Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10000543
Fusion event
HBV-PTPRD integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
AF090842.1;AB033554.1;AB014381.1;M32138.1;AB032431.1;AB036910.1;AB064310;AY090454.1
Host Sequence
Chromosome
chr9
Cytoband
p23
Reference genome
Start
End
10200468/10200468 (Hg38)
Location type
Intronic
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/4192564; hsa-let-7a-1/Downstream/8372838;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/1341760, chr9-CpG: 76/Downstream/412167
Nearest cancer related gene
PTPRD(TSG, No orient, 0)
Downstream sequence
AAGAATTATCTAGGCCAAAATATTAATAGTGCAGTTGAAAAACGAAATGCTAGATGTTT
Junction sequence
CTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAGGCCTTGCCCAAGGTCTTACACAAGAGGACTCTTGGACTCCCAGCAAGAATTATCTAGGCCAAAATATTAATAGTGCAGTTGAAAAACGAAATGCTAGATGTTT
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
Reference
Zhao, L. H., et al.Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma. Nat Commun ,2016,7: 12992.