SPATA12 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004097
Fusion event
HPV-SPATA12 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
E6
Start
365
Host Sequence
Chromosome
chr3
Cytoband
p14.3
Reference genome
GRCh37/hg19
Start
57098409/57064381 (Hg38)
End
57098409/57064381 (Hg38)
Location type
Intron1
Target gene
SPATA12
miRNAs that regulate target gene
hsa-let-7b-5p ; hsa-mir-302a-5p ; hsa-mir-153-5p
Nearest miRNA
hsa-let-7g/Upstream/1211787; hsa-mir-12124/Downstream/3553424;
Nearest TSS
ENST00000440867/Upstream/3940; ENST00000607541/Downstream/14434;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/262199, chr3-CpG: 112/Downstream/14340
Upstream sequence
ttttttttttttgagacagagtctcgctctggttgcccaggctggagtgcaacggcgcgatctcaactcatcgcaatctctgcctcctgggttcaagcga
Downstream sequence
ggcaagatcacggctcactgcagcctcaacttccctgactcaagtgatcctcccatctcagcccccaagtagctgagattacaggtgcatgccaccacgc
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.
Curate