VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004091

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

E4

Start

451

Host Sequence

Chromosome

chr1

Cytoband

p36.21

Reference genome

GRCh37/hg19

Start

16066506/15740011 (Hg38)

End

16066506/15740011 (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/3160988; hsa-mir-101-1/Downstream/1118938;

Nearest TSS

ENST00000473358/Upstream/976; ENST00000465575/Downstream/2411;

Nearest CpG islands

None/Target, chr1-CpG: 111/Upstream/8001, chr1-CpG: 18/Downstream/4122

Upstream sequence

GCTCTACACTCCCCTTCACCCCTATACAAAAGTCATCCTCAACCCTTTCAGACTCTGACATCTCAAATTATATCCCCCTTCATGTGGATACCCTCCTCAC

Downstream sequence

CCCACTTTGGCTCTAGCACCCCATGCTAGGCCACTGCTCCAGTTGGGCTCCAATATACCCTTTCAGGCCACTGCTACTATCCCTTCTTCCCATCTCACTT

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.