Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10019713
Fusion event
HBV-SHROOM3 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2017
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Start
1807
Integrated sequence
CTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCA| |CCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGA
Host Sequence
Chromosome
chr4
Cytoband
q21.1
Reference genome
Start
End
77467928/76546775 (Hg38)
Location type
Intron1
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-6514-3p ; hsa-mir-4314 ; hsa-mir-7977 ; hsa-mir-3649 ; hsa-mir-6847-3p ; hsa-mir-6811-3p ; hsa-mir-214-5p ; hsa-mir-6506-5p ; hsa-mir-619-5p ; hsa-mir-3192-5p ; hsa-mir-4646-5p ; hsa-mir-204-3p ; hsa-mir-383-3p ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-30e-5p ; hsa-mir-30d-5p ; hsa-mir-30c-5p ; hsa-mir-30b-5p ; hsa-mir-30a-5p ; hsa-mir-1537-5p ; hsa-mir-3607-3p ; hsa-mir-6817-5p ; hsa-mir-4769-3p ; hsa-mir-3925-3p ; hsa-mir-766-3p ; hsa-mir-338-3p ; hsa-mir-4530 ; hsa-mir-646
Nearest miRNA
hsa-mir-12113/Upstream/10269847; hsa-mir-1243/Downstream/26793;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/125221, chr4-CpG: 23/Downstream/39149
Upstream sequence
GCCTCTGAATCATAGCACAGAGGATTGACCTGACAGAAGCCAGGTCTCCACTTGGGGCCCTGTCTGTTCCCACCCAAGGAAAGTCTCCACTTACCTGAAT
Downstream sequence
GGTTATGTTGCATTAACTGTGAGTGACTGAAGTGCCCCTCAATCACATACCCCTGCCTTTATCTTCATCTAGGAATGAAAGTAGCCAGGAAAGGCAAAGA
Reference
Cancer Genome Atlas Research Network. Electronic address, w. b. e. and N. Cancer Genome Atlas Research . Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell ,2017,169(7): 1327-1341 e13