Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005158
Fusion event
HBV-PTPRD integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1338
Orient
+
Integrated sequence
TGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCAGCTTGTTTTGCTCGCAGCCGGTCTGGAGCAAAACTTATCGGGACTGACAAC| |TCTGTTGTCCTCTCTCGGAAATACACCTCCTTCCCATGGCTGCTCGGGTGTGCTGCCAACTGGATCCTGCGCGGGACGTCCTTTGTCTACGTCCCGTCGG
Host Sequence
Chromosome
chr9
Cytoband
p23
Reference genome
Start
End
9880419/9880419 (Hg38)
Orient
+
Location type
Intron
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/3872515; hsa-let-7a-1/Downstream/8692887;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/1021711, chr9-CpG: 76/Downstream/732216
Nearest cancer related gene
PTPRD(TSG, No orient, 0)
Upstream sequence
TGATTGTCAAGAGTAACCTAGGCAGCTTCACTGACTTCCTTCCTATAAGACTGAAAATTGTCACTTCTTACTTGCAAAGGAACTAAAAATATCCTGCTTA
Downstream sequence
GTTATTTACTTTTTTAGAATTTCAAAAATCAGATATCACCATTATCACTGTGTATAATTCTAAACAGTATAGAATTTATATACAAATTAAAATTATCATA
Reference
Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).