hsa-mir-548ai _LIHC.png
PCDH9 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018639
Fusion event
HBV-PCDH9 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2017
PubMed ID
29212479
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
1817
Integrated sequence
TGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCAT| |GCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCT
Host Sequence
Chromosome
chr13
Cytoband
q21.32
Reference genome
GRCh37.55
Start
67599307/67025175 (Hg38)
End
67599307/67025175 (Hg38)
Location type
Intron2
Fragile sites / regions
FRA13B
Target gene
PCDH9
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-188-5p ; hsa-mir-127-5p ; hsa-mir-4635 ; hsa-mir-7843-3p ; hsa-mir-4735-3p ; hsa-mir-1264 ; hsa-mir-18b-5p ; hsa-mir-18a-5p ; hsa-mir-570-5p ; hsa-mir-548ba ; hsa-mir-548ai ; hsa-mir-548ag ; hsa-mir-548m
Nearest miRNA
hsa-mir-1297/Upstream/806851; hsa-mir-1267/Downstream/10672837;
Nearest TSS
ENST00000623511/Upstream/34289; ENST00000415120/Downstream/204643;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/3180629, chr13-CpG: 92/Downstream/205201
Nearest cancer related gene
PCDH9(TSG, No orient, 0)
Upstream sequence
ACTATTAGTTATATATATATTTTCATAAAGAAACTTTAAGaaacattcagggcaggtaatttctatggtatgttaatacttccagaacatgggagaggag
Downstream sequence
tgggtagaaagctctcaattttattttctgaaagaagtatggtattgaaacctaaagaaacactgagaagactataagccaatatcatatatggcaattg
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.
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