Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004093
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
E7
Start
3390
Host Sequence
Chromosome
chr10
Cytoband
q25.2
Reference genome
End
112327466/110567708 (Hg38)
Location type
Exon1
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/6299303; hsa-mir-202/Downstream/330382;
Nearest CpG islands
chr10-CpG: 91/Target, None/Upstream, None/Downstream
Upstream sequence
caaagagatccaaataaccacttgtagactttacagacagagtgtttccaaactgctcaattaaaagaaaggttaaactctgtgagttgaacgcacacat
Downstream sequence
cacaaagtagtttctgagaatgattctctgtagcttttatatgaagatatttacatttctaacattggcgtcaaatcgcttgaaatctccacttgcaaaa
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.