Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10007022
Fusion event
HBV-APTX integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Subtype
C
Reference genome
Not given
Start
2053
End
2238
Orient
+
Host Sequence
Chromosome
chr9
Cytoband
p21.1
Reference genome
Start
End
32948812/32948814 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-342-3p ; hsa-mir-7977 ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-5693 ; hsa-mir-6783-3p ; hsa-mir-4279 ; hsa-mir-1343-3p ; hsa-mir-377-3p ; hsa-mir-23b-5p ; hsa-mir-23a-5p ; hsa-mir-6829-3p ; hsa-mir-6791-3p ; hsa-mir-2276-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-1281 ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-660-3p ; hsa-mir-4485-5p ; hsa-mir-1228-3p ; hsa-mir-6722-5p ; hsa-mir-6884-5p ; hsa-mir-485-5p ; hsa-mir-383-3p ; hsa-mir-4478 ; hsa-mir-4419b ; hsa-mir-3929 ; hsa-mir-1304-3p ; hsa-mir-1307-3p ; hsa-mir-4638-5p ; hsa-mir-6741-3p ; hsa-mir-6890-3p ; hsa-mir-891a-3p
Nearest miRNA
hsa-mir-101-2/Upstream/4059859; hsa-let-7a-1/Downstream/159878;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/165187, chr9-CpG: 52/Downstream/6839
Upstream sequence
aggattccctatttaataaatggtgctgggaaaactggctagccatatgtagaaagctgaaactggatcccttccttacaccttatacaaaaatcaattc
Downstream sequence
ctcttctctccctagaggctggagggtggggctggaagttggagccctctaatcatgccttggcctttccagtgaccagccctcatcctgaagatctcta
Reference
Kawai-Kitahata, F., et al. Comprehensive analyses of mutations and hepatitis B virus integration in hepatocellular carcinoma with clinicopathological features. J Gastroenterol ,2016,51(5): 473-486.