Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018567
Fusion event
HBV-SHISAL1 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2017
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1752
Integrated sequence
TACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGA| |GATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTT
Host Sequence
Chromosome
chr22
Cytoband
q13.31
Reference genome
Start
End
44720012/44324132 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-26b-5p ; hsa-mir-1226-3p ; hsa-mir-218-5p ; hsa-mir-7855-5p ; hsa-mir-4710 ; hsa-mir-504-3p ; hsa-mir-4792 ; hsa-mir-6778-3p ; hsa-mir-6133 ; hsa-mir-6130 ; hsa-mir-6129 ; hsa-mir-6127 ; hsa-mir-4510 ; hsa-mir-6873-5p ; hsa-mir-4419a ; hsa-mir-6856-5p ; hsa-mir-6758-5p ; hsa-mir-510-3p ; hsa-mir-502-5p ; hsa-mir-7162-5p ; hsa-mir-516b-3p ; hsa-mir-516a-3p ; hsa-mir-2115-5p ; hsa-mir-6776-3p ; hsa-mir-497-3p
Nearest miRNA
hsa-mir-1281/Upstream/2400830; hsa-let-7a-3/Downstream/876822;
Nearest CpG islands
None/Target, chr22-CpG: 279/Upstream/299217, chr22-CpG: 154/Downstream/6604
Nearby gene
Upstream sequence
acagccaggaggagtggagactgggatttgaaatcttactgtctctctagagCTTAGGGGTAAAACATAATGGTTAGCAATGTAACTGACCCAGctgtcc
Downstream sequence
gttacaatccccgcctcaaatcctcacaagccactcaggttattatcatcattattagccctatgttgaaaatgaggatgctgaggctcagagggaaata
Target sequence
caaat
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.