IFT140 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003951
Fusion event
HPV-IFT140 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
28928286
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Not given
Gene
E1
Start
2253
Host Sequence
Chromosome
chr16
Cytoband
p13.3
Reference genome
GRCh37/hg19
Start
1611947/1561946 (Hg38)
End
1611947/1561946 (Hg38)
Location type
Exon18
Target gene
IFT140
miRNAs that regulate target gene
hsa-mir-93-3p ; hsa-mir-6874-5p ; hsa-mir-6500-5p ; hsa-mir-4633-3p ; hsa-mir-6080 ; hsa-mir-558 ; hsa-mir-6849-5p ; hsa-mir-3681-5p ; hsa-mir-22-3p
Nearest miRNA
hsa-mir-3176/Upstream/791669; hsa-mir-11401/Downstream/173039;
Nearest TSS
ENST00000527434/Upstream/28373; ENST00000563162/Downstream/2164;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/6602, chr16-CpG: 424/Downstream/48107
Upstream sequence
CATCACTCTAGACCAGCAGTTCTGAGCCTTGGTTGCACCTTAGAGTCACCCTATCAGAATTCCTATCAGAATCTGGTTTTGTTTTTGttttaaggcttcc
Downstream sequence
GATCAGAAGACACCTGTGCGGATGTCGTGGCTTCGTACCTTTCTTGTGAAGTAGTAATAAGGCACTTCCATCCCCAGGAGACTGTGGGAGGTGGCAGGCC
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.
Curate