Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10007053
Fusion event
HBV-KDR 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
1498
End
1790
Orient
-
Host Sequence
Chromosome
chr4
Cytoband
q12
Reference genome
Start
End
55950831/55084664 (Hg38)
Orient
-
Location type
Intron
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-19b-1-5p ; hsa-mir-200b-3p ; hsa-mir-16-5p ; hsa-mir-335-5p ; hsa-mir-1236-3p ; hsa-mir-17-3p ; hsa-mir-200c-3p ; hsa-mir-15b-5p ; hsa-mir-4799-5p ; hsa-mir-548ay-3p ; hsa-mir-548at-3p ; hsa-mir-548as-3p ; hsa-mir-548t-3p ; hsa-mir-548ap-3p ; hsa-mir-548aa ; hsa-mir-296-5p ; hsa-mir-199a-3p ; hsa-mir-195-5p
Nearest miRNA
hsa-mir-12113/Upstream/2371917; hsa-mir-1243/Downstream/5837955;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/425534, chr4-CpG: 64/Downstream/40571
Upstream sequence
gttgggttagggttagggtcagggtcagggtcagggtcagggtcagggtcagggttaggggttaggggttagggtcagggttagggttagggttagggtt
Downstream sequence
gccttcagacactaaagcccatgTGAAGTTTTTGTTTTGTTTTACTCTACTCCATACAGACTCCCTTGGAAGAGTATCAGGAGGGAAAAGAAAGAAGAAA
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.