IFT140 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003956
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
807
Host Sequence
Chromosome
chr16
Cytoband
p13.3
Reference genome
GRCh37/hg19
Start
1612203/1562202 (Hg38)
End
1612203/1562202 (Hg38)
Location type
Intron17
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/791925; hsa-mir-11401/Downstream/172783;
Nearest TSS
ENST00000527434/Upstream/28629; ENST00000563162/Downstream/1908;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/6858, chr16-CpG: 424/Downstream/47851
Upstream sequence
GCTCTTCGGAAATGAAGAAGGACAGGATCAAAACATCTGCCTGGGAGAGAAAGAAAAGTACTGTTCTGTTTTTTTTTTTAACTTACATAAATTTCTGGGG
Downstream sequence
TGCGTCACGGTGGGGTCGTTGCTACACACTGCGTCATGGTGGGGTCGGGTGCTTTGCTTTGATTACACCACCTTTTATCTGCTCCACTTGGGAAAAACCA
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