Identification of Hub Genes and Immune-Related Pathways for Membranous Nephropathy by Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35812314", "kind": "science-record", "revision": 5, "content_hash": "sha256:27ab69a67c5d462d281c9d2603ea23ea533cbd441ff87a102ea95f49767c2bb0", "created_at": "2026-11-01T18:14:52Z", "updated_at": "2026-11-01T22:49:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub Genes and Immune-Related Pathways for Membranous Nephropathy by Bioinformatics Analysis.", "doi": "10.3389/fphys.2022.914382", "pmid": "35812314", "authors": ["Xiao-Yu Cai", "Zu-Feng Wang", "Shu-Wang Ge", "Gang Xu"], "journal": "Frontiers in physiology", "year": 2022, "abstract": "OBJECTIVE: We aim to explore the detailed molecular mechanisms of membrane nephropathy (MN) related genes by bioinformatics analysis. METHODS: Two microarray datasets (GSE108109 and GSE104948) with glomerular gene expression data from 65 MN patients and 9 healthy donors were obtained from the Gene Expression Omnibus (GEO) database. After processing the raw data, DEGs screening was conducted using the LIMMA (linear model for microarray data) package and Gene set enrichment analysis (GSEA) was performed with GSEA software (v. 3.0), followed by gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. The protein-protein interaction (PPI) network analysis was carried out to determine the hub genes, by applying the maximal clique centrality (MCC) method, which was visualized by Cytoscape. Finally, utilizing the Nephroseq v5 online platform, we analyzed subgroups associated with hub genes. The findings were further validated by immunohistochemistry (IHC) staining in renal tissues from MN or control patients. RESULTS: A sum of 370 DEGs (188 up-regulated genes, 182 down-regulated genes) and 20 hub genes were ascertained. GO and KEGG enrichment analysis demonstrated that DEGs of MN were preponderantly associated with cell damage and complement cascade-related immune responses. Combined with literature data and hub gene-related MN subset analysis, CTSS, ITGB2, and HCK may play important roles in the pathological process of MN. CONCLUSION: This study identified novel hub genes in MN using bioinformatics. We found that some hub genes such as CTSS, ITGB2, and HCK might contribute to MN immunopathological process, providing new insights for further study of the molecular mechanisms underlying glomerular injury of MN.", "claims": [{"id": "claim-method", "statement": "To test for differentially expressed genes across renal glomerular tissues from MN and healthy controls, we utilized the LIMMA (linear model of microarray data) (Smyth, 2004) package of R program.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35812314", "locator": "sections[4] \"Data Preprocessing and Differentially Expressed Genes Identification\" paragraph 2", "quote": "To test for differentially expressed genes across renal glomerular tissues from MN and healthy controls, we utilized the LIMMA (linear model of microarray data) (Smyth, 2004) package of R program."}], "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:35812314", "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 in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In conclusion, we identified 370 DEGs and 10 hub genes that may serve as diagnostic indicators and therapeutic targets for prevention of MN occurrence and development.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35812314", "locator": "sections[1] \"Introduction\" paragraph 4", "quote": "In conclusion, we identified 370 DEGs and 10 hub genes that may serve as diagnostic indicators and therapeutic targets for prevention of MN occurrence and development."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In conclusion, we identified 370 DEGs and 10 hub genes that may serve as diagnostic indicators and therapeutic targets for prevention of MN occurrence and development.", "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:35812314"], "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. 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