VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20003903

Fusion event

HPV-ERBB2 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

755

Host Sequence

Chromosome

chr17

Cytoband

q12

Reference genome

GRCh37/hg19

Start

37879571/39723318 (Hg38)

End

37879571/39723318 (Hg38)

Location type

Exon20

Target gene

ERBB2

miRNAs that regulate target gene

hsa-mir-559 ; hsa-mir-548d-3p ; hsa-mir-125b-5p ; hsa-mir-21-5p ; hsa-mir-125a-5p ; hsa-mir-331-3p ; hsa-mir-205-5p ; hsa-mir-199b-5p ; hsa-mir-199a-5p ; hsa-mir-124-3p ; hsa-mir-326 ; hsa-mir-375 ; hsa-mir-25-3p ; hsa-mir-670-3p ; hsa-mir-4326 ; hsa-mir-552-3p ; hsa-mir-541-3p ; hsa-mir-498 ; hsa-mir-323b-5p ; hsa-mir-193a-5p ; hsa-mir-193a-3p ; hsa-mir-134-5p ; hsa-mir-6739-3p ; hsa-mir-4677-5p ; hsa-mir-7156-5p ; hsa-mir-4273 ; hsa-mir-7109-5p ; hsa-mir-4790-5p ; hsa-mir-6868-3p ; hsa-mir-3127-5p ; hsa-mir-22-5p ; hsa-mir-2116-5p ; hsa-mir-593-3p ; hsa-mir-6885-5p ; hsa-mir-328-5p ; hsa-mir-6887-5p ; hsa-mir-486-3p ; hsa-mir-6795-5p ; hsa-mir-3140-3p ; hsa-mir-3116 ; hsa-mir-1254 ; hsa-mir-4790-3p ; hsa-mir-6730-3p ; hsa-mir-4680-3p ; hsa-mir-5187-3p ; hsa-mir-4427 ; hsa-mir-4653-5p ; hsa-mir-3921 ; hsa-mir-301b-5p ; hsa-mir-301a-5p ; hsa-mir-4315 ; hsa-mir-146a-3p ; hsa-mir-3667-3p ; hsa-mir-6734-3p ; hsa-mir-6891-3p ; hsa-mir-6072 ; hsa-mir-6754-5p ; hsa-mir-4441 ; hsa-mir-4270 ; hsa-mir-211-3p ; hsa-mir-4748 ; hsa-mir-329-5p ; hsa-mir-4464 ; hsa-mir-7845-5p ; hsa-mir-888-3p ; hsa-mir-4506 ; hsa-mir-34a-5p ; hsa-mir-155-3p ; hsa-mir-130b-3p ; hsa-mir-1296-5p ; hsa-mir-133a-3p ; hsa-mir-3622b-5p ; hsa-mir-22-3p

Nearest miRNA

hsa-mir-1180/Upstream/425809; hsa-mir-10226/Downstream/3177;

Nearest TSS

ENST00000595228/Upstream/5889; ENST00000584888/Downstream/5068;

Nearest CpG islands

None/Target, chr17-CpG: 26/Upstream/22680, chr17-CpG: 17/Downstream/82

Nearest cancer related gene

ERBB2(OG, No orient, 0)

Upstream sequence

CTTCATCTTCACTTGAAGCCAAATGAAGTTTGATTTTTAATTCACCTTGCAGAGTCATAAAGCAAACCAGTGATTGCAGTTAATGCTCAAACTCTGTCTC

Downstream sequence

CCCTCTGACGTCCATCATCTCTGCGGTGGTTGGCATTCTGCTGGTCGTGGTCTTGGGGGTGGTCTTTGGGATCCTCATCAAGCGACGGCAGCAGAAGATC

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.