Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10007044
Fusion event
HBV-GRK4 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
46
End
239
Orient
+
Host Sequence
Chromosome
chr4
Cytoband
p16.3
Reference genome
Start
End
2983521/2981794 (Hg38)
Orient
-
Location type
Intron
Target gene
miRNAs that regulate target gene
hsa-mir-19b-3p ; hsa-mir-5582-3p ; hsa-mir-548f-3p ; hsa-mir-548e-3p ; hsa-mir-548az-3p ; hsa-mir-548ar-3p ; hsa-mir-548a-3p ; hsa-mir-6776-5p ; hsa-mir-7977 ; hsa-mir-143-5p ; hsa-mir-6781-5p ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-6499-3p ; hsa-mir-5693 ; hsa-mir-4279 ; hsa-mir-6778-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-2116-3p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-122-3p ; hsa-mir-6837-5p ; hsa-mir-4685-5p ; hsa-mir-7113-5p ; hsa-mir-6823-5p ; hsa-mir-340-3p ; hsa-mir-4434 ; hsa-mir-4516 ; hsa-mir-4531 ; hsa-mir-4645-5p ; hsa-mir-4662a-5p ; hsa-mir-4673 ; hsa-mir-4676-5p ; hsa-mir-4684-5p ; hsa-mir-4755-3p ; hsa-mir-4802-3p ; hsa-mir-548c-3p ; hsa-mir-5703 ; hsa-mir-575 ; hsa-mir-6771-3p ; hsa-mir-6827-3p ; hsa-mir-6858-3p
Nearest miRNA
hsa-mir-4800/Upstream/731638; hsa-mir-12113/Downstream/2941481;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/17507, chr4-CpG: 39/Downstream/59497
Upstream sequence
CAACATCCTCAGAAGAAAATGGAGCTCCATAAGTAAATCAATGTGAAGTGAACATTAACATCAAGCTATGAAACTGAAAAAGAATGCCCATGATGACTGT
Downstream sequence
aggagcctgtctgcctcctgcccttgttcatggtgccctggctgtttgtgtgccctggcctgcactgagctgaactcagccacgccttggcctccctgcc
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.