Table 1.
Integration targeted genes in hotspots and relationship with tumors
| Hotspots | Integrated times | Fragile sites | ITGs in the hotspot and relationship with tumors | |||
|---|---|---|---|---|---|---|
|
|
|
|||||
| HPV16 | HPV18 | Other types | Y | N | ||
| 14q32 | 43 | - | - | - | CLMN c, GOLGA5 c, CYP46A1, DDX24, DYNC1H1 | RPL3P4 d, AL162151.3 d, HSP90AA1 c, IFI27L1 c, AB019438.66, CTD-2240H23.2, HHIPL1, HOMER2P1, IFI27, IFI27L2, IGHV1-67, IGHV1-68, IGHV1-69, IGHV2-70, IGHV3-38, IGHV3-41, IGHV3-42, IGHV3-43, IGHV3-63, IGHV3-64, IGHV3-65, IGHV3-66, IGHV3-71, IGHV3-72, IGHV4-39, IGHV7-40, IGHVII-40-1, IGHVII-43-1, IGHVII-44-2, IGHVII-62-1, IGHVII-65-1, IGHVII-67-1, IGHVIII-38-1, IGHVIII-44, IGHVIII-67-2, IGHVIII-67-3, IGHVIII-67-4, IGHVIV-44-1, LINC00221, OTUB2, RN7SL472P, RP11-1017G21.4, RP11-543C4.3, RP11-725G5.3, SLC20A1P1 |
| 12q15 | 3 | - | - | - | IFNG-AS1 c,d, IL26 d, DYRK2, IFNG, IL22 | MDM1, RP11-335O4.1, RP11-335O4.3, RP11-444B24.2 |
| 9p23 | 4 | - | - | - | PES1P2, RP11-23D5.1, RP11-284P20.3, RPL3P11 | |
| 2q34 | - | - | 4 | FRA2I | IKZF2 c,d | RP11-105N14.1 d, RP11-105N14.3 d, AC079610.1 c |
| 15q22 | 5 | - | - | FRA15A a | RORA c,d, SMAD3 c, CA12 | FAM81A c, RP11-219B17.1 c, RP11-321G12.1 c, AAGAB, AC007950.1, CTD-2501E16.1, CTD-2501E16.2, NARG2, RP11-342M21.2, RP11-356M20.1, RP11-356M20.2, RPS24P16, Y_RNA |
| 5p14 | 6 | - | - | FRA5E a | - | CDH18 c,d, CTD-2061E9.1, HSPD1P15, MSNP1, RNU6-909P |
| 1q24 | 2 | - | 2 | FRA1G | POU2F1 c, UCK2 | LINC00970 c,d, RPL29P7 d, SUMO1P2 d, RP11-525G13.2, RP11-52A20.2, RP11-7G12.2 |
| 7q33 | 3 | - | - | FRA7H | EXOC4 c,d | AC083875.1, AC083875.2, AC091736.1 |
| 8p21 | 5 | - | - | - | DPYSL2 c, U3 | AC100802.3 c, RP11-108E14.1 c, AC021613.1, RP11-1G11.2, RP11-404E12.1, RPL30P9, SLC18A1 |
| 7p15 | 4 | - | - | - | CREB5 c,d, EVX1, NPY | AC005105.2 d, RPL35P4 c, AC004485.3, EVX1-AS, RP1-170O19.17, snoU13 |
| 7p21 | 6 | - | - | FRA7B | THSD7A c,d, PHF14 c, AC004538.3, AC004543.2, TMEM106B | |
| 6q21 | 4 | - | - | FRA16B b, FRA16C | LAMA4 c, SLC22A16, TUBE1, U3, WISP3 | HS3ST5 c, LRP3-399L15.3 c, CTA-331P3.1, FAM229B, RN7SL617P, RP1-142L7.5, RP1-249H1.2 |
| Xq27 | 4 | - | - | FRAXD, FRAXA a,b | HNRNPCP10, RNU6-382P, RP11-434J24.2, RP11-434J24.3, RP3-406C18.1 | |
| 11p15 | 4 | - | - | FRA11C, FRA11I b | IGF2 c, SBF2 c, SPON1 c, INS, INS-IGF2, MIR483 | RIC3 c, RP11-1H15.2 c, AC132217.4, IGF2-AS, MIR4686, RNA5SP332, RP11-379P15.1, TH, TUB |
| 3q22 | 4 | - | - | - | NCK1 c, PIK3CB c | COL6A4P2 c, IL20RB c, TMCC1 c, AC083799.1, AC130888.1, ENPP7P3, IL20RB-AS1, RNU6-1142P, RP11-85F14.1, RP11-93K22.14, TMCC1-AS1, Y_RNA |
| 1q41 | 4 | - | - | FRA1H | GPATCH2 c, KCNK2, TLR5 | AURKAPS1, MORF4L1P1, RAB3GAP2, RP11-239E10.2, RP11-302I18.1, RP11-323K10.1, XRCC6P3 |
