Bioinformatics analysis of pathways of renal infiltrating macrophages in different renal disease models.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35070815", "kind": "science-record", "revision": 4, "content_hash": "sha256:e0169daf1754f6a94947313ab35d693228574c1b93a5f5b7e6bdfb4905200616", "created_at": "2026-11-01T17:36:48Z", "updated_at": "2026-11-01T21:27:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of pathways of renal infiltrating macrophages in different renal disease models.", "doi": "10.21037/tau-21-761", "pmid": "35070815", "authors": ["Yin Celeste Cheuk", "Pingbao Zhang", "Shihao Xu", "Jiyan Wang", "Tian Chen", "Yongxin Mao", "Yamei Jiang", "Yongsheng Luo", "Jingjing Guo", "Weixi Wang", "Ruiming Rong"], "journal": "Translational andrology and urology", "year": 2021, "abstract": "BACKGROUND: Recent studies have suggested that macrophages are significantly involved in different renal diseases. However, the role of these renal infiltrating macrophages has not been entirely uncovered. To further clarify the underlying mechanism and identify therapeutic targets, a bioinformatic analysis based on transcriptome profiles was performed.\nMETHODS: Three transcription profiling datasets, GSE27045, GSE51466 and GSE75808, were obtained from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were assessed by Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene set enrichment analysis (GSEA).\nRESULTS: The classic signaling pathways and metabolic pathways of macrophages infiltrating the kidney in different pathophysiological processes, including lupus nephritis (LN), renal crystal formation and renal ischemia-reperfusion injury (IRI), were analysed. Furthermore, the common classical pathways significantly altered in the three renal disorders were the oxidative phosphorylation, VEGF signaling and JAK/STAT signaling pathways, while the renin-angiotensin system was uniquely altered in LN, the glycolysis and gluconeogenesis pathways were uniquely altered in models of renal crystal formation, and the calcium signaling pathway was specific to renal IRI.\nCONCLUSIONS: Via bioinformatics analysis, this study revealed the transcriptional features of macrophages in murine LN, renal crystal formation and IRI models, which may serve as promising targets for mechanistic research and the clinical treatment of multiple renal diseases.", "claims": [{"id": "claim-method", "statement": "We used GEO2R to identify DEGs, and the thresholds were set as |logFC| >1 and P<0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35070815", "locator": "sections[6] \"Statistical analysis\" paragraph 2", "quote": "We used GEO2R to identify DEGs, and the thresholds were set as |logFC| >1 and P<0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In the GSE27045 dataset, F4/80hi macrophages were isolated from NZB/W mice in the early stage of lupus, during lupus nephritis and after induction of remission using flow cytometry.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35070815", "locator": "sections[3] \"Data preparation\" paragraph 3", "quote": "In the GSE27045 dataset, F4/80hi macrophages were isolated from NZB/W mice in the early stage of lupus, during lupus nephritis and after induction of remission using flow cytometry."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differentially expressed genes were identified using GEO2R, and their functions were assessed using GO annotation, KEGG pathway analysis, and GSEA.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35070815", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were assessed by Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene set enrichment analysis (GSEA)."}, {"asset": "source:pmid:35070815", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "DEGs were identified by using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differentially expressed genes were identified using GEO2R, and their functions were assessed using GO annotation, KEGG pathway analysis, and GSEA.", "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:35070815"], "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:GSE27045"], "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:GSE27045"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35070815", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tau-21-761", "sha256": 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