CDH12 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10019781
Fusion event
HBV-CDH12 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2017
PubMed ID
29212479
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
1804
Integrated sequence
ATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGC| |GCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCAT
Host Sequence
Chromosome
chr5
Cytoband
p14.3
Reference genome
GRCh37.55
Start
22529168/22529059 (Hg38)
End
22529225/22529116 (Hg38)
Location type
Intron14
Fragile sites / regions
FRA5E
Target gene
CDH12
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-4455 ; hsa-mir-5010-3p ; hsa-mir-147a ; hsa-mir-6818-5p ; hsa-mir-8068 ; hsa-mir-6867-5p ; hsa-mir-574-5p ; hsa-mir-759 ; hsa-mir-4433a-5p ; hsa-mir-4433b-5p ; hsa-mir-4646-3p
Nearest miRNA
hsa-mir-10397/Upstream/5373067; hsa-mir-103a-1/Downstream/9406986;
Nearest TSS
ENST00000502646/Upstream/315309; ENST00000507674/Downstream/109878;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/1069316, chr5-CpG: 68/Downstream/2661278
Upstream sequence
gtggaggcagcctaggtgtccatcaactgatgatgaatgggtagagtgtggtgtgtctgtgcaatggcaaattacccagccgtaaaaagaaacaaagtgt
Downstream sequence
tgcaaaacatgaatatatgcatatatatacacatatatatacacatgtgtatatatatatatatatatatatagagagagagagagagagagagagagag
Target sequence
tatatgtatatatgcatatatatgcatgcaaaacatgaatatatgcatatatatgca
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.
Curate