Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004098
Fusion event
HPV-SPEN 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
694
Host Sequence
Chromosome
chr1
Cytoband
p36.21
Reference genome
Start
End
16199313/15872818 (Hg38)
Location type
Exon2
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-151a-5p ; hsa-mir-877-3p ; hsa-mir-23b-5p ; hsa-mir-769-5p ; hsa-mir-615-3p ; hsa-mir-193b-3p ; hsa-mir-423-3p ; hsa-mir-324-5p ; hsa-mir-331-3p ; hsa-mir-328-3p ; hsa-mir-106b-5p ; hsa-mir-320a ; hsa-mir-186-5p ; hsa-mir-125b-5p ; hsa-mir-196a-5p ; hsa-mir-92a-3p ; hsa-mir-16-5p ; hsa-mir-18a-5p ; hsa-mir-18b-5p ; hsa-mir-214-3p ; hsa-mir-3619-5p ; hsa-mir-4722-5p ; hsa-mir-4735-3p ; hsa-mir-4768-3p ; hsa-mir-6165 ; hsa-mir-761 ; hsa-mir-885-3p
Nearest miRNA
hsa-mir-12136/Upstream/3293795; hsa-mir-101-1/Downstream/986131;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/23196, chr1-CpG: 22/Downstream/61557
Upstream sequence
ttatctgggtggtagctacatgactatatagaaacgcaaaaagcactgggctgtagacataaaatttatgtattttacttatgtaaattgctcaataaat
Downstream sequence
caaacatttaaaaaTATTTAATTAAAATATTAAACATTTCATGTAAAATATTAAAGCTGTTAAGCTCAAAATAAAGATTTTGCCAAGGGTTAGCAACCAA
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.