Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10007054
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
765
End
1080
Orient
+
Host Sequence
Chromosome
chr4
Cytoband
q12
Reference genome
Start
End
55950887/55084720 (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/2371973; hsa-mir-1243/Downstream/5837899;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/425590, chr4-CpG: 64/Downstream/40515
Upstream sequence
agggttagggttagggttagggttagggttaagggttagggttagggttagggttagggttagggttagggttagggtggttagggttagggttagggtt
Downstream sequence
CAGACTCCCTTGGAAGAGTATCAGGAGGGAAAAGAAAGAAGAAAACAGCAGACACAATTGTTCAAGCCAttattaagcacccagtatgtgcacagcactg
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.