VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004090

Fusion event

HPV-SLC25A34 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

833

Host Sequence

Chromosome

chr1

Cytoband

p36.21

Reference genome

GRCh37/hg19

Start

16066376/15739881 (Hg38)

End

16066376/15739881 (Hg38)

Location type

Exon5

Fragile sites / regions

FRA1A

Target gene

SLC25A34

miRNAs that regulate target gene

hsa-mir-1273e ; hsa-mir-4266 ; hsa-mir-486-3p ; hsa-mir-4722-5p ; hsa-mir-6721-5p ; hsa-mir-4779 ; hsa-mir-219b-3p ; hsa-mir-4695-5p ; hsa-mir-302f ; hsa-mir-6513-5p ; hsa-mir-887-5p ; hsa-mir-3913-5p ; hsa-mir-3122 ; hsa-mir-450a-1-3p ; hsa-mir-6780a-5p ; hsa-mir-6779-5p ; hsa-mir-3689c ; hsa-mir-3689b-3p ; hsa-mir-3689a-3p ; hsa-mir-30b-3p ; hsa-mir-1273h-5p ; hsa-mir-6788-5p ; hsa-mir-30c-2-3p ; hsa-mir-30c-1-3p ; hsa-mir-6799-5p ; hsa-mir-6883-5p ; hsa-mir-6785-5p ; hsa-mir-4728-5p ; hsa-mir-149-3p ; hsa-mir-7106-5p ; hsa-mir-3922-5p ; hsa-mir-6849-5p ; hsa-mir-3681-5p ; hsa-mir-4753-5p ; hsa-mir-7977 ; hsa-mir-383-3p ; hsa-mir-4284 ; hsa-mir-7160-5p ; hsa-mir-4755-3p ; hsa-mir-6089 ; hsa-mir-5008-5p ; hsa-mir-4649-3p ; hsa-mir-338-3p ; hsa-mir-7157-5p ; hsa-mir-4310 ; hsa-mir-4786-5p ; hsa-mir-3922-3p ; hsa-mir-3176 ; hsa-mir-3190-5p ; hsa-mir-622 ; hsa-mir-4433a-3p ; hsa-mir-4459 ; hsa-mir-4768-3p ; hsa-mir-6500-3p ; hsa-mir-3614-5p

Nearest miRNA

hsa-mir-12136/Upstream/3160858; hsa-mir-101-1/Downstream/1119068;

Nearest TSS

ENST00000473358/Upstream/846; ENST00000465575/Downstream/2541;

Nearest CpG islands

None/Target, chr1-CpG: 111/Upstream/7871, chr1-CpG: 18/Downstream/4252

Upstream sequence

GATTCTCCCAGAGATGAAGTTACTATATTGTTTTATTCCTTTCTACTGTCTTCTTTGCTAAAATGTTCCCACCTCCCAACTTAATAAAGAAATCCACAAC

Downstream sequence

CCTGTCTCATGCATAAGTAGCTATGACCCATCTCTCTCCTTTCATTCCCAATCAGTAGTTGTGAATGGTTTCCCACGATCATCACCTTCACAGCTATTCA

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.