Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016523
Fusion event
HBV-PTPRD integration
Validated
No
Detection method
WGS
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2012
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
463
End
498
Orient
-
Integrated sequence
TGTTGCCCGTTTGTCCTCTAATTCCAGGATCCTCAA
Host Sequence
Chromosome
chr9
Cytoband
p23
Reference genome
Start
End
10227982/10227982 (Hg38)
Orient
-
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-429 ; hsa-mir-200a-3p ; hsa-mir-200c-3p ; hsa-mir-141-3p ; hsa-mir-1-3p ; hsa-mir-200b-3p ; hsa-mir-190a-3p ; hsa-mir-5011-5p ; hsa-mir-374b-3p ; hsa-mir-3924 ; hsa-mir-340-5p ; hsa-mir-4524b-5p ; hsa-mir-4791 ; hsa-mir-4524a-5p ; hsa-mir-3201 ; hsa-mir-891b ; hsa-mir-1246 ; hsa-mir-8076 ; hsa-mir-3163 ; hsa-mir-646 ; hsa-mir-5583-3p ; hsa-mir-503-5p ; hsa-mir-424-5p ; hsa-mir-15a-5p ; hsa-mir-497-5p ; hsa-mir-6838-5p ; hsa-mir-15b-5p ; hsa-mir-16-5p ; hsa-mir-195-5p ; hsa-mir-135a-5p
Nearest miRNA
hsa-mir-101-2/Upstream/4220043; hsa-let-7a-1/Downstream/8345324;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/1369239, chr9-CpG: 76/Downstream/384653
Nearest cancer related gene
PTPRD(TSG, No orient, 0)
Upstream sequence
cccagaggcatctgctataAAGATACAGTCTCTGCCTTTAAGGAGTTTGTAAAAAGAGCAACTGACTTGTCTTCCTTCTTGAGGTCTAGGACAAACTTGT
Downstream sequence
AATATAACTACAGAAAGGCTAAAGTAAAAATTCTGGCTGTAATATAGGTGGTCATTTGTTACACATTTTAGGCCCATTATGATTAAAAGAGATTTTGGAT
Target sequence
CAGTCATTCAGAAAGGCCTAGAAATTTTTCTTGTT
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.