Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003897
Fusion event
HPV-DUSP5 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
3388
Host Sequence
Chromosome
chr10
Cytoband
q25.2
Reference genome
End
112258133/110498375 (Hg38)
Location type
Exon1
Target gene
miRNAs that regulate target gene
hsa-mir-181a-5p ; hsa-mir-335-5p ; hsa-mir-27b-3p ; hsa-mir-27a-3p ; hsa-mir-16-1-3p ; hsa-mir-25-3p ; hsa-mir-32-5p ; hsa-mir-92a-3p ; hsa-mir-203a-3p ; hsa-mir-222-5p ; hsa-mir-363-3p ; hsa-mir-367-3p ; hsa-mir-92b-3p ; hsa-mir-627-5p ; hsa-mir-924 ; hsa-mir-3912-5p ; hsa-mir-181b-5p ; hsa-mir-181c-5p ; hsa-mir-181d-5p ; hsa-mir-302a-5p ; hsa-mir-26a-5p
Nearest miRNA
hsa-mir-107/Upstream/6229970; hsa-mir-202/Downstream/399715;
Nearest CpG islands
chr10-CpG: 187/Target, None/Upstream, None/Downstream
Nearest cancer related gene
DUSP5(TSG, No orient, 0)
Upstream sequence
CCTCCCAGCTCAGGCAAGCCTAGCGTGGACACAGAAACCCTTGACACTGAGCCAATATCTCTTCCCCCTGTATGGCTTGAATTTCAGATATATTGATGTT
Downstream sequence
GAGCCCTTCTGGCCGGCAGTGGGACTCCCCTTGGCCTTACATAGGTAATGCCTATATCCTGGCCTGGGCTTTTCCAAGAAGCCAGACTCTGGGAAGGACC
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.