Identification of Hub Genes Correlated with the Initiation and Progression of CKD in the Unilateral Ureteral Obstruction Model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40564035", "kind": "science-record", "revision": 4, "content_hash": "sha256:dce21e3d3220239bc00de746e0d39b6c305e3581507171aa1c9f97328e711edb", "created_at": "2026-11-01T20:30:39Z", "updated_at": "2026-11-01T22:56:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub Genes Correlated with the Initiation and Progression of CKD in the Unilateral Ureteral Obstruction Model.", "doi": "10.3390/biomedicines13061316", "pmid": "40564035", "authors": ["Xinxin Li", "Junjie Li", "Xiaobing Yao", "Jun Yang"], "journal": "Biomedicines", "year": 2025, "abstract": "Background: Chronic kidney disease (CKD) is a global health problem marked by a persistent deterioration in the function of the nephrons and kidneys. To identify novel therapies for CKD, we investigated the molecular targets associated with the initiation and progression of the disease. Methods: The transcriptional profile dataset of GSE42303 was downloaded from GEO (The Gene Expression Omnibus). Utilizing the R package limma, the differentially expressed genes (DEGs) were identified between control (Con) and unilateral ureteral obstruction (UUO) mice. Then, functional enrichment, protein-protein interactions (PPI) and subsequent hub genes were identified by multiple bioinformatics approaches. Further validations of these hub genes were confirmed through the GSE118339 dataset and in vivo experiments. Results: We found 381 DEGs between Con and UUO mice (308 up-regulated genes and 73 down-regulated genes). GO functions and pathway analysis indicated that DEGs were mainly enriched in activities associated with inflammation and fibrosis. The mRNA expressions of nine hub genes were identified and confirmed by dataset GSE118339 and in vivo experiments. Conclusions: The hub genes Fgg, Penk, Ckap4, and Gpc3 may be new prospective targets for the treatment of the initiation and progression of CKD.", "claims": [{"id": "claim-method", "statement": "Then, by comparing UUO with Sham samples, we identified DEGs using the R package limma.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40564035", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "Then, by comparing UUO with Sham samples, we identified DEGs using the R package limma."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Any interested party is welcome to access the datasets used in this study by contacting the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40564035", "locator": "sections[29] \"Data Availability Statement\" paragraph 2", "quote": "Any interested party is welcome to access the datasets used in this study by contacting the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We found 381 DEGs between Con and UUO mice (308 up-regulated genes and 73 down-regulated genes).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40564035", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found 381 DEGs between Con and UUO mice (308 up-regulated genes and 73 down-regulated genes)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We found 381 DEGs between Con and UUO mice (308 up-regulated genes and 73 down-regulated genes).", "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:40564035"], "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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Results: We found 381 DEGs betw", "ified and confirmed by dataset GSE118339 and in vivo experiments. Conclusions: The hub genes Fgg,", "12 weeks were utilized in this research. The mice were bred in a sterile environment devoid of path", "same surgery without obstructing the ureter. Mice were kept breeding for 3, 7, and 14 days after su"], "order_basis": "paper_text_order:875", "id": "assay:1"}, {"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": ["Then, by comparing UUO with Sham samples, we identified DEGs using the R package limma."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}