | 0.04 | -0.949 | 0.944
4q | 1049 | 0.00 | -1.5 | 0.944 | 0.07 | -0.155 | 0.944
5p | 270 | 0.07 | -0.319 | 0.862 | 0.00 | -1.59 | 0.944
5q | 1427 | 0.04 | -0.787 | 0.871 | 0.00 | -1.48 | 0.944
6p | 1173 | 0.11 | 0.644 | 0.693 | 0.04 | -0.707 | 0.944
6q | 839 | 0.08 | -0.0336 | 0.854 | 0.12 | 0.624 | 0.944
7p | 641 | 0.29 | 3.84 | 0.00123 | 0.00 | -1.36 | 0.944
7q | 1277 | 0.25 | 3.45 | 0.00377 | 0.00 | -1.32 | 0.944
8p | 580 | 0.08 | -0.0276 | 0.854 | 0.15 | 1.26 | 0.944
8q | 859 | 0.08 | -0.0872 | 0.854 | 0.08 | -0.0872 | 0.944
9p | 422 | 0.07 | -0.234 | 0.854 | 0.04 | -0.875 | 0.944
9q | 1113 | 0.07 | -0.141 | 0.854 | 0.00 | -1.49 | 0.944
10p | 409 | 0.11 | 0.446 | 0.771 | 0.04 | -0.833 | 0.944
10q | 1268 | 0.07 | -0.0525 | 0.854 | 0.04 | -0.734 | 0.944
11p | 862 | 0.14 | 1.18 | 0.393 | 0.00 | -1.46 | 0.944
11q | 1515 | 0.29 | 4.29 | 0.000362 | 0.00 | -1.26 | 0.944
12p | 575 | 0.12 | 0.556 | 0.722 | 0.08 | -0.089 | 0.944
12q | 1447 | 0.15 | 1.45 | 0.266 | 0.04 | -0.615 | 0.944
13q | 654 | 0.07 | -0.186 | 0.854 | 0.04 | -0.838 | 0.944
14q | 1341 | 0.07 | -0.0894 | 0.854 | 0.00 | -1.46 | 0.944
15q | 1355 | 0.04 | -0.585 | 0.871 | 0.19 | 2.15 | 0.632
16p | 872 | 0.12 | 0.705 | 0.687 | 0.12 | 0.705 | 0.944
16q | 702 | 0.17 | 1.47 | 0.266 | 0.17 | 1.47 | 0.944
17p | 683 | 0.04 | -0.789 | 0.871 | 0.11 | 0.515 | 0.944
17q | 1592 | 0.04 | -0.717 | 0.871 | 0.04 | -0.717 | 0.944
18p | 143 | 0.19 | 1.82 | 0.172 | 0.09 | -0.0522 | 0.944
18q | 446 | 0.19 | 1.92 | 0.157 | 0.09 | 0.00796 | 0.944
19p | 995 | 0.04 | -0.823 | 0.871 | 0.04 | -0.823 | 0.944
19q | 1709 | 0.04 | -0.736 | 0.871 | 0.00 | -1.44 | 0.944
20p | 355 | 0.07 | -0.248 | 0.854 | 0.04 | -0.886 | 0.944
20q | 753 | 0.04 | -0.864 | 0.871 | 0.04 | -0.864 | 0.944
21q | 509 | 0.22 | 2.53 | 0.0453 | 0.05 | -0.675 | 0.944
22q | 921 | 0.00 | -1.51 | 0.944 | 0.07 | -0.183 | 0.944
Xq | 1312 | 0.12 | 0.824 | 0.63 | 0.12 | 0.824 | 0.944

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

- Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

- Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

- CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

- Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

- Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

- Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

- Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

- Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

- Confidence Level: Confidence level used to calculate the region containing a driver.

- Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

- Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

- Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

- Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/DLBC-TP/8016616/GDAC_MergeDataFiles_4929834/DLBC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 28 Input Tumor Samples.

Tumor Sample Names
TCGA-FA-8693-01A-11D-2389-01
TCGA-FA-A4BB-01A-11D-A31W-01
TCGA-FA-A4XK-01A-11D-A31W-01
TCGA-FA-A6HN-01A-11D-A31W-01
TCGA-FA-A6HO-01A-11D-A31W-01
TCGA-FF-8041-01A-11D-2209-01
TCGA-FF-8042-01A-11D-2209-01
TCGA-FF-8043-01A-11D-2209-01
TCGA-FF-8046-01A-11D-2209-01
TCGA-FF-8047-01A-11D-2209-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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