VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10018941

Fusion event

HBV-NLGN4X integration

Validated

No

Detection method

VirusFinder

Data source

Curated

Sample type

Nontumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2017

PubMed ID

29212479

Virus Sequence

Virus name

HBV

Reference genome

NC_003977

Start

1822

Integrated sequence

GTTTAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAAC| |TTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAA

Host Sequence

Chromosome

chrX

Cytoband

p22.32

Reference genome

GRCh37.55

Start

5863798/5945757 (Hg38)

End

5863798/5945757 (Hg38)

Location type

Intron3

Target gene

NLGN4X

miRNAs that regulate target gene

hsa-mir-148b-3p ; hsa-mir-26b-5p ; hsa-mir-6848-3p ; hsa-mir-6843-3p ; hsa-mir-4666b ; hsa-mir-5011-3p ; hsa-mir-502-3p ; hsa-mir-501-3p ; hsa-mir-6718-5p ; hsa-mir-203b-5p ; hsa-mir-6507-5p ; hsa-mir-574-5p ; hsa-mir-1277-5p ; hsa-mir-6083 ; hsa-mir-190a-3p ; hsa-mir-6867-5p ; hsa-mir-223-5p ; hsa-mir-5011-5p ; hsa-mir-6501-3p ; hsa-mir-4797-5p ; hsa-mir-6128 ; hsa-mir-1324 ; hsa-mir-6504-3p ; hsa-mir-1243 ; hsa-mir-3654 ; hsa-mir-323a-3p ; hsa-mir-429 ; hsa-mir-200c-3p ; hsa-mir-200b-3p ; hsa-mir-7-2-3p ; hsa-mir-7-1-3p ; hsa-mir-23b-3p ; hsa-mir-23a-3p ; hsa-mir-130a-5p ; hsa-mir-23c ; hsa-mir-6831-3p ; hsa-mir-8066 ; hsa-mir-550b-3p ; hsa-mir-6758-3p ; hsa-mir-153-5p ; hsa-mir-1250-3p ; hsa-mir-5003-3p ; hsa-mir-6809-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-4753-3p ; hsa-mir-6873-3p ; hsa-mir-139-3p ; hsa-mir-942-5p ; hsa-mir-130b-5p ; hsa-mir-6817-3p ; hsa-mir-7110-3p ; hsa-mir-1248 ; hsa-mir-1237-3p

Nearest miRNA

hsa-mir-3690-1/Upstream/3336503; hsa-let-7f-2/Downstream/438149;

Nearest TSS

ENST00000429181/Upstream/42404; ENST00000217961/Downstream/205709;

Nearest CpG islands

None/Target, chrX-CpG: 62/Upstream/42099, chrX-CpG: 138/Downstream/280322

Upstream sequence

tcattgatcttttgtattttttatttcaaattcatttatttctgctctgatctttatgatttctttccttctactctttttaggtttgatttgctcttgc

Downstream sequence

actggggcctacttgagggtgaagggtgggggtagggagaggatcaaaaaaataactaatgcgtacttggctcaatacctggatgatgaaataatctgta

Reference

Yoo, S., et al. A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC Med ,2017, 15(1): 214.