VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10016030

Fusion event

HBV-PPFIA4 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

1818

Orient

-

Host Sequence

Chromosome

chr1

Cytoband

q32.1

Reference genome

GRCh37/hg19

Start

203022097/203052969 (Hg38)

End

203022097/203052969 (Hg38)

Orient

+

Location type

Intron

Target gene

PPFIA4

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-21-5p ; hsa-mir-6857-5p ; hsa-mir-6788-5p ; hsa-mir-30c-2-3p ; hsa-mir-30c-1-3p ; hsa-mir-4450 ; hsa-mir-8085 ; hsa-mir-6731-5p ; hsa-mir-6878-5p ; hsa-mir-5589-5p ; hsa-mir-5192 ; hsa-mir-4731-5p ; hsa-mir-4693-3p ; hsa-mir-8089 ; hsa-mir-4700-5p ; hsa-mir-4667-5p

Nearest miRNA

hsa-mir-101-1/Upstream/1049733; hsa-mir-1182/Downstream/2395333;

Nearest TSS

ENST00000473358/Upstream/1729; ENST00000600447/Downstream/734;

Nearest CpG islands

None/Target, chr1-CpG: 111/Upstream/25912, chr1-CpG: 67/Downstream/22625

Upstream sequence

CTACCTGGGCTTATATGTTATGCAGTCAGTGAGACTGTTACTCGGAAACTTTTTCATTAAAATAAGGTGGTTACAGTTTAAAAAGGCCCTGAGCTTTTCT

Downstream sequence

GATCATAAGATTTAGGGCCCGCGTCACCCTGTCTTTTTAACTCTGTGAGAGTACCAGAACAAAGATTTCATATTATTAACTTTGAAGGATTTGTACCTAG

Reference

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