Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004094
Fusion event
HPV-SMC3 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
3450
Host Sequence
Chromosome
chr10
Cytoband
q25.2
Reference genome
End
112328694/110568936 (Hg38)
Location type
Exon2
Target gene
miRNAs that regulate target gene
hsa-mir-340-5p ; hsa-mir-196a-5p ; hsa-mir-615-3p ; hsa-mir-193b-3p ; hsa-mir-92a-3p ; hsa-mir-3163 ; hsa-let-7a-2-3p ; hsa-let-7g-3p ; hsa-mir-382-5p ; hsa-mir-3613-5p ; hsa-mir-526b-5p ; hsa-mir-27b-5p ; hsa-mir-4680-3p ; hsa-mir-5187-3p ; hsa-mir-4427 ; hsa-mir-4762-5p ; hsa-mir-4668-3p ; hsa-mir-493-5p ; hsa-let-7c-3p ; hsa-mir-524-5p ; hsa-mir-520d-5p ; hsa-mir-302a-5p ; hsa-mir-4700-3p ; hsa-mir-10a-3p ; hsa-mir-7844-5p
Nearest miRNA
hsa-mir-107/Upstream/6300531; hsa-mir-202/Downstream/329154;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/506, chr10-CpG: 137/Downstream/74259
Upstream sequence
cccccaatgtgttggtatttggaggtggggcatttgggatgttactattatccatttagatgacgtcatgagagttgtgccctggagacagaattagtac
Downstream sequence
ctacacctgatcttggacttcccagcctccagcaggaaagtgagaaataaatttcttttcttttcttttttcttttttttttttgagacggagtttcact
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.