Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10004304
Fusion event
HBV-chr3 integration
Validated
No
Detection method
HIVID
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
AF090842.1;AB033554.1;AB014381.1;M32138.1;AB032431.1;AB036910.1;AB064310;AY090454.1
Host Sequence
Chromosome
chr3
Cytoband
p21.31
Reference genome
Start
End
48948847/48911414 (Hg38)
Location type
Promoter;downstream
miRNAs that regulate target gene
hsa-mir-221-3p ; hsa-mir-19a-3p ; hsa-mir-93-5p ; hsa-mir-1301-3p ; hsa-mir-342-3p ; hsa-mir-1229-5p ; hsa-mir-1304-5p ; hsa-mir-6134 ; hsa-mir-6769a-5p ; hsa-mir-6806-5p ; hsa-mir-6769b-5p ; hsa-mir-8055 ; hsa-mir-6516-5p ; hsa-mir-455-3p ; hsa-mir-3132 ; hsa-mir-197-5p ; hsa-mir-7854-3p ; hsa-mir-449c-5p ; hsa-mir-34b-5p ; hsa-mir-2682-5p ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-6808-5p ; hsa-mir-6511a-5p ; hsa-mir-1910-3p ; hsa-mir-610 ; hsa-mir-4319 ; hsa-mir-125b-5p ; hsa-mir-125a-5p ; hsa-mir-6777-3p ; hsa-mir-5195-5p ; hsa-mir-640 ; hsa-mir-378a-5p ; hsa-mir-6821-3p ; hsa-mir-6790-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-1281 ; hsa-mir-6777-3p ; hsa-mir-5698 ; hsa-mir-143-5p ; hsa-mir-4430 ; hsa-mir-3652 ; hsa-mir-566 ; hsa-mir-6789-3p ; hsa-mir-122-5p ; hsa-mir-504-3p ; hsa-mir-3135b ; hsa-mir-6499-3p ; hsa-mir-4431 ; hsa-mir-5693 ; hsa-mir-6812-3p
Nearest miRNA
hsa-mir-12127/Upstream/267134; hsa-let-7g/Downstream/108734;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/12390, chr3-CpG: 137/Downstream/6963
Upstream sequence
aagggagggagggagggaggggaaagaaaagaaaagaaaggaaagaaagggaagggaaggggaggggagggaagggaagggaagaaagagagagaaagag
Downstream sequence
agccaccgtgtccggcTCACGGTGataatttttatttttatttttCTTGTATTTCCATCCAGTGCACTCACAGTGGTAATTTGATACTTATTGTTGAATT
Reference
Zhao, L. H., et al.Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma. Nat Commun ,2016,7: 12992.