Identification and bioinformatics analysis of genes associated with pyroptosis in spinal cord injury of rat and mouse.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38890348", "kind": "science-record", "revision": 4, "content_hash": "sha256:41b05c2d2aec13ee718f22d5776f673a5660b76c7d9b9256267f807a179623a6", "created_at": "2026-11-01T20:28:57Z", "updated_at": "2026-11-01T22:54:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and bioinformatics analysis of genes associated with pyroptosis in spinal cord injury of rat and mouse.", "doi": "10.1038/s41598-024-64843-6", "pmid": "38890348", "authors": ["Fu-Sheng Liu", "Hai-Long Huang", "Lin-Xia Deng", "Qian-Shi Zhang", "Xiao-Bin Wang", "Jing Li", "Fu-Bing Liu"], "journal": "Scientific reports", "year": 2024, "abstract": "The mechanism of spinal cord injury (SCI) is highly complex, and an increasing number of studies have indicated the involvement of pyroptosis in the physiological and pathological processes of secondary SCI. However, there is limited bioinformatics research on pyroptosis-related genes (PRGs) in SCI. This study aims to identify and validate differentially expressed PRGs in the GEO database, perform bioinformatics analysis, and construct regulatory networks to explore potential regulatory mechanisms and therapeutic targets for SCI. We obtained high-throughput sequencing datasets of SCI in rats and mice from the GEO database. Differential analysis was conducted using the \"limma\" package in R to identify differentially expressed genes (DEGs). These genes were then intersected with previously reported PRGs, resulting in a set of PRGs in SCI. GO and KEGG enrichment analyses, as well as correlation analysis, were performed on the PRGs in both rat and mouse models of SCI. Additionally, a protein-protein interaction (PPI) network was constructed using the STRING website to examine the relationships between proteins. Hub genes were identified using Cytoscape software, and the intersection of the top 5 hub genes in rats and mice were selected for subsequent experimentally validated. Furthermore, a competing endogenous RNA (ceRNA) network was constructed to explore potential regulatory mechanisms. The gene expression profiles of GSE93249, GSE133093, GSE138637, GSE174549, GSE45376, GSE171441_3d and GSE171441_35d were selected in this study. We identified 10 and 12 PRGs in rats and mice datasets respectively. Six common DEGs were identified in the intersection of rats and mice PRGs. Enrichment analysis of these DEGs indicated that GO analysis was mainly focused on inflammation-related factors, while KEGG analysis showed that the most genes were enriched on the NOD-like receptor signaling pathway. We constructed a ceRNA regulatory network that consisted of five important PRGs, as well as 24 miRNAs and 34 lncRNAs. This network revealed potential regulatory mechanisms. Additionally, the three hub genes obtained from the intersection were validated in the rat model, showing high expression of PRGs in SCI. Pyroptosis is involved in secondary SCI and may play a significant role in its pathogenesis. The regulatory mechanisms associated with pyroptosis deserve further in-depth research.", "claims": [{"id": "claim-method", "statement": "The “limma” R package was utilized to perform the differential expression analysis between SCI group and sham surgery group from GEO databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38890348", "locator": "sections[4] \"Gene differential expression analysis\" paragraph 2", "quote": "The “limma” R package was utilized to perform the differential expression analysis between SCI group and sham surgery group from GEO databases."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data relevant to the study are included in the article or uploaded as supplementary information.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38890348", "locator": "sections[23] \"Data availability\" paragraph 2", "quote": "All data relevant to the study are included in the article or uploaded as supplementary information."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 10 and 12 PRGs in rats and mice datasets respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38890348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 10 and 12 PRGs in rats and mice datasets respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 10 and 12 PRGs in rats and mice datasets respectively.", "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:38890348"], "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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