Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10008452
Fusion event
HBV-PRKCB integration
Validated
No
Detection method
NGS
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Region type
Polymerase|
Start
1042
Orient
+
Integrated sequence
AATGTTTTAGAAAACTTCCTATTAACAGGCCTATTGATTGGAAAGTATGTCAACGAATTGTGGGTCTTTTGGGTTTTGCTGCCCCTTTTACACAATGTGG| |TTATCCTGCGTTGATGCCTTTGTATGCATGTATTCAATCTAAGCAGGCTTTCACTTTCTCGCCAACTTACAAGGCCTTTCTGTGTAAACAATACCTGAAC
Host Sequence
Chromosome
chr16
Cytoband
p12.2
Reference genome
Start
End
24154006/24142685 (Hg38)
Orient
-
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-142-5p ; hsa-mir-3650 ; hsa-mir-4796-3p ; hsa-mir-5590-3p ; hsa-mir-6867-5p ; hsa-mir-1261 ; hsa-mir-3614-5p ; hsa-mir-381-3p ; hsa-mir-300 ; hsa-mir-890 ; hsa-mir-574-5p ; hsa-mir-4455 ; hsa-mir-4999-5p ; hsa-mir-4718 ; hsa-mir-1537-5p ; hsa-mir-4742-3p ; hsa-mir-93-5p ; hsa-mir-526b-3p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-20a-5p ; hsa-mir-17-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-548ah-5p ; hsa-mir-3609 ; hsa-mir-6868-3p ; hsa-mir-627-3p ; hsa-mir-1248 ; hsa-mir-3667-3p ; hsa-mir-6734-3p ; hsa-mir-6074 ; hsa-mir-4753-3p ; hsa-mir-6809-3p ; hsa-mir-130b-5p ; hsa-mir-3180-5p ; hsa-mir-6780a-3p ; hsa-mir-6881-3p ; hsa-mir-525-5p ; hsa-mir-520a-5p ; hsa-mir-877-3p ; hsa-mir-488-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-4778-3p ; hsa-mir-184 ; hsa-mir-33a-5p
Nearest miRNA
hsa-mir-1225/Upstream/2636550; hsa-mir-11401/Downstream/60431;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/305904, chr16-CpG: 44/Downstream/113034
Nearest cancer related gene
PRKCB(TSG, No orient, 0)
Upstream sequence
gtctagagtgtggcccaagcatcggcttctaaaacctccacagggagttctaatatgcagcagggagaagcaGCAGCTCAGTGCAGCAGGCAAGGCTCGT
Downstream sequence
CCACGGAAGGGCTGGGGGAAGGAAGGAGATCATATTTGCCTTAAAACTTGGAGTTGAGCTCATCTGACCTACCCTCTGCAGGTCTTCAGGGGGACTGGGA
Reference
Yang, L., et al. Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma. J Cancer ,2018,9(18): 3225-3235.