Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018436
Fusion event
HBV-NRXN1 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2017
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1620
Integrated sequence
ACGGGGCGCACCTCTCTTTACGCGGACTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCAC| |CGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGT
Host Sequence
Chromosome
chr2
Cytoband
p16.3
Reference genome
Start
End
50249937/50022799 (Hg38)
Location type
Intron2
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-196a-5p ; hsa-mir-16-5p ; hsa-mir-616-5p ; hsa-mir-498 ; hsa-mir-1537-5p ; hsa-mir-302a-5p ; hsa-mir-3607-3p ; hsa-mir-548as-3p ; hsa-mir-548z ; hsa-mir-548h-3p ; hsa-mir-548d-3p ; hsa-mir-548bb-3p ; hsa-mir-548ac ; hsa-mir-574-5p ; hsa-mir-4752 ; hsa-mir-6867-5p ; hsa-mir-8056 ; hsa-mir-3691-5p ; hsa-mir-376c-5p ; hsa-mir-376b-5p ; hsa-mir-7114-5p ; hsa-mir-6818-5p ; hsa-mir-4320
Nearest miRNA
hsa-mir-1301/Upstream/963141; hsa-mir-10b/Downstream/673373;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/1267053, chr2-CpG: 74/Downstream/324104
Upstream sequence
GTGGTTGCTGGGATCAGGCCATTGACACCCTCATGTGACTGTAATTAAATGGACTGGTCACCTGACAGTTTTCCATAGTCAGTATAGACCAtgacatagc
Downstream sequence
AGTCACTGAAATATCAAGACACAACAATGTTAGACTTTCATTCAGTGGCCTGTAAATTTACTGGTTGCCAGAATATCTTATATAGTAGGTAAAAATAGAG
Reference
Yoo, S., et al. A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC Med ,2017, 15(1): 214.