Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018896
Fusion event
HBV-PDE4D 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
1822
Integrated sequence
GTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAAC| |TTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAA
Host Sequence
Chromosome
chr5
Cytoband
q11.2
Reference genome
Start
End
58755048/59459222 (Hg38)
Location type
Intron14
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-340-5p ; hsa-mir-7-5p ; hsa-mir-103a-3p ; hsa-mir-19b-3p ; hsa-mir-18a-5p ; hsa-mir-16-5p ; hsa-mir-3148 ; hsa-mir-4668-5p ; hsa-mir-4457 ; hsa-mir-5590-3p ; hsa-mir-142-5p ; hsa-mir-6783-5p ; hsa-mir-6838-5p ; hsa-mir-497-5p ; hsa-mir-424-5p ; hsa-mir-195-5p ; hsa-mir-15b-5p ; hsa-mir-15a-5p ; hsa-mir-6835-3p ; hsa-mir-548z ; hsa-mir-548h-3p ; hsa-mir-548d-3p ; hsa-mir-548bb-3p ; hsa-mir-7158-3p ; hsa-mir-548ac ; hsa-mir-31-3p ; hsa-mir-302f ; hsa-mir-4760-3p ; hsa-mir-4282 ; hsa-mir-18b-5p ; hsa-mir-4735-3p ; hsa-mir-4439 ; hsa-mir-3136-5p ; hsa-mir-6857-3p ; hsa-mir-6855-3p ; hsa-mir-4513 ; hsa-mir-4502 ; hsa-mir-4682 ; hsa-mir-1324 ; hsa-mir-4422 ; hsa-mir-3611 ; hsa-mir-4325 ; hsa-mir-4266 ; hsa-mir-642b-3p ; hsa-mir-642a-3p ; hsa-mir-6080 ; hsa-mir-6888-5p ; hsa-mir-3120-3p ; hsa-mir-3646 ; hsa-mir-424-3p ; hsa-mir-199a-5p ; hsa-mir-139-5p
Nearest miRNA
hsa-mir-10397/Upstream/929113; hsa-mir-103a-1/Downstream/244384;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/419168, chr5-CpG: 47/Downstream/433997
Upstream sequence
CTTCATATCATGTCCCATATATTATAGATGTTAACTTATTAGTTATCTCATTGAAGTAAAAAAAATTCTTCTGctaagtttctcaggataatattcagga
Downstream sequence
ACCCTGTCTTATGTACTGAAAAAACCAGGTTAATTTTTAAAAGTATTCATTTGGGAAGCAACTTTCTGAGAGGCGAAATATTCTTACATCAGAAAAGACA
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.