Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003887
Fusion event
HPV-CD274 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
E4
Start
6952
Host Sequence
Chromosome
chr9
Cytoband
p24.1
Reference genome
Start
End
5464507/5464507 (Hg38)
Location type
Intron4
Target gene
miRNAs that regulate target gene
hsa-mir-513a-5p ; hsa-mir-103a-3p ; hsa-mir-16-5p ; hsa-mir-570-3p ; hsa-mir-651-3p ; hsa-mir-3978 ; hsa-mir-593-3p ; hsa-mir-885-3p ; hsa-mir-380-5p ; hsa-mir-124-3p ; hsa-mir-601 ; hsa-mir-708-5p ; hsa-mir-34b-5p ; hsa-mir-665 ; hsa-mir-940 ; hsa-mir-326 ; hsa-mir-363-5p ; hsa-mir-214-3p ; hsa-mir-29c-3p ; hsa-mir-3977 ; hsa-mir-5706 ; hsa-mir-4782-5p ; hsa-mir-516b-5p ; hsa-mir-1299 ; hsa-mir-103a-2-5p ; hsa-mir-4790-3p ; hsa-mir-6128 ; hsa-mir-875-3p ; hsa-mir-4496 ; hsa-mir-138-5p ; hsa-mir-324-5p ; hsa-mir-338-5p ; hsa-mir-34a-3p ; hsa-mir-152-5p ; hsa-mir-200b-3p ; hsa-mir-152-3p ; hsa-mir-1273a ; hsa-mir-1273c ; hsa-mir-15a-5p ; hsa-mir-15b-5p ; hsa-mir-194-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-4503 ; hsa-mir-497-5p ; hsa-mir-6792-5p ; hsa-mir-6838-5p
Nearest miRNA
hsa-mir-101-2/Upstream/614132; hsa-let-7a-1/Downstream/543319;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/13878, chr9-CpG: 107/Downstream/164063
Upstream sequence
cagccaaatgtgcaactgggtatagggggtctaacaaatgtcttcaggattcaaattgtctctatcatttcttcactctgtttcctttttgttgatgcca
Downstream sequence
tttcctccaagtatattaatgtccttttcctggagaagtggaattcttcctcttttccccttgaatttggactggctttaatgacttctttgaccataga
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.