VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004136

Fusion event

HPV-TNFSF4 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

180

Host Sequence

Chromosome

chr1

Cytoband

q25.1

Reference genome

GRCh37/hg19

Start

173175941/173206802 (Hg38)

End

173175941/173206802 (Hg38)

Location type

Exon1

Fragile sites / regions

FRA1G

Target gene

TNFSF4

miRNAs that regulate target gene

hsa-mir-6869-5p ; hsa-mir-4303 ; hsa-mir-3182 ; hsa-mir-4682 ; hsa-mir-8485 ; hsa-mir-3941 ; hsa-mir-603 ; hsa-mir-362-3p ; hsa-mir-329-3p

Nearest miRNA

hsa-mir-101-1/Upstream/1062158; hsa-mir-1182/Downstream/2761568;

Nearest TSS

ENST00000473358/Upstream/1078; ENST00000460950/Downstream/511;

Nearest CpG islands

None/Target, chr1-CpG: 111/Upstream/673397, chr1-CpG: 100/Downstream/270037

Upstream sequence

TCTGAGAAAACTTCATCTTTGTAACATTTTAGCTTAAAGCAATATTGTATTTTGTTATTATTGTTATAATAATGACTAAAATTTGTTTTCTCCCTTGTTT

Downstream sequence

TTAGTTCTATGAGTACTGTGTCTTATATGGAAGAACCCAGTCAGCGTGATGATATCTCTCGCCTTACAGTTCAGATGGAAAACACCTATCAGTTGGGTGT

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.