Bioinformatic analysis identifies potential key genes in the pathogenesis of age-related macular degeneration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36018119", "kind": "science-record", "revision": 5, "content_hash": "sha256:b1ff85eb2ed6b08e97ecc7a57aa52c42402970182a48e7b117cef1c7523a6696", "created_at": "2026-11-01T18:15:10Z", "updated_at": "2026-11-01T22:49:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis identifies potential key genes in the pathogenesis of age-related macular degeneration.", "doi": "10.4103/ijo.IJO_3211_21", "pmid": "36018119", "authors": ["Zhiyue Wang", "Xinyu Huang", "Xiao Lv", "Chao Chen", "Shen Qu", "Xiaoyu Ma", "Li Zhang", "Yanlong Bi"], "journal": "Indian journal of ophthalmology", "year": 2022, "abstract": "Purpose: Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in older individuals. More studies focused on screening the genes, which may be correlated with the development of AMD. With advances in various technologies like multiple microarray datasets, researchers could identify differentially expressed genes (DEGs) more accurately. Exploring abnormal gene expression in disease status can help to understand pathophysiological changes in complex diseases. This study aims to identify the key genes and upstream regulators in AMD and reveal factors, especially genetic association, and the prognosis of the development of this disease.\nMethods: Data from expression profile GSE125564 and profile GSE29801 were obtained from the Gene Expression Omnibus (GEO) database. We analyzed DEGs using R software (version 3.6.3). Functional enrichment and PPI network analysis were performed using the R package and online database STRING (version 11.0).\nResults: We compared AMD with normal and found 68 up-regulated genes (URGs) and 25 down-regulated genes (DRGs). We also compared wet AMD with dry AMD and found 41 DRGs in dry AMD. Further work including PPI network analysis, GO classification, and KEGG analysis was done to find connections with AMD. The URGs were mainly enriched in the biological process such as DNA replication, nucleoplasm, extracellular exosome, and cadherin binding. Besides, DRGs were mainly enriched in these functions such as an integral component of membrane and formation of the blood-aqueous barrier (BAB).\nConclusion: This study implied that core genes might involve in the process of AMD. Our findings may contribute to revealing the pathogenesis, developing new biomarkers, and raising strategies of treatment for AMD.", "claims": [{"id": "claim-method", "statement": "We used the Limma package in R software (version 3.6.3) to analyze GSE125564 and GSE29801 aiming to identify DEGs. We used multiple testing and controlled the false discovery rate (FDR) to calculate the P values of each differential expression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36018119", "locator": "sections[4] \"Identify DEGs in AMD\" paragraph 2", "quote": "We used the Limma package in R software (version 3.6.3) to analyze GSE125564 and GSE29801 aiming to identify DEGs. We used multiple testing and controlled the false discovery rate (FDR) to calculate the P values of each differential expression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "There were RPE samples differentiated from induced pluripotent stem cells (iPScs) of four advanced AMD donor eyes and age-matched three non-AMD donors (normal controls) in GSE125564.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36018119", "locator": "sections[3] \"Qualified gene expression data of AMD\" paragraph 2", "quote": "There were RPE samples differentiated from induced pluripotent stem cells (iPScs) of four advanced AMD donor eyes and age-matched three non-AMD donors (normal controls) in GSE125564."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper identified differentially expressed genes in AMD by comparing AMD with normal eyes and wet AMD with dry AMD, followed by PPI, GO, and KEGG analyses.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36018119", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We compared AMD with normal and found 68 up-regulated genes (URGs) and 25 down-regulated genes (DRGs). We also compared wet AMD with dry AMD and found 41 DRGs in dry AMD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper identified differentially expressed genes in AMD by comparing AMD with normal eyes and wet AMD with dry AMD, followed by PPI, GO, and KEGG analyses.", "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:36018119"], "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:GSE125564"], "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": {"fdr_threshold": "Limma with false discovery rate control"}, "inputs": ["data:geo:GSE125564"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36018119", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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