Screening and Bioinformatics Analysis of IgA Nephropathy Gene Based on GEO Databases.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31392215", "kind": "science-record", "revision": 5, "content_hash": "sha256:c87fcd33b8e03e983e38cc6b8e11dc0d532c108e6b41d7c5f8530ee52b72f1cf", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T22:00:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and Bioinformatics Analysis of IgA Nephropathy Gene Based on GEO Databases.", "doi": "10.1155/2019/8794013", "pmid": "31392215", "authors": ["Wang Qian", "Wang Xiaoyi", "Ye Zi"], "journal": "BioMed research international", "year": 2019, "abstract": "PURPOSE: To identify novel biomarkers of IgA nephropathy (IgAN) through bioinformatics analysis and elucidate the possible molecular mechanism.\nMETHODS: The GSE93798 and GSE73953 datasets containing microarray data from IgAN patients and healthy controls were downloaded from the GEO database and analyzed by the GEO2R web tool to obtain different expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, protein-protein interaction (PPI), and Biological Networks Gene Oncology tool (BiNGO) were then performed to elucidate the molecular mechanism of IgAN.\nRESULTS: A total of 223 DEGs were identified, of which 21 were hub genes, and involved in inflammatory response, cellular response to lipopolysaccharide, transcription factor activity, extracellular exosome, TNF signaling pathway, and MAPK signaling pathway.\nCONCLUSIONS: TNF and MAPK pathways likely form the basis of IgAN progression, and JUN/JUNB, FOS, NR4A1/2, EGR1, and FOSL1/2 are novel prognostic biomarkers of IgAN.", "claims": [{"id": "claim-method", "statement": "The DEGs between IgAN patients and normal subjects were analyzed using the GEO2R web tool (http://www.ncbi.nlm.nih.gov/geo/geo2r).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31392215", "locator": "sections[3] \"2.1. Identification of DEGs\" paragraph 2", "quote": "The DEGs between IgAN patients and normal subjects were analyzed using the GEO2R web tool (http://www.ncbi.nlm.nih.gov/geo/geo2r)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31392215", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31392215"], "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:GSE73953"], "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:GSE73953"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31392215", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2019/8794013", "sha256": "sha256:871c8b2601ba4d658bbcb33306feef2fc2e9e01229350d15d026870c110f831e", "bytes": 20577, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2019/8794013", "version": null, "note": "Full article fetched from PMC; 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