VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20003919

Fusion event

HPV-FGD1 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

E4

Start

2495

Host Sequence

Chromosome

chrX

Cytoband

p11.22

Reference genome

GRCh37/hg19

Start

54519473

End

(Hg38)

Location type

intron1

Target gene

FGD1

miRNAs that regulate target gene

hsa-mir-4640-3p ; hsa-mir-2355-3p ; hsa-mir-676-3p ; hsa-mir-6749-3p ; hsa-mir-6852-3p ; hsa-mir-3909 ; hsa-mir-7151-5p ; hsa-mir-4446-5p ; hsa-mir-5006-3p ; hsa-mir-4755-5p ; hsa-mir-670-5p

Nearest CpG islands

None/Target, None/Upstream, None/Downstream

Upstream sequence

GGGATGAAGAGTAGGAAGGGGAGAGAGAAGTGAGCAAACATGGATGTACTATGTGTTTTTCCTTAAGAATGGTGAAGTTGTTTTTTTTTTTTAAAAAAAG

Downstream sequence

TGATTTGTAATTTGAATGAATTGGTGGATTGGGAAGGCATACTCAGAATCATCACCTTGTATTGATTACAGAGGCCAGAGACTGGGGGTCTAGACATTGC

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.