Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018292
Fusion event
HBV-EXTL3 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
2247
Host Sequence
Chromosome
chr8
Cytoband
p21.1
Reference genome
Start
End
28508835/28651318 (Hg38)
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-500a-5p ; hsa-mir-125b-5p ; hsa-mir-10b-5p ; hsa-mir-10a-5p ; hsa-mir-99a-5p ; hsa-mir-4474-3p ; hsa-mir-644a ; hsa-mir-6505-3p ; hsa-mir-617 ; hsa-mir-4673 ; hsa-mir-4302 ; hsa-mir-4645-5p ; hsa-mir-199a-5p ; hsa-mir-199b-5p ; hsa-mir-6828-3p ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-642a-5p ; hsa-mir-920 ; hsa-mir-6726-5p ; hsa-mir-5591-5p ; hsa-mir-4300 ; hsa-mir-6090 ; hsa-mir-6827-5p ; hsa-mir-505-5p ; hsa-mir-6847-3p ; hsa-mir-767-3p ; hsa-mir-6728-3p ; hsa-mir-4469 ; hsa-mir-6870-3p ; hsa-mir-2276-5p ; hsa-mir-6892-3p ; hsa-mir-4793-5p ; hsa-mir-5196-3p ; hsa-mir-141-5p ; hsa-mir-887-5p ; hsa-mir-6780a-5p ; hsa-mir-6779-5p ; hsa-mir-3689c ; hsa-mir-3689b-3p ; hsa-mir-3689a-3p ; hsa-mir-30b-3p ; hsa-mir-1273h-5p ; hsa-mir-6788-5p ; hsa-mir-30c-2-3p ; hsa-mir-30c-1-3p ; hsa-mir-514b-5p ; hsa-mir-513c-5p ; hsa-mir-566 ; hsa-mir-6789-3p ; hsa-mir-134-3p ; hsa-mir-7114-5p ; hsa-mir-4315 ; hsa-mir-101-3p ; hsa-mir-1276 ; hsa-mir-1323 ; hsa-mir-548o-3p
Nearest miRNA
hsa-mir-124-1/Upstream/146136; hsa-mir-10400/Downstream/1305954;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/28037, chr8-CpG: 145/Downstream/49753
Nearest cancer related gene
EXTL3(TSG, No orient, 0)
Upstream sequence
aatataaatgaagggaaaatagatgtttattgtattaatattcaagctttctttagatttaatttttttccaaataaTATTTGAGAAAAGAACaagaaac
Downstream sequence
AGAACAGtttcttctgtttttttcaaagacagggtctaactttgtcccccacgctggagtgcagtggcactatcatgactcactgcagcctcgaactcct
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