Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016522
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
2959
End
2994
Orient
+
Integrated sequence
CAAGGACACCTGGCCAGACGCCAACAAGGTAGGAGC
Host Sequence
Chromosome
chr9
Cytoband
p23
Reference genome
Start
End
9215664/9215664 (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/3207725; hsa-let-7a-1/Downstream/9357642;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/356921, chr9-CpG: 76/Downstream/1396971
Nearest cancer related gene
PTPRD(TSG, No orient, 0)
Upstream sequence
taacagagatgaacctttcttttgatagagcagttttgaaacactctttgtagaatctgcaagtggatatttcgagagctttgaggatttcgttggaaag
Downstream sequence
CAACCCAGGAGGTTAATCTAATACAACTGGATTAAACCCTGCTTTACAAGTAACACATGTAGCTGTTCATGACTTTCTTCATTCCATCGTACATTGattc
Target sequence
TTGGGACGAAGGGAGCAGCTCCTCAGGGGGCTGTA
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.