Bioinformatics Analysis of Gene Expression Profiles for Risk Prediction in Patients with Septic Shock.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31838482", "kind": "science-record", "revision": 5, "content_hash": "sha256:4dbe480416dd46b497c1a5b57e7bd7798b9ba2f5f37dd73ba31cf85f217b5ea7", "created_at": "2026-11-01T15:40:53Z", "updated_at": "2026-11-01T22:01:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis of Gene Expression Profiles for Risk Prediction in Patients with Septic Shock.", "doi": "10.12659/MSM.918491", "pmid": "31838482", "authors": ["Yingchun Hu", "Lingxia Cheng", "Wu Zhong", "Muhu Chen", "Qian Zhang"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2019, "abstract": "BACKGROUND Septic shock occurs when sepsis is associated with critically low blood pressure, and has a high mortality rate. This study aimed to undertake a bioinformatics analysis of gene expression profiles for risk prediction in septic shock. MATERIAL AND METHODS Two good quality datasets associated with septic shock were downloaded from the Gene Expression Omnibus (GEO) database, GSE64457 and GSE57065. Patients with septic shock had both sepsis and hypotension, and a normal control group was included. The differentially expressed genes (DEGs) were identified using OmicShare tools based on R. Functional enrichment of DEGs was analyzed using DAVID. The protein-protein interaction (PPI) network was established using STRING. Survival curves of key genes were constructed using GraphPad Prism version 7.0. Each putative central gene was analyzed by receiver operating characteristic (ROC) curves using MedCalc statistical software. RESULTS GSE64457 and GSE57065 included 130 RNA samples derived from whole blood from 97 patients with septic shock and 33 healthy volunteers to obtain 975 DEGs, 455 of which were significantly down-regulated and 520 were significantly upregulated (P<0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified significantly enriched DEGs in four signaling pathways, MAPK, TNF, HIF-1, and insulin. Six genes, WDR82, ASH1L, NCOA1, TPR, SF1, and CREBBP in the center of the PPI network were associated with septic shock, according to survival curve and ROC analysis. CONCLUSIONS Bioinformatics analysis of gene expression profiles identified four signaling pathways and six genes, potentially representing molecular mechanisms for the occurrence, progression, and risk prediction in septic shock.", "claims": [{"id": "claim-method", "statement": "After logarithmic pretreatment of the original data, OmicShare online tools based on R (www.omicshare.com/tools) were used to identify the DEGs in the septic shock and control cases. The P-value was corrected for the occurrence of false-positive results, and the genes with a P-value <0.05 were considered as initial DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31838482", "locator": "sections[4] \"Data preprocessing and analysis of differentially expressed genes (DEGs)\" paragraph 2", "quote": "After logarithmic pretreatment of the original data, OmicShare online tools based on R (www.omicshare.com/tools) were used to identify the DEGs in the septic shock and control cases. The P-value was corrected for the occurrence of false-positive results, and the genes with a P-value <0.05 were considered as initial DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Two good quality datasets associated with septic shock were downloaded from the Gene Expression Omnibus (GEO) database, GSE64457 and GSE57065. The gene expression profile data of GSE64457 included 15 cases of septic shock and eight healthy volunteers with data on whole blood-derived RNA samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31838482", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Two good quality datasets associated with septic shock were downloaded from the Gene Expression Omnibus (GEO) database, GSE64457 and GSE57065."}, {"asset": "source:pmid:31838482", "locator": "sections[3] \"Data sources\" paragraph 2", "quote": "The gene expression profile data of GSE64457 included 15 cases of septic shock and eight healthy volunteers with data on whole blood-derived RNA samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31838482"], "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:GSE57065"], "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:GSE57065"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31838482", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.918491", "sha256": "sha256:0041ba1ccd2dcf27c05e0bdc80d46a4cd8622f18b06ac68ae839ed95f876054d", "bytes": 19989, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.918491", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6929537", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE57065", "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=GSE57065", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57065", "version": null, "note": "Two good quality datasets associated with septic shock were downloaded from the Gene Expression Omnibus (GEO) database, GSE64457 and GSE57065. 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licence not read", "asset:data:geo:GSE64457 not downloaded", "asset:data:geo:GSE64457 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE65682 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC analysis"}}, {"id": "method-3", "family": null, "specific": null, "label": "Differentially expressed genes were identified using OmicShare online tools based on R, with the P-value corrected for false-positive results and genes having P<0.05 considered initial DEGs.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "After logarithmic pretreatment of the original data, OmicShare online tools based on R (www.omicshare.com/tools) were used to identify the DEGs in the septic shock and control cases. The P-value was corrected for the occurrence of false-positive results, and the genes with a P-value <0.05 were considered as initial DEGs."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE64457", "GSE57065", "GSE65682"], "resolved_accessions": ["GSE64457", "GSE57065", "GSE65682"], "statements": ["Two good quality datasets associated with septic shock were downloaded from the Gene Expression Omnibus (GEO) database, GSE64457 and GSE57065. The gene expression profile data of GSE64457 included 15 cases of septic shock and eight healthy volunteers with data on whole blood-derived RNA samples."], "basis": "The paper names GSE64457, GSE57065, GSE65682 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:31838482", "data:geo:GSE57065"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE57065"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:22Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 14888, "completion_tokens": 1425, "cached_tokens": 793}}, "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:31838482", "type": "paper", "label": "pmid:31838482"}, {"id": "source:pmid:31838482", "type": "manuscript", "label": "PMID 31838482 full text"}, {"id": "data:geo:GSE57065", "type": "dataset", "label": "GEO GSE57065"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31838482", "type": "paper", "label": "pmid:31838482"}, {"id": "source:pmid:31838482", "type": "manuscript", "label": "PMID 31838482 full text"}, {"id": "data:geo:GSE57065", "type": "dataset", "label": "GEO GSE57065"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31838482", "type": "extraction", "used": ["source:pmid:31838482"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE57065", "type": "accession_resolution", "used": ["data:geo:GSE57065"], "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:31838482", "parent_hash": "sha256:d7143c9818cb101d3c72d0390718162f576be39276c33f1375ffc2eebe82f535", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE57065 licence not read", "asset:data:geo:GSE57065 not downloaded", "asset:data:geo:GSE64457 licence not read", "asset:data:geo:GSE64457 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE65682 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}