Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004001
Fusion event
HPV-MAML3 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
L1
Start
3536
Host Sequence
Chromosome
chr4
Cytoband
q31.1
Reference genome
End
140810511/139889357 (Hg38)
Location type
Exon3
Fragile sites / regions
Target gene
miRNAs that regulate target gene
hsa-mir-3682-3p ; hsa-mir-4424 ; hsa-mir-4679 ; hsa-mir-1273g-3p ; hsa-mir-1272 ; hsa-mir-1255b-2-3p ; hsa-mir-4477b ; hsa-mir-5684 ; hsa-mir-651-3p ; hsa-mir-548c-3p ; hsa-mir-452-3p ; hsa-mir-576-3p ; hsa-mir-539-3p ; hsa-mir-485-3p ; hsa-mir-101-3p ; hsa-mir-144-3p ; hsa-mir-499a-3p ; hsa-mir-499b-3p ; hsa-mir-505-3p ; hsa-mir-5696 ; hsa-mir-579-3p ; hsa-mir-664b-3p
Nearest miRNA
hsa-mir-12113/Upstream/14382050; hsa-mir-1305/Downstream/3454103;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/29078, chr4-CpG: 20/Downstream/261012
Upstream sequence
atatatatacacatatatatacgtatatatatacatatatacgtgtatatatacatatatatatacacgtatatatatatacatatatatatacacgtat
Downstream sequence
TGACCGTGGGATGGAAGTGCAGCGTAAGCCATGGGCTGATTCATCACTCCTTTCTGCTTCATGAGAAGCAGGCGTTTCTGGTCTTCGCTCAGGTGTGCCC
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.