Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018286
Fusion event
HBV-LSAMP integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2017
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Not given
Start
1760
Host Sequence
Chromosome
chr3
Cytoband
q13.31
Reference genome
End
115814086/116095239 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-26b-5p ; hsa-mir-369-3p ; hsa-mir-5584-3p ; hsa-mir-552-5p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-5006-3p ; hsa-mir-4755-5p ; hsa-mir-3977 ; hsa-mir-6873-3p ; hsa-mir-211-5p ; hsa-mir-204-5p ; hsa-mir-623 ; hsa-mir-103a-2-5p ; hsa-mir-302d-5p ; hsa-mir-302b-5p ; hsa-mir-942-5p ; hsa-mir-4680-3p ; hsa-mir-6845-3p ; hsa-mir-6832-3p ; hsa-mir-345-3p ; hsa-mir-3162-3p ; hsa-mir-3150b-5p ; hsa-mir-3150a-5p ; hsa-mir-6756-3p ; hsa-mir-4469 ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-6818-3p ; hsa-mir-6888-3p ; hsa-mir-593-3p ; hsa-mir-6895-3p ; hsa-mir-630 ; hsa-mir-3120-5p ; hsa-mir-4742-3p ; hsa-mir-6817-3p ; hsa-mir-7110-3p ; hsa-mir-361-3p ; hsa-mir-4778-5p ; hsa-mir-629-3p ; hsa-mir-4279 ; hsa-mir-6867-3p ; hsa-mir-4713-5p ; hsa-mir-6868-3p ; hsa-mir-6763-3p ; hsa-mir-5581-5p ; hsa-mir-4297 ; hsa-mir-3124-3p ; hsa-mir-1976 ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-7113-3p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-660-3p ; hsa-mir-3127-3p ; hsa-mir-553 ; hsa-mir-4762-3p ; hsa-mir-29b-2-5p ; hsa-mir-4256 ; hsa-mir-6719-3p ; hsa-mir-4526 ; hsa-mir-3660 ; hsa-mir-6730-3p ; hsa-mir-296-3p ; hsa-mir-192-3p ; hsa-mir-342-3p
Nearest miRNA
hsa-let-7g/Upstream/1351714; hsa-mir-12124/Downstream/755038;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/310505, chr3-CpG: 75/Downstream/1901478
Nearest cancer related gene
LSAMP(TSG, No orient, 0)
Upstream sequence
AGACTTGACTTTTGGGCTTCAGCAAGATGTGGAAACTTTTTTAAAAGAATTTTTGCTTTCTTTCTCTCTAAATTTTCCTTCCGTGCTTTGATGCGGGCTC
Downstream sequence
ATCACCTGAAAGTGCAAAAGTTCACATGGCAAATGGCAAAACCCAGACAAGCTGCGCAATTTCTGGAGCAATGAAAAGGCCTCCATAGACATGCTTTTTG
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