Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004054
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
E6
Start
835
Host Sequence
Chromosome
chr14
Cytoband
q24.1
Reference genome
Start
End
68963838/68497121 (Hg38)
Location type
Intron10
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/1055191; hsa-mir-1185-1/Downstream/4019699;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/821956, chr14-CpG: 40/Downstream/131177
Upstream sequence
CTGGACTACTGGCAATGAGTAATGTCTGGACTTCATGTGAAATGCCATCTCAAGAAAGGGCATCTGAAAGCGTGCTTTTACCATTTCATTTCAGGCACTT
Downstream sequence
AGCCTATGGAAATTCCTAGAGACAGATAAATGTGCAAACCTGTTCATCTTGCCAAGAAAAATCCGCTTTTCTGCCACAGAAACAAAATATTGGGAAAGAG
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.