VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10006831

Fusion event

HBV-PHF20 integration

Validated

Yes

Detection method

Alu PCR and sequencing

Data source

Curated

Sample type

Tumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Good

Reported year

2015

PubMed ID

25815780

Virus Sequence

Virus name

HBV

Reference genome

Not given

Start

1612

Host Sequence

Chromosome

chr20

Cytoband

q11.23

Reference genome

GRCh38/hg38

Start

35833665 (Hg38)

End

35833819 (Hg38)

Orient

+

Location type

Intronic 1

Target gene

PHF20

miRNAs that regulate target gene

hsa-mir-197-3p ; hsa-mir-21-5p ; hsa-mir-1303 ; hsa-mir-5096 ; hsa-mir-3187-3p ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-6802-3p ; hsa-mir-411-5p ; hsa-mir-6832-5p ; hsa-mir-193b-5p ; hsa-mir-3620-3p ; hsa-mir-6865-3p ; hsa-mir-483-5p ; hsa-mir-10b-5p ; hsa-mir-10a-5p

Nearest miRNA

hsa-mir-103a-2/Upstream/379568; hsa-mir-1-1/Downstream/2682744;

Nearest TSS

ENST00000382410/Upstream/61632; ENST00000496305/Downstream/15570;

Nearest CpG islands

None/Target, chr20-CpG: 39/Upstream/61337, chr20-CpG: 146/Downstream/119861

Upstream sequence

TTTTTAAAAATTACATCTGGTGAACCTTTATTGAATGTCTAATATATGCAGGATACCCTGGGGGAGATTCAGACTCTTGATCTCTGAAGGTTTGATCCAA

Downstream sequence

gaggctgaggcgggcagatcacgaagtcaggagttcaagaccagcctggccaacatggtgaaaccccgtctctactaaaaatacaaaaattggccaggca

Target sequence

AGGCTAAGTCTTCTCTGAACCCTTTCCCAACCCTCTAGTTAGAAAAAATGGGACTCTGATGAAAAAGTTTAATGTGGGCTTTAGAATGAAGGGTTAAAAAAAATAAAAAATAgaccaggcacagcggttcatgcctgtaatcccagcactttgg

Reference

Zhang, X., et al. DNA methylation consistency implicates the primary tumor cell origin of recurrent hepatocellular carcinoma. Epigenomics,2015, 7(4): 581-592.