| 20p11 | 4 | - | - | FRA20A a,b | - | DZANK1 c, RALGAPA2 c, RP1-122P22.2 c, AL121761.1, AL121761.2, FAM182B, GCNT1P1, LINC00851, MIR3192, POLR3F, RNA5SP476, RP13-401N8.1, RPL12L3, VN1R108P, ZNF337 |
| 1q42 | 5 | - | - | FRA1H a | ABCB10, B3GALNT2, EGLN1, EXOC8, SPRTN | NVL c, TBCE c, BTNL10, CNIH4, GNPAT, HIST3H2A, HIST3H2BA, HIST3H2BB, HMGN2P19, MIR4666A, RNA5SP78, RNA5SP80, RNF187, RNU4-21P, RNU6-1008P, RP11-293G6__A.2, RP11-293G6__A.3, RP11-365O16.5, snoU13, TAF5L, URB2 |
| 9q33 | 5 | - | - | FRA9B b, FRA9E | CRB2, STOM | ASTN2 c, BRINP1 c, RP11-162D16.2 c, GGTA1P, RN7SKP125, RP11-787B4.2, STRBP |
| Xq25 | 2 | - | 1 | - | U3 | - |
| 8q13 | 3 | - | - | - | ARFGEF1 c, MTFR1 c, PDE7A | CPA6, RP11-707M3.3, RP11-7F18.2 |
| 9p21 | 5 | - | - | FRA9A a,b, FRA9C a | FOCAD c, MLLT3 c | LINGO2 c, MIR4474, RP11-321L2.2, RP11-32I2.1, RP11-73E6.2, SNORA30 |
| 4q22 | 4 | - | - | - | PPM1K | CCSER1 c, RP11-10L7.1 c, HERC6, Y_RNA |
| 2p12 | 3 | - | - | FRA2E | - | LRRTM4 c, AC073628.1, RNU6-812P, RNU6-827P |
| 7q31 | 7 | - | - | FRA7F, FRA7G a | FOXP2 c, MDFIC c, MET | RP11-328J2.1 c, SLC13A1 c, AC006159.3, AC006926.1, RP11-500M10.1, RP11-95P9.1 |
| 18q22 | 4 | - | - | FRA18B, FRA18C | TSHZ1 | CDH19 c, RP11-638L3.1, RP11-659F24.1, ZADH2 |
| 6p22 | 3 | - | 2 | FRA6A b, FRA6C a | ZNF322, RNF144B c, TPMT c, KDM1B | RP11-457M11.2 d, VN1R14P d, ABT1, NHLRC1, RP11-457M11.5, RP11-457M11.6, snoU13 |
| 9q31 | 4 | - | - | FRA9B b, FRA9E | - | RNA5SP293, RP11-380I20.2, RP11-436F21.1, RPL36AP6 |
| 16q21 | 3 | - | - | FRA16B b, FRA16C | - | AC012322.1 c, LINC00922 c, RP11-351A20.1, RP11-744D14.1 |
| 2q36 | 3 | - | - | - | DNER c | SPHKAP c, AC007559.1 |
| 8q24 | 9 | - | - | FRA8C a, FRA8E a,b, FRA8D a | ASAP1 c, GSDMC c, KHDRBS3 c, TG c, ZFAT | DENND3 c, RP11-1082L8.3 c, RP11-30J20.1 c, RP11-369K17.1 c, AC083843.1, AC131568.1, CTD-2182N23.1, CTD-2342N23.3, LINC00964, MAPRE1P1, MIR4662B, RNU6-1255P, RP11-1082L8.4, RP11-274M4.1, RP11-809O17.1, SLC45A4, SNORA12 |
| 3p12 | 4 | - | - | - | CADM2 c,d | CADM2-AS2 c, RP11-260O18.1 c, RPL7AP23 |
| 2q31 | 4 | - | - | FRA2G a | CERKL c, ZNF385B c, ITGA4 c | AC013410.1, AC068706.1, AC068706.2, AC073069.2, MTX2 |
| 2p11 | 3 | - | - | FRA2A b | RPIA | ANKRD36BP2 c, AC096579.1, AC096579.13, AC128677.4, MIR4436A |
| 6q24 | 3 | - | - | - | GRM1 c,d | FUNDC2P3 |
| 7q21 | 6 | - | - | FRA7J, FRA7E a | MAGI2 c, SHFM1 c | ANKIB1 c, MTERF c, AC007566.11, AC073958.2, AC092013.1, RP11-682N22.1 |
| 5q31 | 4 | - | - | FRA5C a | DIAPH1 c, SLC22A5 | AC005592.2 c,d, AC116366.5 c, C5orf56 c, AC116366.6, CTD-2024I7.13, PCDHGA1, PCDHGA10, PCDHGA11, PCDHGA12, PCDHGA2, PCDHGA3, PCDHGA4, PCDHGA5, PCDHGA6, PCDHGA7, PCDHGA8, PCDHGA9, PCDHGB1, PCDHGB2, PCDHGB3, PCDHGB4, PCDHGB6, PCDHGB7, PCDHGC3, PCDHGC4, PCDHGC5, RN7SL68P, Y_RNA |
| 14q31 | 3 | - | - | - | - | CTD-2128A3.2 c, RP11-526N18.1 c, CTD-2128A3.3, EML5, LINC00911, PTPN21, RNU4-22P, RP11-507K2.2, RP11-507K2.3, ZC3H14 |
