Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004058
Fusion event
HPV-RAD51B 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
E4
Start
717
Host Sequence
Chromosome
chr14
Cytoband
q24.1
Reference genome
Start
End
68699686/68232969 (Hg38)
Location type
Intron7
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-484 ; hsa-mir-4668-5p ; hsa-mir-2053 ; hsa-mir-6780a-5p ; hsa-mir-6779-5p ; hsa-mir-3689c ; hsa-mir-3689b-3p ; hsa-mir-30b-3p ; hsa-mir-3689a-3p ; hsa-mir-1273h-5p ; hsa-mir-569 ; hsa-mir-6799-5p ; hsa-mir-6883-5p ; hsa-mir-6785-5p ; hsa-mir-4728-5p ; hsa-mir-149-3p ; hsa-mir-7106-5p ; hsa-mir-766-5p ; hsa-mir-6871-5p ; hsa-mir-4496 ; hsa-mir-4506
Nearest miRNA
hsa-mir-208a/Upstream/791039; hsa-mir-1185-1/Downstream/4283851;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/557804, chr14-CpG: 40/Downstream/395329
Upstream sequence
TCTGACTCATTCAGGCCTCTAGAAAAATAGCTGTAGGTACTGGAAGGGCTATGTAGATCAAGGAGGTCAGATAAATTGGCTTGATGTTGGTCTATAGAAA
Downstream sequence
AATCTAGAAGATATTGCCAAAAGCTTTTAAGCATACCGTCTTCAGATGCTGGGATGTGGGCTATATCCACAGGCCATTGGCTCATTCATGTGTTTGAAGC
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.