Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003918
Fusion event
HPV-ETS2 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
2510
Host Sequence
Chromosome
chr21
Cytoband
q22.2
Reference genome
Start
End
40190657/38818733 (Hg38)
Location type
Intron7
Target gene
miRNAs that regulate target gene
hsa-mir-199a-3p ; hsa-mir-199a-5p ; hsa-mir-218-5p ; hsa-mir-877-5p ; hsa-mir-149-5p ; hsa-mir-18a-5p ; hsa-mir-196b-5p ; hsa-mir-455-5p ; hsa-mir-548t-3p ; hsa-mir-3646 ; hsa-mir-3662 ; hsa-mir-548aa ; hsa-mir-548ap-3p ; hsa-mir-548as-3p ; hsa-mir-548at-3p ; hsa-mir-548ay-3p ; hsa-mir-587 ; hsa-mir-1468-3p ; hsa-mir-548f-5p ; hsa-mir-548g-5p ; hsa-mir-548x-5p ; hsa-mir-548aj-5p ; hsa-mir-548aw ; hsa-mir-410-3p ; hsa-mir-582-5p ; hsa-mir-944 ; hsa-mir-607 ; hsa-mir-3671 ; hsa-mir-190a-3p ; hsa-mir-205-3p ; hsa-mir-338-5p
Nearest miRNA
hsa-let-7c/Upstream/3097925; hsa-mir-3197/Downstream/628277;
Nearest CpG islands
None/Target, chr21-CpG: 261/Upstream/11990, chr21-CpG: 21/Downstream/3987
Nearest cancer related gene
ETS2(OG, No orient, 0)
Upstream sequence
ACCAACAATTCTGGTAAGATTGGAAGCATCTTTCAACAAGGCTGTTGCTTTGATTCTGAGAACCCCAGAGCCATAATGAACCTCTTAATAAATACTTCCT
Downstream sequence
GGATTCAGCCATTAGAGAAGGGGGTCAAAGCCCATGTTCTAAGTGGATTtccaacaagcatacccctaatatgtttcaggcactggcccaggtactgcag
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.