Liver Hepatocellular Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara
(Broad Institute)
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 2.0.16 (cga svn revision 38839).
Summary
There were 53 tumor samples used in this analysis: 21 significant arm-level results, 15 significant focal amplifications, and 35 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 - 15 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 |
|---|---|---|---|---|
| 11q13.2 | 9.6605e-05 | 9.6605e-05 | chr11:68713597-68771449 | 0 [MYEOV] |
| 6p21.1 | 0.0097933 | 0.0097933 | chr6:43876809-43886368 | 0 [VEGFA] |
| 1q23.3 | 0.0097933 | 0.011247 | chr1:158773709-159925403 | 40 |
| 13q33.3 | 0.066106 | 0.066106 | chr13:106978732-114142980 | 43 |
| 17q25.3 | 0.10175 | 0.10175 | chr17:76596751-78239374 | 62 |
| 3q26.31 | 0.17594 | 0.17594 | chr3:173737376-173779556 | 0 [TNFSF10] |
| 7q21.13 | 0.17594 | 0.17594 | chr7:90288913-92559550 | 15 |
| 16q11.2 | 0.17594 | 0.17594 | chr16:31813563-46192072 | 20 |
| 5p15.33 | 0.18058 | 0.18058 | chr5:1009672-1339515 | 5 |
| 6q12 | 0.18058 | 0.18058 | chr6:67601419-67634943 | 0 [MCART3P] |
| 4q13.3 | 0.19184 | 0.19184 | chr4:74503551-74538973 | 2 |
| 5q31.1 | 0.20526 | 0.20526 | chr5:133799381-133822028 | 0 [CDKN2AIPNL] |
| 20q13.2 | 0.21798 | 0.21798 | chr20:50693176-54369134 | 10 |
| 2p24.1 | 0.23604 | 0.23604 | chr2:1-27538143 | 146 |
| 1q21.2 | 0.0072315 | 1 | chr1:1-247249719 | 2207 |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 1q23.3.
Table S1. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| FCGR2B |
| SDHC |
| APOA2 |
| CD48 |
| FCER1G |
| FCGR2A |
| FCGR3A |
| FCGR3B |
| HSPA6 |
| HSPA7 |
| LY9 |
| MPZ |
| NDUFS2 |
| NIT1 |
| PFDN2 |
| PPOX |
| SLAMF1 |
| USF1 |
| B4GALT3 |
| CD84 |
| FCGR2C |
| DEDD |
| ADAMTS4 |
| NR1I3 |
| USP21 |
| F11R |
| UFC1 |
| CD244 |
| ITLN1 |
| SLAMF7 |
| PVRL4 |
| TOMM40L |
| KLHDC9 |
| ITLN2 |
| ARHGAP30 |
| C1orf192 |
| RPL31P11 |
| LOC642502 |
| PCP4L1 |
| TSTD1 |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 13q33.3.
Table S2. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| hsa-mir-1267 |
| ATP4B |
| COL4A1 |
| COL4A2 |
| F7 |
| F10 |
| GAS6 |
| ING1 |
| LAMP1 |
| LIG4 |
| GRK1 |
| SOX1 |
| TFDP1 |
| CUL4A |
| IRS2 |
| PROZ |
| ARHGEF7 |
| CDC16 |
| TUBGCP3 |
| TNFSF13B |
| RASA3 |
| MYO16 |
| ATP11A |
| MCF2L |
| TMCO3 |
| DCUN1D2 |
| ANKRD10 |
| RAB20 |
| CARKD |
| PCID2 |
| UPF3A |
| CARS2 |
| GRTP1 |
| ABHD13 |
| ADPRHL1 |
| C13orf16 |
| C13orf28 |
| C13orf29 |
| ZNF828 |
| FAM70B |
| C13orf35 |
| FLJ44054 |
| FAM155A |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 17q25.3.
Table S3. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| ASPSCR1 |
| hsa-mir-1250 |
| ACTG1 |
| ARHGDIA |
| CD7 |
| CSNK1D |
| SLC25A10 |
| FASN |
| UTS2R |
| GPS1 |
| FOXK2 |
| MAFG |
| P4HB |
| PDE6G |
| PYCR1 |
| PCYT2 |
| RAC3 |
| RFNG |
| MRPL12 |
| SECTM1 |
| SLC16A3 |
| HGS |
| AATK |
| THOC4 |
| BAIAP2 |
| RAB40B |
| AZI1 |
| FSCN2 |
| NARF |
| DCXR |
| ANAPC11 |
| SIRT7 |
| NPLOC4 |
| WDR45L |
| BAHCC1 |
| DUS1L |
| C17orf62 |
| C17orf101 |
| C17orf70 |
| TSPAN10 |
| LOC92659 |
| DYSFIP1 |
| SLC38A10 |
| C17orf56 |
| NOTUM |
| STRA13 |
| LRRC45 |
| MYADML2 |
| NPB |
| CCDC57 |
| HEXDC |
| C17orf89 |
| C17orf55 |
| TMEM105 |
| C17orf90 |
| CCDC137 |
| ARL16 |
| LOC388428 |
| TEX19 |
| FLJ90757 |
| MIR338 |
| MIR657 |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 7q21.13.
Table S4. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| CDK6 |
| AKAP9 |
| hsa-mir-1285-1 |
| KRIT1 |
| CYP51A1 |
| PEX1 |
| PFTK1 |
| MTERF |
| FZD1 |
| ANKIB1 |
| GATAD1 |
| C7orf64 |
| MGC16142 |
| FAM133B |
| LOC401387 |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 16q11.2.
Table S5. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| hsa-mir-1826 |
| PHKB |
| DNAJA2 |
| ZNF267 |
| ORC6L |
| TP53TG3 |
| VPS35 |
| SHCBP1 |
| ITFG1 |
| NETO2 |
| GPT2 |
| MYLK3 |
| ANKRD26P1 |
| LOC146481 |
| LOC283914 |
| SLC6A10P |
| C16orf87 |
| HERC2P4 |
| UBE2MP1 |
| TP53TG3B |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 5p15.33.
Table S6. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| TERT |
| SLC12A7 |
| NKD2 |
| SLC6A19 |
| SLC6A18 |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 4q13.3.
Table S7. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| AFP |
| ALB |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 20q13.2.
Table S8. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| CYP24A1 |
| MC3R |
| PFDN4 |
| ZNF217 |
| BCAS1 |
| DOK5 |
| C20orf108 |
| TSHZ2 |
| CBLN4 |
| SUMO1P1 |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 2p24.1.
Table S9. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| DNMT3A |
| MYCN |
| NCOA1 |
| hsa-mir-1301 |
| ACP1 |
| ADCY3 |
| APOB |
| RHOB |
| CAD |
| CENPA |
| DDX1 |
| DTNB |
| E2F6 |
| FKBP1B |
| FTHL3P |
| GTF3C2 |
| HADHA |
| HADHB |
| HPCAL1 |
| ID2 |
| KCNF1 |
| KCNK3 |
| KCNS3 |
| KHK |
| KIF3C |
| MATN3 |
| MPV17 |
| ODC1 |
| POMC |
| PPM1G |
| RPS7 |
| RRM2 |
| SDC1 |
| SOX11 |
| ADAM17 |
| TPO |
| TSSC1 |
| UCN |
| VSNL1 |
| SLC30A3 |
| PXDN |
| KLF11 |
| ASAP2 |
| SLC5A6 |
| EIF2B4 |
| TAF1B |
| ITGB1BP1 |
| OTOF |
| ROCK2 |
| TP53I3 |
| GREB1 |
| LAPTM4A |
| RNF144A |
| SNX17 |
| PREB |
| PDIA6 |
| MYCNOS |
| CGREF1 |
| RAB10 |
| YWHAQ |
| EMILIN1 |
| MAPRE3 |
| EFR3B |
| MYT1L |
| LPIN1 |
| PUM2 |
| NTSR2 |
| IFT172 |
| SH3YL1 |
| TRIB2 |
| GRHL1 |
| NRBP1 |
| ITSN2 |
| TTC15 |
| DNAJC27 |
| C2orf28 |
| NBAS |
| SF3B14 |
| CPSF3 |
| SNTG2 |
| ATAD2B |
| TMEM214 |
| C2orf18 |
| ASXL2 |
| ADI1 |
| ALLC |
| DPYSL5 |
| TRIM54 |
| KIDINS220 |
| WDR35 |
| RDH14 |
| AGBL5 |
| C2orf43 |
| HS1BP3 |
| COLEC11 |
| CENPO |
| SMC6 |
| NOL10 |
| C2orf44 |
| FAM49A |
| ABHD1 |
| SELI |
| RSAD2 |
| C2orf39 |
| NT5C1B |
| KLHL29 |
| CMPK2 |
| MBOAT2 |
| TMEM18 |
| CIB4 |
| OSR1 |
| TTC32 |
| ZNF513 |
| C2orf50 |
| PQLC3 |
| LOC150622 |
| TCF23 |
| FAM84A |
| GDF7 |
| GPR113 |
| UBXN2A |
| CYS1 |
| KRTCAP3 |
| ATP6V1C2 |
| RNASEH1 |
| FAM150B |
| DNAJC5G |
| IAH1 |
| C2orf70 |
| C2orf53 |
| LOC339788 |
| MSGN1 |
| GEN1 |
| C2orf48 |
| PFN4 |
| LOC375190 |
| MFSD2B |
| C2orf90 |
| C2orf79 |
| LOC400940 |
| FAM110C |
| C2orf84 |
| RAD51AP2 |
| LOC730811 |
| LOC100128731 |
| SNORA80B |
Genes in Wide Peak
This is the comprehensive list of amplified genes in the wide peak for 1q21.2.
Table S10. Genes in bold are cancer genes as defined by The Sanger Institute's 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-1537 |
| hsa-mir-1182 |
| hsa-mir-320b-2 |
| hsa-mir-664 |
| hsa-mir-194-1 |
| hsa-mir-205 |
| hsa-mir-29b-2 |
| hsa-mir-135b |
| hsa-mir-1231 |
| hsa-mir-181a-1 |
| hsa-mir-1278 |
| hsa-mir-488 |
| hsa-mir-199a-2 |
| hsa-mir-1295 |
| hsa-mir-557 |
| hsa-mir-1255b-2 |
| hsa-mir-921 |
| hsa-mir-556 |
| hsa-mir-765 |
| hsa-mir-9-1 |
| hsa-mir-555 |
| hsa-mir-92b |
| hsa-mir-190b |
| hsa-mir-554 |
| hsa-mir-942 |
| hsa-mir-320b-1 |
| hsa-mir-197 |
| hsa-mir-553 |
| hsa-mir-137 |
| hsa-mir-760 |
| hsa-mir-186 |
| hsa-mir-1262 |
| hsa-mir-101-1 |
| hsa-mir-30c-1 |
| hsa-mir-552 |
| hsa-mir-1976 |
| hsa-mir-1256 |
| hsa-mir-1290 |
| hsa-mir-34a |
| hsa-mir-551a |
| hsa-mir-429 |
| hsa-mir-1977 |
| hsa-mir-1302-2 |
| ABCA4 |
| ACADM |
| ACTA1 |
| ACTN2 |
| ADAR |
| ADORA1 |
| ADORA3 |
| PARP1 |
| ADSS |
| AGL |
| AGT |
| AK2 |
| AK3L1 |
| 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 |
| CDC2L1 |
| 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 |
| LGTN |
| 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 |
| GBAP |
| 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 |
| ORC1L |
| OVGP1 |
| PAFAH2 |
| PRDX1 |
| PCTK3 |
| PDC |
| PDE4B |
| PDZK1 |
| PEX10 |
| PEX14 |
| PFDN2 |
| PFKFB2 |
| PGD |
| PGM1 |
| PIGC |
| PIGR |
| PIK3C2B |
| PIK3CD |
| PI4KB |
| PIN1L |
| 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 |
| SFRS4 |
| 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 |
| SFRS11 |
| 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 |
| KIAA0562 |
| 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 |
| SFRS13A |
| 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 |
| TNRC4 |
| MSTP2 |
| DDX20 |
| DUSP10 |
| MSTP9 |
| 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 |
| BAT2D1 |
| FBXO28 |
| RPRD2 |
| OTUD3 |
| KIAA1026 |
| CAMTA1 |
| LPHN2 |
| CAMSAP1L1 |
| KIAA1107 |
| ZCCHC11 |
| KIAA0467 |
| 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 |
| C1orf77 |
| 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 |
| RNF11 |
| USP21 |
| FOXD3 |
| C1orf107 |
| TRAPPC3 |
| TAF5L |
| CACYBP |
| HSPB7 |
| CHIA |
| SLC39A1 |
| DISC2 |
| DISC1 |
| ARHGEF16 |
| AHDC1 |
| RNF115 |
| KLHL20 |
| TEKT2 |
| SMPDL3B |
| ANGPTL3 |
| ROBLD3 |
| FLVCR1 |
| PRO0611 |
| UBE2T |
| HSPC157 |
| CNIH4 |
| SSU72 |
| TMOD4 |
| GNL2 |
| GPSM2 |
| UBIAD1 |
| PYCR2 |
| NME7 |
| ALG6 |
| NENF |
| PADI1 |
| IL19 |
| LASS2 |
| SLC25A24 |
| PLA2G2E |
| DNTTIP2 |
| WDR8 |
| CRNN |
| G0S2 |
| IL20 |
| SLC45A1 |
| DCAF8 |
| HP1BP3 |
| F11R |
| TMED5 |
| RRP15 |
| GLRX2 |
| BOLA1 |
| PPPDE1 |
| CELA2B |
| ZNF593 |
| ZBTB7B |
| ZNF691 |
| TXNDC12 |
| TNNI3K |
| C1orf66 |
| 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 |
| C1orf26 |
| GDAP2 |
| FAM46C |
| GON4L |
| GPATCH4 |
| PALMD |
| FNBP1L |
| ST7L |
| PQLC2 |
| CASZ1 |
| LAX1 |
| RHBDL2 |
| DUSP23 |
| ADPRHL2 |
| TRNAU1AP |
| C1orf27 |
| C1orf109 |
| C1orf56 |
| CPSF3L |
| C1orf123 |
| C1orf159 |
| MOSC2 |
| 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 |
| C1orf103 |
| FAM63A |
| ADCY10 |
| DCAF6 |
| ASH1L |
| LENEP |
| CTTNBP2NL |
| RCC2 |
| C1orf183 |
| DMAP1 |
| AJAP1 |
| GNG12 |
| RAG1AP1 |
| C1orf91 |
| FAM54B |
| SERTAD4 |
| CCBL2 |
| ERO1LB |
| FMN2 |
| SLAMF8 |
| CDC42SE1 |
| UBQLN4 |
| TMEM167B |
| OLFML3 |
| SMYD2 |
| LHX9 |
| OTUD7B |
| CABC1 |
| CTNNBIP1 |
| C1orf63 |
| AGTRAP |
| C1orf128 |
| RAB25 |
| PGLYRP4 |
| ZNF695 |
| RHBG |
| MAN1C1 |
| SCYL3 |
| GJC2 |
| CAMK1G |
| NIPAL3 |
| SEPN1 |
| ATP8B2 |
| KIAA0495 |
| VANGL2 |
| 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 |
| SPATA1 |
| LEPRE1 |
| TFB2M |
| SEMA4A |
| TOR3A |
| RFWD2 |
| GREM2 |
| RGS18 |
| PLA2G2F |
| HIAT1 |
| NUCKS1 |
| SMAP2 |
| ACBD3 |
| SMYD3 |
| ATPAF1 |
| MOSC1 |
| S100PBP |
| MEAF6 |
| DEM1 |
| CCDC21 |
| ARV1 |
| NMNAT1 |
| ELOVL1 |
| AIDA |
| VWA1 |
| DCLRE1B |
| MRPS15 |
| MRPL9 |
| PINK1 |
| JMJD4 |
| MARCKSL1 |
| PRAMEF1 |
| PRAMEF2 |
| INTS3 |
| NADK |
| ZNF643 |
| C1orf163 |
| PHACTR4 |
| C1orf135 |
| SCNM1 |
| ERI3 |
| C1orf50 |
| WDR77 |
| C1orf116 |
| MGC4473 |
| CCDC28B |
| C1orf35 |
| EFHD2 |
| MMEL1 |
| C1orf89 |
| FCRL2 |
| DLEU2L |
| OR4F5 |
| NKAIN1 |
| TTC13 |
| EPS8L3 |
| CDC73 |
| MRPL24 |
| MUL1 |
| PGBD5 |
| TNFAIP8L2 |
| C1orf54 |
| TMEM53 |
| AKIRIN1 |
| HECTD3 |
| BEND5 |
| VTCN1 |
| YRDC |
| ZYG11B |
| NOL9 |
| PPCS |
| LIN28 |
| C1orf113 |
| TTLL7 |
| SNIP1 |
| C1orf115 |
| HHIPL2 |
| VASH2 |
| AGMAT |
| WDR78 |
| ZMYM1 |
| NCRNA00115 |
| ZNF669 |
| RPAP2 |
| ZNF672 |
| MORN1 |
| GRRP1 |
| KIAA0319L |
| DHDDS |
| PAQR6 |
| DENND2D |
| GPR177 |
| 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 |
| C1orf14 |
| C1orf25 |
| 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 |
| C1orf57 |
| EFCAB2 |
| DDI2 |
| ACBD6 |
| LZIC |
| PROK1 |
| KIAA1804 |
| EFCAB7 |
| ZBTB37 |
| NT5C1A |
| LCE3D |
| TRIM63 |
| PSRC1 |
| FAM167B |
| C1orf97 |
| MGC12982 |
| C1orf170 |
| CROCCL1 |
| FCRLA |
| ANKRD36BL1 |
| ZNF496 |
| HPDL |
| C1orf203 |
| 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 |
| C1orf156 |
| GORAB |
| C1orf105 |
| TMEM183A |
| HIST3H2A |
| PIGM |
| IGSF8 |
| C1orf158 |
| LEMD1 |
| ZNF670 |
| FBXO44 |
| ATPIF1 |
| SNORD46 |
| SNORD38A |
| SNORD38B |
| C1orf85 |
| MED8 |
| KTI12 |
| C1orf212 |
| ADC |
| TMEM54 |
| C1orf59 |
| TOE1 |
| NLRP3 |
| ERMAP |
| PGLYRP3 |
| CSMD2 |
| MYSM1 |
| GNRHR2 |
| CROCCL2 |
| 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 |
| C1orf231 |
| TDRD10 |
| SHE |
| C1orf172 |
| C1orf96 |
| AADACL3 |
| PUSL1 |
| B3GALT6 |
| WDR63 |
| KLHDC9 |
| C1orf125 |
| C1orf161 |
| IFFO2 |
| HIST2H3C |
| SLC44A3 |
| ATXN7L2 |
| C1orf194 |
| LYPLAL1 |
| OR2M5 |
| OR2M3 |
| OR2T12 |
| OR14C36 |
| OR2T34 |
| OR2T10 |
| OR2T4 |
| OR2T11 |
| ATP6V1G3 |
| ASB17 |
| TYW3 |
| C1orf173 |
| LRRIQ3 |
| TPRG1L |
| C1orf93 |
| MYOM3 |
| DMBX1 |
| OR10J5 |
| TMCO2 |
| ZNF684 |
| C1orf83 |
| 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 |
| 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 |
| C1orf58 |
| SAMD11 |
| LOC148413 |
| SAMD13 |
| C1orf52 |
| PHF13 |
| C1orf51 |
| TMEM56 |
| NBPF4 |
| UBE2U |
| SLC35F3 |
| LOC148696 |
| LOC148709 |
| PTPRV |
| HFE2 |
| ANKRD35 |
| FAM163A |
| B3GALNT2 |
| MFSD4 |
| PM20D1 |
| C1orf150 |
| LOC148824 |
| SLC30A7 |
| CCDC27 |
| C1orf213 |
| KNCN |
| MOBKL2C |
| GLIS1 |
| LELP1 |
| RC3H1 |
| MGC27382 |
| DCDC2B |
| ZNF362 |
| DCST1 |
| CNIH3 |
| LOC149134 |
| MANEAL |
| IL23R |
| METTL11B |
| FAM78B |
| SHISA4 |
| EXOC8 |
| PDIK1L |
| BNIPL |
| CLDN19 |
| WDR65 |
| C1orf210 |
| C1orf84 |
| CCDC24 |
| BTBD19 |
| CCDC17 |
| C1orf92 |
| C1orf64 |
| RNF187 |
| LOC149620 |
| 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 |
| C1orf168 |
| TMEM201 |
| TMEM61 |
| CYP4Z1 |
| C1orf86 |
| CDCP2 |
| SLC5A9 |
| CC2D1B |
| LOC200030 |
| NUDT17 |
| FLJ23867 |
| TXLNA |
| TCTEX1D1 |
| PLD5 |
| C1orf100 |
| SPAG17 |
| SLFNL1 |
| KRTCAP2 |
| CRTC2 |
| C1orf126 |
| C1orf69 |
| HIPK1 |
| SLC44A5 |
| ATAD3C |
| AKR7L |
| AFARP1 |
| TMEM9 |
| FNDC5 |
| EPHX4 |
| TTLL10 |
| AKNAD1 |
| SLC41A1 |
| OR2T6 |
| LCE5A |
| TMCO4 |
| MCOLN2 |
| COL24A1 |
| PCSK9 |
| SYT14 |
| ST6GALNAC3 |
| C1orf101 |
| ZNF683 |
| ARHGAP30 |
| C1orf192 |
| NEGR1 |
| ASPM |
| CYP4X1 |
| MAGI3 |
| TIPRL |
| NPHP4 |
| BEST4 |
| PGBD2 |
| FAM19A3 |
| C1orf230 |
| THEM5 |
| OR2L13 |
| SLC9A11 |
| OR14A16 |
| CYP4A22 |
| C1orf185 |
| LOC284551 |
| NBPF15 |
| C1orf157 |
| LOC284578 |
| FAM41C |
| FAM102B |
| SYPL2 |
| CYB561D1 |
| ANKRD34A |
| C1orf104 |
| LOC284632 |
| RSPO1 |
| EPHA10 |
| LOC284661 |
| C1orf204 |
| C1orf111 |
| LOC284688 |
| ZNF326 |
| BTBD8 |
| NCRNA00201 |
| RIMKLA |
| SLC25A34 |
| ESPNP |
| LIN9 |
| VN1R5 |
| HIST2H2AB |
| PPM1J |
| HIST2H3A |
| HIST2H2BA |
| FAM151A |
| S100A7A |
| LINGO4 |
| RXFP4 |
| ANKRD45 |
| C1orf174 |
| KLHL17 |
| C1orf70 |
| TMEM52 |
| FAM5C |
| MTMR9L |
| ZBTB8OS |
| TFAP2E |
| ZNF678 |
| PRSS38 |
| C1orf110 |
| FAM58B |
| LOC339524 |
| 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 |
| C1orf223 |
| C1orf175 |
| FAM73A |
| PEAR1 |
| SFT2D2 |
| MIA3 |
| C1orf95 |
| FAM89A |
| AGRN |
| RPS10P7 |
| APITD1 |
| CATSPER4 |
| NSUN4 |
| GPR153 |
| ILDR2 |
| FAM132A |
| HES5 |
| LOC388588 |
| RNF207 |
| TMEM82 |
| TRNP1 |
| CD164L2 |
| LDLRAD1 |
| GBP7 |
| C1orf146 |
| FAM69A |
| SLC6A17 |
| NOTCH2NL |
| FLJ39739 |
| LOC388692 |
| LYSMD1 |
| HRNR |
| FLG2 |
| C1orf189 |
| FMO6P |
| 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 |
| LOC400759 |
| C1orf226 |
| LOC400794 |
| C1orf220 |
| LOC400804 |
| NBPF20 |
| FAM177B |
| PRAMEF3 |
| LDLRAD2 |
| OR2T2 |
| OR2T5 |
| OR14I1 |
| 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 |
| C1orf151 |
| FAM183A |
| ZYG11A |
| BCL2L15 |
| HIST2H2BF |
| ETV3L |
| LRRC52 |
| C1orf186 |
| TRIM67 |
| MAP1LC3C |
| LOC440926 |
| LOC441869 |
| PRAMEF7 |
| LOC441897 |
| OR10J3 |
| OR2W5 |
| OR13G1 |
| MIR135B |
| KPRP |
| LCE6A |
| SUMO1P3 |
| LOC492303 |
| RBMXL1 |
| C1orf190 |
| PEF1 |
| MIR429 |
| HIST2H4B |
| DUSP5P |
| C1orf133 |
| MIR488 |
| CYB5RL |
| SNORD74 |
| RPL31P11 |
| FAM138F |
| LOC642502 |
| LOC642587 |
| LQK1 |
| CYMP |
| KIAA0754 |
| LOC643837 |
| TMEM88B |
| PPIAL4G |
| C1orf200 |
| PPIAL4D |
| LOC645166 |
| PRAMEF19 |
| PRAMEF20 |
| FAM138A |
| LOC645676 |
| S100A7L2 |
| LOC646471 |
| LOC646627 |
| LOC647121 |
| LOC648740 |
| LOC649330 |
| ZBTB8A |
| NBPF6 |
| PPIAL4B |
| GPR89A |
| LOC653566 |
| PPIAL4C |
| HIST2H3D |
| PRAMEF22 |
| PRAMEF15 |
| WASH5P |
| TMEM183B |
| FAM72B |
| PRAMEF16 |
| PCP4L1 |
| FAM138C |
| SCARNA3 |
| SCARNA2 |
| SCARNA4 |
| SCARNA1 |
| SNORA14B |
| SNORA36B |
| SNORA42 |
| SNORA44 |
| SNORA55 |
| SNORA61 |
| SNORA77 |
| SNORA59B |
| SNORA59A |
| SNORA16A |
| SNORD45C |
| SNORA16B |
| SNORD75 |
| SNORD76 |
| SNORD77 |
| SNORD78 |
| SNORD85 |
| SNORD99 |
| SNORD103A |
| MIR551A |
| MIR553 |
| MIR554 |
| MIR555 |
| MIR556 |
| MIR557 |
| MIR92B |
| HIST2H2AA4 |
| ZBTB8B |
| LOC728448 |
| CCDC30 |
| CDC2L2 |
| LOC728661 |
| LOC728855 |
| LOC728875 |
| NBPF11 |
| GPR89C |
| NBPF16 |
| PDZK1P1 |
| PPIAL4F |
| RPS15AP10 |
| LOC728989 |
| LOC729467 |
| PRAMEF14 |
| FAM72A |
| FLJ37453 |
| OR4F29 |
| PPIAL4E |
| LOC731275 |
| SNHG3-RCC1 |
| C1orf152 |
| MIR765 |
| MIR942 |
| MIR190B |
| MIR760 |
| MIR921 |
| LOC100128003 |
| LOC100128071 |
| LOC100128842 |
| C1orf68 |
| MSTO2P |
| LOC100129534 |
| LOC100130093 |
| LOC100130331 |
| FLJ39609 |
| LOC100130557 |
| TSTD1 |
| LOC100132062 |
| LOC100132111 |
| LOC100132287 |
| NBPF10 |
| FCGR1C |
| LOC100133331 |
| LOC100133612 |
| C2CD4D |
| LOC100286793 |
| LOC100288778 |
| LOC100302401 |
| TSNAX-DISC1 |
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 - 35 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 |
|---|---|---|---|---|
| 1p36.23 | 7.7868e-08 | 7.7868e-08 | chr1:1-8309316 | 134 |
| 13q14.2 | 0.00030558 | 0.00085033 | chr13:47731768-47962808 | 2 |
| 14q31.3 | 0.0059411 | 0.0059411 | chr14:74536625-106368585 | 314 |
| 19p13.3 | 0.0075482 | 0.012098 | chr19:6619605-6686925 | 1 |
| 2q34 | 0.017434 | 0.017434 | chr2:208838538-242951149 | 261 |
| 10q26.2 | 0.012098 | 0.019034 | chr10:123231113-135374737 | 91 |
| 8p23.2 | 0.022767 | 0.022462 | chr8:2080589-6255647 | 1 |
| 22q13.31 | 0.024075 | 0.022806 | chr22:40804400-49691432 | 109 |
| 2q23.1 | 0.027339 | 0.027339 | chr2:138435310-165520964 | 67 |
| 18q21.2 | 0.039499 | 0.038451 | chr18:46509167-46959369 | 4 |
| 9p21.3 | 0.04488 | 0.046925 | chr9:21020852-23680570 | 26 |
| 10q23.31 | 0.012515 | 0.051476 | chr10:88837980-90024018 | 11 |
| 16q24.2 | 0.059144 | 0.056098 | chr16:70485567-88827254 | 147 |
| 13q32.3 | 0.066172 | 0.062681 | chr13:99428994-100055448 | 3 |
| 3p21.1 | 0.088143 | 0.09176 | chr3:52547488-52919124 | 13 |
| 4q22.3 | 0.0031499 | 0.09176 | chr4:76699973-123507109 | 222 |
| 17p12 | 0.095983 | 0.092912 | chr17:15832052-16062027 | 2 |
| 4q31.3 | 0.038028 | 0.12018 | chr4:151397952-152240226 | 2 |
| 9p24.1 | 0.12242 | 0.12184 | chr9:7786330-12683402 | 2 |
| 2p15 | 0.13818 | 0.13818 | chr2:62267493-207340787 | 728 |
| 11q14.1 | 0.096761 | 0.14987 | chr11:77555851-94349006 | 75 |
| 19p13.12 | 0.12184 | 0.16414 | chr19:10621992-17905559 | 216 |
| 1p33 | 0.19242 | 0.19242 | chr1:50652354-51210952 | 2 |
| 11q24.3 | 0.056755 | 0.19242 | chr11:102421578-134452384 | 269 |
| 12q24.31 | 0.20028 | 0.19242 | chr12:109829625-132349534 | 191 |
| 17p13.2 | 0.20077 | 0.19242 | chr17:1-4658761 | 99 |
| 6q26 | 0.16298 | 0.20182 | chr6:44330865-170899992 | 548 |
| 13q14.3 | 0.024497 | 0.20182 | chr13:1-94080173 | 276 |
| 18q22.1 | 0.20308 | 0.20182 | chr18:50644442-76117153 | 86 |
| 6q15 | 0.13818 | 0.22392 | chr6:44330865-170414665 | 543 |
| 9q31.1 | 0.17657 | 0.22392 | chr9:101620195-140273252 | 439 |
| 4q35.1 | 0.0026302 | 0.25613 | chr4:1-191273063 | 806 |
| 7q34 | 0.24123 | 0.25613 | chr7:1-158821424 | 1031 |
| 9q34.13 | 0.15068 | 0.25613 | chr9:1-140273252 | 890 |
| 4q24 | 0.0031689 | 0.77436 | chr4:1-191273063 | 806 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 1p36.23.
