Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10016046
Fusion event
HBV-SEMA5A integration
Validated
Yes
Detection method
LM PCR
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2012
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Not given
Start
1812
Orient
-
Host Sequence
Chromosome
chr5
Cytoband
p15.31
Reference genome
Start
End
9437224/9437112 (Hg38)
Orient
+
Location type
Exon
Target gene
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-218-5p ; hsa-mir-6811-5p ; hsa-mir-6511b-5p ; hsa-mir-6722-3p ; hsa-mir-1909-3p ; hsa-mir-6836-5p ; hsa-mir-6132 ; hsa-mir-6754-5p ; hsa-mir-4441 ; hsa-mir-100-3p ; hsa-mir-4270 ; hsa-mir-4709-3p ; hsa-mir-4645-3p ; hsa-mir-3185 ; hsa-mir-144-3p ; hsa-mir-8077 ; hsa-mir-496 ; hsa-mir-216a-5p ; hsa-mir-548c-3p ; hsa-mir-4695-3p ; hsa-mir-4772-3p ; hsa-mir-6787-3p ; hsa-mir-1304-3p ; hsa-mir-660-3p ; hsa-mir-6736-3p ; hsa-mir-6890-3p ; hsa-mir-4714-3p
Nearest miRNA
hsa-mir-4277/Upstream/383217; hsa-mir-10397/Downstream/965252;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/978952, chr5-CpG: 138/Downstream/107468
Upstream sequence
CATACAAATATCACCTCCAGTGAATTCGTTTGGAAAAGAAACTCAAAGCAAGGCCAGACaaagaaaacaaaaataaaagaaaagaaagggaaaggacagg
Downstream sequence
GTGGTATGCACTGCAAATAAGTGGGGGCAGCGCACAGAGGTAACTGCAGGAGACAAAACTGAAACCAGGTAGGCAGTCACACTGGGGCGCAGAAGATGCT
Reference
Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.