KDM4C _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005435
Fusion event
HBV-KDM4C integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
29861854
Virus Sequence
Virus name
HBV
Reference genome
AP011098
Start
1803
Orient
-
Integrated sequence
TACTTCAAAGACTGTTTGTTTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTT| |CACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATG
Host Sequence
Chromosome
chr9
Cytoband
p24.1
Reference genome
GRCh37/hg19
Start
7056365/7056365 (Hg38)
End
7056365/7056365 (Hg38)
Orient
-
Location type
Intron
Target gene
KDM4C
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-409-3p ; hsa-mir-432-5p
Nearest miRNA
hsa-mir-101-2/Upstream/1048461; hsa-let-7a-1/Downstream/11516941;
Nearest TSS
ENST00000422679/Upstream/7173; ENST00000466673/Downstream/47903;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/297493, chr9-CpG: 43/Downstream/742990
Nearest cancer related gene
KDM4C(OG, No orient, 0)
Upstream sequence
tgcttcagaggattgttgagggcattaaggaatctatctgaaaagccctccgtacaatccctgacactgtactgctaagtgctcagtgaatggcagACAC
Downstream sequence
CATTAGTAGCTGTATAGTACTTAACTGTCAGAATGATTTGCTACAGGGACTAGATCCTATTGCAAGCTGTCAAATTTGTATATTGCTGTAATACCAAACC
Reference
Tu, T., et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol ,2018,92(11).
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