Discovering genetic linkage between periodontitis and type 1 diabetes: A bioinformatics study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37051594", "kind": "science-record", "revision": 4, "content_hash": "sha256:52c28a2ec6d6e1a34dea2ff3154459e2d6d816a04f2b01f90f6d1445c1693678", "created_at": "2026-11-01T19:01:42Z", "updated_at": "2026-11-01T22:51:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Discovering genetic linkage between periodontitis and type 1 diabetes: A bioinformatics study.", "doi": "10.3389/fgene.2023.1147819", "pmid": "37051594", "authors": ["Junqi Liu", "Bo Zhang", "Guanyin Zhu", "Chenlu Liu", "Shuangcheng Wang", "Zhihe Zhao"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Background: Relationship between periodontitis (PD) and type 1 diabetes (T1D) has been reported, but the detailed pathogenesis requires further elucidation. This study aimed to reveal the genetic linkage between PD and T1D through bioinformatics analysis, thereby providing novel insights into scientific research and clinical treatment of the two diseases. Methods: PD-related datasets (GSE10334, GSE16134, GSE23586) and T1D-related datasets(GSE162689)were downloaded from NCBI Gene Expression Omnibus (GEO). Following batch correction and merging of PD-related datasets as one cohort, differential expression analysis was performed (adjusted p-value <0.05 and ∣log2 fold change| > 0.5), and common differentially expressed genes (DEGs) between PD and T1D were extracted. Functional enrichment analysis was conducted via Metascape website. The protein-protein interaction (PPI) network of common DEGs was generated in The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Hub genes were selected by Cytoscape software and validated by receiver operating characteristic (ROC) curve analysis. Results: 59 common DEGs of PD and T1D were identified. Among these DEGs, 23 genes were commonly upregulated, and 36 genes were commonly downregulated in both PD- and T1D-related cohorts. Functional enrichment analysis indicated that common DEGs were mainly enriched in tube morphogenesis, supramolecular fiber organization, 9 + 0 non-motile cilium, plasma membrane bounded cell projection assembly, glomerulus development, enzyme-linked receptor protein signaling pathway, endochondral bone morphogenesis, positive regulation of kinase activity, cell projection membrane and regulation of lipid metabolic process. After PPI construction and modules selection, 6 hub genes (CD34, EGR1, BBS7, FMOD, IGF2, TXN) were screened out and expected to be critical in linking PD and T1D. ROC analysis showed that the AUC values of hub genes were all greater than 70% in PD-related cohort and greater than 60% in T1D-related datasets. Conclusion: Shared molecular mechanisms between PD and T1D were revealed in this study, and 6 hub genes were identified as potential targets in treating PD and T1D.", "claims": [{"id": "claim-method", "statement": "To identify the DEGs between disease and normal samples, the “limma” package and “DESeq2” package in R language software were used for PD- and T1D-related datasets respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37051594", "locator": "sections[4] \"2.2 Identification of DEGs\" paragraph 2", "quote": "To identify the DEGs between disease and normal samples, the “limma” package and “DESeq2” package in R language software were used for PD- and T1D-related datasets respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number (s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37051594", "locator": "sections[16] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number (s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 59 common differentially expressed genes between periodontitis and type 1 diabetes and selected six hub genes: CD34, EGR1, BBS7, FMOD, IGF2, and TXN.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37051594", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "59 common DEGs of PD and T1D were identified."}, {"asset": "source:pmid:37051594", "locator": "sections[11] \"3.3 PPI network construction and hub genes selection\" paragraph 2", "quote": "6 hub genes were identified in this study: CD34, EGR1, BBS7, FMOD, IGF2, TXN."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 59 common differentially expressed genes between periodontitis and type 1 diabetes and selected six hub genes: CD34, EGR1, BBS7, FMOD, IGF2, and TXN.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37051594"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE10334"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE10334"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37051594", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2023.1147819", "sha256": "sha256:edec603894dc38758bbca9844b8f293227cf87de493bf1975edadf8172f33a3d", "bytes": 53169, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2023.1147819", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10083320", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10334", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10334", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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