VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20005044

Fusion event

HPV-PLCXD2 integration

Validated

No

Detection method

WGS, RNA-seq, Whole-Exome sequencing, PCR

Data source

Curated

Sample type

Tumor

Disease

Head and neck squamous cell carcinoma (HNSCC)

Quality evaluation

Perfect

Reported year

2014

PubMed ID

25313082

Virus Sequence

Virus name

HPV

Subtype

HPV33

Reference genome

Not given

Gene

E1

Start

2495

Host Sequence

Chromosome

chr3

Cytoband

q13.2

Reference genome

GRCh37/hg19

Start

111493569/111774722 (Hg38)

End

111493569/111774722 (Hg38)

Location type

Intronic

Target gene

PLCXD2

miRNAs that regulate target gene

hsa-mir-1-3p ; hsa-mir-16-5p ; hsa-mir-92a-3p ; hsa-mir-1273e ; hsa-mir-6783-3p ; hsa-mir-1343-3p ; hsa-mir-503-3p ; hsa-mir-6861-5p ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-4291 ; hsa-mir-193a-5p ; hsa-mir-205-5p ; hsa-mir-7157-5p ; hsa-mir-4310

Nearest miRNA

hsa-let-7g/Upstream/2171825; hsa-mir-12124/Downstream/338079;

Nearest TSS

ENST00000440867/Upstream/42225; ENST00000478922/Downstream/84458;

Nearest CpG islands

None/Target, chr3-CpG: 148/Upstream/100025, chr3-CpG: 59/Downstream/84668

Junction sequence

GCATTTGTATTTGAGGTAAGAAGCAGTGGTGGACATTTTAATTGCACTAATGCCCTATGTTTCACATCTATT---TACTAGGCCCCAAATTCGTGGTGTTTTTA

* Color: Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence

Reference

Parfenov, M., et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A,2014,111(43): 15544-15549.