Table S11. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| RPL22 |
| TNFRSF14 |
| PRDM16 |
| hsa-mir-551a |
| hsa-mir-429 |
| hsa-mir-1977 |
| hsa-mir-1302-2 |
| CDC2L1 |
| DFFB |
| DVL1 |
| MEGF6 |
| GABRD |
| GNB1 |
| ZBTB48 |
| TNFRSF9 |
| PEX10 |
| PRKCZ |
| SCNN1D |
| SKI |
| TP73 |
| TNFRSF4 |
| MMP23B |
| MMP23A |
| KCNAB2 |
| TNFRSF25 |
| TNFRSF18 |
| PER3 |
| VAMP3 |
| ISG15 |
| PLCH2 |
| KIAA0562 |
| KLHL21 |
| SLC35E2 |
| UTS2 |
| RER1 |
| PARK7 |
| ACOT7 |
| CAMTA1 |
| ICMT |
| CHD5 |
| NOC2L |
| OR4F3 |
| ARHGEF16 |
| SSU72 |
| WDR8 |
| SDF4 |
| ERRFI1 |
| MXRA8 |
| HES2 |
| CPSF3L |
| C1orf159 |
| AURKAIP1 |
| MRPL20 |
| ATAD3A |
| PANK4 |
| DNAJC11 |
| AJAP1 |
| KIAA0495 |
| PLEKHG5 |
| LRRC47 |
| HES4 |
| VWA1 |
| NADK |
| MMEL1 |
| OR4F5 |
| NOL9 |
| NCRNA00115 |
| MORN1 |
| GLTPD1 |
| TAS1R1 |
| OR4F16 |
| CCNL2 |
| ESPN |
| TAS1R3 |
| ATAD3B |
| PLEKHN1 |
| C1orf170 |
| KIAA1751 |
| THAP3 |
| LOC115110 |
| ACAP3 |
| UBE2J2 |
| PUSL1 |
| B3GALT6 |
| TPRG1L |
| C1orf93 |
| ACTRT2 |
| MIB2 |
| SAMD11 |
| LOC148413 |
| PHF13 |
| CCDC27 |
| CALML6 |
| C1orf86 |
| ATAD3C |
| TTLL10 |
| NPHP4 |
| FAM41C |
| LOC284661 |
| C1orf174 |
| KLHL17 |
| C1orf70 |
| TMEM52 |
| AGRN |
| GPR153 |
| FAM132A |
| HES5 |
| LOC388588 |
| RNF207 |
| HES3 |
| MIR200A |
| MIR200B |
| FLJ42875 |
| LOC441869 |
| MIR429 |
| FAM138F |
| LOC643837 |
| TMEM88B |
| FAM138A |
| WASH5P |
| FAM138C |
| MIR551A |
| CDC2L2 |
| LOC728661 |
| OR4F29 |
| LOC100128003 |
| LOC100128842 |
| LOC100129534 |
| FLJ39609 |
| LOC100132062 |
| LOC100132287 |
| LOC100133331 |
| LOC100133612 |
| LOC100288778 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 13q14.2.
Table S12. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| RB1 |
| LPAR6 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 14q31.3.
Table S13. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| AKT1 |
| TSHR |
| TCL1A |
| TRIP11 |
| GOLGA5 |
| DICER1 |
| TCL6 |
| BCL11B |
| hsa-mir-203 |
| hsa-mir-1247 |
| hsa-mir-656 |
| hsa-mir-370 |
| hsa-mir-770 |
| hsa-mir-345 |
| hsa-mir-342 |
| hsa-mir-1260 |
| SERPINA3 |
| ACYP1 |
| BCYRN1 |
| BDKRB1 |
| BDKRB2 |
| CALM1 |
| SERPINA6 |
| FOXN3 |
| CHGA |
| CKB |
| CRIP1 |
| CRIP2 |
| DIO2 |
| DIO3 |
| DYNC1H1 |
| EIF5 |
| EML1 |
| ESRRB |
| FOS |
| GALC |
| GSTZ1 |
| GTF2A1 |
| BRF1 |
| HSP90AA1 |
| IFI27 |
| ITPK1 |
| JAG2 |
| KLC1 |
| MARK3 |
| ATXN3 |
| NDUFB1 |
| SERPINA5 |
| SERPINA1 |
| SERPINA4 |
| PPP2R5C |
| LGMN |
| PSMC1 |
| RAGE |
| SEL1L |
| TGFB3 |
| TNFAIP2 |
| TRAF3 |
| VRK1 |
| WARS |
| XRCC3 |
| YY1 |
| GPR68 |
| GPR65 |
| ADAM6 |
| DLK1 |
| CCNK |
| ALKBH1 |
| EIF2B2 |
| MTA1 |
| RPS6KA5 |
| NRXN3 |
| SPTLC2 |
| BAG5 |
| C14orf2 |
| CDC42BPB |
| TCL1B |
| KIAA0125 |
| TECPR2 |
| FBLN5 |
| BATF |
| SIVA1 |
| AHSA1 |
| CYP46A1 |
| PAPOLA |
| TMED10 |
| PTPN21 |
| C14orf1 |
| VASH1 |
| SNW1 |
| TTLL5 |
| RCOR1 |
| PACS2 |
| ANGEL1 |
| PPP1R13B |
| FLRT2 |
| KIF26A |
| C14orf109 |
| MLH3 |
| PRO1768 |
| GPR132 |
| POMT2 |
| SERPINA10 |
| GLRX5 |
| EVL |
| C14orf129 |
| CINP |
| ASB2 |
| CPSF2 |
| KCNK10 |
| CDCA4 |
| C14orf102 |
| ATG2B |
| UBR7 |
| MEG3 |
| FLVCR2 |
| C14orf118 |
| SMEK1 |
| BTBD7 |
| TDP1 |
| ZNF839 |
| SPATA7 |
| KCNK13 |
| C14orf132 |
| DDX24 |
| ADCK1 |
| TMEM63C |
| KIAA1409 |
| BEGAIN |
| PPP4R4 |
| NGB |
| C14orf133 |
| MOAP1 |
| DIO3OS |
| C14orf4 |
| INF2 |
| OTUB2 |
| ZFYVE21 |
| MEG8 |
| WDR25 |
| C14orf139 |
| FAM164C |
| CLMN |
| CATSPERB |
| ZC3H14 |
| RIN3 |
| C14orf159 |
| TMEM121 |
| AMN |
| C14orf156 |
| IFI27L2 |
| SETD3 |
| C14orf153 |
| HHIPL1 |
| C14orf142 |
| STON2 |
| KIAA1737 |
| FAM181A |
| BTBD6 |
| C14orf143 |
| NEK9 |
| C14orf73 |
| WDR20 |
| C14orf179 |
| AHNAK2 |
| TRMT61A |
| TDRD9 |
| ANKRD9 |
| AK7 |
| IFI27L1 |
| C14orf79 |
| PLD4 |
| ADSSL1 |
| C14orf148 |
| JDP2 |
| TTC8 |
| TC2N |
| SLC24A4 |
| SLC25A29 |
| DEGS2 |
| C14orf72 |
| GSC |
| SERPINA12 |
| PRIMA1 |
| C14orf166B |
| ISM2 |
| C14orf145 |
| TTC7B |
| C14orf49 |
| C14orf174 |
| EML5 |
| MGC23270 |
| NUDT14 |
| C14orf48 |
| SERPINA11 |
| ZDHHC22 |
| TMED8 |
| C14orf178 |
| C14orf86 |
| SNHG10 |
| C14orf177 |
| C14orf68 |
| C14orf70 |
| KIAA0284 |
| C14orf80 |
| CCDC85C |
| NCRNA00203 |
| SERPINA9 |
| COX8C |
| ASPG |
| SERPINA13 |
| C14orf64 |
| RTL1 |
| TMEM179 |
| FLJ45244 |
| C14orf180 |
| MIR127 |
| MIR134 |
| MIR136 |
| MIR154 |
| MIR203 |
| MIR299 |
| CCDC88C |
| MIR323 |
| MIR337 |
| MIR342 |
| MIR345 |
| MIR376C |
| MIR369 |
| MIR376A1 |
| MIR377 |
| MIR379 |
| MIR380 |
| MIR381 |
| MIR382 |
| MIR433 |
| MIR431 |
| MIR329-1 |
| MIR329-2 |
| MIR453 |
| MIR409 |
| MIR412 |
| MIR410 |
| MIR376B |
| MIR485 |
| MIR493 |
| MIR432 |
| MIR494 |
| MIR495 |
| MIR496 |
| MIR487A |
| C14orf184 |
| MIR539 |
| MIR376A2 |
| MIR487B |
| SCARNA13 |
| SNORA28 |
| SNORA79 |
| SNORD112 |
| MIR411 |
| MIR654 |
| MIR655 |
| MIR656 |
| SNORD113-1 |
| SNORD113-2 |
| SNORD113-3 |
| SNORD113-4 |
| SNORD113-5 |
| SNORD113-6 |
| SNORD113-7 |
| SNORD113-8 |
| SNORD113-9 |
| SNORD114-1 |
| SNORD114-2 |
| SNORD114-3 |
| SNORD114-4 |
| SNORD114-5 |
| SNORD114-6 |
| SNORD114-7 |
| SNORD114-8 |
| SNORD114-9 |
| SNORD114-10 |
| SNORD114-11 |
| SNORD114-12 |
| SNORD114-13 |
| SNORD114-14 |
| SNORD114-15 |
| SNORD114-16 |
| SNORD114-17 |
| SNORD114-18 |
| SNORD114-19 |
| SNORD114-20 |
| SNORD114-21 |
| SNORD114-22 |
| SNORD114-23 |
| SNORD114-24 |
| SNORD114-25 |
| SNORD114-26 |
| SNORD114-27 |
| SNORD114-28 |
| SNORD114-29 |
| SNORD114-30 |
| SNORD114-31 |
| MIR758 |
| MIR668 |
| MIR770 |
| SNORA11B |
| MIR300 |
| MIR541 |
| MIR665 |
| MIR543 |
| MIR889 |
| ZBTB42 |
| LOC100133469 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 19p13.3.
Table S14. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| C3 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 2q34.
Table S15. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| ATIC |
| ACSL3 |
| PAX3 |
| FEV |
| hsa-mir-149 |
| hsa-mir-562 |
| hsa-mir-1471 |
| hsa-mir-1244 |
| hsa-mir-153-1 |
| hsa-mir-375 |
| hsa-mir-26b |
| hsa-mir-548f-2 |
| AAMP |
| ACADL |
| AGXT |
| ALPI |
| ALPP |
| ALPPL2 |
| KIF1A |
| BARD1 |
| BCS1L |
| BOK |
| CHRND |
| CHRNG |
| COL4A3 |
| COL4A4 |
| COL6A3 |
| CPS1 |
| CRYBA2 |
| CYP27A1 |
| DES |
| DTYMK |
| EPHA4 |
| ERBB4 |
| FN1 |
| GBX2 |
| GPC1 |
| GPR35 |
| HDLBP |
| AGFG1 |
| DNAJB2 |
| HTR2B |
| SP110 |
| IGFBP2 |
| IGFBP5 |
| IHH |
| IL8RA |
| IL8RB |
| IL8RBP |
| INHA |
| INPP5D |
| IRS1 |
| KCNJ13 |
| MAP2 |
| MYL1 |
| NCL |
| NDUFA10 |
| SEPT2 |
| NEU2 |
| NPPC |
| PDCD1 |
| PDE6D |
| SERPINE2 |
| PPP1R7 |
| PSMD1 |
| PTH2R |
| PTMA |
| PTPRN |
| SNORD20 |
| RPE |
| RPL37A |
| SAG |
| CCL20 |
| SLC4A3 |
| SLC11A1 |
| SP100 |
| SPP2 |
| TNP1 |
| TNS1 |
| TUBA4A |
| VIL1 |
| WNT6 |
| XRCC5 |
| ZNF142 |
| SCG2 |
| CUL3 |
| DGKD |
| STK16 |
| PER2 |
| CDK5R2 |
| RQCD1 |
| LRRFIP1 |
| GPR55 |
| TRIP12 |
| ECEL1 |
| EIF4E2 |
| TTLL4 |
| HDAC4 |
| FARP2 |
| FARSB |
| ABCB6 |
| ARPC2 |
| ARL4C |
| RAMP1 |
| SPEG |
| LANCL1 |
| NMUR1 |
| STK25 |
| COPS8 |
| CAPN10 |
| SP140 |
| IKZF2 |
| PASK |
| ATG4B |
| OBSL1 |
| DNPEP |
| SH3BP4 |
| KCNE4 |
| NGEF |
| SNORD82 |
| PNKD |
| SNED1 |
| GIGYF2 |
| TRAF3IP1 |
| ABCA12 |
| C2orf24 |
| STK36 |
| LOC29034 |
| GMPPA |
| SMARCAL1 |
| ANO7 |
| PRLH |
| THAP4 |
| ANKMY1 |
| SCLY |
| ASB1 |
| CAB39 |
| PRKAG3 |
| UGT1A10 |
| UGT1A8 |
| UGT1A7 |
| UGT1A6 |
| UGT1A5 |
| UGT1A9 |
| UGT1A4 |
| UGT1A1 |
| UGT1A3 |
| PID1 |
| ATG16L1 |
| ANKZF1 |
| USP40 |
| HJURP |
| HES6 |
| ACCN4 |
| DOCK10 |
| MREG |
| PECR |
| C2orf83 |
| MFF |
| CXCR7 |
| RNPEPL1 |
| MARCH4 |
| WDFY1 |
| KIAA1486 |
| USP37 |
| CTDSP1 |
| GAL3ST2 |
| TMBIM1 |
| RAB17 |
| RNF25 |
| COPS7B |
| MRPL44 |
| TRPM8 |
| ATG9A |
| MLPH |
| FAM134A |
| GLB1L |
| SPAG16 |
| CHPF |
| IQCA1 |
| NHEJ1 |
| FAM124B |
| TM4SF20 |
| C2orf54 |
| TUBA4B |
| ARMC9 |
| EFHD1 |
| SPHKAP |
| WNT10A |
| SLC19A3 |
| ILKAP |
| ITM2C |
| RHBDD1 |
| ING5 |
| PLCD4 |
| MGC16025 |
| TMEM169 |
| DNER |
| B3GNT7 |
| SP140L |
| STK11IP |
| MOGAT1 |
| AGAP1 |
| DIS3L2 |
| NEU4 |
| AP1S3 |
| SGPP2 |
| SPATA3 |
| TMEM198 |
| ZFAND2B |
| FBXO36 |
| MTERFD2 |
| UBE2F |
| OTOS |
| MYEOV2 |
| OR6B3 |
| C2orf67 |
| LOC151174 |
| CCDC140 |
| SLC23A3 |
| LOC151300 |
| GPBAR1 |
| SLC16A14 |
| C2orf52 |
| MSL3L2 |
| WDR69 |
| C2orf57 |
| PIKFYVE |
| TIGD1 |
| CCDC108 |
| C2orf72 |
| C2orf85 |
| UNC80 |
| RUFY4 |
| DUSP28 |
| ESPNL |
| ECEL1P2 |
| C2orf62 |
| RBM44 |
| AQP12A |
| KLHL30 |
| RESP18 |
| C2orf82 |
| OR6B2 |
| ASB18 |
| VWC2L |
| MIR149 |
| MIR153-1 |
| MIR26B |
| DNAJB3 |
| MIR375 |
| LOC643387 |
| PRR21 |
| AQP12B |
| SNORA75 |
| SCARNA6 |
| SCARNA5 |
| D2HGDH |
| LOC728323 |
| DIRC3 |
| PP14571 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 10q26.2.
Table S16. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| FGFR2 |
| DUX4 |
| hsa-mir-202 |
| ACADSB |
| ADAM8 |
| BNIP3 |
| CTBP2 |
| CYP2E1 |
| DMBT1 |
| DOCK1 |
| ECHS1 |
| GPR26 |
| HMX2 |
| INPP5A |
| MGMT |
| MKI67 |
| OAT |
| HTRA1 |
| PTPRE |
| UROS |
| ADAM12 |
| UTF1 |
| BUB3 |
| FAM53B |
| GLRX3 |
| DPYSL4 |
| TACC2 |
| TUBGCP2 |
| ATE1 |
| FAM175B |
| C10orf137 |
| VENTX |
| CUZD1 |
| CALY |
| CHST15 |
| ZRANB1 |
| NSMCE4A |
| DHX32 |
| PPP2R2D |
| BCCIP |
| PLEKHA1 |
| LHPP |
| IKZF5 |
| C10orf88 |
| LRRC27 |
| GPR123 |
| NKX6-2 |
| KNDC1 |
| MTG1 |
| FANK1 |
| SYCE1 |
| PRAP1 |
| ZNF511 |
| C10orf90 |
| BTBD16 |
| FAM24A |
| PSTK |
| MMP21 |
| CLRN3 |
| CPXM2 |
| C10orf91 |
| PWWP2B |
| PAOX |
| FAM24B |
| EBF3 |
| C10orf93 |
| TCERG1L |
| C10orf125 |
| JAKMIP3 |
| STK32C |
| HMX3 |
| FLJ46361 |
| ARMS2 |
| C10orf122 |
| NKX1-2 |
| C10orf120 |
| LOC399815 |
| METTL10 |
| FOXI2 |
| FRG2B |
| SPRN |
| MIR202 |
| NPS |
| LOC619207 |
| FAM196A |
| LOC653543 |
| LOC653544 |
| LOC653545 |
| LOC653548 |
| LOC728410 |
| LOC100169752 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 8p23.2.
Table S17. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| CSMD1 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 22q13.31.
Table S18. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| hsa-let-7b |
| hsa-mir-1249 |
| ACR |
| ARSA |
| BIK |
| TSPO |
| MPPED1 |
| CHKB |
| CPT1B |
| CYP2D7P1 |
| CYP2D6 |
| CYB5R3 |
| TYMP |
| FBLN1 |
| NDUFA6 |
| PPARA |
| MAPK11 |
| MAPK12 |
| SBF1 |
| TCF20 |
| UPK3A |
| WNT7B |
| CELSR1 |
| SAPS2 |
| ZBED4 |
| SCO2 |
| PKDREJ |
| NUP50 |
| RABL2B |
| PACSIN2 |
| GRAMD4 |
| TTLL12 |
| MLC1 |
| C22orf9 |
| MAPK8IP2 |
| PLXNB2 |
| BRD1 |
| ARHGAP8 |
| TBC1D22A |
| TTLL1 |
| SAMM50 |
| ATXN10 |
| FAM19A5 |
| SULT4A1 |
| RIBC2 |
| ARFGAP3 |
| SMC1B |
| RRP7A |
| MCAT |
| PARVB |
| NCAPH2 |
| GTSE1 |
| A4GALT |
| MOV10L1 |
| FAM118A |
| TTC38 |
| C22orf26 |
| MIOX |
| PRR5 |
| TRMU |
| PANX2 |
| PARVG |
| CERK |
| EFCAB6 |
| ALG12 |
| CRELD2 |
| ADM2 |
| SCUBE1 |
| TRABD |
| PNPLA3 |
| SELO |
| HDAC10 |
| LDOC1L |
| POLDIP3 |
| KIAA1644 |
| SHANK3 |
| TUBGCP6 |
| LOC90834 |
| LMF2 |
| C22orf32 |
| RRP7B |
| SERHL |
| PHF21B |
| KLHDC7B |
| NFAM1 |
| PNPLA5 |
| LOC150381 |
| C22orf40 |
| CN5H6.4 |
| TTLL8 |
| SERHL2 |
| RNU12 |
| ATP5L2 |
| RPL23AP82 |
| C22orf34 |
| CHKB-CPT1B |
| NCRNA00207 |
| LOC400931 |
| IL17REL |
| MIRLET7A3 |
| MIRLET7B |
| FAM116B |
| PIM3 |
| ODF3B |
| PRR5-ARHGAP8 |
| C22orf41 |
| LOC730668 |
| LOC100144603 |
| LOC100271722 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 2q23.1.
Table S19. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| hsa-mir-1978 |
| ACVR1 |
| ACVR2A |
| RND3 |
| CACNB4 |
| DPP4 |
| FAP |
| GCG |
| GPD2 |
| GRB14 |
| HNMT |
| ITGB6 |
| KCNJ3 |
| KIF5C |
| LY75 |
| NEB |
| NR4A2 |
| ORC4L |
| RBMS1 |
| TNFAIP6 |
| PKP4 |
| KYNU |
| NMI |
| CYTIP |
| ZEB2 |
| CD302 |
| TANK |
| PSMD14 |
| STAM2 |
| TBR1 |
| GALNT5 |
| NXPH2 |
| COBLL1 |
| PLA2R1 |
| GCA |
| EPC2 |
| ARL5A |
| MMADHC |
| BAZ2B |
| LRP1B |
| FIGN |
| RIF1 |
| PRPF40A |
| MBD5 |
| ARHGAP15 |
| RPRM |
| SLC4A10 |
| ERMN |
| IFIH1 |
| MARCH7 |
| GTDC1 |
| TANC1 |
| KCNH7 |
| DAPL1 |
| FMNL2 |
| GALNT13 |
| ACVR1C |
| LYPD6 |
| LYPD6B |
| CCDC148 |
| ARL6IP6 |
| SLC38A11 |
| WDSUB1 |
| UPP2 |
| SPOPL |
| RBM43 |
| PABPCP2 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 18q21.2.
Table S20. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| SMAD4 |
| ME2 |
| ELAC1 |
| MRO |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 9p21.3.
Table S21. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| hsa-mir-31 |
| CDKN2A |
| CDKN2B |
| IFNA1 |
| IFNA2 |
| IFNA4 |
| IFNA5 |
| IFNA6 |
| IFNA7 |
| IFNA8 |
| IFNA10 |
| IFNA13 |
| IFNA14 |
| IFNA16 |
| IFNA17 |
| IFNA21 |
| IFNB1 |
| IFNW1 |
| MTAP |
| C9orf53 |
| KLHL9 |
| DMRTA1 |
| IFNE |
| MIR31 |
| LOC554202 |
| CDKN2BAS |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 10q23.31.
Table S22. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| PTEN |
| PAPSS2 |
| MINPP1 |
| FAM35A |
| ATAD1 |
| CFLP1 |
| LOC439994 |
| FAM22A |
| FAM22D |
| LOC728190 |
| KILLIN |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 16q24.2.
