Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10019796
Fusion event
HBV-PTPRD 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
1665
Integrated sequence
CATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGAC| |TCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAG
Host Sequence
Chromosome
chr9
Cytoband
p24.1
Reference genome
Start
End
8960394/8960394 (Hg38)
Location type
Intron35
Target gene
miRNAs that regulate target gene
hsa-mir-429 ; hsa-mir-200a-3p ; hsa-mir-200c-3p ; hsa-mir-141-3p ; hsa-mir-1-3p ; hsa-mir-200b-3p ; hsa-mir-190a-3p ; hsa-mir-5011-5p ; hsa-mir-374b-3p ; hsa-mir-3924 ; hsa-mir-340-5p ; hsa-mir-4524b-5p ; hsa-mir-4791 ; hsa-mir-4524a-5p ; hsa-mir-3201 ; hsa-mir-891b ; hsa-mir-1246 ; hsa-mir-8076 ; hsa-mir-3163 ; hsa-mir-646 ; hsa-mir-5583-3p ; hsa-mir-503-5p ; hsa-mir-424-5p ; hsa-mir-15a-5p ; hsa-mir-497-5p ; hsa-mir-6838-5p ; hsa-mir-15b-5p ; hsa-mir-16-5p ; hsa-mir-195-5p ; hsa-mir-135a-5p
Nearest miRNA
hsa-mir-101-2/Upstream/2952490; hsa-let-7a-1/Downstream/9612912;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/101686, chr9-CpG: 76/Downstream/1652241
Nearest cancer related gene
PTPRD(TSG, No orient, 0)
Upstream sequence
CAGCTGCTGCTTCGAGGGGCAAGGGGTGTAAGTGTCTTTAAGGAAACACCTTGGCTAAGGGATTTGGACCAGTTAAACCACTGTGGAATCACAGCTGCTC
Downstream sequence
AGAATGGTAGAAGGATGAATATCACTCTAGGAAGAGATCAGTCAGTTAAGTTCAAGAGAGCTGTCATCTAGCCCTGAAAAATCAAGACTTTTTATACTTG
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.