Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10014904
Fusion event
HBV-CCNE1 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2012
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Region type
HBVgp3 X protein
Start
1652
End
1779
Orient
-
Integrated sequence
TACATAAGAGGACTCTTGGACTCTCAGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGA
Host Sequence
Chromosome
chr19
Cytoband
q12
Reference genome
Start
End
30304305/29813398 (Hg38)
Orient
-
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-15b-5p ; hsa-mir-503-5p ; hsa-mir-424-5p ; hsa-mir-16-5p ; hsa-mir-15a-5p ; hsa-mir-107 ; hsa-mir-185-5p ; hsa-mir-103a-3p ; hsa-mir-26b-5p ; hsa-mir-26a-5p ; hsa-mir-16-1-3p ; hsa-mir-195-5p ; hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-151a-3p ; hsa-mir-342-5p ; hsa-mir-125b-5p ; hsa-mir-92a-3p ; hsa-mir-383-3p ; hsa-mir-497-5p ; hsa-mir-4524a-5p ; hsa-mir-4694-3p ; hsa-mir-4524b-5p ; hsa-mir-6838-5p ; hsa-mir-7-5p ; hsa-mir-4477a ; hsa-mir-524-5p ; hsa-mir-520d-5p ; hsa-mir-5191 ; hsa-mir-646 ; hsa-mir-25-5p ; hsa-mir-30c-2-3p ; hsa-mir-144-5p ; hsa-mir-892b
Nearest miRNA
hsa-mir-10395/Upstream/9413915; hsa-let-7e/Downstream/5309302;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/495, chr19-CpG: 21/Downstream/30135
Nearest cancer related gene
CCNE1(OG, No orient, 0)
Upstream sequence
TGGCCCAGCACTGTACCTGTCAGTGGGCACTGGCCTCTGCCAGTCCTGGGATTCCAGGAAGCTTGGTGTTCCTGACTGGCACCGTCTGAGATTACAGATA
Downstream sequence
gggCTCTCGGCCTTGTCTGTAAAAGCTGGTGAACTGGGGGAGGGTTCCTGGGTGTTTATAAGCAACAACTTTCCCCCTATCTACACCTATTTTTCTTGTC
Target sequence
TGTGCCTAGCCTGGAagaaccagaatggacatcacagtattcagtcctccccttctgcccaggaggaaactgagactcagttagaggaagaaagtaacccagagtcctgtgccatccaggggcaaagtt
Reference
Sung, W. K., et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet,2012, 44(7): 765-769.