Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016371
Fusion event
HBV-SDC2 integration
Validated
No
Detection method
RNA-Seq
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
1782
End
1804
Orient
-
Integrated sequence
CTGTAGGCATAAATTGGTCTGCG
Host Sequence
Chromosome
chr8
Cytoband
q22.1
Reference genome
Start
End
97591478/96579250 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-3202 ; hsa-mir-2467-3p ; hsa-mir-3616-3p ; hsa-mir-4784 ; hsa-mir-3150b-3p ; hsa-mir-3179 ; hsa-mir-6847-5p ; hsa-mir-7843-5p ; hsa-mir-6879-5p ; hsa-mir-6735-5p ; hsa-mir-4632-5p ; hsa-mir-4436b-3p ; hsa-mir-6876-5p ; hsa-mir-4476 ; hsa-mir-577 ; hsa-mir-6859-5p ; hsa-mir-3916 ; hsa-mir-3125 ; hsa-mir-7-2-3p ; hsa-mir-7-1-3p ; hsa-mir-5688 ; hsa-mir-495-3p
Nearest miRNA
hsa-mir-12123/Upstream/1506189; hsa-mir-10400/Downstream/1814395;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/83806, chr8-CpG: 67/Downstream/65696
Upstream sequence
cgtctaaatctgtattactggtttgcctctgctctctcctttgtggattggccttttaaaacaatttccctttctgaggagatttggaaaagaggaaaaa
Downstream sequence
GATTATGTTGTGCTTTCCTTTAATGTCTAATCTGGAAATTGGCTGTTGATGCTAGTGAGGGTTTTTAATATAAGTTTTAAATGAAAATGCCAAATTGCTT
Target sequence
TTCGTTTTATGTATGGCATTTTAATAAAGTCTTAATTTTTTTTCTTCTAAACAGATAACAGACTA
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.