Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004035
Fusion event
HPV-PDCD1LG2 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Not given
Gene
E1
Start
165
Host Sequence
Chromosome
chr9
Cytoband
p24.1
Reference genome
Start
End
5549340/5549340 (Hg38)
Location type
Exon4
Target gene
Nearest miRNA
hsa-mir-101-2/Upstream/698965; hsa-let-7a-1/Downstream/458486;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/98711, chr9-CpG: 107/Downstream/79230
Upstream sequence
CAAAACTGAACCAAACTGATAAAATGGCAAATCTTAGAAGGAGAATTGTGATTCATATTAGGTTTTTTCTTTTTTAATCTGGCAAGTGAATGTGGTTACC
Downstream sequence
TAATACCTTTAGAATTCATCCCCATACATACTAGCCTGGTTTCCTCTAATGTTAAGTTAACAAAATCTTATGATTCTTTTGAAGTATAAGACTTTTCCTG
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.