Table S23. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| CBFA2T3 |
| FANCA |
| MAF |
| hsa-mir-1910 |
| AFG3L1 |
| APRT |
| ZFHX3 |
| C16orf3 |
| CA5A |
| CDH13 |
| CDH15 |
| COX4I1 |
| CTRB1 |
| CYBA |
| DHODH |
| DPEP1 |
| FOXF1 |
| FOXL1 |
| FOXC2 |
| GALNS |
| GAS8 |
| GCSH |
| GLG1 |
| HP |
| HPR |
| HSBP1 |
| HSD17B2 |
| IRF8 |
| KARS |
| MC1R |
| CHST6 |
| MVD |
| CHMP1A |
| PLCG2 |
| PSMD7 |
| RPL13 |
| SPG7 |
| GAN |
| SLC7A5 |
| CDK10 |
| MBTPS1 |
| TAF1C |
| USP10 |
| BCAR1 |
| C16orf7 |
| KIAA0513 |
| FAM38A |
| DHX38 |
| KIAA0174 |
| ATP2C2 |
| CLEC3A |
| MPHOSPH6 |
| COX4NB |
| TUBB3 |
| CFDP1 |
| PRDM7 |
| GABARAPL2 |
| MON1B |
| TCF25 |
| ZCCHC14 |
| KIAA0182 |
| ATMIN |
| COTL1 |
| MLYCD |
| ADAT1 |
| CHST5 |
| CPNE7 |
| IL17C |
| ANKRD11 |
| OSGIN1 |
| GINS2 |
| TRAPPC2L |
| WWOX |
| BCMO1 |
| TERF2IP |
| NECAB2 |
| KLHDC4 |
| DEF8 |
| TXNL4B |
| BANP |
| RFWD3 |
| ZDHHC7 |
| CENPN |
| C16orf61 |
| JPH3 |
| VAT1L |
| KIAA1609 |
| WFDC1 |
| MTHFSD |
| DBNDD1 |
| FA2H |
| TMEM231 |
| WDR59 |
| KLHL36 |
| FBXO31 |
| CMIP |
| CDT1 |
| MAP1LC3B |
| PMFBP1 |
| DYNLRB2 |
| HSDL1 |
| CRISPLD2 |
| SPIRE2 |
| ZNF469 |
| ZNRF1 |
| CNTNAP4 |
| CENPBD1 |
| ZNF276 |
| KCNG4 |
| SDR42E1 |
| PKD1L2 |
| RNF166 |
| C16orf46 |
| LRRC50 |
| SPATA2L |
| C16orf55 |
| ZC3H18 |
| CDYL2 |
| TMEM170A |
| SLC38A8 |
| FLJ30679 |
| ZFPM1 |
| ADAD2 |
| ZFP1 |
| ADAMTS18 |
| MGC23284 |
| LDHD |
| MLKL |
| ZNF778 |
| ACSF3 |
| C16orf81 |
| HTA |
| LOC283922 |
| NUDT7 |
| SNAI3 |
| FAM92B |
| PKD1L3 |
| CTU2 |
| LOC390748 |
| C16orf74 |
| CTRB2 |
| CLEC18B |
| SNORD68 |
| LOC732275 |
| LOC100129637 |
| LOC100130015 |
| SYCE1L |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 13q32.3.
Table S24. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| PCCA |
| ZIC2 |
| A2LD1 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 3p21.1.
Table S25. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| PBRM1 |
| ITIH1 |
| ITIH3 |
| ITIH4 |
| NEK4 |
| GNL3 |
| SPCS1 |
| GLT8D1 |
| TMEM110 |
| MUSTN1 |
| SNORD19 |
| SNORD69 |
| SNORD19B |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 4q22.3.
Table S26. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| RAP1GDS1 |
| TET2 |
| hsa-mir-1973 |
| hsa-mir-577 |
| hsa-mir-1243 |
| hsa-mir-302b |
| hsa-mir-297 |
| hsa-mir-576 |
| hsa-mir-1255a |
| hsa-mir-575 |
| ADH1A |
| ADH1B |
| ADH1C |
| ADH4 |
| ADH5 |
| ADH6 |
| ADH7 |
| ANK2 |
| ANXA3 |
| ANXA5 |
| ART3 |
| ATOH1 |
| BMP3 |
| BMPR1B |
| CAMK2D |
| CASP6 |
| CCNA2 |
| CCNG2 |
| SCARB2 |
| CDS1 |
| CENPE |
| DMP1 |
| DSPP |
| EGF |
| EIF4E |
| ENPEP |
| FABP2 |
| FGF5 |
| GK2 |
| GRID2 |
| H2AFZ |
| HADH |
| HNRNPD |
| IBSP |
| CFI |
| CXCL10 |
| MAD2L1 |
| MANBA |
| CXCL9 |
| AFF1 |
| MTTP |
| NFKB1 |
| NKX6-1 |
| PDHA2 |
| PITX2 |
| PKD2 |
| EXOSC9 |
| PPEF2 |
| PPP3CA |
| PRKG2 |
| MAPK10 |
| PTPN13 |
| RPL34 |
| CXCL11 |
| SNCA |
| SPP1 |
| TACR3 |
| TMSL3 |
| TRPC3 |
| UBE2D3 |
| UGT8 |
| SPARCL1 |
| PRSS12 |
| USO1 |
| UNC5C |
| MAPKSP1 |
| PDE5A |
| HERC3 |
| STBD1 |
| CDKL2 |
| PAPSS1 |
| AIMP1 |
| NDST3 |
| ABCG2 |
| SEC24D |
| G3BP2 |
| HNRPDL |
| TSPAN5 |
| FAM13A |
| SEC24B |
| CXCL13 |
| PDLIM5 |
| RRH |
| HPSE |
| CCNI |
| PRDM5 |
| SEC31A |
| MMRN1 |
| WDFY3 |
| METAP1 |
| PPA2 |
| DAPP1 |
| DKK2 |
| NAAA |
| COQ2 |
| HPGDS |
| MRPS18C |
| COPS4 |
| HSD17B11 |
| LEF1 |
| HERC5 |
| PLAC8 |
| LARP7 |
| EMCN |
| MYOZ2 |
| NUDT9 |
| NUP54 |
| GAR1 |
| USP53 |
| FLJ20184 |
| HERC6 |
| CCDC109B |
| BANK1 |
| SDAD1 |
| BBS7 |
| C4orf21 |
| AP1AR |
| BMP2K |
| SEPT11 |
| BDH2 |
| SMARCAD1 |
| MEPE |
| PRDM8 |
| INTS12 |
| KLHL8 |
| SHROOM3 |
| METTL14 |
| ENOPH1 |
| OSTC |
| NEUROG2 |
| SLC39A8 |
| NDST4 |
| AGXT2L1 |
| MRPL1 |
| ELOVL6 |
| C4orf31 |
| ARSJ |
| THAP9 |
| GSTCD |
| TNIP3 |
| SCD5 |
| DNAJB14 |
| FRAS1 |
| ALPK1 |
| CXXC4 |
| PLA2G12A |
| ARHGAP24 |
| C4orf17 |
| QRFPR |
| FAM175A |
| KIAA1109 |
| COL25A1 |
| ARD1B |
| AGPAT9 |
| PIGY |
| TIFA |
| RG9MTD2 |
| TBCK |
| HELQ |
| CYP2U1 |
| DDIT4L |
| GDEP |
| ANTXR2 |
| TMEM155 |
| LIN54 |
| C4orf32 |
| C4orf36 |
| TRAM1L1 |
| NHEDC2 |
| NHEDC1 |
| PAQR3 |
| C4orf26 |
| PPM1K |
| RASGEF1B |
| TIGD2 |
| SGMS2 |
| SYNPO2 |
| CNOT6L |
| C4orf22 |
| NPNT |
| LOC256880 |
| NAP1L5 |
| LOC285456 |
| FAM13AOS |
| GPRIN3 |
| C4orf37 |
| CCDC158 |
| ANKRD56 |
| LRIT3 |
| SLC10A6 |
| HSD17B13 |
| PCNAP1 |
| FAM190A |
| C4orf3 |
| C4orf12 |
| MIR302A |
| C4orf11 |
| TMEM150C |
| EEF1AL7 |
| MIR302B |
| MIR302C |
| MIR302D |
| MIR367 |
| CISD2 |
| LOC641518 |
| CEP170L |
| SNORA24 |
| MIR575 |
| MIR577 |
| SNHG8 |
| FAM47E |
| LOC100192379 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 17p12.
Table S27. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| NCOR1 |
| TTC19 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 4q31.3.
Table S28. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| LRBA |
| MAB21L2 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 9p24.1.
Table S29. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| PTPRD |
| C9orf123 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 2p15.
Table S30. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| CHN1 |
| ERCC3 |
| HOXD11 |
| HOXD13 |
| NFE2L2 |
| PMS1 |
| PAX8 |
| TTL |
| hsa-mir-1245 |
| hsa-mir-561 |
| hsa-mir-1258 |
| hsa-mir-1246 |
| hsa-mir-10b |
| hsa-mir-933 |
| hsa-mir-1978 |
| hsa-mir-128-1 |
| hsa-mir-663b |
| hsa-mir-1302-3 |
| hsa-mir-1285-2 |
| ACTG2 |
| ACVR1 |
| ACVR2A |
| ADD2 |
| ADRA2B |
| BIN1 |
| ANXA4 |
| AOX1 |
| RND3 |
| ATP5G3 |
| ATP6V1B1 |
| AUP1 |
| BMPR2 |
| BUB1 |
| CACNB4 |
| CAPG |
| CASP8 |
| CASP10 |
| CCNT2 |
| CD8A |
| CD8B |
| CD28 |
| CHRNA1 |
| CLK1 |
| CNGA3 |
| COL3A1 |
| COL5A2 |
| COX5B |
| ATF2 |
| CTLA4 |
| CTNNA2 |
| DARS |
| DBI |
| DCTN1 |
| DGUOK |
| DLX1 |
| DLX2 |
| DNAH6 |
| DYNC1I2 |
| DOK1 |
| DPP4 |
| DUSP2 |
| EEF1B2 |
| EGR4 |
| EMX1 |
| EN1 |
| FABP1 |
| FAP |
| FHL2 |
| FRZB |
| GAD1 |
| GALNT3 |
| GCG |
| MSTN |
| GFPT1 |
| GGCX |
| GLI2 |
| GLS |
| GPD2 |
| GPR1 |
| GPR17 |
| GPR39 |
| GRB14 |
| GYPC |
| HK2 |
| HNMT |
| TLX2 |
| HOXD1 |
| HOXD3 |
| HOXD4 |
| HOXD8 |
| HOXD9 |
| HOXD10 |
| HOXD12 |
| HSPD1 |
| HSPE1 |
| IL1A |
| IL1B |
| IL1R1 |
| IL1RN |
| INHBB |
| INPP1 |
| INPP4A |
| ITGA6 |
| ITGA4 |
| ITGAV |
| ITGB6 |
| KCNJ3 |
| KIF5C |
| AFF3 |
| LCT |
| LIMS1 |
| LRP2 |
| LY75 |
| MXD1 |
| MAL |
| MAT2A |
| MCM6 |
| MDH1 |
| MEIS1 |
| MGAT5 |
| MYO1B |
| MYO7B |
| NAB1 |
| NEB |
| NDUFB3 |
| NDUFS1 |
| NEUROD1 |
| NPAS2 |
| NPHP1 |
| NR4A2 |
| ORC2L |
| ORC4L |
| OTX1 |
| REG3A |
| PCBP1 |
| PDE1A |
| PDK1 |
| PLCL1 |
| PLEK |
| PLGLB2 |
| PLGLB1 |
| POLR2D |
| POU3F3 |
| PPP3R1 |
| PROC |
| PTPN4 |
| RAB1A |
| RALB |
| RANBP2 |
| RBMS1 |
| REG1A |
| REG1B |
| REG1P |
| RPL31 |
| RTKN |
| SCN1A |
| SCN2A |
| SCN3A |
| SCN7A |
| SCN9A |
| SCTR |
| SFTPB |
| SLC1A4 |
| SLC9A2 |
| SLC20A1 |
| SNRPG |
| SP3 |
| SPR |
| SSB |
| SSFA2 |
| STAT1 |
| STAT4 |
| SULT1C2 |
| TACR1 |
| C2orf3 |
| TFPI |
| TGFA |
| TIA1 |
| TNFAIP6 |
| TSN |
| TTN |
| SUMO1 |
| UGP2 |
| WIPF1 |
| ZAP70 |
| ZNF2 |
| ALMS1 |
| MOGS |
| RNF103 |
| IL1R2 |
| MALL |
| CXCR4 |
| DYSF |
| FZD7 |
| SDPR |
| NCK2 |
| DUSP11 |
| PKP4 |
| HAT1 |
| AGPS |
| PRKRA |
| SLC25A12 |
| ABCB11 |
| VAMP8 |
| MARCO |
| B3GALT1 |
| ADAM23 |
| SUCLG1 |
| IL18RAP |
| IL1RL2 |
| IL18R1 |
| NRP2 |
| CFLAR |
| ST3GAL5 |
| DDX18 |
| KYNU |
| NAT8 |
| NMI |
| TMSB10 |
| IL1RL1 |
| STK17B |
| GTF3C3 |
| PPIG |
| CIAO1 |
| TGFBRAP1 |
| HS6ST1 |
| MAP4K4 |
| EIF2AK3 |
| CHST10 |
| CIR1 |
| CYTIP |
| GCC2 |
| EIF5B |
| BZW1 |
| SERTAD2 |
| MRPL19 |
| ZEB2 |
| TLK1 |
| CD302 |
| ARHGAP25 |
| TANK |
| BCL2L11 |
| ACTR3 |
| ACTR2 |
| ACTR1B |
| ABI2 |
| DHRS9 |
| TXNDC9 |
| MPHOSPH10 |
| CALCRL |
| PSMD14 |
| STAM2 |
| SMYD5 |
| KBTBD10 |
| C1D |
| MERTK |
| UBE2E3 |
| SEMA4F |
| CCT7 |
| GNLY |
| STAMBP |
| TGOLN2 |
| MTX2 |
| B3GNT2 |
| USP39 |
| TBR1 |
| MAP3K2 |
| NCKAP1 |
| VAMP5 |
| MTHFD2 |
| ARID5A |
| PROKR1 |
| EDAR |
| IMMT |
| SNRNP27 |
| RAPGEF4 |
| TBC1D8 |
| RABL2A |
| GALNT5 |
| NXPH2 |
| GPR45 |
| MGAT4A |
| COBLL1 |
| AAK1 |
| PLA2R1 |
| RAB3GAP1 |
| RPIA |
| SNRNP200 |
| CEP68 |
| UBXN4 |
| EXOC6B |
| EHBP1 |
| SATB2 |
| CLASP1 |
| NCAPH |
| SF3B1 |
| TMEM131 |
| R3HDM1 |
| PSD4 |
| WBP1 |
| TMEFF2 |
| GCA |
| VAX2 |
| MOBKL3 |
| POLR1A |
| CNRIP1 |
| UNC50 |
| GORASP2 |
| SPATS2L |
| RAB11FIP5 |
| EPC2 |
| ARL5A |
| HIBCH |
| PTPN18 |
| CNNM4 |
| CNNM3 |
| IL1F5 |
| SNORD51 |
| IL1F8 |
| IL1F7 |
| IL1F6 |
| SULT1C4 |
| NFU1 |
| MMADHC |
| BMP10 |
| ZNF638 |
| STK39 |
| HTRA2 |
| METTL5 |
| HSPC159 |
| OLA1 |
| C2orf27A |
| TFCP2L1 |
| ICOS |
| BAZ2B |
| SLC40A1 |
| KCNIP3 |
| CD207 |
| ARHGEF4 |
| PDE11A |
| TPRKB |
| FAHD2A |
| C2orf86 |
| INSIG2 |
| ANKRD39 |
| FAM178B |
| RNF181 |
| MRPL30 |
| KRCC1 |
| MRPL35 |
| PCYOX1 |
| GULP1 |
| REV1 |
| NAT8B |
| VPS54 |
| LIPT1 |
| NOP58 |
| VPS24 |
| FKBP7 |
| ZAK |
| LRP1B |
| PPIL3 |
| DNAJC10 |
| ETAA1 |
| CCDC93 |
| ASNSD1 |
| AFTPH |
| MFSD6 |
| RETSAT |
| INO80D |
| SEMA4C |
| C2orf42 |
| PTCD3 |
| PLEKHB2 |
| FIGN |
| RIF1 |
| MOBKL1B |
| STEAP3 |
| THNSL2 |
| ACOXL |
| WDR33 |
| STRADB |
| C2orf29 |
| NAGK |
| SMPD4 |
| TMEM127 |
| PRPF40A |
| IWS1 |
| LIMS2 |
| KIAA1310 |
| WDR12 |
| MBD5 |
| KDM3A |
| ARHGAP15 |
| ZC3H15 |
| CFC1 |
| DNAH7 |
| GKN1 |
| IL1F9 |
| RPRM |
| CYP26B1 |
| POLE4 |
| UGGT1 |
| KCMF1 |
| PNO1 |
| STARD7 |
| PELI1 |
| SLC39A10 |
| SLC4A10 |
| CYP20A1 |
| SPC25 |
| ERMN |
| HECW2 |
| DPP10 |
| EPB41L5 |
| ALS2 |
| ZDBF2 |
| CWC22 |
| ANKRD36B |
| G6PC2 |
| SLC4A5 |
| MPP4 |
| SLC5A7 |
| NIF3L1 |
| PCGEM1 |
| IFIH1 |
| OSGEPL1 |
| GMCL1 |
| TTC31 |
| ANAPC1 |
| RMND5A |
| MARCH7 |
| OBFC2A |
| MRPS9 |
| MRPS5 |
| REEP1 |
| RAPH1 |
| PFTK2 |
| ALS2CR4 |
| NBEAL1 |
| ANKRD57 |
| PLEKHA3 |
| TRAK2 |
| BOLL |
| PDCL3 |
| C2orf49 |
| TMEM185B |
| OR7E91P |
| C2orf47 |
| SAP130 |
| SCRN3 |
| FASTKD1 |
| GTDC1 |
| ALS2CR8 |
| TTC21B |
| METTL8 |
| CYBRD1 |
| ANKRD53 |
| CSRNP3 |
| PGAP1 |
| LRRTM4 |
| DCAF17 |
| FAM128B |
| YSK4 |
| UXS1 |
| COQ10B |
| SLC35F5 |
| TSGA10 |
| THSD7B |
| TMEM177 |
| KIAA1715 |
| LMAN2L |
| TMEM163 |
| TCF7L1 |
| INO80B |
| AMMECR1L |
| CDCA7 |
| WDR54 |
| ZRANB3 |
| RAB6C |
| WDR75 |
| FAM176A |
| ANTXR1 |
| POLR1B |
| ELMOD3 |
| RGPD5 |
| CHCHD5 |
| C2orf7 |
| C2orf88 |
| CCDC115 |
| MKI67IP |
| C2orf40 |
| ZC3H8 |
| ST6GAL2 |
| IL1F10 |
| MCEE |
| LOXL3 |
| PCGF1 |
| MGC13005 |
| MFSD9 |
| SFT2D3 |
| CCDC142 |
| ZNF514 |
| FAM136A |
| TMEM87B |
| ATOH8 |
| LOC84931 |
| TANC1 |
| LBX2 |
| KCNH7 |
| FER1L5 |
| CCDC74A |
| LOC90784 |
| LOC91149 |
| SESTD1 |
| CCDC74B |
| ANKRD44 |
| ZNF804A |
| TTC30A |
| DAPL1 |
| IMP4 |
| MARS2 |
| NEURL3 |
| SFXN5 |
| ORMDL1 |
| LIMS3 |
| NCRNA00152 |
| TUBA3E |
| TEX261 |
| TUBA3D |
| FMNL2 |
| GALNT13 |
| OSBPL6 |
| NOSTRIN |
| DIRC1 |
| WDR92 |
| LYPD1 |
| MRPL53 |
| PARD3B |
| RPL23AP7 |
| C2orf89 |
| TMEM150A |
| NUP35 |
| XIRP2 |
| C2orf60 |
| NMS |
| LYG1 |
| MITD1 |
| CNTNAP5 |
| FBLN7 |
| RBM45 |
| TRIM43 |
| BBS5 |
| C2orf77 |
| ACMSD |
| ICA1L |
| FAM168B |
| REG3G |
| RFTN2 |
| C2orf76 |
| ACVR1C |
| UBR3 |
| KCTD18 |
| ALS2CR12 |
| LYPD6 |
| LYPD6B |
| MDH1B |
| TMEM182 |
| CCDC148 |
| C2orf65 |
| MYO3B |
| TMEM37 |
| DUSP19 |
| CKAP2L |
| CBWD2 |
| TEKT4 |
| LOC150527 |
| FLJ32063 |
| LOC150568 |
| SMYD1 |
| C2orf15 |
| PROM2 |
| ANKAR |
| FBXO41 |
| TTC30B |
| GPAT2 |
| ITPRIPL1 |
| LOC150776 |
| LOC150786 |
| FAM117B |
| LOC151009 |
| SEPT10 |
| ZSWIM2 |
| ZNF385B |
| LOC151162 |
| ARL6IP6 |
| KLHL23 |
| PPP1R1C |
| SGOL2 |
| ALS2CR11 |
| SLC38A11 |
| FAHD2B |
| ASPRV1 |
| WDSUB1 |
| UPP2 |
| LOC151534 |
| GPR155 |
| BZW1L1 |
| LONRF2 |
| CCDC138 |
| FAM171B |
| C1QL2 |
| CLEC4F |
| DQX1 |
| FOXD4L1 |
| PCDP1 |
| VWA3B |
| CREG2 |
| ALMS1P |
| TET3 |
| GKN2 |
| C2orf51 |
| ANKRD23 |
| APLF |
| LOC200726 |
| TMEM17 |
| SPRED2 |
| FAM123C |
| NCRNA00116 |
| C2orf69 |
| HNRNPA3 |
| LASS6 |
| MAP1D |
| LYG2 |
| SH2D6 |
| CCDC150 |
| RNF149 |
| CCDC141 |
| LOC285033 |
| LOC285074 |
| FAM126B |
| PLGLA |
| RGPD4 |
| SPOPL |
| CYP27C1 |
| C2orf55 |
| FIGLA |
| NOTO |
| NCKAP5 |
| FOXI3 |
| EVX2 |
| AOX2P |
| SH3RF3 |
| GPR148 |
| LRRTM1 |
| ANKRD36 |
| WASH2P |
| RBM43 |
| CERKL |
| ZC3H6 |
| LOC388955 |
| C2orf78 |
| BOLA3 |
| C2orf81 |
| LOC388965 |
| C2orf68 |
| SLC9A4 |
| LOC389033 |
| SP5 |
| DYTN |
| PAIP2B |
| RGPD1 |
| LOC401010 |
| C2orf66 |
| MIR10B |
| MIR128-1 |
| C2orf27B |
| ASTL |
| FKSG73 |
| LOC440895 |
| LOC440905 |
| LOC440925 |
| SULT1C3 |
| POTEE |
| C2orf64 |
| PHOSPHO2 |
| DFNB59 |
| LOC541471 |
| NCRNA00164 |
| FBXO48 |
| SNORA41 |
| GGT8P |
| FLJ40330 |
| TRIM43B |
| CFC1B |
| RGPD3 |
| FAM128A |
| LOC654342 |
| FAM138B |
| LOC654433 |
| SNORD11 |
| SNORD70 |
| SNORD89 |
| SNORD94 |
| MIR561 |
| RGPD8 |
| POTEF |
| PABPCP2 |
| LOC729121 |
| ANKRD20B |
| LOC729234 |
| RGPD6 |
| RGPD2 |
| RFX8 |
| SNORD11B |
| SNORA36C |
| MIR933 |
| LOC100130691 |
| TMEM194B |
| SP9 |
| LOC100132215 |
| C2orf14 |
| LOC100133985 |
| RNU4ATAC |
| SNAR-H |
| LOC100189589 |
| LIMS3-LOC440895 |
| LOC100287216 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 11q14.1.
Table S31. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| PICALM |
| hsa-mir-548l |
| hsa-mir-1304 |
| hsa-mir-1261 |
| hsa-mir-708 |
| CTSC |
| DLG2 |
| FUT4 |
| GRM5 |
| MRE11A |
| MTNR1B |
| PRCP |
| TYR |
| FZD4 |
| EED |
| MED17 |
| GAB2 |
| NAALAD2 |
| ME3 |
| GPR83 |
| PRSS23 |
| RAB38 |
| PANX1 |
| ODZ4 |
| CHORDC1 |
| RAB30 |
| C11orf54 |
| NOX4 |
| C11orf73 |
| CWC15 |
| PCF11 |
| SYTL2 |
| ANKRD49 |
| TMEM126B |
| C11orf75 |
| TRIM49 |
| USP35 |
| CREBZF |
| CCDC90B |
| CCDC81 |
| TMEM135 |
| TAF1D |
| NARS2 |
| TMEM126A |
| KIAA1731 |
| SLC36A4 |
| FAT3 |
| TRIM64 |
| PIWIL4 |
| AMOTL1 |
| CCDC67 |
| FOLH1B |
| C11orf82 |
| CCDC83 |
| FAM181B |
| CCDC89 |
| KCTD21 |
| ANKRD42 |
| HEPHL1 |
| C11orf90 |
| TRIM77 |
| FOLR4 |
| SCARNA9 |
| TRIM64B |
| TRIM53 |
| UBTFL1 |
| SNORA8 |
| SNORA1 |
| SNORA18 |
| SNORA40 |
| SNORA25 |
| SNORA32 |
| SNORD5 |
| SNORD6 |
| LOC729384 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 19p13.12.
Table S32. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| JAK3 |
| LYL1 |
| SMARCA4 |
| TPM4 |
| BRD4 |
| hsa-mir-1470 |
| hsa-mir-639 |
| hsa-mir-181d |
| hsa-mir-199a-1 |
| hsa-mir-638 |
| ACP5 |
| ASNA1 |
| BST2 |
| CACNA1A |
| CALR |
| CD97 |
| CNN1 |
| DHPS |
| DNASE2 |
| DNM2 |
| ELAVL3 |
| EPOR |
| NR2F6 |
| FARSA |
| GCDH |
| DNAJB1 |
| ILF3 |
| INSL3 |
| JUNB |
| LDLR |
| CYP4F3 |
| MAN2B1 |
| RAB8A |
| MYO9B |
| NDUFB7 |
| NFIX |
| NOTCH3 |
| PRKACA |
| PKN1 |
| PRKCSH |
| PTGER1 |
| RAD23A |
| RFX1 |
| RPL18A |
| SLC1A6 |
| SLC5A5 |
| PRDX2 |
| ZNF20 |
| ZNF69 |
| ZNF136 |
| CYP4F2 |
| STX10 |
| AP1M1 |
| F2RL3 |
| MED26 |
| IL27RA |
| TECR |
| RAB3D |
| IER2 |
| DDX39 |
| ZNF443 |
| AKAP8 |
| B3GNT3 |
| KLF2 |
| CARM1 |
| CHERP |
| RNASEH2A |
| KLF1 |
| GIPC1 |
| ILVBL |
| TMED1 |
| CYP4F8 |
| LPHN1 |
| MAST1 |
| UNC13A |
| FCHO1 |
| SIN3B |
| CASP14 |
| PGLS |
| KANK2 |
| FAM32A |
| OR7A17 |
| TSPAN16 |
| OR10H3 |
| OR10H2 |
| OR10H1 |
| OR7C2 |
| OR7A5 |
| OR7C1 |
| SNORA68 |
| SNORD41 |
| AKAP8L |
| CPAMD8 |
| C19orf53 |
| C19orf62 |
| HOOK2 |
| TNPO2 |
| EMR2 |
| ECSIT |
| C19orf56 |
| ZNF44 |
| BEST2 |
| CC2D1A |
| MAP1S |
| ZNF823 |
| TRMT1 |
| ASF1B |
| USE1 |
| LOC55908 |
| RGL3 |
| ZNF490 |
| DOCK6 |
| ANO8 |
| CYP4F11 |
| EPS15L1 |
| WIZ |
| LPPR2 |
| RASAL3 |
| MRPL34 |
| ZSWIM4 |
| CYP4F12 |
| YIPF2 |
| C19orf43 |
| DDA1 |
| TMEM38A |
| C19orf42 |
| C19orf57 |
| ABHD8 |
| OCEL1 |
| GLT25D1 |
| EPHX3 |
| PODNL1 |
| SLC35E1 |
| ZNF442 |
| CCDC130 |
| QTRT1 |
| PLVAP |
| RTBDN |
| USHBP1 |
| C19orf44 |
| MRI1 |
| FBXW9 |
| MORG1 |
| ELOF1 |
| ZNF333 |
| EMR3 |
| GTPBP3 |
| HSH2D |
| SYDE1 |
| SAMD1 |
| DCAF15 |
| GADD45GIP1 |
| ZNF799 |
| C19orf52 |
| ZNF625 |
| ZNF700 |
| ZNF439 |
| HAUS8 |
| FAM125A |
| NACC1 |
| LOC113230 |
| PGLYRP2 |
| NXNL1 |
| CCDC151 |
| ZNF653 |
| CIB3 |
| RLN3 |
| CALR3 |
| ZNF441 |
| ZNF491 |
| ZNF440 |
| C19orf39 |
| CCDC159 |
| OR1I1 |
| CCDC105 |
| CYP4F22 |
| LOC126536 |
| OR10H4 |
| ANKLE1 |
| LOC147727 |
| ZNF563 |
| SPC24 |
| FLJ25328 |
| ZNF791 |
| ZNF564 |
| ZNF709 |
| ZNF433 |
| ZNF627 |
| DAND5 |
| FAM129C |
| C19orf38 |
| SYCE2 |
| ZNF763 |
| ZNF844 |
| OR10H5 |
| NWD1 |
| NANOS3 |
| PALM3 |
| TMEM205 |
| SLC27A1 |
| ZNF788 |
| CLEC17A |
| RPL18AP3 |
| OR7A10 |
| ZNF833 |
| MIR181C |
| MIR199A1 |
| MIR23A |
| MIR24-2 |
| MIR27A |
| MIR181D |
| UCA1 |
| MIR638 |
| MIR639 |
| ZNF878 |
| LOC100130932 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 1p33.
