Screening of periodontitis-related genes and immune cells based on an integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35722384", "kind": "science-record", "revision": 5, "content_hash": "sha256:340edf047cc3f5b297c9e68af4a8dfba1d34807e75fcedc41622fa528876f296", "created_at": "2026-11-01T18:14:44Z", "updated_at": "2026-11-01T22:49:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of periodontitis-related genes and immune cells based on an integrated bioinformatics analysis.", "doi": "10.21037/atm-22-1592", "pmid": "35722384", "authors": ["Qiang Ban", "Xiaofang Ling", "Hui Ding", "Jiansheng Meng", "Yuan Li", "Juanfei Zhang", "Mingyi Zhu"], "journal": "Annals of translational medicine", "year": 2022, "abstract": "Background: Periodontitis is a serious health issue; however, there are few reports on periodontitis and immune related. The study sought to analyze differences in gene expression between periodontitis patients before and after treatment using bioinformatics techniques.\nMethods: The GSE6751 data set was screened for differentially expressed genes (DEGs) and immune-related genes using the Gene Expression Omnibus (GEO) database, a gene expression data analysis tool. Enrichment, protein-protein interaction (PPI) network construction, and immune cell correlation analyses were also performed on these genes.\nResults: A total of 327 DEGs in periodontitis were identified, including 149 upregulated genes, 178 downregulated genes, and 27 immune-related genes. The immune-related DEGs were mainly involved in granulocyte chemotaxis, granulocyte migration, leukocyte chemotaxis, cytokine receptor binding, Toll-like receptor (TLR) binding, the phosphatidylinositol-3-kinase and protein kinase b signaling pathway, viral protein interactions with cytokines and cytokine receptors, the Ras-proximate-1 signaling pathway, the Ras signaling pathway, natural killer cell mediated cytotoxicity, and immune response related pathways. IFNG and TLR2 were the key core genes in the constructed PPI network.\nConclusions: The pathogenesis of periodontitis is closely related to changes in the expression of genes, such as PF4, ANGPT1, TNFRSF1B, IFNG and TLR2, among which IFNG and TLR2 are potential therapeutic targets for periodontitis.", "claims": [{"id": "claim-method", "statement": "The Wilcoxon rank-sum test was used to compare differences in gene expression between pre- and post-treatment periodontitis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35722384", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "The Wilcoxon rank-sum test was used to compare differences in gene expression between pre- and post-treatment periodontitis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE6751 data set was obtained. A total of 59 samples were obtained, 29 of which were from 1 week before periodontitis treatment and 30 of which were from 6–10 weeks after treatment.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35722384", "locator": "sections[3] \"Data acquisition\" paragraph 2", "quote": "The GSE6751 data set was obtained. A total of 59 samples were obtained, 29 of which were from 1 week before periodontitis treatment and 30 of which were from 6–10 weeks after treatment."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 327 DEGs in periodontitis were identified, including 149 upregulated genes, 178 downregulated genes, and 27 immune-related genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35722384", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 327 DEGs in periodontitis were identified, including 149 upregulated genes, 178 downregulated genes, and 27 immune-related genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 327 DEGs in periodontitis were identified, including 149 upregulated genes, 178 downregulated genes, and 27 immune-related genes.", "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:35722384"], "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:GSE6751"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE6751"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35722384", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-22-1592", "sha256": "sha256:d1258bfabf03e89cd317f1a8c85f435c1a368f7058a9185f839ee290a4937836", "bytes": 28838, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm-22-1592", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9201185", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE6751", "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=GSE6751", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6751", "version": null, "note": "The GSE6751 data set was obtained. 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