Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10015439
Fusion event
HBV-CYP2C19 integration
Validated
No
Detection method
HIVID
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2013
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Host Sequence
Chromosome
chr10
Cytoband
q23.33
Reference genome
Start
End
96587309/94827552 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-6516-5p ; hsa-mir-620 ; hsa-mir-1270 ; hsa-mir-455-3p ; hsa-mir-4325 ; hsa-mir-7703 ; hsa-mir-6880-5p ; hsa-mir-6851-5p ; hsa-mir-3689d ; hsa-mir-4683 ; hsa-mir-6499-3p ; hsa-mir-767-5p ; hsa-mir-6134 ; hsa-mir-4537 ; hsa-mir-5186 ; hsa-mir-665 ; hsa-mir-4459 ; hsa-mir-92b-3p ; hsa-mir-92a-3p ; hsa-mir-367-3p ; hsa-mir-363-3p ; hsa-mir-32-5p ; hsa-mir-25-3p ; hsa-mir-3180-5p ; hsa-mir-3912-5p ; hsa-mir-874-3p ; hsa-mir-3157-3p ; hsa-mir-5195-3p ; hsa-mir-145-5p ; hsa-mir-6886-3p ; hsa-mir-938 ; hsa-mir-6780b-3p ; hsa-mir-10b-3p ; hsa-mir-29a-3p
Nearest miRNA
hsa-mir-107/Upstream/5234725; hsa-mir-1287/Downstream/1236763;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/281416, chr10-CpG: 63/Downstream/355886
Upstream sequence
GCGGCTGGGCTGGACGGTGTGATCCTGAGGTGGGCCGAGGCGGCTGGGCTGGACGGTGTGACCCGGAGGTGGGCCGAGGCGGCTGGGCTGGACGGTGTGA
Downstream sequence
TCCTGAGGTGGGCCGAGGCTGGACGAGGTGCCCCAGAGGTGGGCCGAGGCAGCTGGGCTGGACGGTGTGGCCCTGAGGTGGGCCGAGGCAGCTGGATGAG
Reference
Li, W., et al. HIVID: an efficient method to detect HBV integration using low coverage sequencing. Genomics,2013, 102(4): 338-344.