Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004125
Fusion event
HPV-TEAD1 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
E6
Start
1192
Host Sequence
Chromosome
chr11
Cytoband
p15.2
Reference genome
Start
End
12897549/12876002 (Hg38)
Location type
Intron5
Target gene
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-98-5p ; hsa-mir-320a ; hsa-mir-215-3p ; hsa-mir-503-3p ; hsa-mir-548at-5p ; hsa-mir-873-5p ; hsa-mir-101-5p ; hsa-mir-377-3p ; hsa-mir-1324 ; hsa-mir-5004-3p ; hsa-mir-1261 ; hsa-mir-4748 ; hsa-mir-4464 ; hsa-mir-624-3p ; hsa-mir-548e-5p ; hsa-mir-7150 ; hsa-mir-580-3p ; hsa-mir-6720-5p ; hsa-mir-6512-3p ; hsa-mir-4736 ; hsa-mir-4763-3p ; hsa-mir-1207-5p ; hsa-mir-6077 ; hsa-mir-5580-5p ; hsa-mir-219a-1-3p ; hsa-mir-6868-5p ; hsa-mir-9500 ; hsa-mir-4267 ; hsa-mir-4445-3p ; hsa-mir-4722-5p ; hsa-mir-1286 ; hsa-mir-548x-5p ; hsa-mir-548g-5p ; hsa-mir-548f-5p ; hsa-mir-548aj-5p ; hsa-mir-494-3p ; hsa-mir-548p ; hsa-mir-561-3p ; hsa-mir-5187-3p ; hsa-mir-6515-3p ; hsa-mir-1236-3p ; hsa-mir-3140-5p ; hsa-mir-4713-5p ; hsa-mir-3156-3p ; hsa-mir-2116-3p ; hsa-mir-532-3p ; hsa-mir-150-5p ; hsa-mir-4301 ; hsa-mir-181a-2-3p
Nearest miRNA
hsa-mir-210/Upstream/712235; hsa-let-7a-2/Downstream/3093531;
Nearest CpG islands
Upstream sequence
TGCGCCCCTCTCAGCCAGCCCGGGAGCCCGCCAGGGGCCGGCGGCTGGCAGCGCTCACCGCGAAGGTGGGCCCGGGCCGCCCGCTCTGCGCCCGCCGCTT
Downstream sequence
ACCTGGCAGGGTCCCGCGGGAACCTGAAGAAGGCCAAGTCGGACTGCGTGCTCTTCCGCGTGCAGTTGGGGGCAGCGCAGAAGTTCGGCATCGTcgcccg
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.