Screening of the Key Genes and Signalling Pathways for Diabetic Nephropathy Using Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35923621", "kind": "science-record", "revision": 5, "content_hash": "sha256:8ad6368c7d148495b4344dd929e34684f904c45a9dda1823750bb8dfa224950b", "created_at": "2026-11-01T18:15:00Z", "updated_at": "2026-11-01T22:49:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of the Key Genes and Signalling Pathways for Diabetic Nephropathy Using Bioinformatics Analysis.", "doi": "10.3389/fendo.2022.864407", "pmid": "35923621", "authors": ["Zukai Li", "Junxia Feng", "Jinting Zhong", "Meizhi Lu", "Xuejuan Gao", "Yunfang Zhang"], "journal": "Frontiers in endocrinology", "year": 2022, "abstract": "Background: This study aimed to identify biological markers for diabetic nephropathy (DN) and explore their underlying mechanisms.\nMethods: Four datasets, GSE30528, GSE47183, GSE104948, and GSE96804, were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the \"limma\" package, and the \"RobustRankAggreg\" package was used to screen the overlapping DEGs. The hub genes were identified using cytoHubba of Cytoscape. Logistic regression analysis was used to further analyse the hub genes, followed by receiver operating characteristic (ROC) curve analysis to predict the diagnostic effectiveness of the hub genes. Correlation analysis and enrichment analysis of the hub genes were performed to identify the potential functions of the hub genes involved in DN.\nResults: In total, 55 DEGs, including 38 upregulated and 17 downregulated genes, were identified from the three datasets. Four hub genes (FN1, CD44, C1QB, and C1QA) were screened out by the \"UpSetR\" package, and FN1 was identified as a key gene for DN by logistic regression analysis. Correlation analysis and enrichment analysis showed that FN1 was positively correlated with four genes (COL6A3, COL1A2, THBS2, and CD44) and with the development of DN through the extracellular matrix (ECM)-receptor interaction pathway.\nConclusions: We identified four candidate genes: FN1, C1QA, C1QB, and CD44. On further investigating the biological functions of FN1, we showed that FN1 was positively correlated with THBS2, COL1A2, COL6A3, and CD44 and involved in the development of DN through the ECM-receptor interaction pathway. THBS2, COL1A2, COL6A3, and CD44 may be novel biomarkers and target therapeutic candidates for DN.", "claims": [{"id": "claim-method", "statement": "“Limma” package was utilised to identify the DEGs between the glomerular tissues of DN patients and controls.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35923621", "locator": "sections[4] \"Identification of the Differentially Expressed Genes\" paragraph 2", "quote": "“Limma” package was utilised to identify the DEGs between the glomerular tissues of DN patients and controls."}], "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:35923621", "locator": "sections[16] \"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": "The analysis identified 55 overlapping differentially expressed genes, comprising 38 upregulated and 17 downregulated genes, across GSE30528, GSE47183, and GSE104948.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35923621", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In total, 55 DEGs, including 38 upregulated and 17 downregulated genes, were identified from the three datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 55 overlapping differentially expressed genes, comprising 38 upregulated and 17 downregulated genes, across GSE30528, GSE47183, and GSE104948.", "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:35923621"], "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:GSE104948"], "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:GSE104948"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35923621", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2022.864407", "sha256": "sha256:f5302d67606f64681bbb6eecd74175abda7171a5f6d411bfeac9669a753a6e4a", "bytes": 31142, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2022.864407", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9340545", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE104948", "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=GSE104948", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE104948", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE30528", "GSE47183", "GSE104948", "GSE96804"], "resolved_accessions": ["GSE30528", "GSE47183", "GSE104948", "GSE96804"], "statements": ["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."], "basis": "The paper names GSE30528, GSE47183, GSE104948, GSE96804 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35923621", "data:geo:GSE104948"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE104948"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:58:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9591, "completion_tokens": 1824, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35923621", "type": "paper", "label": "pmid:35923621"}, {"id": "source:pmid:35923621", "type": "manuscript", "label": "PMID 35923621 full text"}, {"id": "data:geo:GSE104948", "type": "dataset", "label": "GEO GSE104948"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35923621", "type": "paper", "label": "pmid:35923621"}, {"id": "source:pmid:35923621", "type": "manuscript", "label": "PMID 35923621 full text"}, {"id": "data:geo:GSE104948", "type": "dataset", "label": "GEO GSE104948"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35923621", "type": "extraction", "used": ["source:pmid:35923621"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE104948", "type": "accession_resolution", "used": ["data:geo:GSE104948"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35923621", "parent_hash": "sha256:75a33ce841271c19aca9ad2d0162885be37d730e5faf96e612e4504d52dda314", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE104948 licence not read", "asset:data:geo:GSE104948 not downloaded", "asset:data:geo:GSE30528 licence not read", "asset:data:geo:GSE30528 not downloaded", "asset:data:geo:GSE47183 licence not read", "asset:data:geo:GSE47183 not downloaded", "asset:data:geo:GSE96804 licence not read", "asset:data:geo:GSE96804 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["“Limma” package was utilised to identify the DEGs between the glomerular tissues of DN patients and controls."], "order_basis": "analysis_only", "id": "assay:1"}]}