Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018312
Fusion event
HBV-chr13 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2017
PubMed ID
Virus Sequence
Virus name
HBV
Reference genome
Not given
Start
1942
Host Sequence
Chromosome
chr13
Cytoband
q14.11
Reference genome
Start
End
41381422/40807286 (Hg38)
Location type
Intronic
miRNAs that regulate target gene
hsa-mir-193b-3p ; hsa-mir-375 ; hsa-mir-7-5p ; hsa-mir-24-3p ; hsa-mir-423-3p ; hsa-mir-218-5p ; hsa-mir-6807-5p ; hsa-mir-5089-5p ; hsa-mir-5589-5p ; hsa-mir-4731-5p ; hsa-mir-6720-3p ; hsa-mir-668-5p ; hsa-mir-4252 ; hsa-mir-6506-5p ; hsa-mir-619-5p ; hsa-mir-3922-3p ; hsa-mir-3176 ; hsa-mir-1273g-3p ; hsa-mir-1295b-3p ; hsa-mir-3186-5p ; hsa-mir-1227-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-4279 ; hsa-mir-4537 ; hsa-mir-455-3p ; hsa-mir-4722-3p ; hsa-mir-6499-3p ; hsa-mir-6516-5p ; hsa-mir-6727-3p ; hsa-mir-6747-3p
Nearest miRNA
hsa-mir-2276/Upstream/79377; hsa-mir-1267/Downstream/3480;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/17081, chr13-CpG: 43/Downstream/114354
Upstream sequence
TCTTCATTTACAAAATCAGCTTCTTCCTTACTAGTGCTTGATCAGATCTGTTAATTGGTTGCAAATGCCCTTGTCTTTTCTTCCTTCCCACCTGCTGTAA
Downstream sequence
CTCCCAGTACAGTGTGGTCTGTCATCAAAAGTATTCTTAGGAAAGATGGCCCCTTGGGGTTCTACCATGGACTCTCAAGCACTTTACTTCGAGAAGTACC
Target sequence
CCGTGCTATCTCTCTGTGTCTC
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