VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10006508

Fusion event

HBV-CDC42BPA integration

Validated

Yes

Detection method

invPCR +Sequencing

Data source

Curated

Sample type

Tumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2016

PubMed ID

27453547

Virus Sequence

Virus name

HBV

Reference genome

V01460.1

Host Sequence

Chromosome

chr1

Cytoband

q42.13

Reference genome

GRCh38

Start

227011883 (Hg38)

End

227011883 (Hg38)

Location type

Intron

Fragile sites / regions

FRA1H

Target gene

CDC42BPA

miRNAs that regulate target gene

hsa-mir-335-5p ; hsa-mir-98-5p ; hsa-let-7c-5p ; hsa-mir-485-5p ; hsa-mir-218-5p ; hsa-mir-4753-3p ; hsa-mir-6868-3p ; hsa-mir-1468-3p ; hsa-mir-3124-3p ; hsa-mir-130b-5p ; hsa-mir-8063 ; hsa-mir-6856-5p ; hsa-mir-6758-5p ; hsa-mir-216b-5p ; hsa-mir-4311

Nearest miRNA

hsa-mir-101-1/Upstream/1089741; hsa-mir-1182/Downstream/929707;

Nearest TSS

ENST00000473358/Upstream/19743; ENST00000424451/Downstream/22834;

Nearest CpG islands

None/Target, chr1-CpG: 111/Upstream/35347, chr1-CpG: 104/Downstream/305862

Upstream sequence

TCCGATTACGCAGGAACTATCACTCAGTAGCCAGTCACCTTCTCTAATGGGAATTTTCAAGATTCAGTTCTTGAAGAACAGTTATGTTTCCAGAAAACAT

Downstream sequence

GATCCCTTCATTAGAGGCAGAGGGTGAATGGCGTGTTGGAGAGAGTGCTAACTGAATCCAGCATGGAATTCACGTTCCCATGAGCTGAGATGAACCTGCT

Reference

Mason, W. S., et al. HBV DNA Integration and Clonal Hepatocyte Expansion in Chronic Hepatitis B Patients Considered Immune Tolerant. Gastroenterology,2016, 151(5): 986-998 e984.