SPATA12 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004095
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
E1
Start
445
Host Sequence
Chromosome
chr3
Cytoband
p14.3
Reference genome
GRCh37/hg19
Start
57094696/57060668 (Hg38)
End
57094696/57060668 (Hg38)
Location type
Exon1
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/1208074; hsa-mir-12124/Downstream/3557137;
Nearest TSS
ENST00000440867/Upstream/227; ENST00000607541/Downstream/18147;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/258486, chr3-CpG: 112/Downstream/18053
Upstream sequence
tttaaaatttttaaatGGTAGATTATATGTCTTAATTTTCCTCTAAAGCCCAATTTGATTAAAAGTGGTTTGTGAACAGTCATTGGCTTCCACCCAGCAT
Downstream sequence
CACTGAGAAAATTCTTTGTGCAGGCTCACCTTCCCCTCATCTCCCCCACTCTTCCTGATCCTGCAGCGTCAGATCCCAGCCTGCAGTATCAGACCTCAAA
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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