Table S33. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| FAF1 |
| DMRTA2 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 11q24.3.
Table S34. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| ATM |
| CBL |
| DDX6 |
| DDX10 |
| FLI1 |
| MLL |
| PAFAH1B2 |
| POU2AF1 |
| SDHD |
| PCSK7 |
| ARHGEF12 |
| hsa-mir-100 |
| hsa-mir-125b-1 |
| hsa-mir-34c |
| ACAT1 |
| ACRV1 |
| APLP2 |
| APOA1 |
| APOA4 |
| APOC3 |
| ARCN1 |
| FXYD2 |
| CXCR5 |
| CASP1 |
| CASP4 |
| CASP5 |
| CD3D |
| CD3E |
| CD3G |
| CHEK1 |
| CRYAB |
| DLAT |
| DPAGT1 |
| DRD2 |
| ETS1 |
| FDX1 |
| SLC37A4 |
| GRIA4 |
| GRIK4 |
| GUCY1A2 |
| H2AFX |
| HMBS |
| HSPA8 |
| HSPB2 |
| HTR3A |
| IL10RA |
| IL18 |
| STT3A |
| KCNJ1 |
| KCNJ5 |
| VWA5A |
| MCAM |
| NCAM1 |
| NFRKB |
| NNMT |
| NPAT |
| NRGN |
| OPCML |
| PPP2R1B |
| PTS |
| PVRL1 |
| RDX |
| RPS25 |
| SC5DL |
| SCN2B |
| SCN4B |
| ST3GAL4 |
| SLN |
| SORL1 |
| SRPR |
| ST14 |
| TAGLN |
| TECTA |
| THY1 |
| UPK2 |
| ZBTB16 |
| ZNF202 |
| CUL5 |
| BARX2 |
| ZNF259 |
| USP2 |
| HTR3B |
| ZW10 |
| UBE4A |
| EI24 |
| FEZ1 |
| RICS |
| C2CD2L |
| RBM7 |
| MPZL2 |
| HYOU1 |
| ATP5L |
| ADAMTS8 |
| TREH |
| CEP164 |
| IGSF9B |
| EXPH5 |
| PHLDB1 |
| SIK2 |
| NCAPD3 |
| SIK3 |
| VSIG2 |
| BACE1 |
| TRIM29 |
| CADM1 |
| POU2F3 |
| HINFP |
| REXO2 |
| OR8G2 |
| OR8B8 |
| OR8G1 |
| TIMM8B |
| OR8B2 |
| ACAD8 |
| B3GAT1 |
| DCPS |
| ZBTB44 |
| THYN1 |
| DDX25 |
| NTM |
| CDON |
| SIDT2 |
| TRAPPC4 |
| SPA17 |
| FXYD6 |
| SIAE |
| C11orf71 |
| ROBO4 |
| SLC35F2 |
| RAB39 |
| BTG4 |
| FAM55D |
| TTC12 |
| C11orf57 |
| ELMOD1 |
| FOXRED1 |
| SCN3B |
| VPS11 |
| TEX12 |
| CRTAM |
| TMPRSS4 |
| C11orf60 |
| PRDM10 |
| DSCAML1 |
| GRAMD1B |
| ARHGAP20 |
| USP28 |
| CARD18 |
| AASDHPPT |
| PKNOX2 |
| TP53AIP1 |
| ABCG4 |
| ROBO3 |
| C11orf1 |
| RNF26 |
| FAM118B |
| DYNC2H1 |
| NLRX1 |
| C11orf61 |
| ALG9 |
| ASAM |
| PDZD3 |
| C11orf63 |
| CCDC15 |
| PDGFD |
| TMPRSS5 |
| PUS3 |
| MFRP |
| JAM3 |
| BCO2 |
| TMPRSS13 |
| DCUN1D5 |
| KIAA1826 |
| KIRREL3 |
| BUD13 |
| TMEM25 |
| RPUSD4 |
| TBRG1 |
| UBASH3B |
| DIXDC1 |
| ZC3H12C |
| GLB1L2 |
| ESAM |
| ALKBH8 |
| FDXACB1 |
| C11orf52 |
| VPS26B |
| GLB1L3 |
| TIRAP |
| CARD16 |
| C1QTNF5 |
| PANX3 |
| APOA5 |
| TMEM45B |
| CASP12 |
| C11orf93 |
| PIH1D2 |
| FAM55A |
| FAM55B |
| AMICA1 |
| KBTBD3 |
| CWF19L2 |
| KDELC2 |
| LAYN |
| TTC36 |
| PATE1 |
| C11orf65 |
| ADAMTS15 |
| MPZL3 |
| C11orf45 |
| HYLS1 |
| TMEM218 |
| SLC37A2 |
| OR8B12 |
| OR8G5 |
| OR10G8 |
| OR10G9 |
| OR10S1 |
| OR6T1 |
| OR4D5 |
| TBCEL |
| TMEM136 |
| SPATA19 |
| HEPACAM |
| OAF |
| ANKK1 |
| RNF214 |
| BCL9L |
| FOXR1 |
| CCDC153 |
| OR8D1 |
| OR8D2 |
| OR8B4 |
| LOC283174 |
| CCDC84 |
| TMEM225 |
| OR8D4 |
| C11orf53 |
| LOC341056 |
| C11orf34 |
| BSX |
| OR6X1 |
| OR6M1 |
| OR10G4 |
| OR10G7 |
| OR8B3 |
| OR8A1 |
| C11orf87 |
| C11orf92 |
| C11orf88 |
| LOC399959 |
| PATE2 |
| PATE4 |
| SNX19 |
| MIRLET7A2 |
| MIR100 |
| MIR125B1 |
| MIR34B |
| MIR34C |
| DDI1 |
| BLID |
| CARD17 |
| NCRNA00167 |
| HEPN1 |
| LOC643923 |
| CLDN25 |
| RPL23AP64 |
| LOC100128239 |
| PATE3 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 12q24.31.
Table S35. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| ALDH2 |
| BCL7A |
| PTPN11 |
| hsa-mir-1178 |
| hsa-mir-620 |
| hsa-mir-1302-1 |
| ACADS |
| SCARB1 |
| COX6A1 |
| DTX1 |
| EIF2B1 |
| STX2 |
| GOLGA3 |
| GTF2H3 |
| HPD |
| MMP17 |
| MSI1 |
| MYL2 |
| NOS1 |
| OAS1 |
| OAS2 |
| OAS3 |
| P2RX4 |
| P2RX7 |
| PEBP1 |
| PLA2G1B |
| POLE |
| PRKAB1 |
| PSMD9 |
| PXMP2 |
| PXN |
| RAN |
| RFC5 |
| RPL6 |
| RPLP0 |
| CLIP1 |
| ATXN2 |
| SFRS8 |
| TBX5 |
| TBX3 |
| HNF1A |
| UBC |
| ZNF10 |
| ZNF26 |
| ZNF84 |
| ZNF140 |
| CDK2AP1 |
| BRAP |
| ULK1 |
| RASAL1 |
| MAPKAPK5 |
| DENR |
| OASL |
| DYNLL1 |
| SFRS9 |
| HRK |
| GPR109B |
| HIP1R |
| PIWIL1 |
| CABP1 |
| NCOR2 |
| KNTC1 |
| MLEC |
| RBM19 |
| RNF10 |
| SH2B3 |
| MPHOSPH9 |
| CAMKK2 |
| ZNF268 |
| TRAFD1 |
| TMED2 |
| ERP29 |
| GCN1L1 |
| SDS |
| RAB35 |
| SNRNP35 |
| CIT |
| FZD10 |
| MLXIP |
| RPH3A |
| P2RX2 |
| FBXO21 |
| SETD1B |
| ANKLE2 |
| CUX2 |
| MED13L |
| SIRT4 |
| ABCB9 |
| RIMBP2 |
| ATP6V0A2 |
| FBXW8 |
| HSPB8 |
| GPR81 |
| GALNT9 |
| C12orf47 |
| ARL6IP4 |
| TAOK3 |
| POP5 |
| ANAPC5 |
| TRIAP1 |
| TPCN1 |
| RHOF |
| VSIG10 |
| TESC |
| SBNO1 |
| ZCCHC8 |
| CHFR |
| WSB2 |
| DIABLO |
| PITPNM2 |
| EP400 |
| DHX37 |
| FBRSL1 |
| DDX55 |
| LHX5 |
| SUDS3 |
| C12orf43 |
| VPS33A |
| RSRC2 |
| AACS |
| DDX54 |
| NOC4L |
| B3GNT4 |
| OGFOD2 |
| VPS37B |
| C12orf49 |
| TCTN2 |
| C12orf30 |
| SLC24A6 |
| RNF34 |
| CCDC92 |
| PUS1 |
| ACAD10 |
| COQ5 |
| SRRM4 |
| CCDC62 |
| KDM2B |
| UNC119B |
| ORAI1 |
| RNFT2 |
| C12orf52 |
| TMEM116 |
| C12orf65 |
| TMEM132C |
| CCDC64 |
| SDSL |
| MGC16384 |
| TMEM132B |
| IQCD |
| LOC116437 |
| TMEM132D |
| SLC15A4 |
| SPPL3 |
| BRI3BP |
| FAM101A |
| ZNF664 |
| TMEM120B |
| WDR66 |
| GLT1D1 |
| FAM109A |
| LOC144742 |
| CCDC60 |
| PGAM5 |
| RILPL2 |
| DNAH10 |
| PLBD2 |
| LRRC43 |
| GPR133 |
| MORN3 |
| C12orf51 |
| KSR2 |
| NME2P1 |
| GATC |
| C12orf27 |
| DDX51 |
| GPR109A |
| LOC338799 |
| EP400NL |
| RILPL1 |
| IL31 |
| CCDC42B |
| TMEM233 |
| SETD8 |
| MAP1LC3B2 |
| SNORA49 |
| MIR620 |
| LOC100128554 |
| LOC100130238 |
| LOC100190940 |
| NCRNA00173 |
| ZNF605 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 17p13.2.
Table S36. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| hsa-mir-1253 |
| hsa-mir-212 |
| hsa-mir-22 |
| ABR |
| ALOX15 |
| ARRB2 |
| ASPA |
| ATP2A3 |
| CRK |
| CTNS |
| DPH1 |
| HIC1 |
| ITGAE |
| MNT |
| MYO1C |
| OR1D2 |
| OR3A1 |
| OR3A2 |
| P2RX1 |
| P2RX5 |
| PAFAH1B1 |
| SERPINF1 |
| PITPNA |
| SERPINF2 |
| PSMB6 |
| RPA1 |
| UBE2G1 |
| TRPV1 |
| YWHAE |
| OR1A1 |
| OR1D4 |
| OR1D5 |
| OR1E1 |
| OR1E2 |
| OR1G1 |
| OR3A3 |
| SCARF1 |
| TM4SF5 |
| RPH3AL |
| SGSM2 |
| MYBBP1A |
| PRPF8 |
| RAP1GAP2 |
| ZZEF1 |
| KIAA0664 |
| SMG6 |
| SHPK |
| OR1A2 |
| PELP1 |
| TIMM22 |
| TAX1BP3 |
| GEMIN4 |
| GLOD4 |
| ANKFY1 |
| INPP5K |
| RNMTL1 |
| VPS53 |
| C17orf85 |
| TSR1 |
| CXCL16 |
| SRR |
| NXN |
| METT10D |
| FAM57A |
| TMEM93 |
| RILP |
| GSG2 |
| ZMYND15 |
| CAMKK1 |
| SPATA22 |
| C17orf91 |
| SMYD4 |
| OVCA2 |
| SLC43A2 |
| CYB5D2 |
| GGT6 |
| SPNS2 |
| WDR81 |
| RTN4RL1 |
| TRPV3 |
| SPNS3 |
| LOC284009 |
| VMO1 |
| TUSC5 |
| SMTNL2 |
| FAM101B |
| GLTPD2 |
| OR3A4 |
| C17orf97 |
| MED11 |
| MIR132 |
| MIR212 |
| MIR22 |
| SNORD91A |
| SNORD91B |
| BHLHA9 |
| TLCD2 |
| ELP2P |
| LOC100306951 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 6q26.
Table S37. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| PRDM1 |
| MLLT4 |
| MYB |
| ROS1 |
| TNFAIP3 |
| STL |
| FGFR1OP |
| GOPC |
| hsa-mir-1913 |
| hsa-mir-1202 |
| hsa-mir-548a-2 |
| hsa-mir-588 |
| hsa-mir-548b |
| hsa-mir-587 |
| hsa-mir-2113 |
| hsa-mir-30a |
| hsa-mir-133b |
| hsa-mir-586 |
| ACAT2 |
| CRISP1 |
| AIM1 |
| AMD1 |
| ARG1 |
| BAI3 |
| BCKDHB |
| BMP5 |
| DST |
| RUNX2 |
| CCNC |
| CDC5L |
| CGA |
| CCR6 |
| CNR1 |
| COL9A1 |
| COL10A1 |
| COL12A1 |
| COL19A1 |
| COX7A2 |
| CTGF |
| EEF1A1 |
| EPB41L2 |
| EPHA7 |
| EYA4 |
| ESR1 |
| FABP7 |
| FOXO3 |
| FRK |
| FUCA2 |
| FYN |
| GABRR1 |
| GABRR2 |
| GJA1 |
| GCLC |
| GPR6 |
| GPR31 |
| GRIK2 |
| GRM1 |
| GSTA1 |
| GSTA2 |
| GSTA3 |
| GSTA4 |
| HCRTR2 |
| HDAC2 |
| HIVEP2 |
| HSF2 |
| HTR1B |
| HTR1E |
| IFNGR1 |
| IGF2R |
| IL17A |
| IMPG1 |
| KIF25 |
| KPNA5 |
| LAMA2 |
| LAMA4 |
| LPA |
| MARCKS |
| MAN1A1 |
| MAS1 |
| MCM3 |
| ME1 |
| MAP3K4 |
| MAP3K5 |
| MEP1A |
| MUT |
| MYO6 |
| NFKBIE |
| NMBR |
| NT5E |
| OPRM1 |
| PARK2 |
| PCMT1 |
| PDCD2 |
| ENPP1 |
| ENPP3 |
| PEX7 |
| PGK2 |
| PGM3 |
| PKHD1 |
| PLAGL1 |
| PLG |
| PLN |
| POU3F2 |
| PREP |
| PRIM2 |
| PKIB |
| PSMB1 |
| PTPRK |
| REV3L |
| RHAG |
| RPS6KA2 |
| RPS12 |
| SGK1 |
| SIM1 |
| SLC22A1 |
| SLC22A3 |
| SLC22A2 |
| SMPD2 |
| SOD2 |
| ELOVL4 |
| T |
| MAP3K7 |
| TBP |
| TCF21 |
| TCP1 |
| TCP10 |
| TCTE3 |
| DYNLT1 |
| TFAP2B |
| THBS2 |
| NR2E1 |
| TPBG |
| TPD52L1 |
| CRISP2 |
| TSPYL1 |
| TTK |
| UTRN |
| EZR |
| VIP |
| PTP4A1 |
| PLA2G7 |
| EPM2A |
| STX7 |
| SUPT3H |
| PEX3 |
| GCM1 |
| DDO |
| RNASET2 |
| STX11 |
| SNX3 |
| RNGTT |
| CD164 |
| WISP3 |
| SYNJ2 |
| VNN2 |
| VNN1 |
| WASF1 |
| TAAR5 |
| MAP7 |
| TBX18 |
| LATS1 |
| TAAR2 |
| TAAR3 |
| HMGN3 |
| MED23 |
| QKI |
| FHL5 |
| AKAP7 |
| ATG5 |
| SLC25A27 |
| TBPL1 |
| BAG2 |
| WTAP |
| AKAP12 |
| TRAM2 |
| KIAA0408 |
| PHACTR2 |
| BCLAF1 |
| ZBTB24 |
| SNAP91 |
| FIG4 |
| CASP8AP2 |
| UST |
| RCAN2 |
| CRISP3 |
| TRDN |
| CITED2 |
| SYNCRIP |
| SLC35A1 |
| FUT9 |
| TRAF3IP2 |
| HBS1L |
| PDE10A |
| SMPDL3A |
| PNRC1 |
| ASCC3 |
| RAB32 |
| KATNA1 |
| BVES |
| SEC63 |
| RBM16 |
| KIAA1009 |
| ICK |
| ENPP4 |
| ANKRD6 |
| RIMS1 |
| DOPEY1 |
| ZNF292 |
| CDC2L6 |
| MAP3K7IP2 |
| MDN1 |
| TSPYL4 |
| SASH1 |
| SYNE1 |
| KIAA0776 |
| PHF3 |
| HEY2 |
| HEBP2 |
| ORC3L |
| CD2AP |
| BRD7P3 |
| MTO1 |
| ASF1A |
| CCDC28A |
| MTHFD1L |
| SFRS18 |
| IBTK |
| MOXD1 |
| IPCEF1 |
| ZNF451 |
| SENP6 |
| TIAM2 |
| FBXL4 |
| C6orf123 |
| FBXO9 |
| FBXO5 |
| SLC17A5 |
| RGS17 |
| SNORD50A |
| PDE7B |
| FILIP1 |
| TNFRSF21 |
| SESN1 |
| TINAG |
| DLL1 |
| OSTM1 |
| TMEM14A |
| MRPL18 |
| NDUFAF4 |
| DSE |
| CLDN20 |
| NOX3 |
| HDDC2 |
| TFB1M |
| CYB5R4 |
| TUBE1 |
| C6orf203 |
| CYP39A1 |
| CDC40 |
| RWDD1 |
| AIG1 |
| SNX9 |
| UBE2J1 |
| VTA1 |
| LGSN |
| BRP44L |
| HECA |
| RAB23 |
| COQ3 |
| CLIC5 |
| IL20RA |
| UNC93A |
| HMGCLL1 |
| MTRF1L |
| AHI1 |
| RMND1 |
| PHIP |
| SOBP |
| AKIRIN2 |
| CENPQ |
| LRRC1 |
| PHF10 |
| QRSL1 |
| VNN3 |
| NCRNA00120 |
| DDX43 |
| FAM46A |
| TMEM30A |
| C6orf70 |
| LMBRD1 |
| ECHDC1 |
| KCNQ5 |
| AGPAT4 |
| TULP4 |
| RARS2 |
| HYMAI |
| PDSS2 |
| C6orf162 |
| GPR126 |
| KIAA1244 |
| NHSL1 |
| LYRM2 |
| SNX14 |
| PLEKHG1 |
| ARID1B |
| AARS2 |
| SERINC1 |
| HACE1 |
| FAM135A |
| TMEM181 |
| ZBTB2 |
| BEND3 |
| KIAA1586 |
| C6orf115 |
| RRAGD |
| ENPP5 |
| PRDM13 |
| PBOV1 |
| BACH2 |
| ELOVL5 |
| TRMT11 |
| SMAP1 |
| C6orf164 |
| PERP |
| SMOC2 |
| POPDC3 |
| ALDH8A1 |
| MICAL1 |
| ULBP3 |
| OR2A4 |
| C6orf211 |
| OGFRL1 |
| FAM184A |
| ZDHHC14 |
| MANEA |
| C6orf103 |
| C6orf155 |
| FRMD1 |
| C6orf59 |
| C6orf208 |
| C6orf97 |
| MYCT1 |
| ULBP2 |
| ULBP1 |
| LPAL2 |
| KHDC1 |
| GPR63 |
| COL21A1 |
| PPP1R14C |
| SPACA1 |
| RNF146 |
| SF3B5 |
| TAAR8 |
| SH3BGRL2 |
| TFAP2D |
| RSPH3 |
| TTLL2 |
| ARMC2 |
| FBXO30 |
| RPF2 |
| L3MBTL3 |
| FAM120B |
| MCHR2 |
| C6orf168 |
| FNDC1 |
| GJA10 |
| RTN4IP1 |
| RSPO3 |
| LRP11 |
| LTV1 |
| SERAC1 |
| USP45 |
| REPS1 |
| PPIL4 |
| PAQR8 |
| SLC22A16 |
| UBE2CBP |
| C6orf142 |
| C6orf176 |
| KIAA1919 |
| ARHGAP18 |
| SYTL3 |
| GTF3C6 |
| MRAP2 |
| RWDD2A |
| IL17F |
| FAM54A |
| SFT2D1 |
| EFHC1 |
| KLHL32 |
| TMEM200A |
| C6orf150 |
| NUS1 |
| C6orf72 |
| IL22RA2 |
| C6orf192 |
| SLC16A10 |
| TAGAP |
| ADAT2 |
| RIPPLY2 |
| IRAK1BP1 |
| CLVS2 |
| TAAR9 |
| TAAR1 |
| STXBP5 |
| NCOA7 |
| HINT3 |
| PACRG |
| B3GAT2 |
| C6orf57 |
| CD109 |
| RAET1E |
| PM20D2 |
| SFRS13B |
| C6orf141 |
| LOC153910 |
| C6orf94 |
| CNKSR3 |
| RAET1L |
| SAMD3 |
| MGC34034 |
| SLC2A12 |
| PNLDC1 |
| RNF217 |
| NKAIN2 |
| C6orf221 |
| C6orf165 |
| LOC154449 |
| PRSS35 |
| LCA5 |
| OLIG3 |
| TXLNB |
| DACT2 |
| C6orf118 |
| OSTCL |
| TCTE1 |
| KHDRBS2 |
| C6orf163 |
| C6orf185 |
| AKD1 |
| NT5DC1 |
| FAM26D |
| ZUFSP |
| FAM162B |
| C6orf170 |
| BEND6 |
| GSTA5 |
| OPN5 |
| GPR115 |
| GPR116 |
| TDRD6 |
| SPATS1 |
| HS3ST5 |
| GPRC6A |
| RFX6 |
| SLC35F1 |
| FAM83B |
| GPR111 |
| VGLL2 |
| DEFB110 |
| DEFB112 |
| DEFB113 |
| DEFB114 |
| LACE1 |
| C6orf191 |
| C6orf167 |
| WDR27 |
| FAM26E |
| MCM9 |
| SCML4 |
| SHPRH |
| GPR110 |
| LOC285733 |
| LOC285735 |
| LOC285740 |
| C6orf182 |
| PPIL6 |
| FLJ34503 |
| DCBLD1 |
| LOC285796 |
| PRR18 |
| TAAR6 |
| SLC35D3 |
| ZC3H12D |
| DPPA5 |
| RSPH4A |
| ECT2L |
| EYS |
| NUP43 |
| C6orf58 |
| RAET1G |
| GUSBL2 |
| GJB7 |
| SNHG5 |
| SUMO4 |
| C6orf147 |
| C6orf173 |
| C6orf174 |
| C6orf204 |
| C6orf120 |
| THEMIS |
| C6orf140 |
| GFRAL |
| LIN28B |
| SAMD5 |
| IYD |
| KLHL31 |
| TCP10L2 |
| C6orf122 |
| DEFB133 |
| GTF2H5 |
| MIR206 |
| MIR30A |
| MIR30C2 |
| TMEM151B |
| OOEP |
| FAM26F |
| LOC441177 |
| C6orf138 |
| MCART3P |
| LOC442245 |
| RFPL4B |
| MIR133B |
| LOC553137 |
| SNORD101 |
| SNORD100 |
| SNORA33 |
| C6orf225 |
| TSG1 |
| CTAGE9 |
| RAET1K |
| C6orf124 |
| SNORA20 |
| SNORA29 |
| SNORD50B |
| MIR548B |
| MIR586 |
| LOC728402 |
| C6orf186 |
| LOC729176 |
| LOC729603 |
| LOC730101 |
| HGC6.3 |
| BET3L |
| KHDC1L |
| C6orf217 |
| LOC100287718 |
| NHEG1 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 13q14.3.
