Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018403
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
1616
Integrated sequence
GACCACGGGGCGCACCTCTCTTTACGCGGACTCCCCGTCTGTGCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGA| |CCACCGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGA
Host Sequence
Chromosome
chr5
Cytoband
q12.1
Reference genome
Start
End
59052454/59756628 (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/52925; hsa-mir-103a-1/Downstream/12412839;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/716574, chr5-CpG: 47/Downstream/136591
Upstream sequence
gcgacagagtgatactccgtctcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaatatatatatatatatatatatatatatatatatatatatatatata
Downstream sequence
TCACCAGGACTTCTAGTCTGGAAGGGTATGGATCCCCCTGGGTGTTCAGCATAAAAGACACAGCAACAGAAGGTATGTTTCTCAATCGATCAAAAAACAA
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.