VMO1 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004145
Fusion event
HPV-VMO1 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
28928286
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
Not given
Gene
E1
Start
2532
Host Sequence
Chromosome
chr17
Cytoband
p13.2
Reference genome
GRCh37/hg19
Start
4689091/4785796 (Hg38)
End
4689091/4785796 (Hg38)
Location type
Intron2
Target gene
VMO1
miRNAs that regulate target gene
hsa-mir-335-5p
Nearest miRNA
hsa-mir-1253/Upstream/2037614; hsa-mir-10226/Downstream/183906;
Nearest TSS
ENST00000595228/Upstream/13904; ENST00000331264/Downstream/575;
Nearest CpG islands
chr17-CpG: 75/Target, None/Upstream, None/Downstream
Upstream sequence
CTGTCTGAGGTGGCATGACTTGGAGTGAGTTTGGATGGGGTGGCCAGGTCTGAGAAGGTCCCCCGCCAGTGTCCTCTGACCCATCTGCTCTCTCCTGCCA
Downstream sequence
TCTTCCATCCACCCTTCGCCTCCCCGGTCTATACTGCCCCGTAGCTCTGGCGGAGCCAGCCTGCCTGTTGCGACGGAGTATGTAATAGAGGGTAAGGGAC
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.
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