GPD2 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20003941
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
E1
Start
781
Host Sequence
Chromosome
chr2
Cytoband
q24.1
Reference genome
GRCh37/hg19
Start
157336234/156479722 (Hg38)
End
157336234/156479722 (Hg38)
Location type
Intron2
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/5111311; hsa-mir-10b/Downstream/2707113;
Nearest TSS
ENST00000437798/Upstream/6130; ENST00000464846/Downstream/91450;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/43225, chr2-CpG: 31/Downstream/1117565
Upstream sequence
atgtgtgtatattAATTTATATTTTAAAAAAATCCAAggccgggcatggtgtctcacacctgtaatcccagcactttgggaggccgaggtgggcagatca
Downstream sequence
CCACAGATAACATCCACATTCCAGGCCTTCCTCAGTTAAGCATCTGAGGGCTTTTAGCGTGGTCTTAGAGTGGCTTCTTCTTCATTTTCTTGTCCCCTTT
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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