PPI-based screening of hub genes related to sepsis migration/pyroptosis and immune infiltration analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41252417", "kind": "science-record", "revision": 4, "content_hash": "sha256:4f319ff63d487af3e6a9ceebcedeee1aec4aeae4a4614bd010e50fdcf7c2541b", "created_at": "2026-11-01T20:31:17Z", "updated_at": "2026-11-01T22:57:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PPI-based screening of hub genes related to sepsis migration/pyroptosis and immune infiltration analysis.", "doi": "10.1371/journal.pone.0336982", "pmid": "41252417", "authors": ["Xu Ma", "Jianhao Wang", "Kun Han", "Jinshuai Lu"], "journal": "PloS one", "year": 2025, "abstract": "BACKGROUND: Sepsis incidence is rising, but its pathogenesis remains unclear. This study aimed to identify therapeutic targets.\nMETHODS: Three GEO datasets (GSE154918, GSE32707, GSE54514) were analyzed after batch correction. Differentially expressed genes (DEGs) were identified, and those related to pyroptosis/migration were cross-analyzed. Functional enrichment (GO/KEGG) and interaction networks (PPI, mRNA-miRNA, mRNA-TF, mRNA-drug) were constructed. External validation used GSE57065, excluding non-significant genes. ROC analysis and immune infiltration were performed.\nRESULTS: 3566 DEGs (1715 up, 1851 down) were identified, with 23 linked to pyroptosis/migration. Enrichment analysis highlighted roles in cell adhesion, cytokine regulation, and pathways like IL-17, TNF, and Toll-like receptor signaling. mRNA-miRNA interactions for 12 key genes were predicted. After validation, eight key genes remained: TLR2, SIRT1, PTGS2, MAPK14, IL18, ICAM1, CD274, and CASP3. Immune infiltration revealed varied effects on MAPK14.\nCONCLUSION: Key gene alterations may serve as sepsis biomarkers, and miRNA dysregulation could play a critical role in sepsis pathophysiology.", "claims": [{"id": "claim-method", "statement": "This dataset was normalized using the R package limma, followed by differential gene expression analysis comparing cases versus controls.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41252417", "locator": "sections[5] \"2.3 Integration and difference analysis of data sets\" paragraph 2", "quote": "This dataset was normalized using the R package limma, followed by differential gene expression analysis comparing cases versus controls."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study is available in the GEO repository. 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GSE154918(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154918), GSE32707(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32707), and GSE54514(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54514)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Three GEO datasets (GSE154918, GSE32707, GSE54514) were analyzed after batch correction.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41252417", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Three GEO datasets (GSE154918, GSE32707, GSE54514) were analyzed after batch correction."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Three GEO datasets (GSE154918, GSE32707, GSE54514) were analyzed after batch correction.", "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:41252417"], "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:GSE154918"], "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:GSE154918"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41252417", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0336982", "sha256": "sha256:8f3aa1f8246d47116233ce69b6a05f836a203493d2f677693721e5c336ffaf1c", "bytes": 62031, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0336982", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12626297", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE154918", "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=GSE154918", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE154918", "version": null, "note": "The datasets analyzed during the current study is available in the GEO repository. 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