Table S38. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| BRCA2 |
| CDX2 |
| FLT3 |
| LCP1 |
| RB1 |
| LHFP |
| hsa-mir-92a-1 |
| hsa-mir-622 |
| hsa-mir-1297 |
| hsa-mir-15a |
| hsa-mir-621 |
| hsa-mir-320d-1 |
| PARP4 |
| ALOX5AP |
| ATP12A |
| ATP7B |
| KLF5 |
| BTF3L1 |
| CDK8 |
| RCBTB2 |
| CLN5 |
| CPB2 |
| DACH1 |
| DCT |
| EDNRB |
| ELF1 |
| ESD |
| FGF9 |
| GPC5 |
| FOXO1 |
| FLT1 |
| GJA3 |
| GJB2 |
| GPR12 |
| MLNR |
| GTF2F2 |
| GTF3A |
| GUCY1B2 |
| HMGB1 |
| HTR2A |
| PDX1 |
| KPNA3 |
| LMO7 |
| MAB21L1 |
| SMAD9 |
| MIPEP |
| NEK3 |
| PABPC3 |
| PCDH8 |
| PCDH9 |
| UBL3 |
| POU4F1 |
| RFC3 |
| RFXAP |
| RNF6 |
| RPL21 |
| ATXN8OS |
| SGCG |
| SLC7A1 |
| TPT1 |
| TRPC4 |
| TUBA3C |
| UCHL3 |
| ZMYM2 |
| IFT88 |
| TNFSF11 |
| SCEL |
| SUCLA2 |
| DLEU2 |
| TSC22D1 |
| CCNA1 |
| MTMR6 |
| DCLK1 |
| ZMYM5 |
| KL |
| ITM2B |
| MTRF1 |
| UTP14C |
| NUPL1 |
| TBC1D4 |
| GPC6 |
| FRY |
| LPAR6 |
| SLC25A15 |
| TRIM13 |
| USPL1 |
| MRPS31 |
| SPRY2 |
| SAP18 |
| DLEU1 |
| N4BP2L2 |
| PIBF1 |
| OLFM4 |
| POSTN |
| GJB6 |
| HSPH1 |
| WASF3 |
| SUGT1 |
| LECT1 |
| WBP4 |
| AKAP11 |
| KLF12 |
| EXOSC8 |
| FNDC3A |
| DIS3 |
| PDS5B |
| MYCBP2 |
| KIAA0564 |
| ZC3H13 |
| SPG20 |
| LRCH1 |
| MTUS2 |
| TGDS |
| SLITRK5 |
| FBXL3 |
| SACS |
| INTS6 |
| LATS2 |
| CKAP2 |
| OR7E37P |
| NUFIP1 |
| SNORD102 |
| NBEA |
| PCDH17 |
| C13orf15 |
| MED4 |
| DNAJC15 |
| ALG5 |
| VPS36 |
| POLR1D |
| CRYL1 |
| PHF11 |
| POMP |
| UFM1 |
| ATP8A2 |
| IL17D |
| NDFIP2 |
| MPHOSPH8 |
| SOHLH2 |
| ENOX1 |
| RCBTB1 |
| PSPC1 |
| NUDT15 |
| KIAA1704 |
| TNFRSF19 |
| FAM48A |
| CENPJ |
| THSD1 |
| RNF17 |
| CYSLTR2 |
| C13orf1 |
| COG6 |
| KLHL1 |
| RBM26 |
| XPO4 |
| PCDH20 |
| MRP63 |
| RNF219 |
| NARG1L |
| RNASEH2B |
| DHRS12 |
| C13orf34 |
| C13orf18 |
| C13orf23 |
| TDRD3 |
| CDADC1 |
| CAB39L |
| DIAPH3 |
| CCDC70 |
| COG3 |
| SETDB2 |
| KATNAL1 |
| KBTBD7 |
| SLITRK6 |
| EBPL |
| C13orf33 |
| KBTBD6 |
| STARD13 |
| N4BP2L1 |
| TPTE2 |
| EPSTI1 |
| SLITRK1 |
| KCTD12 |
| ARL11 |
| WDFY2 |
| CG030 |
| LOC121838 |
| CSNK1A1L |
| RXFP2 |
| C13orf26 |
| SLAIN1 |
| PRR20A |
| LOC144776 |
| C13orf30 |
| C13orf31 |
| HNRNPA1L2 |
| FAM10A4 |
| B3GALTL |
| DGKH |
| CCDC122 |
| GPR180 |
| STOML3 |
| COMMD6 |
| EEF1DP3 |
| FAM123A |
| USP12 |
| MTIF3 |
| GSX1 |
| FAM194B |
| SPERT |
| DLEU7 |
| FAM124A |
| LOC220115 |
| LOC220429 |
| N6AMT2 |
| SKA3 |
| EFHA1 |
| SPATA13 |
| LNX2 |
| SLC25A30 |
| ZDHHC20 |
| PAN3 |
| DKFZp686A1627 |
| OR7E156P |
| SUGT1L1 |
| SIAH3 |
| KCNRG |
| FLJ37307 |
| SLC46A3 |
| LOC284232 |
| C1QTNF9 |
| FREM2 |
| NEK5 |
| LOC348021 |
| LOC374491 |
| THSD1P |
| KCTD4 |
| RASL11A |
| C1QTNF9B |
| SHISA2 |
| NHLRC3 |
| SERP2 |
| C13orf36 |
| MIR15A |
| MIR16-1 |
| MIR17 |
| MIR18A |
| MIR19A |
| MIR19B1 |
| MIR20A |
| MIR92A1 |
| MIR17HG |
| ATP5EP2 |
| ALG11 |
| C13orf37 |
| PCOTH |
| SNORA27 |
| LOC646405 |
| PRHOXNB |
| ZAR1L |
| LOC646982 |
| SERPINE3 |
| LOC647288 |
| SNORA31 |
| MIR548A2 |
| MIR621 |
| C13orf38 |
| PRR20B |
| PRR20C |
| PRR20D |
| PRR20E |
| LOC100101938 |
| RPL21P28 |
| LOC100188949 |
| LOC100190939 |
| LOC100288730 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 18q22.1.
Table S39. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| BCL2 |
| MALT1 |
| hsa-mir-122 |
| CDH7 |
| CYB5A |
| FECH |
| KDSR |
| GALR1 |
| GRP |
| LMAN1 |
| MBP |
| MC4R |
| NARS |
| NFATC1 |
| SERPINB2 |
| ATP8B1 |
| SERPINB5 |
| SERPINB8 |
| SERPINB10 |
| SERPINB13 |
| PMAIP1 |
| RAB27B |
| SERPINB3 |
| SERPINB4 |
| TCF4 |
| ZNF236 |
| SERPINB7 |
| TNFRSF11A |
| CTDP1 |
| SOCS6 |
| TXNL1 |
| ONECUT2 |
| VPS4B |
| ZNF516 |
| TSHZ1 |
| CD226 |
| TXNL4A |
| ADNP2 |
| PHLPP1 |
| NEDD4L |
| WDR7 |
| PIGN |
| RTTN |
| KCNG2 |
| SALL3 |
| CDH20 |
| CDH19 |
| C18orf55 |
| RAX |
| ST8SIA3 |
| TMX3 |
| ZCCHC2 |
| ZNF532 |
| ZNF407 |
| CNDP2 |
| KIAA1468 |
| CCDC102B |
| C18orf22 |
| PQLC1 |
| CCDC68 |
| NETO1 |
| PARD6G |
| CNDP1 |
| SERPINB12 |
| SERPINB11 |
| SEC11C |
| DSEL |
| ALPK2 |
| FAM69C |
| CCBE1 |
| CBLN2 |
| FBXO15 |
| DOK6 |
| RNF152 |
| C18orf20 |
| ZADH2 |
| C18orf62 |
| LOC284276 |
| HMSD |
| CPLX4 |
| ATP9B |
| LOC390858 |
| LOC400657 |
| MIR122 |
| HSBP1L1 |
| LOC100130522 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 6q15.
Table S40. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| PRDM1 |
| MLLT4 |
| MYB |
| ROS1 |
| TNFAIP3 |
| STL |
| FGFR1OP |
| GOPC |
| hsa-mir-1913 |
| hsa-mir-1202 |
| hsa-mir-548a-2 |
| hsa-mir-588 |
| hsa-mir-548b |
| hsa-mir-587 |
| hsa-mir-2113 |
| hsa-mir-30a |
| hsa-mir-133b |
| hsa-mir-586 |
| ACAT2 |
| CRISP1 |
| AIM1 |
| AMD1 |
| ARG1 |
| BAI3 |
| BCKDHB |
| BMP5 |
| DST |
| RUNX2 |
| CCNC |
| CDC5L |
| CGA |
| CCR6 |
| CNR1 |
| COL9A1 |
| COL10A1 |
| COL12A1 |
| COL19A1 |
| COX7A2 |
| CTGF |
| EEF1A1 |
| EPB41L2 |
| EPHA7 |
| EYA4 |
| ESR1 |
| FABP7 |
| FOXO3 |
| FRK |
| FUCA2 |
| FYN |
| GABRR1 |
| GABRR2 |
| GJA1 |
| GCLC |
| GPR6 |
| GPR31 |
| GRIK2 |
| GRM1 |
| GSTA1 |
| GSTA2 |
| GSTA3 |
| GSTA4 |
| HCRTR2 |
| HDAC2 |
| HIVEP2 |
| HSF2 |
| HTR1B |
| HTR1E |
| IFNGR1 |
| IGF2R |
| IL17A |
| IMPG1 |
| KIF25 |
| KPNA5 |
| LAMA2 |
| LAMA4 |
| LPA |
| MARCKS |
| MAN1A1 |
| MAS1 |
| MCM3 |
| ME1 |
| MAP3K4 |
| MAP3K5 |
| MEP1A |
| MUT |
| MYO6 |
| NFKBIE |
| NMBR |
| NT5E |
| OPRM1 |
| PARK2 |
| PCMT1 |
| ENPP1 |
| ENPP3 |
| PEX7 |
| PGK2 |
| PGM3 |
| PKHD1 |
| PLAGL1 |
| PLG |
| PLN |
| POU3F2 |
| PREP |
| PRIM2 |
| PKIB |
| PTPRK |
| REV3L |
| RHAG |
| RPS6KA2 |
| RPS12 |
| SGK1 |
| SIM1 |
| SLC22A1 |
| SLC22A3 |
| SLC22A2 |
| SMPD2 |
| SOD2 |
| ELOVL4 |
| T |
| MAP3K7 |
| TCF21 |
| TCP1 |
| TCP10 |
| TCTE3 |
| DYNLT1 |
| TFAP2B |
| THBS2 |
| NR2E1 |
| TPBG |
| TPD52L1 |
| CRISP2 |
| TSPYL1 |
| TTK |
| UTRN |
| EZR |
| VIP |
| PTP4A1 |
| PLA2G7 |
| EPM2A |
| STX7 |
| SUPT3H |
| PEX3 |
| GCM1 |
| DDO |
| RNASET2 |
| STX11 |
| SNX3 |
| RNGTT |
| CD164 |
| WISP3 |
| SYNJ2 |
| VNN2 |
| VNN1 |
| WASF1 |
| TAAR5 |
| MAP7 |
| TBX18 |
| LATS1 |
| TAAR2 |
| TAAR3 |
| HMGN3 |
| MED23 |
| QKI |
| FHL5 |
| AKAP7 |
| ATG5 |
| SLC25A27 |
| TBPL1 |
| BAG2 |
| WTAP |
| AKAP12 |
| TRAM2 |
| KIAA0408 |
| PHACTR2 |
| BCLAF1 |
| ZBTB24 |
| SNAP91 |
| FIG4 |
| CASP8AP2 |
| UST |
| RCAN2 |
| CRISP3 |
| TRDN |
| CITED2 |
| SYNCRIP |
| SLC35A1 |
| FUT9 |
| TRAF3IP2 |
| HBS1L |
| PDE10A |
| SMPDL3A |
| PNRC1 |
| ASCC3 |
| RAB32 |
| KATNA1 |
| BVES |
| SEC63 |
| RBM16 |
| KIAA1009 |
| ICK |
| ENPP4 |
| ANKRD6 |
| RIMS1 |
| DOPEY1 |
| ZNF292 |
| CDC2L6 |
| MAP3K7IP2 |
| MDN1 |
| TSPYL4 |
| SASH1 |
| SYNE1 |
| KIAA0776 |
| PHF3 |
| HEY2 |
| HEBP2 |
| ORC3L |
| CD2AP |
| BRD7P3 |
| MTO1 |
| ASF1A |
| CCDC28A |
| MTHFD1L |
| SFRS18 |
| IBTK |
| MOXD1 |
| IPCEF1 |
| ZNF451 |
| SENP6 |
| TIAM2 |
| FBXL4 |
| C6orf123 |
| FBXO9 |
| FBXO5 |
| SLC17A5 |
| RGS17 |
| SNORD50A |
| PDE7B |
| FILIP1 |
| TNFRSF21 |
| SESN1 |
| TINAG |
| OSTM1 |
| TMEM14A |
| MRPL18 |
| NDUFAF4 |
| DSE |
| CLDN20 |
| NOX3 |
| HDDC2 |
| TFB1M |
| CYB5R4 |
| TUBE1 |
| C6orf203 |
| CYP39A1 |
| CDC40 |
| RWDD1 |
| AIG1 |
| SNX9 |
| UBE2J1 |
| VTA1 |
| LGSN |
| BRP44L |
| HECA |
| RAB23 |
| COQ3 |
| CLIC5 |
| IL20RA |
| UNC93A |
| HMGCLL1 |
| MTRF1L |
| AHI1 |
| RMND1 |
| PHIP |
| SOBP |
| AKIRIN2 |
| CENPQ |
| LRRC1 |
| PHF10 |
| QRSL1 |
| VNN3 |
| NCRNA00120 |
| DDX43 |
| FAM46A |
| TMEM30A |
| C6orf70 |
| LMBRD1 |
| ECHDC1 |
| KCNQ5 |
| AGPAT4 |
| TULP4 |
| RARS2 |
| HYMAI |
| PDSS2 |
| C6orf162 |
| GPR126 |
| KIAA1244 |
| NHSL1 |
| LYRM2 |
| SNX14 |
| PLEKHG1 |
| ARID1B |
| AARS2 |
| SERINC1 |
| HACE1 |
| FAM135A |
| TMEM181 |
| ZBTB2 |
| BEND3 |
| KIAA1586 |
| C6orf115 |
| RRAGD |
| ENPP5 |
| PRDM13 |
| PBOV1 |
| BACH2 |
| ELOVL5 |
| TRMT11 |
| SMAP1 |
| C6orf164 |
| PERP |
| SMOC2 |
| POPDC3 |
| ALDH8A1 |
| MICAL1 |
| ULBP3 |
| OR2A4 |
| C6orf211 |
| OGFRL1 |
| FAM184A |
| ZDHHC14 |
| MANEA |
| C6orf103 |
| C6orf155 |
| FRMD1 |
| C6orf59 |
| C6orf208 |
| C6orf97 |
| MYCT1 |
| ULBP2 |
| ULBP1 |
| LPAL2 |
| KHDC1 |
| GPR63 |
| COL21A1 |
| PPP1R14C |
| SPACA1 |
| RNF146 |
| SF3B5 |
| TAAR8 |
| SH3BGRL2 |
| TFAP2D |
| RSPH3 |
| TTLL2 |
| ARMC2 |
| FBXO30 |
| RPF2 |
| L3MBTL3 |
| MCHR2 |
| C6orf168 |
| FNDC1 |
| GJA10 |
| RTN4IP1 |
| RSPO3 |
| LRP11 |
| LTV1 |
| SERAC1 |
| USP45 |
| REPS1 |
| PPIL4 |
| PAQR8 |
| SLC22A16 |
| UBE2CBP |
| C6orf142 |
| C6orf176 |
| KIAA1919 |
| ARHGAP18 |
| SYTL3 |
| GTF3C6 |
| MRAP2 |
| RWDD2A |
| IL17F |
| FAM54A |
| SFT2D1 |
| EFHC1 |
| KLHL32 |
| TMEM200A |
| C6orf150 |
| NUS1 |
| C6orf72 |
| IL22RA2 |
| C6orf192 |
| SLC16A10 |
| TAGAP |
| ADAT2 |
| RIPPLY2 |
| IRAK1BP1 |
| CLVS2 |
| TAAR9 |
| TAAR1 |
| STXBP5 |
| NCOA7 |
| HINT3 |
| PACRG |
| B3GAT2 |
| C6orf57 |
| CD109 |
| RAET1E |
| PM20D2 |
| SFRS13B |
| C6orf141 |
| LOC153910 |
| C6orf94 |
| CNKSR3 |
| RAET1L |
| SAMD3 |
| MGC34034 |
| SLC2A12 |
| PNLDC1 |
| RNF217 |
| NKAIN2 |
| C6orf221 |
| C6orf165 |
| LOC154449 |
| PRSS35 |
| LCA5 |
| OLIG3 |
| TXLNB |
| DACT2 |
| C6orf118 |
| OSTCL |
| TCTE1 |
| KHDRBS2 |
| C6orf163 |
| C6orf185 |
| AKD1 |
| NT5DC1 |
| FAM26D |
| ZUFSP |
| FAM162B |
| C6orf170 |
| BEND6 |
| GSTA5 |
| OPN5 |
| GPR115 |
| GPR116 |
| TDRD6 |
| SPATS1 |
| HS3ST5 |
| GPRC6A |
| RFX6 |
| SLC35F1 |
| FAM83B |
| GPR111 |
| VGLL2 |
| DEFB110 |
| DEFB112 |
| DEFB113 |
| DEFB114 |
| LACE1 |
| C6orf191 |
| C6orf167 |
| WDR27 |
| FAM26E |
| MCM9 |
| SCML4 |
| SHPRH |
| GPR110 |
| LOC285733 |
| LOC285735 |
| LOC285740 |
| C6orf182 |
| PPIL6 |
| FLJ34503 |
| DCBLD1 |
| LOC285796 |
| PRR18 |
| TAAR6 |
| SLC35D3 |
| ZC3H12D |
| DPPA5 |
| RSPH4A |
| ECT2L |
| EYS |
| NUP43 |
| C6orf58 |
| RAET1G |
| GUSBL2 |
| GJB7 |
| SNHG5 |
| SUMO4 |
| C6orf147 |
| C6orf173 |
| C6orf174 |
| C6orf204 |
| C6orf120 |
| THEMIS |
| C6orf140 |
| GFRAL |
| LIN28B |
| SAMD5 |
| IYD |
| KLHL31 |
| TCP10L2 |
| C6orf122 |
| DEFB133 |
| GTF2H5 |
| MIR206 |
| MIR30A |
| MIR30C2 |
| TMEM151B |
| OOEP |
| FAM26F |
| LOC441177 |
| C6orf138 |
| MCART3P |
| LOC442245 |
| RFPL4B |
| MIR133B |
| LOC553137 |
| SNORD101 |
| SNORD100 |
| SNORA33 |
| C6orf225 |
| TSG1 |
| CTAGE9 |
| RAET1K |
| C6orf124 |
| SNORA20 |
| SNORA29 |
| SNORD50B |
| MIR548B |
| MIR586 |
| LOC728402 |
| C6orf186 |
| LOC729176 |
| LOC729603 |
| LOC730101 |
| HGC6.3 |
| BET3L |
| KHDC1L |
| C6orf217 |
| LOC100287718 |
| NHEG1 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 9q31.1.
Table S41. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| ABL1 |
| NOTCH1 |
| RALGDS |
| SET |
| TAL2 |
| TSC1 |
| NR4A3 |
| BRD3 |
| NUP214 |
| FNBP1 |
| hsa-mir-602 |
| hsa-mir-126 |
| hsa-mir-219-2 |
| hsa-mir-199b |
| hsa-mir-181b-2 |
| hsa-mir-601 |
| hsa-mir-600 |
| hsa-mir-147 |
| hsa-mir-455 |
| hsa-mir-32 |
| ABCA1 |
| ABCA2 |
| ABO |
| AK1 |
| ALAD |
| ALDOB |
| AMBP |
| ASS1 |
| BAAT |
| C5 |
| C8G |
| CACNA1B |
| CCBL1 |
| TNFSF8 |
| ENTPD2 |
| CDK9 |
| CEL |
| CELP |
| COL5A1 |
| SLC31A1 |
| SLC31A2 |
| CRAT |
| CYLC2 |
| DBC1 |
| DBH |
| SARDH |
| DNM1 |
| TOR1A |
| LPAR1 |
| MEGF9 |
| ENDOG |
| ENG |
| STOM |
| FKTN |
| FCN1 |
| FCN2 |
| FPGS |
| NR5A1 |
| FUT7 |
| NR6A1 |
| GGTA1 |
| GLE1 |
| GNG10 |
| GOLGA1 |
| GOLGA2 |
| GPR21 |
| RAPGEF1 |
| GRIN1 |
| GSN |
| HSPA5 |
| TNC |
| LCN1 |
| LCN2 |
| LMX1B |
| MUSK |
| NDUFA8 |
| ODF2 |
| ORM1 |
| ORM2 |
| PAEP |
| PAPPA |
| PDCL |
| PBX3 |
| PPP2R4 |
| PPP3R2 |
| PPP6C |
| PSMB7 |
| PSMD5 |
| PTGDS |
| PTGS1 |
| PTPN3 |
| RAD23B |
| RGS3 |
| RPL7A |
| RPL12 |
| RXRA |
| SNAPC4 |
| SPTAN1 |
| STXBP1 |
| SURF1 |
| SURF2 |
| SURF4 |
| MED22 |
| SURF6 |
| TLR4 |
| TRAF1 |
| TRAF2 |
| TTF1 |
| TXN |
| UGCG |
| VAV2 |
| ZFP37 |
| ZNF79 |
| ZNF189 |
| LHX3 |
| GFI1B |
| IKBKAP |
| TMEFF1 |
| SSNA1 |
| EDF1 |
| CTNNAL1 |
| DPM2 |
| FUBP3 |
| CLIC3 |
| PRPF4 |
| KLF4 |
| GTF3C5 |
| GTF3C4 |
| LHX2 |
| MED27 |
| PTGES |
| ATP6V1G1 |
| RALGPS1 |
| ADAMTSL2 |
| KIAA0649 |
| SEC16A |
| TNFSF15 |
| ROD1 |
| SH2D3C |
| RABEPK |
| LAMC3 |
| TUBB2C |
| UBAC1 |
| OLFM1 |
| ZER1 |
| AGPAT2 |
| POMT1 |
| SMC2 |
| ZBTB6 |
| NEK6 |
| SDCCAG3 |
| NOXA1 |
| USP20 |
| ACTL7B |
| ACTL7A |
| SLC27A4 |
| CEP110 |
| WDR5 |
| C9orf9 |
| ADAMTS13 |
| C9orf7 |
| SLC2A6 |
| AKAP2 |
| RPL35 |
| MAN1B1 |
| DOLK |
| PTGR1 |
| TRIM32 |
| SETX |
| ERP44 |
| ZBTB43 |
| PMPCA |
| ASTN2 |
| FKBP15 |
| KIAA0368 |
| EXOSC2 |
| FREQ |
| SLC44A1 |
| ANGPTL2 |
| NUP188 |
| RABGAP1 |
| C9orf5 |
| C9orf4 |
| CIZ1 |
| DFNB31 |
| COBRA1 |
| NIPSNAP3A |
| NELF |
| GPSM1 |
| LOC26102 |
| GAPVD1 |
| PHF19 |
| FBXW2 |
| OR1J4 |
| OR2K2 |
| GBGT1 |
| LHX6 |
| OR1L3 |
| OR1L1 |
| OR1J2 |
| SNORA65 |
| SNORD62A |
| SNORD36C |
| SNORD36B |
| SNORD36A |
| SNORD24 |
| TRUB2 |
| ST6GALNAC4 |
| INVS |
| NDOR1 |
| TOR1B |
| TOR2A |
| METTL11A |
| PHPT1 |
| ANAPC2 |
| PKN3 |
| DPP7 |
| SLC2A8 |
| OBP2B |
| OBP2A |
| ST6GALNAC6 |
| DEC1 |
| MRPS2 |
| COQ4 |
| CERCAM |
| EGFL7 |
| PRRX2 |
| C9orf114 |
| RAB14 |
| C9orf78 |
| POLE3 |
| FBXW5 |
| MRPL50 |
| RC3H2 |
| EPB41L4B |
| TBC1D13 |
| BSPRY |
| C9orf167 |
| TEX10 |
| LPPR1 |
| EXD3 |
| C9orf6 |
| STX17 |
| TMEM38B |
| NIPSNAP3B |
| STRBP |
| C9orf86 |
| CDK5RAP2 |
| RNF20 |
| LRRC8A |
| INPP5E |
| NPDC1 |
| BARHL1 |
| SH3GLB2 |
| REXO4 |
| DOLPP1 |
| KCNT1 |
| ZBTB26 |
| DENND1A |
| GPR107 |
| SLC46A2 |
| C9orf27 |
| C9orf80 |
| ZNF462 |
| PRDM12 |
| CARD9 |
| SUSD1 |
| DDX31 |
| FAM129B |
| MRPL41 |
| C9orf16 |
| MAPKAP1 |
| EHMT1 |
| SVEP1 |
| PTGES2 |
| AKNA |
| C9orf45 |
| URM1 |
| ARPC5L |
| HDHD3 |
| AIF1L |
| UCK1 |
| FSD1L |
| GARNL3 |
| HSDL2 |
| C9orf125 |
| NTNG2 |
| BAT2L |
| PPAPDC3 |
| ZDHHC12 |
| FAM73B |
| FIBCD1 |
| KIAA1984 |
| SNHG7 |
| TMEM141 |
| C9orf37 |
| COL27A1 |
| FAM125B |
| WDR34 |
| C9orf140 |
| C9orf69 |
| LRSAM1 |
| C9orf30 |
| UAP1L1 |
| MRRF |
| RBM18 |
| ARRDC1 |
| WDR85 |
| TMEM203 |
| KIF12 |
| PALM2 |
| SLC25A25 |
| WDR31 |
| ZNF618 |
| ZMYND19 |
| GRIN3A |
| RNF183 |
| NACC2 |
| C9orf116 |
| LCN8 |
| FAM69B |
| PTRH1 |
| PIP5KL1 |
| OR13C5 |
| OR13C8 |
| OR13C3 |
| OR13C4 |
| OR13F1 |
| OR1L8 |
| OR1N2 |
| OR1N1 |
| ASB6 |
| SLC34A3 |
| DAB2IP |
| CAMSAP1 |
| C9orf163 |
| MAMDC4 |
| LCN6 |
| C9orf98 |
| OR1Q1 |
| TTLL11 |
| TTC16 |
| ZNF483 |
| C9orf84 |
| KIAA1958 |
| C9orf96 |
| OLFML2A |
| QSOX2 |
| LOC169834 |
| C9orf91 |
| NAIF1 |
| CDC26 |
| LOC253039 |
| PHYHD1 |
| MORN5 |
| OR1L4 |
| TXNDC8 |
| C9orf43 |
| NCRNA00094 |
| CRB2 |
| SCAI |
| C9orf117 |
| LCN12 |
| C9orf142 |
| C9orf75 |
| C9orf109 |
| FAM78A |
| OR13C9 |
| OR13D1 |
| LOC286367 |
| GPR144 |
| QRFP |
| OR1J1 |
| OR1B1 |
| MURC |
| GLT6D1 |
| C9orf119 |
| C9orf50 |
| PNPLA7 |
| C9orf169 |
| ENTPD8 |
| LOC389791 |
| IER5L |
| C9orf171 |
| LCN15 |
| C9orf172 |
| LRRC26 |
| TMEM8C |
| OR13C2 |
| OR1L6 |
| OR5C1 |
| OR1K1 |
| LCN9 |
| FAM102A |
| C9orf152 |
| SNX30 |
| WDR38 |
| LCNL1 |
| C9orf139 |
| FAM166A |
| LOC402377 |
| SOHLH1 |
| ZBTB34 |
| MIR126 |
| MIR147 |
| MIR181A2 |
| MIR181B2 |
| MIR199B |
| MIR219-2 |
| MIR32 |
| C9orf106 |
| LCN10 |
| C9orf173 |
| NRARP |
| PALM2-AKAP2 |
| DNAJC25 |
| DNAJC25-GNG10 |
| MIR455 |
| FAM163B |
| FLJ40292 |
| TUBBP5 |
| SNORA17 |
| SNORA43 |
| SNORD62B |
| SNORD90 |
| MIR548D1 |
| MIR600 |
| MIR601 |
| MIR602 |
| RNF208 |
| DNLZ |
| SNORA70C |
| C9orf110 |
| LOC100129034 |
| LOC100131193 |
| FAM157B |
| RNU6ATAC |
| LOC100272217 |
| LOC100289341 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 4q35.1.
