Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10005646
Fusion event
HBV-EML4 integration
Validated
No
Detection method
PCR and Ultra-deep sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1822
Orient
+
Integrated sequence
TTAAGGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGTTCACCAGCACCATGCAACTT| |TTTCACCTCTGCCTAATCATCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCGTATAAAG
Host Sequence
Chromosome
chr2
Cytoband
p21
Reference genome
Start
End
42456686/42229546 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-30b-5p ; hsa-mir-16-5p ; hsa-mir-877-3p ; hsa-mir-652-3p ; hsa-mir-148b-3p ; hsa-mir-651-3p ; hsa-mir-551b-5p ; hsa-mir-548c-3p ; hsa-let-7f-2-3p ; hsa-mir-30a-5p ; hsa-mir-30c-5p ; hsa-mir-30d-5p ; hsa-mir-30e-5p ; hsa-mir-1185-2-3p ; hsa-mir-1185-1-3p ; hsa-mir-142-3p ; hsa-mir-552-5p ; hsa-mir-302c-5p ; hsa-mir-5683 ; hsa-mir-212-3p ; hsa-mir-132-3p ; hsa-mir-107 ; hsa-mir-103a-3p ; hsa-mir-548o-3p ; hsa-mir-1323 ; hsa-mir-587 ; hsa-mir-377-3p ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485
Nearest miRNA
hsa-mir-1301/Upstream/6758060; hsa-mir-10b/Downstream/5148129;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/59753, chr2-CpG: 61/Downstream/131386
Nearest cancer related gene
EML4(OG, No orient, 0)
Upstream sequence
ACACATGAACTTTGTATTCCAGGAACAGTTATGTTAGTAAAATATTAAATGGTAGAGAATTTTTTCATAAAGCAAGACAGATAACTGTCTTGCAAGAGTC
Downstream sequence
ACCCATTCACCACGAGAGAGAAAAATAAAAGAAATGTGAGTGAGTGAGTTTAGGGCTAAATACATGTAAATACTGAGTTTGTCAGAGGAATCAGGGAGGG
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).