Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004100
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
E6
Start
483
Host Sequence
Chromosome
chr9
Cytoband
q31.1
Reference genome
End
102677474/99915192 (Hg38)
Location type
Exon2
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/1685975; hsa-mir-12126/Downstream/6685736;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/8001, chr9-CpG: 69/Downstream/183301
Upstream sequence
GTAGTGTATGCGACTTCAAAAGGCTTCCGTAATTCACAAATTACCAGTAAAAGGGGAAAAAGATTATACACTTAAAATACAGCTCACTTGAGCATGCTAC
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.