Table S42. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| FGFR3 |
| IL2 |
| KDR |
| KIT |
| PDGFRA |
| RAP1GDS1 |
| WHSC1 |
| PHOX2B |
| DUX4 |
| CHIC2 |
| TET2 |
| FBXW7 |
| FIP1L1 |
| hsa-mir-1305 |
| hsa-mir-1979 |
| hsa-mir-548g |
| hsa-mir-2054 |
| hsa-mir-1973 |
| hsa-mir-577 |
| hsa-mir-1243 |
| hsa-mir-302b |
| hsa-mir-297 |
| hsa-mir-576 |
| hsa-mir-1255a |
| hsa-mir-575 |
| hsa-mir-1269 |
| hsa-mir-574 |
| hsa-mir-1255b-1 |
| hsa-mir-573 |
| hsa-mir-218-1 |
| hsa-mir-572 |
| hsa-mir-548i-2 |
| hsa-mir-95 |
| hsa-mir-943 |
| hsa-mir-571 |
| ADD1 |
| ADH1A |
| ADH1B |
| ADH1C |
| ADH4 |
| ADH5 |
| ADH6 |
| ADH7 |
| ADRA2C |
| AFM |
| AFP |
| AGA |
| ALB |
| AMBN |
| ANK2 |
| SLC25A4 |
| ANXA2P1 |
| ANXA3 |
| ANXA5 |
| APBB2 |
| AREG |
| RHOH |
| ART3 |
| ATOH1 |
| ATP5I |
| NKX3-2 |
| BMP3 |
| BMPR1B |
| BST1 |
| BTC |
| CAMK2D |
| CASP3 |
| CASP6 |
| CCKAR |
| CCNA2 |
| CCNG2 |
| SCARB2 |
| CD38 |
| LRBA |
| CDS1 |
| CLGN |
| CENPC1 |
| CENPE |
| CLCN3 |
| CNGA1 |
| CPE |
| CRMP1 |
| CSN1S1 |
| CSN2 |
| CSN3 |
| CTBP1 |
| CTSO |
| DGKQ |
| DCK |
| DCTD |
| DHX15 |
| DMP1 |
| DRD5 |
| DSPP |
| EDNRA |
| EGF |
| EIF4E |
| ELF2 |
| ENPEP |
| EPHA5 |
| EREG |
| ETFDH |
| EVC |
| F11 |
| FABP2 |
| ACSL1 |
| FAT1 |
| FGA |
| FGB |
| FGF2 |
| FGF5 |
| FGG |
| FRG1 |
| GAB1 |
| GABRA2 |
| GABRA4 |
| GABRB1 |
| GABRG1 |
| GAK |
| GC |
| GK2 |
| GK3P |
| GLRB |
| GNRHR |
| GPM6A |
| GRK4 |
| GRIA2 |
| GRID2 |
| CXCL1 |
| CXCL2 |
| CXCL3 |
| GRSF1 |
| GUCY1A3 |
| GUCY1B3 |
| GYPA |
| GYPB |
| GYPE |
| H2AFZ |
| HADH |
| HTT |
| HGFAC |
| UBE2K |
| HMGB2 |
| HNRNPD |
| HPGD |
| HTN1 |
| HTN3 |
| IBSP |
| IDUA |
| CFI |
| IGFBP7 |
| IGJ |
| RBPJ |
| IL8 |
| IL15 |
| ING2 |
| CXCL10 |
| IRF2 |
| KLKB1 |
| LETM1 |
| LRPAP1 |
| MAD2L1 |
| SMAD1 |
| MANBA |
| MGST2 |
| CXCL9 |
| AFF1 |
| NR3C2 |
| MSX1 |
| MTNR1A |
| MTTP |
| MUC7 |
| MYL5 |
| NDUFC1 |
| NEK1 |
| NFKB1 |
| NKX6-1 |
| NPY1R |
| NPY2R |
| NPY5R |
| PCDH7 |
| PDE6B |
| PDHA2 |
| PET112L |
| PF4 |
| PF4V1 |
| PITX2 |
| PKD2 |
| PLRG1 |
| EXOSC9 |
| POLR2B |
| POU4F2 |
| PPEF2 |
| PPAT |
| PPBP |
| PPID |
| PPP2R2C |
| PPP3CA |
| PRKG2 |
| MAPK10 |
| PTPN13 |
| QDPR |
| REST |
| RFC1 |
| RGS12 |
| RNF4 |
| ABCE1 |
| RPL9 |
| RPL34 |
| RPS3A |
| S100P |
| SC4MOL |
| CXCL6 |
| CXCL11 |
| CXCL5 |
| SFRP2 |
| SGCB |
| SH3BP2 |
| SNCA |
| SOD3 |
| SPINK2 |
| SPP1 |
| SRP72 |
| STATH |
| SULT1E1 |
| TACR3 |
| TDO2 |
| TEC |
| TLL1 |
| TLR1 |
| TLR2 |
| TLR3 |
| TMSL3 |
| TRPC3 |
| TXK |
| UBE2D3 |
| UCHL1 |
| UCP1 |
| UGDH |
| UGT2B4 |
| UGT2B7 |
| UGT2B10 |
| UGT2B15 |
| UGT2B17 |
| UGT8 |
| VEGFC |
| WFS1 |
| WHSC2 |
| ZNF141 |
| SLBP |
| GLRA3 |
| ACOX3 |
| SPARCL1 |
| SMARCA5 |
| SORBS2 |
| PRSS12 |
| CPZ |
| NOP14 |
| FAM193A |
| USO1 |
| UNC5C |
| MAPKSP1 |
| PDE5A |
| SLC4A4 |
| SAP30 |
| INPP4B |
| PROM1 |
| HERC3 |
| SNORD73A |
| STBD1 |
| CDKL2 |
| PAPSS1 |
| LDB2 |
| LRAT |
| AIMP1 |
| NDST3 |
| SLIT2 |
| RAB28 |
| TMPRSS11D |
| ABCG2 |
| HAND2 |
| ADAMTS3 |
| CLOCK |
| CEP135 |
| RAPGEF2 |
| KIAA0232 |
| MFAP3L |
| SEC24D |
| G3BP2 |
| WDR1 |
| HS3ST1 |
| FGFBP1 |
| HNRPDL |
| TSPAN5 |
| ENAM |
| C4orf6 |
| FAM13A |
| MFSD10 |
| SPRY1 |
| MAEA |
| TLR6 |
| PCGF3 |
| ANAPC10 |
| ATP8A1 |
| SPON2 |
| PGRMC2 |
| SEC24B |
| TACC3 |
| SLC30A9 |
| CXCL13 |
| SLC34A2 |
| MAB21L2 |
| PAICS |
| MXD4 |
| PDLIM5 |
| RRH |
| CORIN |
| UGT2B11 |
| PLK4 |
| PTTG2 |
| CPLX1 |
| HPSE |
| SLC26A1 |
| NMU |
| SMR3B |
| NPFFR2 |
| PPARGC1A |
| PPBPL2 |
| MORF4 |
| UGT2A1 |
| CCNI |
| LIAS |
| ADAM29 |
| PRDM5 |
| LSM6 |
| NUDT6 |
| ANXA10 |
| KLHL2 |
| SCRG1 |
| HSPA4L |
| SEC31A |
| RUFY3 |
| MMRN1 |
| LIMCH1 |
| WDFY3 |
| PALLD |
| DCUN1D4 |
| TBC1D9 |
| METAP1 |
| TBC1D1 |
| SEL1L3 |
| KIAA0922 |
| PDS5A |
| LPHN3 |
| TRIM2 |
| MAN2B2 |
| ANP32C |
| SLC7A11 |
| CCRN4L |
| PARM1 |
| FAM149A |
| RCHY1 |
| ANKRD17 |
| STAP1 |
| FBXL5 |
| FBXO8 |
| SMR3A |
| D4S234E |
| PPA2 |
| DAPP1 |
| DKK2 |
| FAM184B |
| INTU |
| NAAA |
| GPR78 |
| COQ2 |
| ARFIP1 |
| SULT1B1 |
| PDLIM3 |
| HPGDS |
| ZNF330 |
| TMPRSS11E |
| ZCCHC4 |
| ANAPC4 |
| SPOCK3 |
| MRPS18C |
| LAP3 |
| KLHL5 |
| SEPSECS |
| COPS4 |
| AADAT |
| HSD17B11 |
| LEF1 |
| HERC5 |
| KLF3 |
| FAM198B |
| PLAC8 |
| LARP7 |
| EMCN |
| MYOZ2 |
| ACCN5 |
| GALNT7 |
| NUDT9 |
| NUP54 |
| STX18 |
| FGFRL1 |
| CLDN22 |
| CYTL1 |
| GAR1 |
| SH3TC1 |
| UGT2B28 |
| RBM47 |
| PCDH18 |
| USP53 |
| OTUD4 |
| DCHS2 |
| FLJ20184 |
| PIGG |
| DCAF16 |
| OCIAD1 |
| COMMD8 |
| ODAM |
| C4orf27 |
| HERC6 |
| CCDC109B |
| MARCH1 |
| BANK1 |
| LARP1B |
| SDAD1 |
| TMEM33 |
| LGI2 |
| BBS7 |
| UBA6 |
| NEIL3 |
| PGM2 |
| C4orf19 |
| TBC1D19 |
| PI4K2B |
| TMEM144 |
| C4orf43 |
| UFSP2 |
| CNO |
| C4orf21 |
| STK32B |
| AP1AR |
| MAML3 |
| CHRNA9 |
| BMP2K |
| DDX60 |
| CDKN2AIP |
| LYAR |
| ODZ3 |
| N4BP2 |
| TMEM184C |
| SEPT11 |
| EXOC1 |
| LRP2BP |
| TMEM165 |
| PDGFC |
| TUBB4Q |
| SLC2A9 |
| FSTL5 |
| BDH2 |
| SMARCAD1 |
| MEPE |
| STOX2 |
| PRDM8 |
| UTP3 |
| INTS12 |
| ANKRD50 |
| ATP10D |
| KIAA0114 |
| KIAA1211 |
| RNF150 |
| KIAA1239 |
| TBC1D14 |
| SORCS2 |
| CC2D2A |
| KLHL8 |
| PCDH10 |
| KIAA1430 |
| FNIP2 |
| SLAIN2 |
| SHROOM3 |
| STIM2 |
| SH3RF1 |
| KIAA1530 |
| METTL14 |
| WDR19 |
| ZFYVE28 |
| GBA3 |
| ENOPH1 |
| PROL1 |
| OSTC |
| IL21 |
| RXFP1 |
| AFAP1 |
| GUF1 |
| SPCS3 |
| SCOC |
| C4orf41 |
| NEUROG2 |
| SLC39A8 |
| NCAPG |
| HHIP |
| NDST4 |
| AGXT2L1 |
| USP46 |
| MRPL1 |
| RASL11B |
| ELOVL6 |
| TNIP2 |
| HAUS3 |
| C4orf31 |
| FAT4 |
| ARSJ |
| SRD5A3 |
| ARHGAP10 |
| FLJ13197 |
| MLF1IP |
| THAP9 |
| NSUN7 |
| UGT2A3 |
| NBLA00301 |
| GSTCD |
| MAP9 |
| TNIP3 |
| PHF17 |
| ABCA11P |
| SCD5 |
| DNAJB14 |
| TMEM156 |
| WWC2 |
| FRAS1 |
| NARG1 |
| CWH43 |
| C4orf29 |
| ALPK1 |
| GRPEL1 |
| MED28 |
| CXXC4 |
| KCNIP4 |
| KIAA1712 |
| SETD7 |
| PLA2G12A |
| TLR10 |
| SLC25A31 |
| RAB33B |
| ARHGAP24 |
| FGFBP2 |
| SNX25 |
| TTC29 |
| MND1 |
| SLC10A7 |
| TKTL2 |
| C4orf17 |
| QRFPR |
| FAM175A |
| KIAA1109 |
| MFSD7 |
| C4orf14 |
| TMEM175 |
| ABLIM2 |
| HOPX |
| COL25A1 |
| USP38 |
| LNX1 |
| C4orf49 |
| LOC84740 |
| ARD1B |
| AGPAT9 |
| CBR4 |
| PIGY |
| TMEM128 |
| C4orf35 |
| ZNF518B |
| FHDC1 |
| MGC45800 |
| PRMT10 |
| CCDC149 |
| DDX60L |
| YTHDC1 |
| C4orf42 |
| TMEM129 |
| NAF1 |
| MOBKL1A |
| TIFA |
| FAM114A1 |
| RG9MTD2 |
| MRFAP1 |
| LOC93622 |
| TADA2B |
| TBCK |
| HTRA3 |
| HELQ |
| CYP2U1 |
| C1QTNF7 |
| MRFAP1L1 |
| DDIT4L |
| CLNK |
| WDR17 |
| ARAP2 |
| GDEP |
| ANTXR2 |
| OCIAD2 |
| SCLT1 |
| C4orf33 |
| TMEM155 |
| PABPC4L |
| ADAD1 |
| ZFP42 |
| LIN54 |
| SPATA18 |
| C4orf32 |
| TMPRSS11B |
| GNPDA2 |
| SPATA4 |
| CPEB2 |
| EVC2 |
| ARL9 |
| AASDH |
| PDCL2 |
| C4orf36 |
| PACRGL |
| TRAM1L1 |
| OTOP1 |
| ENPP6 |
| NHEDC2 |
| ASB5 |
| NHEDC1 |
| ZNF827 |
| SH3D19 |
| NFXL1 |
| NIPAL1 |
| PAQR3 |
| SHISA3 |
| SCFD2 |
| C4orf38 |
| ZNF595 |
| C4orf39 |
| JAKMIP1 |
| THAP6 |
| C4orf26 |
| KLB |
| FAM53A |
| PPM1K |
| C4orf45 |
| C4orf23 |
| RASGEF1B |
| SPATA5 |
| BBS12 |
| DCLK2 |
| GPR125 |
| TRIM60 |
| MMAA |
| ZNF509 |
| TIGD2 |
| RASSF6 |
| RBM46 |
| SGMS2 |
| COX7B2 |
| GSX2 |
| ZNF721 |
| SYNPO2 |
| C4orf46 |
| SLC10A4 |
| TIGD4 |
| TMEM154 |
| C4orf34 |
| TMEM192 |
| RWDD4A |
| CCDC111 |
| TAPT1 |
| FLJ39653 |
| TRIML2 |
| CNOT6L |
| TECRL |
| LCORL |
| C4orf22 |
| EPGN |
| ZNF718 |
| ELMOD2 |
| NPNT |
| CCDC110 |
| MFSD8 |
| LOC256880 |
| CCDC96 |
| BOD1L |
| C4orf7 |
| NAP1L5 |
| LOC285419 |
| DCAF4L1 |
| CYP4V2 |
| LOC285456 |
| CRIPAK |
| DOK7 |
| RNF212 |
| LOC285501 |
| FAM13AOS |
| GPRIN3 |
| COX18 |
| YIPF7 |
| FRYL |
| RNF175 |
| LOC285548 |
| LOC285550 |
| C4orf37 |
| CSN1S2A |
| C4orf10 |
| CSN1S2B |
| ZAR1 |
| CCDC158 |
| TMPRSS11A |
| TRIML1 |
| LRRC66 |
| NAT8L |
| LOC340017 |
| LOC344967 |
| PRSS48 |
| ANKRD56 |
| LRIT3 |
| C4orf44 |
| SLC10A6 |
| HSD17B13 |
| LOC348926 |
| ANKRD37 |
| POLN |
| PCNAP1 |
| NCRNA00099 |
| KCTD8 |
| C4orf50 |
| C4orf52 |
| BEND4 |
| GRXCR1 |
| TMPRSS11F |
| USP17L6P |
| USP17 |
| HSP90AB2P |
| TRIM61 |
| TRIM75 |
| HELT |
| C4orf48 |
| DTHD1 |
| LOC401127 |
| SYT14L |
| FLJ41562 |
| C4orf40 |
| AMTN |
| FAM190A |
| C4orf3 |
| RPL21P44 |
| FAM92A3 |
| C4orf12 |
| MIR218-1 |
| MIR302A |
| C4orf11 |
| MTHFD2L |
| TMEM150C |
| EEF1AL7 |
| LOC441046 |
| C4orf47 |
| GALNTL6 |
| MIR302B |
| MIR302C |
| MIR302D |
| MIR367 |
| FRG2 |
| CISD2 |
| LOC550112 |
| UGT2A2 |
| LOC641518 |
| ZNF876P |
| SLED1 |
| LOC644145 |
| DEFB131 |
| CLRN2 |
| CEP170L |
| C4orf51 |
| LOC650293 |
| LOC653543 |
| LOC653544 |
| LOC653545 |
| LOC653548 |
| ZNF732 |
| SCARNA22 |
| SNORA24 |
| SNORA26 |
| MIR572 |
| MIR573 |
| MIR574 |
| MIR575 |
| MIR577 |
| MIR578 |
| PPBPL1 |
| LOC728410 |
| LOC729338 |
| FAM160A1 |
| FLJ36777 |
| RELL1 |
| PSAPL1 |
| SNHG8 |
| MIR943 |
| FAM47E |
| LOC100130017 |
| LOC100130872 |
| LOC100192379 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 7q34.
Table S43. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| BRAF |
| CDK6 |
| EGFR |
| ELN |
| ETV1 |
| EZH2 |
| HIP1 |
| HNRNPA2B1 |
| HOXA9 |
| HOXA11 |
| HOXA13 |
| MET |
| PMS2 |
| SMO |
| AKAP9 |
| IKZF1 |
| SBDS |
| KIAA1549 |
| MLL3 |
| CREB3L2 |
| CARD11 |
| JAZF1 |
| hsa-mir-595 |
| hsa-mir-153-2 |
| hsa-mir-671 |
| hsa-mir-1975 |
| hsa-mir-548f-4 |
| hsa-mir-490 |
| hsa-mir-29b-1 |
| hsa-mir-335 |
| hsa-mir-183 |
| hsa-mir-129-1 |
| hsa-mir-593 |
| hsa-mir-592 |
| hsa-mir-548o |
| hsa-mir-106b |
| hsa-mir-591 |
| hsa-mir-489 |
| hsa-mir-1285-1 |
| hsa-mir-590 |
| hsa-mir-1200 |
| hsa-mir-548n |
| hsa-mir-550-2 |
| hsa-mir-550-1 |
| hsa-mir-196b |
| hsa-mir-148a |
| hsa-mir-1183 |
| hsa-mir-1302-6 |
| hsa-mir-589 |
| hsa-mir-339 |
| ABP1 |
| ACHE |
| ACTB |
| ADCY1 |
| ADCYAP1R1 |
| AEBP1 |
| AHR |
| AKR1B1 |
| AMPH |
| AOAH |
| AQP1 |
| ARF5 |
| ASL |
| ASNS |
| AZGP1 |
| OPN1SW |
| BLVRA |
| BPGM |
| CACNA2D1 |
| CALCR |
| CALD1 |
| CALU |
| CAMK2B |
| CAPZA2 |
| CASP2 |
| CAV1 |
| CAV2 |
| KRIT1 |
| CCT6A |
| CD36 |
| SEPT7 |
| CDK5 |
| CFTR |
| CHN2 |
| CHRM2 |
| AP1S1 |
| CLCN1 |
| CLK2P |
| COL1A2 |
| CPA1 |
| CPA2 |
| CLDN4 |
| CLDN3 |
| CRHR2 |
| CUX1 |
| CYP3A7 |
| CYP3A4 |
| CYP3A5 |
| CYP51A1 |
| DGKB |
| DDC |
| DFNA5 |
| DLD |
| DLX5 |
| DLX6 |
| DYNC1I1 |
| DPP6 |
| SLC26A3 |
| EN2 |
| EPHA1 |
| EPHB4 |
| EPHB6 |
| EPO |
| EVX1 |
| FLNC |
| GARS |
| GBAS |
| GBX1 |
| GCK |
| GHRHR |
| GLI3 |
| GNA12 |
| GNAI1 |
| GNB2 |
| GNG11 |
| GNGT1 |
| GPR22 |
| GPER |
| GPR37 |
| GRB10 |
| GRM3 |
| GRM8 |
| GTF2I |
| GTF2IP1 |
| GUSB |
| HGF |
| MNX1 |
| HOXA1 |
| HOXA2 |
| HOXA3 |
| HOXA4 |
| HOXA5 |
| HOXA6 |
| HOXA7 |
| HOXA10 |
| HPVC1 |
| AGFG2 |
| HSPB1 |
| HTR5A |
| HUS1 |
| ICA1 |
| IFRD1 |
| IGFBP1 |
| IGFBP3 |
| IL6 |
| IMPDH1 |
| INHBA |
| INSIG1 |
| IRF5 |
| ITGB8 |
| KCND2 |
| KCNH2 |
| KEL |
| LAMB1 |
| LEP |
| LFNG |
| LIMK1 |
| LRCH4 |
| MCM7 |
| DNAJB9 |
| MDH2 |
| MEOX2 |
| MEST |
| MKLN1 |
| NUDT1 |
| NDUFA4 |
| NDUFA5 |
| NDUFB2 |
| NOS3 |
| CNOT4 |
| NPY |
| NPTX2 |
| NRCAM |
| NRF1 |
| OCM2 |
| OGDH |
| ORC5L |
| SERPINE1 |
| PAX4 |
| PCOLCE |
| PDE1C |
| PDGFA |
| PDK4 |
| SLC26A4 |
| PEX1 |
| PFTK1 |
| PGAM2 |
| ABCB1 |
| ABCB4 |
| PHKG1 |
| PIK3CG |
| PIP |
| PMS2L1 |
| PMS2L2 |
| PMS2L4 |
| PMS2L5 |
| PMS2L3 |
| PODXL |
| POLD2 |
| POLR2J |
| PON1 |
| PON2 |
| PON3 |
| POR |
| PPIA |
| PPP1R3A |
| PRKAR1B |
| PRKAR2B |
| PRSS1 |
| PRSS2 |
| RELN |
| PSMA2 |
| PSMC2 |
| PSPH |
| TAS2R38 |
| PTN |
| PTPN12 |
| PTPRN2 |
| PTPRZ1 |
| PURB |
| RAC1 |
| RALA |
| RARRES2 |
| RFC2 |
| RHEB |
| RP9 |
| RPA3 |
| CCL24 |
| SFRP4 |
| SHH |
| SLC4A2 |
| SLC13A1 |
| SMARCD3 |
| FSCN1 |
| SP4 |
| SPAM1 |
| SRI |
| AKR1D1 |
| SRPK2 |
| SSBP1 |
| STX1A |
| SYPL1 |
| TAC1 |
| TAF6 |
| TBXAS1 |
| TFR2 |
| TRIP6 |
| TWIST1 |
| UBE2H |
| UPP1 |
| VGF |
| VIPR2 |
| ZAN |
| EIF4H |
| CLIP2 |
| LAT2 |
| WNT2 |
| XRCC2 |
| YWHAG |
| ZNF3 |
| ZNF12 |
| ZKSCAN1 |
| ZSCAN21 |
| ZNF138 |
| ZP3 |
| ZYX |
| AIMP2 |
| MAFK |
| MTERF |
| SHFM1 |
| TFPI2 |
| ST7 |
| ARHGEF5 |
| ZNF212 |
| TRRAP |
| FZD1 |
| FZD9 |
| MAD1L1 |
| ZNF282 |
| CUL1 |
| TPST1 |
| FKBP6 |
| CDC2L5 |
| EIF3B |
| DNAH11 |
| TRIM24 |
| TAX1BP1 |
| BUD31 |
| SGCE |
| SKAP2 |
| MGAM |
| WASL |
| PLOD3 |
| BAZ1B |
| CLDN12 |
| DGKI |
| AP4M1 |
| TBRG4 |
| STK17A |
| CYTH3 |
| BCL7B |
| ATP6V1F |
| ACCN3 |
| PMPCB |
| ATP5J2 |
| GTF2IRD1 |
| CREB5 |
| PDIA4 |
| NFE2L3 |
| PHF14 |
| UBE3C |
| FAM131B |
| SEMA3E |
| DOCK4 |
| HDAC9 |
| FAM115A |
| RAPGEF5 |
| SCRN1 |
| KIAA0087 |
| ELMO1 |
| MAGI2 |
| TRIL |
| POM121 |
| KIAA0415 |
| DMTF1 |
| DNAJB6 |
| ABCF2 |
| MUC12 |
| ARPC1B |
| ARL4A |
| NAMPT |
| RASA4 |
| AASS |
| SLC25A13 |
| LRRC17 |
| POP7 |
| RAMP3 |
| BET1 |
| CCL26 |
| SEMA3A |
| NOD1 |
| FAM3C |
| GPNMB |
| COG5 |
| ZNHIT1 |
| SEMA3C |
| AGR2 |
| ARPC1A |
| SH2B2 |
| IGF2BP3 |
| YKT6 |
| STAG3 |
| ZNF273 |
| C7orf16 |
| FGL2 |
| CPSF4 |
| FASTK |
| DBF4 |
| COPS6 |
| KDELR2 |
| ADAP1 |
| ZPBP |
| DUS4L |
| NUPL2 |
| HIBADH |
| ZNF277 |
| INMT |
| ABCB8 |
| TP53TG1 |
| POU6F2 |
| FKBP9 |
| PDAP1 |
| CBX3 |
| TFEC |
| LAMB4 |
| LMTK2 |
| POMZP3 |
| PAXIP1 |
| KLHDC10 |
| HECW1 |
| AVL9 |
| PEG10 |
| SSPO |
| NACAD |
| SNX13 |
| NUP205 |
| COBL |
| IQCE |
| DPY19L1 |
| UNC84A |
| KIAA0895 |
| AHCYL2 |
| NUDCD3 |
| SEC61G |
| TNPO3 |
| HYAL4 |
| TSPAN12 |
| CLEC5A |
| MKRN1 |
| LSM5 |
| ZKSCAN5 |
| CLDN15 |
| BRI3 |
| TECPR1 |
| SUMF2 |
| POT1 |
| SOSTDC1 |
| KBTBD2 |
| PTCD1 |
| OSBPL3 |
| CNTNAP2 |
| AUTS2 |
| HYALP1 |
| WIPI2 |
| TES |
| GIMAP2 |
| INTS1 |
| OR2F1 |
| FBXO24 |
| SLC13A4 |
| TBL2 |
| STEAP1 |
| COPG2 |
| HBP1 |
| DNAJC2 |
| TPK1 |
| SND1 |
| VPS41 |
| TSPAN13 |
| C7orf54 |
| EIF2AK1 |
| DENND2A |
| ZNF777 |
| BBS9 |
| CRCP |
| RABGEF1 |
| POLM |
| PCLO |
| TMEM176B |
| BZW2 |
| DBNL |
| HIPK2 |
| WDR91 |
| REPIN1 |
| NPC1L1 |
| SNX8 |
| SNX10 |
| TRA2A |
| C7orf68 |
| FTSJ2 |
| MDFIC |
| PILRB |
| PILRA |
| FSCN3 |
| NXPH1 |
| ATP6V0A4 |
| PNPLA8 |
| TAS2R3 |
| TAS2R4 |
| TAS2R16 |
| FIS1 |
| MLXIPL |
| CHCHD2 |
| CPA4 |
| NT5C3 |
| TXNDC3 |
| ZNF117 |
| MRPS17 |
| WNT16 |
| ACTL6B |
| PRKAG2 |
| ZNF107 |
| ZC3HC1 |
| SRRT |
| C7orf20 |
| UBE2D4 |
| C7orf28A |
| LUC7L2 |
| MRPS33 |
| STYXL1 |
| ASB4 |
| NUB1 |
| MPP6 |
| LSM8 |
| ADAM22 |
| PION |
| CYCS |
| GPR85 |
| TAS2R5 |
| STAG3L1 |
| ANLN |
| ANKIB1 |
| MIOS |
| RNF216 |
| CHPF2 |
| CPVL |
| PUS7 |
| TOMM7 |
| ING3 |
| DDX56 |
| TMEM106B |
| LRRN3 |
| CROT |
| EPDR1 |
| ZNF853 |
| ALKBH4 |
| SAMD9 |
| NCAPG2 |
| CYP2W1 |
| HEATR2 |
| CHCHD3 |
| FKBP14 |
| ZCWPW1 |
| C7orf42 |
| WDR60 |
| RBM28 |
| ZDHHC4 |
| TYW1 |
| C7orf43 |
| TMEM140 |
| GIMAP4 |
| GIMAP5 |
| TMEM176A |
| CHST12 |
| TRPV6 |
| CDCA7L |
| PPP1R9A |
| CCDC132 |
| URG4 |
| NSUN5 |
| RADIL |
| C7orf44 |
| AGK |
| METTL2B |
| MLL5 |
| LANCL2 |
| BAIAP2L1 |
| SLC25A40 |
| BCAP29 |
| KLHL7 |
| STK31 |
| MEPCE |
| TRPV5 |
| ANKRD7 |
| ZC3HAV1 |
| PAPOLB |
| C1GALT1 |
| FAM20C |
| SLC12A9 |
| ACN9 |
| C7orf36 |
| AKR1B10 |
| ANKMY2 |
| TBX20 |
| SMURF1 |
| PHTF2 |
| ACTR3B |
| KIAA1147 |
| RHBDD2 |
| FAM40B |
| ESYT2 |
| ZNF398 |
| CCDC146 |
| RBAK |
| GATAD1 |
| MYL7 |
| EXOC4 |
| RINT1 |
| GALNT11 |
| NEUROD6 |
| FIGNL1 |
| MYO1G |
| LRRC4 |
| NPVF |
| HERPUD2 |
| LMBR1 |
| WBSCR17 |
| TMEM168 |
| C7orf4 |
| NOM1 |
| MOSPD3 |
