Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004031
Fusion event
HPV-PARP14 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
HPV33
Reference genome
Not given
Gene
E1
Start
4050
Host Sequence
Chromosome
chr3
Cytoband
q21.1
Reference genome
End
122421840/122702993 (Hg38)
Location type
Intron6
Target gene
miRNAs that regulate target gene
Nearest miRNA
hsa-let-7g/Upstream/1653278; hsa-mir-12124/Downstream/458801;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/21650, chr3-CpG: 28/Downstream/90645
Upstream sequence
ACATCCTTTGTAGACTAGTCCCTTTAGTCACTGCTCTGTGGCCATGCCCCTCAACATGGCTGTACCTGGAAGCTCATAGTCCTGGCAGAGCTGGCTGCTG
Downstream sequence
aaaaaaaaaaaaaaaaacaaaaaaaaaaaacaaaaaacaaaaaacaGTCATAGTTTGCTTTCCTTTCACTCCCATAGATGCTTAGCTTCCATGGCTGTAA
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.