Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003893
Fusion event
HPV-CRAT 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
E7
Start
738
Host Sequence
Chromosome
chr9
Cytoband
q34.11
Reference genome
End
131857621/129095342 (Hg38)
Location type
Exon15
Target gene
miRNAs that regulate target gene
Nearest miRNA
hsa-let-7a-1/Upstream/702628; hsa-mir-12126/Downstream/774263;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/13873, chr9-CpG: 135/Downstream/15003
Upstream sequence
TAAAAATCAGTGGTTTCATAAAGAAAAAAACAAGTCACTCAAGGTCAGCATTAGAAATATTCTATTTATTGATTTAGAATAAATTGTAAAACTAATCGTT
Downstream sequence
AGCTTTATTCCTAGGACACCAACACTAGATACCTAAACTGAAAGCTTCCGCCGATTTCACCGAAGGTCAGGAAAGTCCAACGCCCGGCAAACTGGATTTG
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.