FN1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10018773
Fusion event
HBV-FN1 integration
Validated
No
Detection method
VirusFinder
Data source
Curated
Sample type
Nontumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Good
Reported year
2017
PubMed ID
29212479
Virus Sequence
Virus name
HBV
Reference genome
NC_003977
Start
2005
Integrated sequence
GACATCGACCCTTATAAAGAATTTGGAGCTACTGTGGAGTTACTCTCGTTTTTGCCTTCTGACTTCTTTCCTTCAGTACGAGATCTTCTAGATACCGCCT| |CAGCTCTGTATCGGGAAGCCTTAGAGTCTCCTGAGCATTGTTCACCTCACCATACTGCACTCAGGCAAGCAATTCTTTGCTGGGGGGAACTAATGACTCT
Host Sequence
Chromosome
chr2
Cytoband
q35
Reference genome
GRCh37.55
Start
216253822/215389099 (Hg38)
End
216253840/215389117 (Hg38)
Location type
Intron21
Target gene
FN1
miRNAs that regulate target gene
hsa-mir-200c-3p ; hsa-mir-200b-3p ; hsa-mir-1-3p ; hsa-let-7g-5p ; hsa-mir-26b-5p ; hsa-mir-615-3p ; hsa-mir-218-5p ; hsa-mir-140-3p
Nearest miRNA
hsa-mir-10b/Upstream/1630940; hsa-mir-1244-1/Downstream/2511396;
Nearest TSS
ENST00000437798/Upstream/5019; ENST00000412951/Downstream/4030;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/76690, chr2-CpG: 43/Downstream/46427
Upstream sequence
GAAGCATTCATCTTTCTTCTCTACTTGTACATTTTTATTTACCTGACAGTGTAAAACCCACAACCAAAAAATAATGGCTTTTTCCCCATTTAAAATACTT
Downstream sequence
ctttttgacgaggttttactctgttgcccaggccggagtgcagtggtgtgatcttggctcactgaaacctctgcctcctgggttcaagtgattctcctgc
Target sequence
ttatttttattatttttt
Reference
Yoo, S., et al. A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC Med ,2017, 15(1): 214.
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