| 8q12 | 3 | - | - | - | CA8 c,d | YTHDF3 c, RN7SL135P, RP11-16E18.1, RP11-16E18.3, YTHDF3-AS1 |
| 1p13 | 3 | - | - | FRA1E | TRIM33 c | NHLH2 c, NTNG1 c, AC114491.1, EIF2S2P5, HNRNPA1P43, PKMP1, RP11-270C12.3, RP4-591B8.2, Y_RNA |
| 7p14 | 4 | - | - | FRA7C a | INHBA, INHBA-AS1 | AC005027.3 c,d, AOAH c, AC007349.4, RP11-85E16.1 |
| 5p15 | 5 | - | - | - | AHRR c,d, PDCD6 c,d, MRPL36, NDUFS6, SDHA | CTD-2143L24.1 c, TAS2R1 c, CTD-2001E22.1, CTD-2083E4.5, CTD-2083E4.6, CTD-2228K2.1, CTD-2228K2.2 |
| 14q24 | 3 | - | - | FRA14C a | RAD51B c | C14orf166B c, ANGEL1, CTD-2566J3.1, DLST, PROX2, RN7SKP17, RN7SL706P, RP11-316E14.2, RP11-316E14.6, RP11-488C13.1, RPS6KL1, YLPM1 |
| 8q23 | 3 | - | - | FRA8C, FRA8E b | TRPS1 c | RP11-790J24.1 c, TMEM74 c, RP11-25P11.2, RP11-790J24.2, RP11-946L20.1, RP11-946L20.2 |
| 5q23 | 4 | - | - | FRA5C | - | AC004769.1, AC093267.1, CTD-2334D19.1, RP11-166A12.1, snoU13, SNX2 |
| 3p22 | 3 | - | - | - | MYD88 c, DLEC1, U8 | Y_RNA d, AC018359.1 c, ULK4 c, AC123023.1, ACAA1, ATP6V0E1P2, OXSR1 |
| 2q14 | 4 | - | - | FRA2B b, FRA2F | CNTNAP c, RN7SKP102 | |
| 12q13 | 3 | - | - | FRA12A a,b | RND1 c, STAT2 c, CNPY2, EIF4B, IL23A, KRT18, KRT8 | AC107016.1, AC107016.2, APOF, CACNB3, CCDC65, DDX23, PAN2, RNU6-600P, RNU7-40P, RP11-302B13.1, RP11-302B13.5, RP11-348M3.2, RP11-977G19.10, RP11-977G19.11, RP11-977G19.12 |
| 22q12 | 3 | - | - | FRA22B | - | RP5-1119A7.14 c, BX470187.1, CTA-929C8.8, FOXRED2, LL22NC03-86D4.1, RPS15AP38, TXN2, Y_RNA |
| 2p24 | 3 | - | - | FRA2C a | - | NBAS c, AC008069.2, RN7SKP168, RP11-32P22.1 |
| 2q22 | 3 | - | - | FRA2F, FRA2K a | ARHGAP15 c, LRP1B c | AC068287.1, AC092652.1, AC093084.1, RNU6-904P, RP11-570L15.1, RP11-570L15.2 |
| 6q25 | 3 | - | - | FRA6E | TFB1M | CLDN20 |
| 6q14 | 3 | - | - | FRA6D | - | FILIP1, KRT18P64, RNU1-34P, RP11-30P6.1, RP11-379B8.1, RP1-161C16.1, RP11-801I18.1, RPL26P20 |
| 1p34 | 3 | - | - | FRA1B | MUTYH | TESK2 c, HPDL, RP11-291L19.1, RP11-329N22.1, RP11-422J8.1, snoU13, TOE1 |
| 2p25 | 3 | - | - | FRA2C | - | FAM110C, AC007463.2 |
| 9q22 | 3 | - | - | FRA9D | C9orf3 c, SPTLC1 | LINC00475, MIR2278, MTND4P15, RP11-100G15.10, RP11-100G15.2, RP11-100G15.3, RP11-100G15.4, RP11-100G15.5, RP11-100G15.7, RP11-23B15.1, RP11-49O14.3, RP11-546O6.4, snoU13, SPTLC1 |
| 6q16 | 3 | - | - | FRA6G, FRA6F | - | RP3-463P15.1 |
Abbreviations: HPV, human papillomavirus; ITGs, integration-targeted cellular genes; Y: Yes; means that these genes had been reported to be tumor-related based on NCBI database; N: no; means that there was no report about the relationship between this gene and tumors.
a
Underlined type indicates integrations that occurred within a fragile site.
b
Rare fragile sites are shown in bold.
c
Underlined Italics indicate genes directly targeted.
d
The bold genes were recurrently integration targeted genes.