Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10019294
Fusion event
HBV-FAM13A integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2012
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Host Sequence
Chromosome
chr4
Cytoband
q22.1
Reference genome
Start
End
89898479/88977328 (Hg38)
Location type
Intron20
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-615-3p ; hsa-mir-10b-5p ; hsa-mir-4291 ; hsa-mir-4777-3p ; hsa-mir-558 ; hsa-mir-545-3p ; hsa-mir-3908 ; hsa-mir-4446-5p ; hsa-mir-3679-3p ; hsa-mir-302c-5p ; hsa-mir-2355-5p ; hsa-mir-3143 ; hsa-mir-4262 ; hsa-mir-181d-5p ; hsa-mir-181c-5p ; hsa-mir-181b-5p ; hsa-mir-181a-5p ; hsa-mir-543 ; hsa-mir-5047 ; hsa-mir-6721-5p ; hsa-mir-1301-3p ; hsa-mir-2115-5p ; hsa-mir-4660
Nearest miRNA
hsa-mir-12113/Upstream/1676745; hsa-mir-1243/Downstream/10020059;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/279425, chr4-CpG: 126/Downstream/133425
Upstream sequence
ATTTTATTAACTTAtttatttatttttgagaccgaatctctgtcgcccaggctggagcacagtggcacgatctcagctcactgcaacctccgcctcccgg
Downstream sequence
gtgcaaagagatgaAGCCATAGAAAGTGAAACTGCAAATAAAGGGATACCACTGTCTATTCCAGAGAAGAGTTCACATATTCTAAAAACTCTGCATCACC
Reference
Sung, W. K., et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet,2012, 44(7): 765-769.