VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10016008

Fusion event

HBV-FN1 integration

Validated

Yes

Detection method

Alu PCR and sequencing

Data source

Curated

Sample type

Nontumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2012

PubMed ID

22962577

Virus Sequence

Virus name

HBV

Reference genome

Not given

Start

1819

Orient

-

Host Sequence

Chromosome

chr2

Cytoband

q35

Reference genome

GRCh37/hg19

Start

216264921/215400198 (Hg38)

End

216264921/215400198 (Hg38)

Orient

+

Location type

Intron

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/1642039; hsa-mir-1244-1/Downstream/2500315;

Nearest TSS

ENST00000437798/Upstream/6477; ENST00000412951/Downstream/9752;

Nearest CpG islands

None/Target, chr2-CpG: 135/Upstream/87789, chr2-CpG: 43/Downstream/35346

Upstream sequence

TTCTCTTCACTCCGCATCAAACAAGGCAAGGTGTGATCACACAGACTATTTGGGGGTGGGTGGCTGTGGGTCGTCATCTCCACAGTGCTTGGTTTCTCTT

Downstream sequence

aaaaaaaaGCTTTACGCTGAATTATTCCACAATAATGGTCAGCTATTTTTGGTTGCAATAAAAGATGCTATATAAAAGTTAAACAAAATCTGCCACCATG

Reference

Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.