GPD2 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003936
Fusion event
HPV-GPD2 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
E7
Start
3412
Host Sequence
Chromosome
chr2
Cytoband
q24.1
Reference genome
GRCh37/hg19
Start
157292174/156435662 (Hg38)
End
157292174/156435662 (Hg38)
Location type
Exon1
Target gene
GPD2
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-30a-5p ; hsa-mir-335-5p ; hsa-mir-21-5p ; hsa-mir-877-3p ; hsa-mir-206
Nearest miRNA
hsa-mir-128-1/Upstream/5067251; hsa-mir-10b/Downstream/2751173;
Nearest TSS
ENST00000437798/Upstream/221; ENST00000416888/Downstream/727;
Nearest CpG islands
chr2-CpG: 89/Target, None/Upstream, None/Downstream
Upstream sequence
CCCTTCTTGACAGCACCTCGGCCCTTCGTTAGGGCACTGCCCCGAGTCCAGTCGCTCCCAGAACccctggccaagcagcagcagtgtcccctgggagtct
Downstream sequence
GGGCGAGGGTTCTGGGCTCTGACGGCGGGGTCGCAGGGTCGCCCGCCTCCTGGACACGTCTGTAGGCCTAGGGAAGCCTGCCGGCCGGGAGGTACAGAGT
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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