Identification of hub genes, pathways, and related transcription factors in systemic lupus erythematosus: A preliminary bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34160465", "kind": "science-record", "revision": 8, "content_hash": "sha256:eac62d39b59df22780ce364d398035d56afcc6d374ad6858d0a6a672ad4d9568", "created_at": "2026-11-01T15:41:39Z", "updated_at": "2026-11-01T22:04:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes, pathways, and related transcription factors in systemic lupus erythematosus: A preliminary bioinformatics analysis.", "doi": "10.1097/MD.0000000000026499", "pmid": "34160465", "authors": ["Yanfeng Wang", "Qian Ma", "Zhenghao Huo"], "journal": "Medicine", "year": 2021, "abstract": "BACKGROUND: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multiple organ damage and the production of a variety of autoantibodies. The pathogenesis of SLE has not been fully defined, and it is difficult to treat. Our study aimed to identify candidate genes that may be used as biomarkers for the screening, diagnosis, and treatment of SLE.\nMETHODS: We used the GEO2R tool to identify the differentially expressed genes (DEGs) in SLE-related datasets retrieved from the Gene Expression Omnibus (GEO). In addition, we also identified the biological functions of the DEGs by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Additionally, we constructed protein-protein interaction (PPI) networks to identify hub genes, as well as the regulatory network of transcription factors related to DEGs.\nRESULTS: Two datasets were identified for use from the GEO (GSE50772, GSE4588), and 34 up-regulated genes and 4 down-regulated genes were identified by GEO2R. Pathway analysis of the DEGs revealed enrichment of the interferon alpha/beta signaling pathway; GO analysis was mainly enriched in response to interferon alpha, regulation of ribonuclease activity. PPIs were constructed through the STRING database and 14 hub genes were selected and 1 significant module (score = 12.923) was obtained from the PPI network. Additionally, 11 key transcription factors that interacted closely with the 14 hub DEGs were identified from the gene transcription factor network.\nCONCLUSIONS: Bioinformatic analysis is an effective tool for screening the original genomic data in the GEO database, and a large number of SLE-related DEGs were identified. The identified hub DEGs may be potential biomarkers of SLE.", "claims": [{"id": "claim-method", "statement": "Using the GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) online data analysis tool to compare the gene expression of the healthy control and SLE group, the original data was downloaded, the DEGs were screened, and the screening standard was set to P < .05 and |log 2 FC| > 1.0.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34160465", "locator": "sections[4] \"Screening of differentially expressed genes\" paragraph 2", "quote": "Using the GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) online data analysis tool to compare the gene expression of the healthy control and SLE group, the original data was downloaded, the DEGs were screened, and the screening standard was set to P < .05 and |log 2 FC| > 1.0."}], "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:34160465"], "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:GSE4588"], "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:GSE4588"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34160465", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000026499", "sha256": "sha256:ae8bdd4d5efefd3c2ec7b974b09a7c3cb47794e5527ed7f1024a6cef24a0e38f", "bytes": 30806, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000026499", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8238284", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE4588", "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=GSE4588", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE4588", "version": null, "note": "A microarray search of GSE50772 and GSE4588 in SLE was conducted in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/) with the keywords “SLE” or “Systemic lupus erythematosus.” The entry type was restricted to “series” and the organism was filtered by “Homo sapiens.” The GSE50772 database contains 81 samples, including 20 control samples and 61 SLE patient samples. Using the GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) online data analysis tool to compare the gene expression of the healthy control and SLE group, the original data was downloaded, the DEGs were screened, and the screening standard was set to P < .05 and |log 2 FC| > 1.0.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "A microarray search of GSE50772 and GSE4588 in SLE was conducted in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/) with the keywords “SLE” or “Systemic lupus erythematosus.” The entry type was restricted to “series” and the organism was filtered by “Homo sapiens.” The GSE50772 database contains 81 samples, including 20 control samples and 61 SLE patient samples. 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