Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003910
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
L1
Start
762
Host Sequence
Chromosome
chr21
Cytoband
q22.2
Reference genome
Start
End
40194647/38822723 (Hg38)
Location type
Exon10
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/3101915; hsa-mir-3197/Downstream/624287;
Nearest CpG islands
chr21-CpG: 21/Target, None/Upstream, None/Downstream
Nearest cancer related gene
ETS2(OG, No orient, 0)
Upstream sequence
TCTTCATTGACAAATTGAGTTTAACTCTTTTCCATCCATGTTCACCAAAGGTGGCCCGCCGGTGGGGAAAGAGGAAAAATAAGCCCAAGATGAACTACGA
Downstream sequence
GAAGCTGAGCCGGGGCTTACGCTACTATTACGACAAGAACATCATCCACAAGACGTCGGGGAAGCGCTACGTGTACCGCTTCGTGTGCGACCTCCAGAAC
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.