Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004102
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
E2
Start
1561
Host Sequence
Chromosome
chr9
Cytoband
q31.1
Reference genome
End
102714439/99952157 (Hg38)
Location type
Intron4
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/1722940; hsa-mir-12126/Downstream/6648771;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/44966, chr9-CpG: 69/Downstream/146336
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.