Evidence map›Paper›PMID 41244916›Full record

ArticleFrontiers in oncology2025

dbGVOSCC: a comprehensive database of genetic variation for systems genetics research on oral squamous cell carcinoma.

Yi Zhou, Yutao Wu, Wenjing Shi, Yingbo Zhang, Xingyun Liu, Yuxin Zhang, Chaoying Zhan, Bingyue Chen, Weidong Tian, Bairong Shen

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PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in oncology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Yi Zhou *Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Yutao Wu *Department of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Wenjing ShiDepartment of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Yingbo ZhangDepartment of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Xingyun LiuDepartment of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Yuxin ZhangDepartment of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Chaoying ZhanDepartment of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Bingyue ChenDepartment of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
Weidong TianState Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Engineering Research Center of Oral Translational Medicine, Ministry of Education & National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
Bairong ShenDepartment of Breast Surgery and Institute for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

cancer heterogeneitydbGVOSCC databasegenetic variationsoral squamous cell carcinomaprecision oncology

Identifiers

PMID41244916
PMCPMC12616376

What Socratic holds

Textmetadata
LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.