Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10019801
Fusion event
HBV-CHRM3 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
1524
Integrated sequence
GTTTACGTCCCGTCGGCGCTGAATCCTGCGGACGACCCTTCTCGGGGTCGCTTGGGACTCTCTCGTCCCCTTCTCCGTCTGCCGTTCCGACCGACCACGG| |GGCGCACCTCTCTTTACGCGGACTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTG
Host Sequence
Chromosome
chr1
Cytoband
q43
Reference genome
End
239950046/239786746 (Hg38)
Location type
Intron3
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-296-3p ; hsa-mir-2467-3p ; hsa-mir-6878-5p ; hsa-mir-6130 ; hsa-mir-6133 ; hsa-mir-6129 ; hsa-mir-6127 ; hsa-mir-4510 ; hsa-mir-4419a ; hsa-mir-6760-5p ; hsa-mir-6873-5p ; hsa-mir-6856-5p ; hsa-mir-5197-3p ; hsa-mir-6758-5p ; hsa-mir-4311 ; hsa-mir-1277-5p ; hsa-mir-4776-3p ; hsa-mir-4659b-5p ; hsa-mir-4659a-5p ; hsa-mir-5590-5p ; hsa-mir-190a-3p ; hsa-mir-4789-5p ; hsa-mir-466 ; hsa-mir-5011-5p ; hsa-mir-4643 ; hsa-mir-4789-3p ; hsa-mir-137 ; hsa-mir-4446-5p ; hsa-mir-5006-3p ; hsa-mir-4755-5p ; hsa-mir-670-5p ; hsa-mir-4445-5p ; hsa-mir-6766-3p ; hsa-mir-4782-3p ; hsa-mir-219a-5p ; hsa-mir-508-3p ; hsa-mir-339-5p ; hsa-mir-6079 ; hsa-mir-5186 ; hsa-mir-4522 ; hsa-mir-372-5p ; hsa-mir-371a-5p ; hsa-mir-616-5p ; hsa-mir-373-5p ; hsa-mir-371b-5p ; hsa-mir-520h ; hsa-mir-520g-3p ; hsa-mir-3973 ; hsa-mir-6888-5p ; hsa-mir-148a-5p ; hsa-mir-4428 ; hsa-mir-8075 ; hsa-mir-4728-3p
Nearest miRNA
hsa-mir-101-1/Upstream/2315555; hsa-mir-3123/Downstream/1345526;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/398707, chr1-CpG: 105/Downstream/210791
Upstream sequence
GAATTTCACGTACACTACAATTATTCTCTCTCTAAACTAATATAAATGGTTAGTTATAGAGTTTACCCCCTAGGGCTCAGGGAGAAGACAAGGATAGCAG
Downstream sequence
AAGGGACTGGAGTGAGTGTGGGAGGAAAATGGAGGGAcagaagggcaaggcagccttgcagagacattaagaacttggatagccagatcttggttcctat
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.