Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003967
Fusion event
HPV-KLF12 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
E1
Start
116
Host Sequence
Chromosome
chr13
Cytoband
q22.1
Reference genome
Start
End
74289504/73715367 (Hg38)
Location type
Exon7
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-101-3p ; hsa-mir-23a-3p ; hsa-mir-4652-3p ; hsa-mir-4743-3p ; hsa-mir-218-5p ; hsa-mir-4679 ; hsa-mir-4677-3p ; hsa-mir-216b-5p ; hsa-mir-1264 ; hsa-mir-6888-3p ; hsa-mir-4775 ; hsa-mir-215-3p ; hsa-mir-6773-3p ; hsa-mir-34a-5p ; hsa-mir-141-3p ; hsa-mir-137 ; hsa-mir-200a-3p ; hsa-mir-4720-3p ; hsa-mir-4804-3p
Nearest miRNA
hsa-mir-1297/Upstream/7497043; hsa-mir-1267/Downstream/3982645;
Nearest CpG islands
Upstream sequence
gtatcacttcacttttcacaaatgtaaaagaaaacttggaatgaaaatgggcaaaatgtatttataagaacatttgatcaaaatgaaaagtcgtgcctca
Downstream sequence
tagaatgatatgcaaatgcatcttctgtagctacagaggtaaaattgtttttgggcatagtcttttaaaactcagtatttaactcttgcaatggatgctg
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.