Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004120
Fusion event
HPV-TCTEX1D1 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
E6
Start
820
Host Sequence
Chromosome
chr1
Cytoband
p31.3
Reference genome
Start
End
67239496/66773813 (Hg38)
Location type
Intron3
Fragile sites / regions
Target gene
Nearest miRNA
hsa-mir-101-1/Upstream/145296; hsa-mir-11399/Downstream/1409705;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/21203, chr1-CpG: 27/Downstream/151384
Upstream sequence
TCCTACATACATAACGCAAATTGTCCAAAAAAAATCTAAAAACTCATTTTGGAAAATTATTGATATGCAGCAATAACGTTGACTTTATTTTTTCCAGATA
Downstream sequence
TGGCCGCGTGGAAAGTGTCAAAATTCTTCCCAAGAGGGGATCTGAAGGAGGAGTGGCTGCCTTTGTGGATTTTGTGGACATCAAAAGTGCACAGAAAGCT
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.