Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004101
Fusion event
HPV-STX17 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
3404
Host Sequence
Chromosome
chr9
Cytoband
q31.1
Reference genome
End
102713340/99951058 (Hg38)
Location type
Exon4
Target gene
miRNAs that regulate target gene
hsa-mir-30b-5p ; hsa-mir-5089-5p ; hsa-mir-6811-5p ; hsa-mir-6511b-5p ; hsa-mir-5589-5p ; hsa-mir-4731-5p ; hsa-mir-210-5p ; hsa-mir-4313 ; hsa-mir-1233-3p ; hsa-mir-6506-5p ; hsa-mir-1225-3p ; hsa-mir-619-5p ; hsa-mir-324-3p ; hsa-mir-1913 ; hsa-mir-6752-3p ; hsa-mir-6810-3p ; hsa-mir-6801-3p ; hsa-mir-512-3p ; hsa-mir-6769a-3p ; hsa-mir-195-5p ; hsa-mir-16-5p ; hsa-mir-15b-5p ; hsa-mir-15a-5p
Nearest miRNA
hsa-let-7a-1/Upstream/1721841; hsa-mir-12126/Downstream/6649870;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/43867, chr9-CpG: 69/Downstream/147435
Upstream sequence
TAGTGTATGCGACTTCAAAAGGCTTCCGTAATTCACAAATTACCAGTAAAAGGGGAAAAAGATTATACACTTAAAATACAGCTCACTTGAGCATGCTACC
Downstream sequence
ttctcagacaagatatctcctcataattacaagatggatgccaATGATTATTAAACCTTTCAGATTCAAATATTTTACAAGAAAAAAAAGCCAGAGTATT
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.