Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10003939
Fusion event
HBV-SMARCD1 integration
Validated
No
Detection method
HIVID
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
AF090842.1;AB033554.1;AB014381.1;M32138.1;AB032431.1;AB036910.1;AB064310;AY090454.1
Host Sequence
Chromosome
chr12
Cytoband
q13.12
Reference genome
Start
End
50489827/50096044 (Hg38)
Location type
Intronic
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-7-5p ; hsa-mir-101-3p ; hsa-let-7b-5p ; hsa-mir-744-5p ; hsa-mir-425-5p ; hsa-let-7c-5p ; hsa-mir-223-3p ; hsa-mir-490-3p ; hsa-mir-940 ; hsa-mir-1827 ; hsa-mir-6808-5p ; hsa-mir-6893-5p ; hsa-mir-619-3p ; hsa-mir-3185 ; hsa-mir-8066 ; hsa-mir-6516-5p ; hsa-mir-455-3p ; hsa-mir-6807-5p ; hsa-mir-650 ; hsa-mir-3612 ; hsa-mir-4327 ; hsa-mir-6499-3p ; hsa-mir-6840-3p ; hsa-mir-665 ; hsa-mir-4459 ; hsa-mir-6511a-5p ; hsa-mir-1910-3p ; hsa-mir-4695-5p ; hsa-mir-1294 ; hsa-mir-4316 ; hsa-mir-6077 ; hsa-mir-3188 ; hsa-mir-6884-5p ; hsa-mir-485-5p ; hsa-mir-2467-5p ; hsa-mir-3975 ; hsa-mir-4719 ; hsa-mir-9500 ; hsa-mir-6873-5p ; hsa-mir-3175 ; hsa-mir-3179 ; hsa-mir-3202 ; hsa-mir-4271 ; hsa-mir-4476 ; hsa-mir-4725-3p ; hsa-mir-483-5p ; hsa-mir-6777-5p ; hsa-mir-6780b-5p ; hsa-mir-6783-5p ; hsa-mir-6876-5p ; hsa-mir-6878-5p ; hsa-mir-6889-5p ; hsa-mir-873-5p
Nearest miRNA
hsa-mir-1244-3/Upstream/1324007; hsa-let-7i/Downstream/138098;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/10498, chr12-CpG: 67/Downstream/15553
Upstream sequence
gatcattaccagtggagggactgatgctatttgtatatagaatgatcacttgcaggaaggtggatggagaataatttgtcaagagggcagggctggaggc
Downstream sequence
aggaagcccagttaggaggctggtgcagtaatccatgtgagacgtgttgaggccctaaatttacagtcccgacagtgagggtggagataagtagatagat
Reference
Zhao, L. H., et al.Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma. Nat Commun ,2016,7: 12992.