Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35615586", "kind": "science-record", "revision": 5, "content_hash": "sha256:cae938d7b8d5e8ccb2563c7829a960bd756eb7edf899c490b532c792dc0c8713", "created_at": "2026-11-01T18:14:32Z", "updated_at": "2026-11-01T22:49:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance.", "doi": "10.3389/fnagi.2022.884367", "pmid": "35615586", "authors": ["Fan Chen", "Na Wang", "Xiaping He"], "journal": "Frontiers in aging neuroscience", "year": 2022, "abstract": "Background: Alzheimer's disease (AD) is a common neurodegenerative disease. The pathogenesis is complex and has not been clearly elucidated, and there is no effective treatment. Recent studies have demonstrated that DNA methylation is closely associated with the pathogenesis of AD, which sheds light on investigating potential biomarkers for the diagnosis of early AD and related possible therapeutic approaches.\nMethods: Alzheimer's disease patients samples and healthy controls samples were collected from two datasets in the GEO database. Using LIMMA software package in R language to find differentially expressed genes (DEGs). Afterward, DEGs have been subjected to enrichment analysis of GO and KEGG pathways. The PPI networks and Hub genes were created and visualized based on the STRING database and Cytoscape. ROC curves were further constructed to analyze the accuracy of these genes for AD diagnosis.\nResults: Analysis of the GSE109887 and GSE97760 datasets showed 477 significant DEGs. GO and KEGG enrichment analysis showed terms related to biological processes related to these genes. The top ten Hub genes were found on the basis of the PPI network using the CytoHubba plugin, and the AUC areas of these top ranked genes were all greater than 0.7, showing satisfactory diagnostic accuracy.\nConclusion: The study identified the top 10 Hub genes associated with AD-related DNA methylation, of which RPSA, RPS23, and RPLP0 have high diagnostic accuracy and excellent AD biomarker potential.", "claims": [{"id": "claim-method", "statement": "We used the R package Limma (version 3.40.6) to perform differential analysis of downloaded expression profile datasets to obtain differential genes between normal and AD groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35615586", "locator": "sections[4] \"Data Processing and Identification of Differentially Expressed Genes\" paragraph 2", "quote": "We used the R package Limma (version 3.40.6) to perform differential analysis of downloaded expression profile datasets to obtain differential genes between normal and AD groups."}], "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 below: https://www.ncbi.nlm.nih.gov/, GSE109887; https://www.ncbi.nlm.nih.gov/, GSE97760.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35615586", "locator": "sections[17] \"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 below: https://www.ncbi.nlm.nih.gov/, GSE109887; https://www.ncbi.nlm.nih.gov/, GSE97760."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Analysis of two GEO datasets identified 477 significant differentially expressed genes, with the 10 hub genes showing AUC values of 0.776–0.848 and RPSA, RPS23, and RPLP0 demonstrating the highest diagnostic accuracy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35615586", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Analysis of the GSE109887 and GSE97760 datasets showed 477 significant DEGs."}, {"asset": "source:pmid:35615586", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The top ten Hub genes were found on the basis of the PPI network using the CytoHubba plugin, and the AUC areas of these top ranked genes were all greater than 0.7, showing satisfactory diagnostic accuracy."}, {"asset": "source:pmid:35615586", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The study identified the top 10 Hub genes associated with AD-related DNA methylation, of which RPSA, RPS23, and RPLP0 have high diagnostic accuracy and excellent AD biomarker potential."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Analysis of two GEO datasets identified 477 significant differentially expressed genes, with the 10 hub genes showing AUC values of 0.776–0.848 and RPSA, RPS23, and RPLP0 demonstrating the highest diagnostic accuracy.", "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:35615586"], "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:GSE109887"], "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:GSE109887"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35615586", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnagi.2022.884367", "sha256": "sha256:6eb55320bb0c58571aae864813fecff197a9edb69379e0cdff0494ad5af120e6", "bytes": 31317, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fnagi.2022.884367", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9125150", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE109887", "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=GSE109887", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE109887", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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