VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10006346

Fusion event

HBV-AFF1 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

chr4

Cytoband

q21.3

Reference genome

GRCh38

Start

87006259 (Hg38)

End

87006259 (Hg38)

Location type

Intron

Target gene

AFF1

miRNAs that regulate target gene

hsa-mir-128b ; hsa-mir-877-5p ; hsa-mir-615-3p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-142-3p ; hsa-mir-6073 ; hsa-mir-1914-5p ; hsa-mir-587 ; hsa-mir-17-5p ; hsa-mir-20a-5p ; hsa-mir-93-5p ; hsa-mir-106b-5p ; hsa-mir-20b-5p ; hsa-mir-519d-3p ; hsa-mir-885-3p ; hsa-mir-5197-5p ; hsa-mir-205-5p ; hsa-mir-1228-3p ; hsa-mir-519e-3p ; hsa-mir-515-3p ; hsa-mir-33b-3p ; hsa-mir-371a-3p ; hsa-mir-371b-3p ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485 ; hsa-mir-4279 ; hsa-mir-361-5p ; hsa-mir-889-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-1324 ; hsa-mir-2115-3p ; hsa-mir-3074-3p ; hsa-mir-5571-5p ; hsa-mir-7161-5p ; hsa-mir-548u ; hsa-mir-4744 ; hsa-mir-1273h-3p ; hsa-mir-143-5p ; hsa-mir-3944-5p ; hsa-mir-5093 ; hsa-mir-4480 ; hsa-mir-3166 ; hsa-mir-4771 ; hsa-mir-6790-3p ; hsa-mir-3691-3p ; hsa-mir-548an ; hsa-mir-31-5p ; hsa-mir-5684 ; hsa-mir-4511 ; hsa-mir-548b-3p ; hsa-mir-5692b ; hsa-mir-5692c

Nearest miRNA

hsa-mir-12113/Upstream/463707; hsa-mir-1243/Downstream/294236;

Nearest TSS

ENST00000502981/Upstream/69849; ENST00000511722/Downstream/729;

Nearest CpG islands

None/Target, chr4-CpG: 46/Upstream/70207, chr4-CpG: 76/Downstream/517

Nearest cancer related gene

AFF1(OG, No orient, 0)

Upstream sequence

AATGTTGTCATGATTCTAGGTAGAAGAACGGAGAGTCCACAGTGCAGGCAGTTATTCAGTATTCATCTAAGAGTCTTCAGCTCCTCCGGTGTGCTGGTCC

Downstream sequence

CTATGAGATGCTGAAGCACAACCTCCCTCCATCCTTGCTCATCCAAGTATTTTCCTGCTTTTGAGGCACGGCTTAAACGCTTTCCATGGTCCTCTGAGTA

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.