Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10007097
Fusion event
HBV-PRKCA integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Subtype
C
Reference genome
Not given
Start
991
End
1229
Orient
-
Host Sequence
Chromosome
chr17
Cytoband
q24.2
Reference genome
Start
End
64468192/66472074 (Hg38)
Orient
+
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-375 ; hsa-mir-505-3p ; hsa-mir-193b-3p ; hsa-mir-92a-3p ; hsa-mir-17-3p ; hsa-mir-203a-3p ; hsa-mir-218-5p ; hsa-mir-371b-5p ; hsa-mir-6828-5p ; hsa-mir-1976 ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-5196-3p ; hsa-mir-6821-5p ; hsa-mir-6842-3p ; hsa-mir-647 ; hsa-mir-6514-3p ; hsa-mir-7977 ; hsa-mir-1268b ; hsa-mir-1268a ; hsa-mir-585-3p ; hsa-mir-5787 ; hsa-mir-4505 ; hsa-mir-4430 ; hsa-mir-3652 ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-6847-3p ; hsa-mir-6811-3p ; hsa-mir-214-5p ; hsa-mir-4486 ; hsa-mir-142-3p ; hsa-mir-150-5p
Nearest miRNA
hsa-mir-10226/Upstream/1649972; hsa-mir-1250/Downstream/314998;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/168575, chr17-CpG: 48/Downstream/362894
Nearest cancer related gene
PRKCA(OG, No orient, 0)
Upstream sequence
ttttaaggacatggtttcgctgtgttgcccgggcaggaatgcagtggctccatcatagatcactgcagcctggaactcctgggctcaagcagtcctttcc
Downstream sequence
tgcctcagccttcagagtagctaggattacaggcttgcaccactgcacctggctaattttttaaatttctgcaaagatgaagtcttgctatgttgcccag
Reference
Kawai-Kitahata, F., et al. Comprehensive analyses of mutations and hepatitis B virus integration in hepatocellular carcinoma with clinicopathological features. J Gastroenterol ,2016,51(5): 473-486.