Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016393
Fusion event
HBV-PTAFR 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
1379
End
1414
Orient
-
Integrated sequence
CTGCTAGGCTGTGCTGCCAACTGGATCCTGCGCGGG
Host Sequence
Chromosome
chr1
Cytoband
p35.3
Reference genome
Start
End
28506888/28180377 (Hg38)
Orient
-
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-6788-3p ; hsa-mir-4635 ; hsa-mir-3663-5p ; hsa-mir-4716-5p ; hsa-mir-4494 ; hsa-mir-4463 ; hsa-mir-6829-3p ; hsa-mir-6791-3p ; hsa-mir-2276-3p ; hsa-mir-1281 ; hsa-mir-4485-5p ; hsa-mir-186-3p ; hsa-mir-208b-5p ; hsa-mir-208a-5p ; hsa-mir-6749-3p ; hsa-mir-3156-3p ; hsa-mir-188-3p ; hsa-mir-3157-5p ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-6778-3p ; hsa-mir-149-5p ; hsa-mir-532-3p ; hsa-mir-8073 ; hsa-mir-221-5p ; hsa-mir-4301 ; hsa-mir-660-3p ; hsa-mir-125b-2-3p ; hsa-mir-5697 ; hsa-mir-562 ; hsa-mir-1307-3p ; hsa-mir-5193
Nearest miRNA
hsa-mir-12136/Upstream/1625749; hsa-mir-101-1/Downstream/2558779;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/91541, chr1-CpG: 36/Downstream/52257
Upstream sequence
ccctaaacaatggagttcaggtagcttccaggttggtgaacacatcgaagtgctgggagggtggtgaggttggaaagagcagagaagctccatcctccca
Downstream sequence
tcaaaaTATATATATATAAAAAAGAAGTTGCAGCTGAGCCTGCAACAggcagggagggaaccaggaaataaatactcaaacctttctcttctcccatcct
Target sequence
gctctccaccctgggcgacagagcaagactctgtc
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.