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dbGVOSCC: a comprehensive database of genetic variation for systems genetics
research on oral squamous cell carcinoma
#MMPMID41244916
Zhou Y
; Wu Y
; Shi W
; Zhang Y
; Liu X
; Zhang Y
; Zhan C
; Chen B
; Tian W
; Shen B
Front Oncol
2025[]; 15
(?): 1692732
PMID41244916
show ga
INTRODUCTION: Oral squamous cell carcinoma (OSCC) is a highly aggressive
malignancy of the oral epithelium, marked by a high rate of lymph node metastasis
and a profound negative impact on patients' quality of life. Despite its
severity, no routine screening program currently exists for OSCC. To address the
genetic heterogeneity underlying OSCC, we have developed a database of genetic
variation in oral squamous cell carcinoma (dbGVOSCC;
http://www.sysbio.org.cn/dbGVOSCC/). METHODS: OSCC literature (1991-2024) was
queried from PubMed and screened manually and via PubTator, following predefined
inclusion/exclusion criteria. Entities and relations were extracted from
qualifying articles and organized into tables. The database adopted a
browser/server architecture using HTML and XAMPP. Front-end was built with HTML
and CSS for web display; server-side used Apache for infrastructure, MySQL for
data management, and PHP/JavaScript for backend-frontend integration.
Bioinformatics included mapping genes to STRING (confidence >0.9), hub gene
identification via PPI degree centrality, and GO/KEGG enrichment with
clusterProfiler (FDR-corrected). Usability was assessed using SUS and NPS
surveys. RESULTS: dbGVOSCC comprises 1,788 somatic genetic variation entries from
400 original studies and 106,079 clinical samples, covering
epimutations/methylations (329), SNPs (411), point mutations excluding SNP (258),
indels (98), CNVs (348), LOH (28), one locus mutation, plus 333 unspecified
mutations. We curated 817 biomarker-linked variations (diagnostic n=71,
therapeutic n=175, prognostic n=291; 277 multi-application). PPI analysis
highlighted 15 key genes (e.g., TP53, CTNNB1, AKT1, EGFR, PIK3CA). Enrichment
implicated proliferation, adhesion/migration, p53/DNA damage response, and
PI3K-Akt signaling. User testing showed SUS 88.75 (grade A) and NPS 90.
DISCUSSION: dbGVOSCC represents a robust and reliable knowledge base, offering
clinicians and researchers an open-source platform for personalized
genotype-phenotype association studies and systems genetics research into the
mechanisms of OSCC.
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