VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20003851

Fusion event

HPV-ARHGEF3 integration

Validated

No

Detection method

RNA-Seq

Data source

Curated

Sample type

Tumor

Disease

Head and neck squamous cell carcinoma (HNSCC)

Quality evaluation

Normal

Reported year

2018

PubMed ID

28928286

Virus Sequence

Virus name

HPV

Subtype

HPV16

Reference genome

Not given

Gene

E6

Start

784

Host Sequence

Chromosome

chr3

Cytoband

p14.3

Reference genome

GRCh37/hg19

Start

57074785/57040757 (Hg38)

End

57074785/57040757 (Hg38)

Location type

Intron1

Target gene

ARHGEF3

miRNAs that regulate target gene

hsa-mir-138-5p ; hsa-mir-373-3p ; hsa-mir-335-5p ; hsa-mir-769-5p ; hsa-mir-377-5p ; hsa-mir-485-5p ; hsa-mir-3680-3p ; hsa-mir-557 ; hsa-mir-507 ; hsa-mir-450b-5p ; hsa-mir-889-3p ; hsa-mir-4793-5p ; hsa-mir-5196-3p

Nearest miRNA

hsa-let-7g/Upstream/1188163; hsa-mir-12124/Downstream/3577048;

Nearest TSS

ENST00000440867/Upstream/63382; ENST00000334325/Downstream/19684;

Nearest CpG islands

None/Target, chr3-CpG: 148/Upstream/238575, chr3-CpG: 112/Downstream/37964

Upstream sequence

ACTTTTCTGAACACTATGGAAGACACTTGACCTGGTCAAGCTCCCAAATACTTGAGTGGCCTAATTGAGACTGAGCTGCTTTAGCTGTTGACAAACCTGA

Downstream sequence

CAGGCCTGTGTCCTTTCACCTCTGAATGAAGCAGACCCCAGCTGACCTCCTCAACACCCACACCACCCTGCCAACCGCTGCCCACCAGACTGACCTGGAA

Reference

Koneva, L. A., et al. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res ,2018,16(1): 90-102.