| GIGYF1 |
| CCDC136 |
| TNS3 |
| PARP12 |
| RABL5 |
| CYP3A43 |
| CASD1 |
| STAG3L4 |
| MRPS24 |
| MRPL32 |
| LRRC61 |
| C7orf49 |
| GGCT |
| C7orf25 |
| ZNF655 |
| C7orf26 |
| PVRIG |
| C7orf23 |
| GCC1 |
| STEAP4 |
| GAL3ST4 |
| PRKRIP1 |
| MICALL2 |
| C7orf10 |
| C7orf63 |
| CBLL1 |
| ZNF767 |
| C7orf58 |
| TTC26 |
| FBXL18 |
| C7orf69 |
| ORAI2 |
| TTYH3 |
| UPK3B |
| EEPD1 |
| JHDM1D |
| OR2AE1 |
| VOPP1 |
| WBSCR16 |
| TSC22D4 |
| TRIM56 |
| ABHD11 |
| TMUB1 |
| CCM2 |
| ZMIZ2 |
| CALN1 |
| ARMC10 |
| TMEM120A |
| STARD3NL |
| IMMP2L |
| CTTNBP2 |
| C7orf64 |
| ZNF394 |
| USP42 |
| GTF2IRD2 |
| MYH16 |
| FAM188B |
| SLC37A3 |
| PSMG3 |
| DNAJC30 |
| C7orf50 |
| KRBA1 |
| TNRC18 |
| FAM126A |
| FAM71F1 |
| PLEKHA8 |
| C7orf70 |
| POLR2J4 |
| MGC16142 |
| SLC35B4 |
| TMEM209 |
| TMEM60 |
| SCIN |
| GTPBP10 |
| TRIM4 |
| OR6W1P |
| ZFAND2A |
| COX19 |
| CCDC126 |
| ZNF479 |
| ADCK2 |
| PLXNA4 |
| ZC3HAV1L |
| MYL10 |
| LOC93432 |
| ST7OT1 |
| ST7OT2 |
| ST7OT3 |
| CADPS2 |
| CPA5 |
| FOXP2 |
| H2AFV |
| TSGA14 |
| GLCCI1 |
| C7orf29 |
| DTX2 |
| WBSCR22 |
| KIAA1908 |
| TSGA13 |
| GPR146 |
| C7orf30 |
| AGAP3 |
| C7orf13 |
| OR9A4 |
| WBSCR28 |
| TRIM50 |
| OR9A2 |
| C7orf34 |
| TMEM139 |
| NOBOX |
| OR2A14 |
| OR6B1 |
| OR2F2 |
| ZNF786 |
| EMID2 |
| PRSS37 |
| KLF14 |
| C7orf45 |
| C7orf57 |
| SVOPL |
| MTPN |
| LRGUK |
| ASB10 |
| TRYX3 |
| MOXD2 |
| C7orf11 |
| SRCRB4D |
| C7orf31 |
| ASZ1 |
| MUC17 |
| RNF32 |
| ASB15 |
| RUNDC3B |
| ABCA13 |
| C7orf60 |
| TRY6 |
| LOC154761 |
| CLEC2L |
| C7orf55 |
| VKORC1L1 |
| LOC154822 |
| IQUB |
| KCTD7 |
| C7orf66 |
| TMEM213 |
| GIMAP8 |
| CRYGN |
| ZNF425 |
| ZNF783 |
| ZNF746 |
| ATP6V0E2 |
| AMZ1 |
| WBSCR27 |
| SBDSP |
| VPS37D |
| NSUN5B |
| RBM33 |
| AGR3 |
| ZNF92 |
| GALNTL5 |
| ZNF679 |
| RNF133 |
| CDC14C |
| THAP5 |
| FLJ36031 |
| LOC168474 |
| PKD1L1 |
| GIMAP7 |
| ZNF467 |
| BHLHA15 |
| BMPER |
| PER4 |
| ZNF800 |
| GIMAP1 |
| WBSCR26 |
| LOC202781 |
| C7orf33 |
| TMEM184A |
| SAMD9L |
| MGC26647 |
| ZNF804B |
| FABP5L3 |
| ZNF498 |
| C7orf38 |
| VWDE |
| PRPS1L1 |
| TWISTNB |
| SP8 |
| HOXA11AS |
| C7orf47 |
| GPC2 |
| C7orf27 |
| SDK1 |
| FOXK1 |
| MMD2 |
| DAGLB |
| C7orf28B |
| THSD7A |
| VSTM2A |
| DKFZp434L192 |
| TMED4 |
| DKFZP586I1420 |
| C7orf41 |
| PRR15 |
| SRRM3 |
| RSBN1L |
| KIAA1324L |
| LRWD1 |
| FAM185A |
| FBXL13 |
| NAPEPLD |
| ATXN7L1 |
| FLJ23834 |
| TMEM130 |
| FERD3L |
| RPL23P8 |
| C7orf51 |
| SLC29A4 |
| RSPH10B |
| CCDC129 |
| ZNRF2 |
| SEMA3D |
| CNPY4 |
| POLR2J2 |
| HEPACAM2 |
| UBN2 |
| FLJ35390 |
| MBLAC1 |
| TMEM196 |
| MGC87042 |
| RPS2P32 |
| SUNC1 |
| FAM133B |
| TAS2R39 |
| TAS2R40 |
| TAS2R41 |
| NSUN5C |
| TFAMP1 |
| STEAP2 |
| POM121L12 |
| CNPY1 |
| INTS4L1 |
| NCRNA00174 |
| C7orf71 |
| LOC285954 |
| SPDYE1 |
| C7orf40 |
| FLJ40852 |
| FAM115C |
| ZNF775 |
| ATG9B |
| DLX6AS |
| ZNF789 |
| LOC286002 |
| C7orf53 |
| LOC286016 |
| MESTIT1 |
| ST7OT4 |
| TAS2R60 |
| ZNF680 |
| UNCX |
| COL28A1 |
| ABCB5 |
| C7orf46 |
| FAM183B |
| CTAGE6 |
| TSPAN33 |
| AGBL3 |
| SEPT14 |
| MACC1 |
| OR6V1 |
| OR2A12 |
| OR2A1 |
| GNAT3 |
| MOGAT3 |
| FAM71F2 |
| STRA8 |
| KLRG2 |
| ZNF713 |
| LOC349114 |
| WDR86 |
| GJC3 |
| DPY19L2P2 |
| GATS |
| GPR141 |
| FKBP9L |
| GSTK1 |
| VWC2 |
| TRIM73 |
| C7orf52 |
| SLC26A5 |
| LHFPL3 |
| KCP |
| TRIM74 |
| FLJ43663 |
| RNF148 |
| NPSR1 |
| LOC389458 |
| LOC389493 |
| SPDYE8P |
| GATSL1 |
| GTF2IRD2B |
| MGC72080 |
| C7orf59 |
| FEZF1 |
| FAM180A |
| OR2A25 |
| ELFN1 |
| TMEM195 |
| GRID2IP |
| OR2A5 |
| RPL13AP17 |
| ZNF815 |
| RASA4P |
| C7orf65 |
| GTF2IRD2P |
| LOC401387 |
| LOC401397 |
| PRRT4 |
| RAB19 |
| OR2A7 |
| OR2A20P |
| LOC401431 |
| OR2A42 |
| FLJ45340 |
| KPNA7 |
| C7orf61 |
| LOC402644 |
| UFSP1 |
| AAA1 |
| MIR106B |
| MIR129-1 |
| MIR148A |
| MIR153-2 |
| MIR182 |
| MIR183 |
| MIR25 |
| MIR29A |
| MIR29B1 |
| MIR93 |
| MIR96 |
| LOC407835 |
| RNF216L |
| PMS2CL |
| LOC441204 |
| LOC441208 |
| RP9P |
| ZNF716 |
| TYW1B |
| SPDYE7P |
| PMS2L11 |
| SPDYE3 |
| SPDYE2 |
| AKR1B15 |
| LOC441294 |
| OR2A9P |
| LOC442308 |
| ZNF727 |
| OR2A2 |
| DPY19L2P4 |
| STAG3L3 |
| STAG3L2 |
| SPDYE5 |
| EIF3IP1 |
| LMOD2 |
| MIR335 |
| MIR339 |
| MIR196B |
| ARHGEF5L |
| TARP |
| GIMAP6 |
| LOC493754 |
| WEE2 |
| LOC541473 |
| POLR2J3 |
| DPY19L2P1 |
| MIR489 |
| MIR490 |
| FDPSL2A |
| SEPT13 |
| CCT6P1 |
| ZNF862 |
| LOC643955 |
| WIPF3 |
| INTS4L2 |
| LOC646762 |
| LOC646999 |
| PL-5283 |
| LOC649395 |
| LOC650226 |
| NCF1 |
| ACTR3C |
| OCM |
| SNORA5A |
| NCF1B |
| NCF1C |
| SNORA5B |
| SNORA5C |
| SNORA9 |
| SNORA14A |
| SNORA15 |
| SNORA22 |
| SNORD93 |
| MIR550-1 |
| MIR550-2 |
| MIR589 |
| MIR590 |
| MIR591 |
| MIR592 |
| MIR593 |
| MIR595 |
| LOC723809 |
| MIR653 |
| RSPH10B2 |
| LOC728743 |
| LOC729156 |
| GATSL2 |
| SPDYE6 |
| ISPD |
| TMEM229A |
| ZNF735 |
| LUZP6 |
| MIR671 |
| LOC100093631 |
| POM121C |
| LOC100124692 |
| LOC100128542 |
| CTAGE4 |
| LOC100128822 |
| RPL19P12 |
| EFCAB10 |
| C7orf72 |
| LOC100132707 |
| LOC100132832 |
| LOC100133091 |
| LOC100134229 |
| LOC100134713 |
| UPLP |
| LOC100216545 |
| LOC100287704 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 9q34.13.
Table S44. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| ABL1 |
| FANCC |
| FANCG |
| GNAQ |
| JAK2 |
| MLLT3 |
| NFIB |
| NOTCH1 |
| OMD |
| PAX5 |
| RALGDS |
| SET |
| SYK |
| TAL2 |
| TSC1 |
| XPA |
| NR4A3 |
| BRD3 |
| NUP214 |
| FNBP1 |
| CD274 |
| hsa-mir-602 |
| hsa-mir-126 |
| hsa-mir-219-2 |
| hsa-mir-199b |
| hsa-mir-181b-2 |
| hsa-mir-601 |
| hsa-mir-600 |
| hsa-mir-147 |
| hsa-mir-455 |
| hsa-mir-32 |
| hsa-mir-1302-8 |
| hsa-mir-24-1 |
| hsa-let-7d |
| hsa-mir-7-1 |
| hsa-mir-204 |
| hsa-mir-1299 |
| hsa-mir-873 |
| hsa-mir-31 |
| hsa-mir-491 |
| hsa-mir-101-2 |
| hsa-mir-1302-2 |
| ABCA1 |
| ABCA2 |
| ABO |
| ACO1 |
| PLIN2 |
| AK1 |
| ALAD |
| ALDH1A1 |
| ALDH1B1 |
| ALDOB |
| AMBP |
| ANXA1 |
| ANXA2P2 |
| NUDT2 |
| APBA1 |
| AQP3 |
| AQP7 |
| ASS1 |
| AUH |
| BAAT |
| BAG1 |
| KLF9 |
| C5 |
| C8G |
| CA9 |
| CACNA1B |
| CCIN |
| CCBL1 |
| TNFSF8 |
| ENTPD2 |
| CD72 |
| CDK9 |
| CDKN2A |
| CDKN2B |
| CEL |
| CELP |
| CKS2 |
| CLTA |
| CNTFR |
| COL5A1 |
| COL15A1 |
| SLC31A1 |
| SLC31A2 |
| CRAT |
| CTSL1 |
| CTSL2 |
| CYLC2 |
| DAPK1 |
| DBC1 |
| DBH |
| SARDH |
| DNM1 |
| DMRT1 |
| ECM2 |
| TOR1A |
| LPAR1 |
| S1PR3 |
| MEGF9 |
| ELAVL2 |
| ENDOG |
| ENG |
| STOM |
| FBP1 |
| FKTN |
| FCN1 |
| FCN2 |
| FOXD4 |
| FOXE1 |
| MLANA |
| FPGS |
| FXN |
| NR5A1 |
| FUT7 |
| GALT |
| GAS1 |
| NR6A1 |
| GCNT1 |
| GGTA1 |
| B4GALT1 |
| GLDC |
| GLE1 |
| GNG10 |
| GOLGA1 |
| GOLGA2 |
| GPR21 |
| RAPGEF1 |
| GRIN1 |
| GSN |
| HNRNPK |
| HSD17B3 |
| DNAJA1 |
| HSPA5 |
| TNC |
| IARS |
| IFNA1 |
| IFNA2 |
| IFNA4 |
| IFNA5 |
| IFNA6 |
| IFNA7 |
| IFNA8 |
| IFNA10 |
| IFNA13 |
| IFNA14 |
| IFNA16 |
| IFNA17 |
| IFNA21 |
| IFNB1 |
| IFNW1 |
| IL11RA |
| INSL4 |
| LCN1 |
| LCN2 |
| LMX1B |
| MTAP |
| MUSK |
| NCBP1 |
| NDUFA8 |
| NDUFB6 |
| NFIL3 |
| NFX1 |
| NINJ1 |
| NPR2 |
| NTRK2 |
| ROR2 |
| ODF2 |
| OGN |
| ORM1 |
| ORM2 |
| PAEP |
| PAPPA |
| PDCL |
| PBX3 |
| PCSK5 |
| PGM5 |
| PHF2 |
| PPP2R4 |
| PPP3R2 |
| PPP6C |
| PRKACG |
| PRSS3 |
| PSMB7 |
| PSMD5 |
| PTCH1 |
| PTGDS |
| PTGS1 |
| PTPN3 |
| PTPRD |
| RAD23B |
| RFX3 |
| RGS3 |
| RLN1 |
| RLN2 |
| RMRP |
| RORB |
| RPL7A |
| RPL12 |
| RPS6 |
| RXRA |
| CCL19 |
| CCL21 |
| SH3GL2 |
| SHB |
| SLC1A1 |
| SMARCA2 |
| SNAPC3 |
| SNAPC4 |
| SPTAN1 |
| STXBP1 |
| SURF1 |
| SURF2 |
| SURF4 |
| MED22 |
| SURF6 |
| TEK |
| TESK1 |
| TGFBR1 |
| TLE1 |
| TLE4 |
| TLN1 |
| TLR4 |
| TMOD1 |
| TPM2 |
| TRAF1 |
| TRAF2 |
| TTF1 |
| TXN |
| TYRP1 |
| UGCG |
| VAV2 |
| VCP |
| VLDLR |
| CORO2A |
| ZFP37 |
| ZNF79 |
| ZNF189 |
| ZFAND5 |
| LHX3 |
| GFI1B |
| PIP5K1B |
| RECK |
| IKBKAP |
| CDC14B |
| TMEFF1 |
| SSNA1 |
| EDF1 |
| CTNNAL1 |
| MPDZ |
| FBP2 |
| DPM2 |
| FUBP3 |
| CLIC3 |
| PRPF4 |
| KLF4 |
| GTF3C5 |
| GTF3C4 |
| CER1 |
| LHX2 |
| PLAA |
| GRHPR |
| FAM189A2 |
| TJP2 |
| MED27 |
| PTGES |
| ATP6V1G1 |
| GABBR2 |
| GDA |
| GNA14 |
| RALGPS1 |
| ADAMTSL2 |
| RGP1 |
| TRIM14 |
| MELK |
| RUSC2 |
| KIAA0649 |
| SEC16A |
| ZBTB5 |
| KIAA0020 |
| TNFSF15 |
| ROD1 |
| GNE |
| SH2D3C |
| RCL1 |
| TOPORS |
| RABEPK |
| SIGMAR1 |
| LAMC3 |
| TUBB2C |
| UBAC1 |
| OLFM1 |
| ZER1 |
| CREB3 |
| UNC13B |
| SEMA4D |
| ANP32B |
| AGPAT2 |
| SPTLC1 |
| POMT1 |
| SMC2 |
| DMRT2 |
| RRAGA |
| ZBTB6 |
| NEK6 |
| SDCCAG3 |
| NOXA1 |
| CCL27 |
| USP20 |
| ACTL7B |
| ACTL7A |
| GADD45G |
| SPIN1 |
| SEC61B |
| SLC27A4 |
| SLC35D2 |
| CEP110 |
| WDR5 |
| C9orf9 |
| ADAMTS13 |
| C9orf7 |
| PSIP1 |
| INSL6 |
| SLC2A6 |
| PTENP1 |
| AKAP2 |
| RPL35 |
| MAN1B1 |
| DCTN3 |
| FRMPD1 |
| DOLK |
| ZNF510 |
| HABP4 |
| PTGR1 |
| TRIM32 |
| SETX |
| ERP44 |
| KDM4C |
| ZBTB43 |
| SMC5 |
| KANK1 |
| FAM120A |
| PMPCA |
| VPS13A |
| ASTN2 |
| AGTPBP1 |
| BICD2 |
| FKBP15 |
| KIAA1045 |
| KIAA0368 |
| EXOSC2 |
| FREQ |
| TDRD7 |
| SLC44A1 |
| ANGPTL2 |
| NUP188 |
| CCRK |
| DDX58 |
| RABGAP1 |
| TMEM2 |
| C9orf5 |
| C9orf4 |
| SLC24A2 |
| CIZ1 |
| DNAJB5 |
| DCAF12 |
| DFNB31 |
| COBRA1 |
| NIPSNAP3A |
| NELF |
| GPSM1 |
| LOC26102 |
| GAPVD1 |
| PHF19 |
| ZNF658 |
| FAM75A7 |
| FBXW2 |
| SPAG8 |
| OR1J4 |
| OR2K2 |
| FBXO10 |
| GBGT1 |
| LHX6 |
| OSTF1 |
| OR1L3 |
| OR1L1 |
| OR1J2 |
| SNORA65 |
| SNORD62A |
| SNORD36C |
| SNORD36B |
| SNORD36A |
| SNORD24 |
| RANBP6 |
| TRUB2 |
| DNAI1 |
| ST6GALNAC4 |
| INVS |
| NDOR1 |
| SIT1 |
| SPINK4 |
| TOR1B |
| TOR2A |
| METTL11A |
| PHPT1 |
| ANAPC2 |
| PKN3 |
| DPP7 |
| PSAT1 |
| UBQLN1 |
| SLC2A8 |
| OBP2B |
| OBP2A |
| ST6GALNAC6 |
| STOML2 |
| DEC1 |
| PCA3 |
| AK3 |
| EXOSC3 |
| FAM108B1 |
| MRPS2 |
| COQ4 |
| CERCAM |
| EGFL7 |
| C9orf53 |
| UBAP1 |
| GOLM1 |
| PRRX2 |
| C9orf114 |
| CHMP5 |
| C9orf156 |
| RAB14 |
| TMEM8B |
| C9orf78 |
| SHC3 |
| POLE3 |
| NANS |
| FBXW5 |
| MRPL50 |
| RC3H2 |
| EPB41L4B |
| C9orf11 |
| TBC1D13 |
| FAM22F |
| DIRAS2 |
| BNC2 |
| HAUS6 |
| ASPN |
| BSPRY |
| APTX |
| C9orf167 |
| CNTLN |
| TEX10 |
| LPPR1 |
| KIAA1797 |
| UBE2R2 |
| EXD3 |
| C9orf6 |
| C9orf95 |
| STX17 |
| NOL8 |
| C9orf68 |
| C9orf40 |
| TMEM38B |
| SMU1 |
| RFK |
| NIPSNAP3B |
| STRBP |
| TBC1D2 |
| HEMGN |
| KIF27 |
| CDC37L1 |
| DENND4C |
| C9orf86 |
| CDK5RAP2 |
| UBAP2 |
| C9orf46 |
| CBWD1 |
| KLHL9 |
| BARX1 |
| RNF20 |
| LRRC8A |
| INPP5E |
| NPDC1 |
| OR2S2 |
| BARHL1 |
| IFNK |
| SH3GLB2 |
| REXO4 |
| DOLPP1 |
| KIAA1161 |
| KCNT1 |
| KIAA1432 |
| KIAA1529 |
| ZBTB26 |
| GBA2 |
| DENND1A |
| GPR107 |
| SLC46A2 |
| C9orf27 |
| C9orf80 |
| ZNF462 |
| DMRT3 |
| PRDM12 |
| MAK10 |
| DMRTA1 |
| SLC28A3 |
| CARD9 |
| SUSD1 |
| POLR1E |
| IPPK |
| DDX31 |
| FAM129B |
| LRRC19 |
| MRPL41 |
| NOL6 |
| WNK2 |
| SECISBP2 |
| C9orf16 |
| MAPKAP1 |
| DCAF10 |
| ZCCHC6 |
| GALNT12 |
| EHMT1 |
| MOBKL2B |
| C9orf82 |
| CNTNAP3 |
| ERMP1 |
| SVEP1 |
| RMI1 |
| TRPM3 |
| PTGES2 |
| IFT74 |
| KIAA1539 |
| GKAP1 |
| PDCD1LG2 |
| AKNA |
| C9orf45 |
| URM1 |
| ISCA1 |
| DOCK8 |
| ARPC5L |
| HDHD3 |
| AIF1L |
| UCK1 |
| ZNF484 |
| FSD1L |
| CEP78 |
| ZCCHC7 |
| ANKRD20A1 |
| GARNL3 |
| HSDL2 |
| C9orf64 |
| C9orf89 |
| HIATL2 |
| C9orf125 |
| NTNG2 |
| HIATL1 |
| HINT2 |
| C9orf24 |
| PIGO |
| BAT2L |
| PPAPDC3 |
| C9orf70 |
| ZDHHC12 |
| FAM73B |
| C9orf100 |
| C9orf3 |
| FIBCD1 |
| KIAA1984 |
| SNHG7 |
| TMEM141 |
| C9orf37 |
| COL27A1 |
| ALG2 |
| FGD3 |
| FAM125B |
| TPD52L3 |
| WDR34 |
| C9orf140 |
| C9orf69 |
| LRSAM1 |
| IL33 |
| C9orf123 |
| C9orf30 |
| UAP1L1 |
| MCART1 |
| MRRF |
| RBM18 |
| ARRDC1 |
| WDR85 |
| ADAMTSL1 |
| LOC92973 |
| TMEM203 |
| KIF12 |
| PALM2 |
| SLC25A25 |
| WDR31 |
| ZNF618 |
| UHRF2 |
| FAM122A |
| ZMYND19 |
| GRIN3A |
| TMC1 |
| RNF183 |
| NACC2 |
| C9orf116 |
| C9orf41 |
| C9orf57 |
| C9orf85 |
| C9orf135 |
| LCN8 |
| FAM69B |
| PTRH1 |
| PIP5KL1 |
| TAF1L |
| PTPDC1 |
| ANKRD19 |
| ARID3C |
| C9orf23 |
| C9orf131 |
| OR13C5 |
| OR13C8 |
| OR13C3 |
| OR13C4 |
| OR13F1 |
| OR1L8 |
| OR1N2 |
| OR1N1 |
| ASB6 |
| TRPM6 |
| SLC34A3 |
| RNF38 |
| GLIPR2 |
| DAB2IP |
| CAMSAP1 |
| C9orf66 |
| NCRNA00032 |
| LINGO2 |
| NXNL2 |
| C9orf163 |
| MAMDC4 |
| LCN6 |
| C9orf98 |
| OR1Q1 |
| TTLL11 |
| RASEF |
| TTC39B |
| C9orf122 |
| RG9MTD3 |
| TTC16 |
| FAM120AOS |
| FAM154A |
| C9orf44 |
| FREM1 |
| KIAA2026 |
| LOC158376 |
| LOC158381 |
| ZNF483 |
| C9orf84 |
| KIAA1958 |
| TSTD2 |
| ZNF782 |
| PRUNE2 |
| C9orf96 |
| KCNV2 |
| OLFML2A |
| C9orf71 |
| QSOX2 |
| GLIS3 |
| LOC169834 |
| ZNF169 |
| C9orf21 |
| ZNF367 |
| C9orf91 |
| C9orf72 |
| C9orf93 |
| NAIF1 |
| C9orf25 |
| CCDC107 |
| ANKS6 |
| SUSD3 |
| CBWD5 |
| CDC26 |
| LOC253039 |
| PHYHD1 |
| MORN5 |
| OR1L4 |
| TXNDC8 |
| MAMDC2 |
| FRMD3 |
| C9orf43 |
| C9orf144B |
| NCRNA00094 |
| CRB2 |
| SCAI |
| C9orf117 |
| C9orf47 |
| C9orf79 |
| LOC286238 |
| LCN12 |
| C9orf142 |
| C9orf75 |
| TUSC1 |
| C9orf109 |
| FAM78A |
| C9orf150 |
| LOC286359 |
| OR13C9 |
| OR13D1 |
| LOC286367 |
| FOXD4L3 |
| IFNE |
| ZDHHC21 |
| ACER2 |
| LOC340508 |
| GPR144 |
| FLJ43950 |
| QRFP |
| OR1J1 |
| OR1B1 |
| KIF24 |
| IGFBPL1 |
| MURC |
| FOXD4L4 |
| GLT6D1 |
| ENHO |
| AQP7P1 |
| PTAR1 |
| C9orf102 |
| C9orf119 |
| C9orf50 |
| PNPLA7 |
| C9orf169 |
| ENTPD8 |
| ZNF322B |
| KGFLP1 |
| LOC389705 |
| C9orf144 |
| FAM75A6 |
| MGC21881 |
| AQP7P2 |
| FLJ43859 |
| FLJ44082 |
| FLJ46321 |
| LOC389765 |
| C9orf153 |
| LOC389791 |
| IER5L |
| C9orf171 |
| LCN15 |
| C9orf172 |
| LRRC26 |
| TMEM8C |
| C9orf128 |
| OR13J1 |
| CTSL3 |
| OR13C2 |
| OR1L6 |
| OR5C1 |
| OR1K1 |
| LCN9 |
| FAM102A |
| FLJ35024 |
| PTPLAD2 |
| TMEM215 |
| TOMM5 |
| FAM74A1 |
| FAM74A4 |
| ZNF658B |
| C9orf170 |
| CENPP |
| C9orf152 |
| SNX30 |
| WDR38 |
| LCNL1 |
| C9orf139 |
| FAM166A |
| LOC402377 |
| SOHLH1 |
| PPAPDC2 |
| ZBTB34 |
| MIRLET7A1 |
| MIRLET7D |
| MIRLET7F1 |
| MIR101-2 |
| MIR126 |
| MIR147 |
| MIR181A2 |
| MIR181B2 |
| MIR199B |
| MIR204 |
| MIR219-2 |
| MIR23B |
| MIR24-1 |
| MIR27B |
| MIR31 |
| MIR32 |
| MIR7-1 |
| C9orf106 |
| C9orf103 |
| LCN10 |
| LOC415056 |
| LOC440173 |
| LOC440839 |
| LOC440896 |
| SUGT1P |
| ANKRD20A3 |
| ANKRD20A2 |
| AQP7P3 |
| FAM75C1 |
| LOC441454 |
| LOC441455 |
| FAM22G |
| C9orf173 |
| NRARP |
| LOC442421 |
| FOXB2 |
| CBWD3 |
| C9orf129 |
| PALM2-AKAP2 |
| FAM27A |
| DNAJC25 |
| DNAJC25-GNG10 |
| LOC554202 |
| LOC572558 |
| MIR491 |
| PGM5P2 |
| MIR455 |
| FAM138F |
| FAM75A2 |
| LOC642313 |
| LOC642929 |
| FAM163B |
| FLJ40292 |
| TUBBP5 |
| CBWD6 |
| FAM138A |
| LOC645961 |
| HRCT1 |
| FAM75A1 |
| RPSAP9 |
| FOXD4L6 |
| FOXD4L5 |
| LOC653501 |
| KGFLP2 |
| FAM138C |
| SCARNA8 |
| SNORA17 |
| SNORA43 |
| SNORD62B |
| MSMP |
| SNORD90 |
| MIR548D1 |
| MIR600 |
| MIR601 |
| MIR602 |
| RNF208 |
| FAM75A3 |
| FAM75A5 |
| DNLZ |
| FAM74A3 |
| ANKRD20A4 |
| CCDC29 |
| FAM166B |
| FOXD4L2 |
| CDKN2BAS |
| SNORD121A |
| SNORD121B |
| SNORA84 |
| SNORA70C |
| MIR876 |
| MIR873 |
| LOC100128076 |
| C9orf110 |
| C9orf130 |
| LOC100129034 |
| LOC100129066 |
| LOC100130426 |
| LOC100131193 |
| FAM157B |
| FAM27C |
| FAM95B1 |
| FAM27B |
| LOC100133920 |
| RNU6ATAC |
| NCRNA00092 |
| LOC100272217 |
| WASH1 |
| LOC100289341 |
Genes in Wide Peak
This is the comprehensive list of deleted genes in the wide peak for 4q24.
