Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10006633
Fusion event
HBV-SCD5 integration
Validated
Yes
Detection method
invPCR +Sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Host Sequence
Chromosome
chr4
Cytoband
q21.22
Reference genome
Start
End
82746892 (Hg38)
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-140-3p ; hsa-mir-324-5p ; hsa-mir-30c-5p ; hsa-mir-92a-3p ; hsa-mir-6513-5p ; hsa-mir-887-5p ; hsa-mir-3913-5p ; hsa-mir-3122 ; hsa-mir-450a-1-3p ; hsa-mir-6780a-5p ; hsa-mir-6779-5p ; hsa-mir-3689c ; hsa-mir-3689b-3p ; hsa-mir-3689a-3p ; hsa-mir-30b-3p ; hsa-mir-1273h-5p ; hsa-mir-6788-5p ; hsa-mir-30c-2-3p ; hsa-mir-30c-1-3p ; hsa-mir-7977 ; hsa-mir-6799-5p ; hsa-mir-6883-5p ; hsa-mir-6785-5p ; hsa-mir-4728-5p ; hsa-mir-149-3p ; hsa-mir-7106-5p ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-9-5p ; hsa-mir-4267 ; hsa-mir-675-5p ; hsa-mir-4466 ; hsa-mir-4746-3p ; hsa-mir-511-5p ; hsa-mir-6885-3p ; hsa-mir-6805-3p ; hsa-mir-5691 ; hsa-mir-6502-5p ; hsa-mir-1301-5p ; hsa-mir-129-2-3p ; hsa-mir-129-1-3p ; hsa-mir-4637 ; hsa-mir-200a-3p ; hsa-mir-141-3p ; hsa-mir-1247-3p ; hsa-mir-25-5p ; hsa-mir-3160-3p ; hsa-mir-4327 ; hsa-mir-4487 ; hsa-mir-455-3p ; hsa-mir-4722-5p ; hsa-mir-4768-3p ; hsa-mir-558 ; hsa-mir-6087 ; hsa-mir-6499-3p ; hsa-mir-6516-5p
Nearest miRNA
hsa-mir-12113/Upstream/6171266; hsa-mir-1243/Downstream/6445;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/184954, chr4-CpG: 118/Downstream/50964
Upstream sequence
caagggctccacccttggtcctgcgcccatggacccaagcgagaataggcactcccacttttacactcaagggttgcattttccaagacccctctggcct
Downstream sequence
accacacccccaatcctgttgccatataaacccgagaccttaagtggacgcagacacaagggcgtcagggggagaggaggaacggggaacacacccacag
Reference
Mason, W. S., et al. HBV DNA Integration and Clonal Hepatocyte Expansion in Chronic Hepatitis B Patients Considered Immune Tolerant. Gastroenterology,2016, 151(5): 986-998 e984.