Identification of Nine mRNA Signatures for Sepsis Using Random Forest.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35345523", "kind": "science-record", "revision": 5, "content_hash": "sha256:7159602599dcfb7ef1616b4e447989b5a1be97ba6142669bc3c3d9797f902a79", "created_at": "2026-11-01T18:14:08Z", "updated_at": "2026-11-01T22:48:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Nine mRNA Signatures for Sepsis Using Random Forest.", "doi": "10.1155/2022/5650024", "pmid": "35345523", "authors": ["Jing Zhou", "Siqing Dong", "Ping Wang", "Xi Su", "Liang Cheng"], "journal": "Computational and mathematical methods in medicine", "year": 2022, "abstract": "Sepsis has high fatality rates. Early diagnosis could increase its curating rates. There were no reliable molecular biomarkers to distinguish between infected and uninfected patients currently, which limit the treatment of sepsis. To this end, we analyzed gene expression datasets from the GEO database to identify its mRNA signature. First, two gene expression datasets (GSE154918 and GSE131761) were downloaded to identify the differentially expressed genes (DEGs) using Limma package. Totally 384 common DEGs were found in three contrast groups. We found that as the condition worsens, more genes were under disorder condition. Then, random forest model was performed with expression matrix of all genes as feature and disease state as label. After which 279 genes were left. We further analyzed the functions of 279 important DEGs, and their potential biological roles mainly focused on neutrophil threshing, neutrophil activation involved in immune response, neutrophil-mediated immunity, RAGE receptor binding, long-chain fatty acid binding, specific granule, tertiary granule, and secretory granule lumen. Finally, the top nine mRNAs (MCEMP1, PSTPIP2, CD177, GCA, NDUFAF1, CLIC1, UFD1, SEPT9, and UBE2A) associated with sepsis were considered as signatures for distinguishing between sepsis and healthy controls. Based on 5-fold cross-validation and leave-one-out cross-validation, the nine mRNA signature showed very high AUC.", "claims": [{"id": "claim-method", "statement": "DEGs were calculated between sepsis samples (uncomplicated infection, sepsis, and septic shock) and healthy control using Limma package [22] with p value < 0.05 and ∣logFC | >1 as threshold.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35345523", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "DEGs were calculated between sepsis samples (uncomplicated infection, sepsis, and septic shock) and healthy control using Limma package [22] with p value < 0.05 and ∣logFC | >1 as threshold."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study have been deposited in the GEO database repository (GSE154918 and GES131761).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35345523", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study have been deposited in the GEO database repository (GSE154918 and GES131761)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "384 common DEGs were found in the above three contrast groups.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35345523", "locator": "sections[8] \"3.1. Identification of DEGs\" paragraph 2", "quote": "530 differentially expressed genes (DEGs) were found in uncomplicated infection patients compared with healthy control, 727 DEGs were found in sepsis samples, 1414 DEGs were found in sepsis shock samples, and 384 common DEGs were found in the above three contrast groups (Figure 2)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "384 common DEGs were found in the above three contrast groups.", "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:35345523"], "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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