Table S45. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].
| Genes |
|---|
| FGFR3 |
| IL2 |
| KDR |
| KIT |
| PDGFRA |
| RAP1GDS1 |
| WHSC1 |
| PHOX2B |
| DUX4 |
| CHIC2 |
| TET2 |
| FBXW7 |
| FIP1L1 |
| hsa-mir-1305 |
| hsa-mir-1979 |
| hsa-mir-548g |
| hsa-mir-2054 |
| hsa-mir-1973 |
| hsa-mir-577 |
| hsa-mir-1243 |
| hsa-mir-302b |
| hsa-mir-297 |
| hsa-mir-576 |
| hsa-mir-1255a |
| hsa-mir-575 |
| hsa-mir-1269 |
| hsa-mir-574 |
| hsa-mir-1255b-1 |
| hsa-mir-573 |
| hsa-mir-218-1 |
| hsa-mir-572 |
| hsa-mir-548i-2 |
| hsa-mir-95 |
| hsa-mir-943 |
| hsa-mir-571 |
| ADD1 |
| ADH1A |
| ADH1B |
| ADH1C |
| ADH4 |
| ADH5 |
| ADH6 |
| ADH7 |
| ADRA2C |
| AFM |
| AFP |
| AGA |
| ALB |
| AMBN |
| ANK2 |
| SLC25A4 |
| ANXA2P1 |
| ANXA3 |
| ANXA5 |
| APBB2 |
| AREG |
| RHOH |
| ART3 |
| ATOH1 |
| ATP5I |
| NKX3-2 |
| BMP3 |
| BMPR1B |
| BST1 |
| BTC |
| CAMK2D |
| CASP3 |
| CASP6 |
| CCKAR |
| CCNA2 |
| CCNG2 |
| SCARB2 |
| CD38 |
| LRBA |
| CDS1 |
| CLGN |
| CENPC1 |
| CENPE |
| CLCN3 |
| CNGA1 |
| CPE |
| CRMP1 |
| CSN1S1 |
| CSN2 |
| CSN3 |
| CTBP1 |
| CTSO |
| DGKQ |
| DCK |
| DCTD |
| DHX15 |
| DMP1 |
| DRD5 |
| DSPP |
| EDNRA |
| EGF |
| EIF4E |
| ELF2 |
| ENPEP |
| EPHA5 |
| EREG |
| ETFDH |
| EVC |
| F11 |
| FABP2 |
| ACSL1 |
| FAT1 |
| FGA |
| FGB |
| FGF2 |
| FGF5 |
| FGG |
| FRG1 |
| GAB1 |
| GABRA2 |
| GABRA4 |
| GABRB1 |
| GABRG1 |
| GAK |
| GC |
| GK2 |
| GK3P |
| GLRB |
| GNRHR |
| GPM6A |
| GRK4 |
| GRIA2 |
| GRID2 |
| CXCL1 |
| CXCL2 |
| CXCL3 |
| GRSF1 |
| GUCY1A3 |
| GUCY1B3 |
| GYPA |
| GYPB |
| GYPE |
| H2AFZ |
| HADH |
| HTT |
| HGFAC |
| UBE2K |
| HMGB2 |
| HNRNPD |
| HPGD |
| HTN1 |
| HTN3 |
| IBSP |
| IDUA |
| CFI |
| IGFBP7 |
| IGJ |
| RBPJ |
| IL8 |
| IL15 |
| ING2 |
| CXCL10 |
| IRF2 |
| KLKB1 |
| LETM1 |
| LRPAP1 |
| MAD2L1 |
| SMAD1 |
| MANBA |
| MGST2 |
| CXCL9 |
| AFF1 |
| NR3C2 |
| MSX1 |
| MTNR1A |
| MTTP |
| MUC7 |
| MYL5 |
| NDUFC1 |
| NEK1 |
| NFKB1 |
| NKX6-1 |
| NPY1R |
| NPY2R |
| NPY5R |
| PCDH7 |
| PDE6B |
| PDHA2 |
| PET112L |
| PF4 |
| PF4V1 |
| PITX2 |
| PKD2 |
| PLRG1 |
| EXOSC9 |
| POLR2B |
| POU4F2 |
| PPEF2 |
| PPAT |
| PPBP |
| PPID |
| PPP2R2C |
| PPP3CA |
| PRKG2 |
| MAPK10 |
| PTPN13 |
| QDPR |
| REST |
| RFC1 |
| RGS12 |
| RNF4 |
| ABCE1 |
| RPL9 |
| RPL34 |
| RPS3A |
| S100P |
| SC4MOL |
| CXCL6 |
| CXCL11 |
| CXCL5 |
| SFRP2 |
| SGCB |
| SH3BP2 |
| SNCA |
| SOD3 |
| SPINK2 |
| SPP1 |
| SRP72 |
| STATH |
| SULT1E1 |
| TACR3 |
| TDO2 |
| TEC |
| TLL1 |
| TLR1 |
| TLR2 |
| TLR3 |
| TMSL3 |
| TRPC3 |
| TXK |
| UBE2D3 |
| UCHL1 |
| UCP1 |
| UGDH |
| UGT2B4 |
| UGT2B7 |
| UGT2B10 |
| UGT2B15 |
| UGT2B17 |
| UGT8 |
| VEGFC |
| WFS1 |
| WHSC2 |
| ZNF141 |
| SLBP |
| GLRA3 |
| ACOX3 |
| SPARCL1 |
| SMARCA5 |
| SORBS2 |
| PRSS12 |
| CPZ |
| NOP14 |
| FAM193A |
| USO1 |
| UNC5C |
| MAPKSP1 |
| PDE5A |
| SLC4A4 |
| SAP30 |
| INPP4B |
| PROM1 |
| HERC3 |
| SNORD73A |
| STBD1 |
| CDKL2 |
| PAPSS1 |
| LDB2 |
| LRAT |
| AIMP1 |
| NDST3 |
| SLIT2 |
| RAB28 |
| TMPRSS11D |
| ABCG2 |
| HAND2 |
| ADAMTS3 |
| CLOCK |
| CEP135 |
| RAPGEF2 |
| KIAA0232 |
| MFAP3L |
| SEC24D |
| G3BP2 |
| WDR1 |
| HS3ST1 |
| FGFBP1 |
| HNRPDL |
| TSPAN5 |
| ENAM |
| C4orf6 |
| FAM13A |
| MFSD10 |
| SPRY1 |
| MAEA |
| TLR6 |
| PCGF3 |
| ANAPC10 |
| ATP8A1 |
| SPON2 |
| PGRMC2 |
| SEC24B |
| TACC3 |
| SLC30A9 |
| CXCL13 |
| SLC34A2 |
| MAB21L2 |
| PAICS |
| MXD4 |
| PDLIM5 |
| RRH |
| CORIN |
| UGT2B11 |
| PLK4 |
| PTTG2 |
| CPLX1 |
| HPSE |
| SLC26A1 |
| NMU |
| SMR3B |
| NPFFR2 |
| PPARGC1A |
| PPBPL2 |
| MORF4 |
| UGT2A1 |
| CCNI |
| LIAS |
| ADAM29 |
| PRDM5 |
| LSM6 |
| NUDT6 |
| ANXA10 |
| KLHL2 |
| SCRG1 |
| HSPA4L |
| SEC31A |
| RUFY3 |
| MMRN1 |
| LIMCH1 |
| WDFY3 |
| PALLD |
| DCUN1D4 |
| TBC1D9 |
| METAP1 |
| TBC1D1 |
| SEL1L3 |
| KIAA0922 |
| PDS5A |
| LPHN3 |
| TRIM2 |
| MAN2B2 |
| ANP32C |
| SLC7A11 |
| CCRN4L |
| PARM1 |
| FAM149A |
| RCHY1 |
| ANKRD17 |
| STAP1 |
| FBXL5 |
| FBXO8 |
| SMR3A |
| D4S234E |
| PPA2 |
| DAPP1 |
| DKK2 |
| FAM184B |
| INTU |
| NAAA |
| GPR78 |
| COQ2 |
| ARFIP1 |
| SULT1B1 |
| PDLIM3 |
| HPGDS |
| ZNF330 |
| TMPRSS11E |
| ZCCHC4 |
| ANAPC4 |
| SPOCK3 |
| MRPS18C |
| LAP3 |
| KLHL5 |
| SEPSECS |
| COPS4 |
| AADAT |
| HSD17B11 |
| LEF1 |
| HERC5 |
| KLF3 |
| FAM198B |
| PLAC8 |
| LARP7 |
| EMCN |
| MYOZ2 |
| ACCN5 |
| GALNT7 |
| NUDT9 |
| NUP54 |
| STX18 |
| FGFRL1 |
| CLDN22 |
| CYTL1 |
| GAR1 |
| SH3TC1 |
| UGT2B28 |
| RBM47 |
| PCDH18 |
| USP53 |
| OTUD4 |
| DCHS2 |
| FLJ20184 |
| PIGG |
| DCAF16 |
| OCIAD1 |
| COMMD8 |
| ODAM |
| C4orf27 |
| HERC6 |
| CCDC109B |
| MARCH1 |
| BANK1 |
| LARP1B |
| SDAD1 |
| TMEM33 |
| LGI2 |
| BBS7 |
| UBA6 |
| NEIL3 |
| PGM2 |
| C4orf19 |
| TBC1D19 |
| PI4K2B |
| TMEM144 |
| C4orf43 |
| UFSP2 |
| CNO |
| C4orf21 |
| STK32B |
| AP1AR |
| MAML3 |
| CHRNA9 |
| BMP2K |
| DDX60 |
| CDKN2AIP |
| LYAR |
| ODZ3 |
| N4BP2 |
| TMEM184C |
| SEPT11 |
| EXOC1 |
| LRP2BP |
| TMEM165 |
| PDGFC |
| TUBB4Q |
| SLC2A9 |
| FSTL5 |
| BDH2 |
| SMARCAD1 |
| MEPE |
| STOX2 |
| PRDM8 |
| UTP3 |
| INTS12 |
| ANKRD50 |
| ATP10D |
| KIAA0114 |
| KIAA1211 |
| RNF150 |
| KIAA1239 |
| TBC1D14 |
| SORCS2 |
| CC2D2A |
| KLHL8 |
| PCDH10 |
| KIAA1430 |
| FNIP2 |
| SLAIN2 |
| SHROOM3 |
| STIM2 |
| SH3RF1 |
| KIAA1530 |
| METTL14 |
| WDR19 |
| ZFYVE28 |
| GBA3 |
| ENOPH1 |
| PROL1 |
| OSTC |
| IL21 |
| RXFP1 |
| AFAP1 |
| GUF1 |
| SPCS3 |
| SCOC |
| C4orf41 |
| NEUROG2 |
| SLC39A8 |
| NCAPG |
| HHIP |
| NDST4 |
| AGXT2L1 |
| USP46 |
| MRPL1 |
| RASL11B |
| ELOVL6 |
| TNIP2 |
| HAUS3 |
| C4orf31 |
| FAT4 |
| ARSJ |
| SRD5A3 |
| ARHGAP10 |
| FLJ13197 |
| MLF1IP |
| THAP9 |
| NSUN7 |
| UGT2A3 |
| NBLA00301 |
| GSTCD |
| MAP9 |
| TNIP3 |
| PHF17 |
| ABCA11P |
| SCD5 |
| DNAJB14 |
| TMEM156 |
| WWC2 |
| FRAS1 |
| NARG1 |
| CWH43 |
| C4orf29 |
| ALPK1 |
| GRPEL1 |
| MED28 |
| CXXC4 |
| KCNIP4 |
| KIAA1712 |
| SETD7 |
| PLA2G12A |
| TLR10 |
| SLC25A31 |
| RAB33B |
| ARHGAP24 |
| FGFBP2 |
| SNX25 |
| TTC29 |
| MND1 |
| SLC10A7 |
| TKTL2 |
| C4orf17 |
| QRFPR |
| FAM175A |
| KIAA1109 |
| MFSD7 |
| C4orf14 |
| TMEM175 |
| ABLIM2 |
| HOPX |
| COL25A1 |
| USP38 |
| LNX1 |
| C4orf49 |
| LOC84740 |
| ARD1B |
| AGPAT9 |
| CBR4 |
| PIGY |
| TMEM128 |
| C4orf35 |
| ZNF518B |
| FHDC1 |
| MGC45800 |
| PRMT10 |
| CCDC149 |
| DDX60L |
| YTHDC1 |
| C4orf42 |
| TMEM129 |
| NAF1 |
| MOBKL1A |
| TIFA |
| FAM114A1 |
| RG9MTD2 |
| MRFAP1 |
| LOC93622 |
| TADA2B |
| TBCK |
| HTRA3 |
| HELQ |
| CYP2U1 |
| C1QTNF7 |
| MRFAP1L1 |
| DDIT4L |
| CLNK |
| WDR17 |
| ARAP2 |
| GDEP |
| ANTXR2 |
| OCIAD2 |
| SCLT1 |
| C4orf33 |
| TMEM155 |
| PABPC4L |
| ADAD1 |
| ZFP42 |
| LIN54 |
| SPATA18 |
| C4orf32 |
| TMPRSS11B |
| GNPDA2 |
| SPATA4 |
| CPEB2 |
| EVC2 |
| ARL9 |
| AASDH |
| PDCL2 |
| C4orf36 |
| PACRGL |
| TRAM1L1 |
| OTOP1 |
| ENPP6 |
| NHEDC2 |
| ASB5 |
| NHEDC1 |
| ZNF827 |
| SH3D19 |
| NFXL1 |
| NIPAL1 |
| PAQR3 |
| SHISA3 |
| SCFD2 |
| C4orf38 |
| ZNF595 |
| C4orf39 |
| JAKMIP1 |
| THAP6 |
| C4orf26 |
| KLB |
| FAM53A |
| PPM1K |
| C4orf45 |
| C4orf23 |
| RASGEF1B |
| SPATA5 |
| BBS12 |
| DCLK2 |
| GPR125 |
| TRIM60 |
| MMAA |
| ZNF509 |
| TIGD2 |
| RASSF6 |
| RBM46 |
| SGMS2 |
| COX7B2 |
| GSX2 |
| ZNF721 |
| SYNPO2 |
| C4orf46 |
| SLC10A4 |
| TIGD4 |
| TMEM154 |
| C4orf34 |
| TMEM192 |
| RWDD4A |
| CCDC111 |
| TAPT1 |
| FLJ39653 |
| TRIML2 |
| CNOT6L |
| TECRL |
| LCORL |
| C4orf22 |
| EPGN |
| ZNF718 |
| ELMOD2 |
| NPNT |
| CCDC110 |
| MFSD8 |
| LOC256880 |
| CCDC96 |
| BOD1L |
| C4orf7 |
| NAP1L5 |
| LOC285419 |
| DCAF4L1 |
| CYP4V2 |
| LOC285456 |
| CRIPAK |
| DOK7 |
| RNF212 |
| LOC285501 |
| FAM13AOS |
| GPRIN3 |
| COX18 |
| YIPF7 |
| FRYL |
| RNF175 |
| LOC285548 |
| LOC285550 |
| C4orf37 |
| CSN1S2A |
| C4orf10 |
| CSN1S2B |
| ZAR1 |
| CCDC158 |
| TMPRSS11A |
| TRIML1 |
| LRRC66 |
| NAT8L |
| LOC340017 |
| LOC344967 |
| PRSS48 |
| ANKRD56 |
| LRIT3 |
| C4orf44 |
| SLC10A6 |
| HSD17B13 |
| LOC348926 |
| ANKRD37 |
| POLN |
| PCNAP1 |
| NCRNA00099 |
| KCTD8 |
| C4orf50 |
| C4orf52 |
| BEND4 |
| GRXCR1 |
| TMPRSS11F |
| USP17L6P |
| USP17 |
| HSP90AB2P |
| TRIM61 |
| TRIM75 |
| HELT |
| C4orf48 |
| DTHD1 |
| LOC401127 |
| SYT14L |
| FLJ41562 |
| C4orf40 |
| AMTN |
| FAM190A |
| C4orf3 |
| RPL21P44 |
| FAM92A3 |
| C4orf12 |
| MIR218-1 |
| MIR302A |
| C4orf11 |
| MTHFD2L |
| TMEM150C |
| EEF1AL7 |
| LOC441046 |
| C4orf47 |
| GALNTL6 |
| MIR302B |
| MIR302C |
| MIR302D |
| MIR367 |
| FRG2 |
| CISD2 |
| LOC550112 |
| UGT2A2 |
| LOC641518 |
| ZNF876P |
| SLED1 |
| LOC644145 |
| DEFB131 |
| CLRN2 |
| CEP170L |
| C4orf51 |
| LOC650293 |
| LOC653543 |
| LOC653544 |
| LOC653545 |
| LOC653548 |
| ZNF732 |
| SCARNA22 |
| SNORA24 |
| SNORA26 |
| MIR572 |
| MIR573 |
| MIR574 |
| MIR575 |
| MIR577 |
| MIR578 |
| PPBPL1 |
| LOC728410 |
| LOC729338 |
| FAM160A1 |
| FLJ36777 |
| RELL1 |
| PSAPL1 |
| SNHG8 |
| MIR943 |
| FAM47E |
| LOC100130017 |
| LOC100130872 |
| LOC100192379 |
Arm-level results
Table 3. Get Full Table Arm-level significance table - 21 significant results found.
| Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value |
|---|---|---|---|---|---|---|---|
| 1p | 1731 | 0.17 | 0.209 | 0.991 | 0.24 | 1.58 | 0.172 |
| 1q | 1572 | 0.60 | 8.94 | 0 | 0.05 | -1.39 | 0.994 |
| 2p | 753 | 0.19 | 1.22 | 0.36 | 0.02 | -2.14 | 0.994 |
| 2q | 1235 | 0.14 | -0.0924 | 0.991 | 0.07 | -1.53 | 0.994 |
| 3p | 853 | 0.06 | -1.45 | 0.991 | 0.12 | -0.342 | 0.994 |
| 3q | 917 | 0.10 | -0.778 | 0.991 | 0.06 | -1.52 | 0.994 |
| 4p | 366 | 0.11 | -0.309 | 0.991 | 0.17 | 0.839 | 0.46 |
| 4q | 865 | 0.12 | -0.218 | 0.991 | 0.27 | 2.7 | 0.0225 |
| 5p | 207 | 0.28 | 3.38 | 0.00356 | 0.08 | -0.877 | 0.994 |
| 5q | 1246 | 0.30 | 3.12 | 0.0071 | 0.08 | -1.15 | 0.994 |
| 6p | 937 | 0.25 | 2.41 | 0.0388 | 0.05 | -1.62 | 0.994 |
| 6q | 692 | 0.12 | -0.212 | 0.991 | 0.25 | 2.38 | 0.0374 |
| 7p | 508 | 0.25 | 2.67 | 0.0246 | 0.05 | -1.5 | 0.994 |
| 7q | 1071 | 0.20 | 1.26 | 0.36 | 0.09 | -0.907 | 0.994 |
| 8p | 495 | 0.25 | 1.77 | 0.168 | 0.62 | 9.98 | 0 |
| 8q | 697 | 0.50 | 7.15 | 8.16e-12 | 0.29 | 2.57 | 0.0247 |
| 9p | 343 | 0.05 | -1.45 | 0.991 | 0.25 | 2.78 | 0.0214 |
| 9q | 916 | 0.05 | -1.66 | 0.991 | 0.24 | 2.02 | 0.0775 |
| 10p | 312 | 0.08 | -0.878 | 0.991 | 0.10 | -0.491 | 0.994 |
| 10q | 1050 | 0.02 | -2.14 | 0.991 | 0.23 | 1.87 | 0.101 |
| 11p | 731 | 0.02 | -2.3 | 0.991 | 0.10 | -0.802 | 0.994 |
| 11q | 1279 | 0.02 | -2.35 | 0.991 | 0.15 | 0.17 | 0.887 |
| 12p | 484 | 0.06 | -1.41 | 0.991 | 0.08 | -1.03 | 0.994 |
| 12q | 1162 | 0.06 | -1.76 | 0.991 | 0.02 | -2.49 | 0.994 |
| 13q | 554 | 0.00 | -2.26 | 0.991 | 0.36 | 4.93 | 4.07e-06 |
| 14q | 1144 | 0.03 | -2.09 | 0.991 | 0.27 | 2.61 | 0.0247 |
| 15q | 1132 | 0.09 | -1.08 | 0.991 | 0.14 | 0.00837 | 0.968 |
| 16p | 719 | 0.05 | -1.6 | 0.991 | 0.24 | 2.13 | 0.0648 |
| 16q | 562 | 0.00 | -2.26 | 0.991 | 0.36 | 4.93 | 4.07e-06 |
| 17p | 575 | 0.06 | -0.947 | 0.991 | 0.67 | 11.6 | 0 |
| 17q | 1321 | 0.31 | 3.38 | 0.00356 | 0.05 | -1.59 | 0.994 |
| 18p | 117 | 0.04 | -1.58 | 0.991 | 0.16 | 0.781 | 0.471 |
| 18q | 340 | 0.05 | -1.61 | 0.991 | 0.18 | 1.09 | 0.336 |
| 19p | 870 | 0.14 | 0.12 | 0.991 | 0.09 | -0.986 | 0.994 |
| 19q | 1452 | 0.17 | 0.341 | 0.991 | 0.11 | -0.716 | 0.994 |
| 20p | 295 | 0.20 | 1.54 | 0.242 | 0.05 | -1.56 | 0.994 |
| 20q | 627 | 0.25 | 2.52 | 0.0329 | 0.03 | -2 | 0.994 |
| 21q | 422 | 0.07 | -1.18 | 0.991 | 0.18 | 1.11 | 0.336 |
| 22q | 764 | 0.14 | 0.0316 | 0.991 | 0.19 | 1.14 | 0.336 |
Methods & Data
Input
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/LIHC/1216611/2.GDAC_MergeDataFiles.Finished/LIHC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt
-
Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt
-
Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat
-
CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt
-
Amplification Threshold = 0.30
-
Deletion Threshold = 0.30
-
Cap Values = 2.0
-
Broad Length Cutoff = 0.5
-
Remove X-Chromosome = 1
-
Confidence Level = 0.99
-
Join Segment Size = 10
-
Arm Level Peel Off = 1
-
Maximum Sample Segments = 10000
Table 4. Get Full Table First 10 out of 53 Input Tumor Samples.
| Tumor Sample Names |
|---|
| TCGA-BC-4072-01B-11D-A151-01 |
| TCGA-BC-4073-01B-02D-A12Y-01 |
| TCGA-BC-A10Q-01A-11D-A12Y-01 |
| TCGA-BC-A10R-01A-11D-A12Y-01 |
| TCGA-BC-A10S-01A-22D-A12Y-01 |
| TCGA-BC-A10T-01A-11D-A12Y-01 |
| TCGA-BC-A10U-01A-11D-A12Y-01 |
| TCGA-BC-A10W-01A-11D-A12Y-01 |
| TCGA-BC-A10X-01A-11D-A12Y-01 |
| TCGA-BC-A10Y-01A-11D-A12Y-01 |
Figure 3. Segmented copy number profiles in the input data
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
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
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)
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