Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018644
Fusion event
HBV-CARHSP1 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
1818
Integrated sequence
GTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATG| |CAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTT
Host Sequence
Chromosome
chr16
Cytoband
p13.2
Reference genome
Start
End
8954916/8861059 (Hg38)
Location type
Intron3
Target gene
miRNAs that regulate target gene
hsa-let-7b-5p ; hsa-mir-155-5p ; hsa-mir-125b-5p ; hsa-mir-10a-5p ; hsa-let-7a-5p ; hsa-mir-3909 ; hsa-mir-6878-3p ; hsa-mir-6744-3p ; hsa-mir-4757-5p ; hsa-mir-4312 ; hsa-mir-372-5p ; hsa-mir-371a-5p ; hsa-mir-616-5p ; hsa-mir-373-5p ; hsa-mir-371b-5p ; hsa-mir-212-5p ; hsa-mir-6747-3p ; hsa-mir-520h ; hsa-mir-520g-3p ; hsa-mir-3973 ; hsa-mir-1278 ; hsa-mir-8054 ; hsa-mir-548k ; hsa-mir-548av-5p ; hsa-mir-3187-3p ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-203b-3p ; hsa-mir-7158-3p ; hsa-mir-4755-3p ; hsa-mir-4680-5p ; hsa-mir-3922-3p ; hsa-mir-3176 ; hsa-mir-4781-3p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-7162-5p ; hsa-mir-516b-3p ; hsa-mir-516a-3p ; hsa-mir-2115-5p ; hsa-mir-150-5p ; hsa-mir-6769b-3p ; hsa-mir-4723-3p ; hsa-mir-3183 ; hsa-mir-6887-3p ; hsa-mir-6814-5p ; hsa-mir-4255 ; hsa-mir-6513-3p
Nearest miRNA
hsa-mir-1225/Upstream/3228493; hsa-mir-11401/Downstream/2445381;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/62988, chr16-CpG: 74/Downstream/7273
Upstream sequence
ctgtatatgtgaaccacatttttaaaaatgcatttctgaacctgaaggacattatgttaagtcaaataagccagacacagacagacaaagacatatgatc
Downstream sequence
aaataaCttttatttttttgagacagtgtctcactgtcacccaggctggagggcagtggcataatcacagttcactgtagccttgacctccatgcctaat
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.