Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016260
Fusion event
HBV-SMAD3 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
1658
End
1693
Orient
-
Integrated sequence
AGAGGACTCTTGGACTCTCAGCAATGTCAACGACCG
Host Sequence
Chromosome
chr15
Cytoband
q22.33
Reference genome
Start
End
67461806/67169468 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-200a-3p ; hsa-mir-18a-5p ; hsa-mir-335-5p ; hsa-mir-155-5p ; hsa-mir-193b-3p ; hsa-mir-17-5p ; hsa-mir-143-3p ; hsa-mir-145-5p ; hsa-mir-3529-3p ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-497-5p ; hsa-mir-142-5p ; hsa-mir-491-5p ; hsa-mir-92b-3p ; hsa-mir-4290 ; hsa-mir-18a-3p ; hsa-mir-323a-3p ; hsa-mir-708-5p ; hsa-mir-199a-5p ; hsa-mir-145-3p ; hsa-mir-590-5p ; hsa-mir-23a-3p ; hsa-mir-23b-5p ; hsa-mir-424-5p ; hsa-mir-29b-1-5p
Nearest miRNA
hsa-mir-10393/Upstream/672399; hsa-mir-11181/Downstream/1632382;
Nearest CpG islands
None/Target, chr15-CpG: 55/Upstream/103009, chr15-CpG: 62/Downstream/84983
Upstream sequence
TTCCAACTTACCGTTTCAAGGCTCTTCTGAAACTCCAGAAGTTTAGCTTCAGCTTCTTTATAATTCCTGAAGAACATACACAGTTCATACATCTCCATCA
Downstream sequence
GGTTAACAAATAGTCTCCttttttatttttattttttgaaacagtctcactgctgcccaggctggtgtgcagtggtgcaaacacagctcgctgcagcctc
Target sequence
TAGATTTCATGGGGTGGAATTAGACCCCATAGGGT
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.