Identifying crucial genes for prognosis in septic patients: Gene integration study based on PRISMA guidelines.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31415393", "kind": "science-record", "revision": 8, "content_hash": "sha256:b5546e4d93b4a89e772092eaa4a85af83dbc461d1210793b9e0dfd7efa493224", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T22:00:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying crucial genes for prognosis in septic patients: Gene integration study based on PRISMA guidelines.", "doi": "10.1097/MD.0000000000016807", "pmid": "31415393", "authors": ["Yingchun Hu", "Wu Zhong", "Muhu Chen", "Qian Zhang"], "journal": "Medicine", "year": 2019, "abstract": "BACKGROUND: Sepsis is a serious clinical condition with a poor prognosis, despite improvements in diagnosis and treatment.Therefore, novel biomarkers are necessary that can help with estimating prognosis and improving clinical outcomes of patients with sepsis.\nMETHODS: The gene expression profiles GSE54514 and GSE63042 were downloaded from the GEO database. DEGs were screened by t test after logarithmization of raw data; then, the common DEGs between the 2 gene expression profiles were identified by up-regulation and down-regulation intersection. The DEGs were analyzed using bioinformatics, and a protein-protein interaction (PPI) survival network was constructed using STRING. Survival curves were constructed to explore the relationship between core genes and the prognosis of sepsis patients based on GSE54514 data.\nRESULTS: A total of 688 common DEGs were identified between survivors and non-survivors of sepsis, and 96 genes were involved in survival networks. The crucial genes Signal transducer and activator of transcription 5A (STAT5A), CCAAT/enhancer-binding protein beta (CEBPB), Myc proto-oncogene protein (MYC), and REL-associated protein (RELA) were identified and showed increased expression in sepsis survivors. These crucial genes had a positive correlation with patients' survival time according to the survival analysis.\nCONCLUSIONS: Our findings indicate that the genes STAT5A, CEBPB, MYC, and RELA may be important in predicting the prognosis of sepsis patients.", "claims": [{"id": "claim-method", "statement": "The DEGs between survivors and non-survivors were selected by t-test, with a P value <.05 considered the cut-off criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31415393", "locator": "sections[4] \"Screening for DEGs\" paragraph 2", "quote": "The DEGs between survivors and non-survivors were selected by t-test, with a P value <.05 considered the cut-off criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Two microarray datasets for sepsis were downloaded from the public Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/): GSE54514[4] and GSE63042.[5]", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31415393", "locator": "sections[3] \"Microarray chip data\" paragraph 2", "quote": "Two microarray datasets for sepsis were downloaded from the public Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/): GSE54514[4] and GSE63042.[5]"}], "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:31415393"], "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:GSE54514"], "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:GSE54514"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31415393", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000016807", "sha256": "sha256:050907d69bec3a69f41ad021f60a5d43866e9cadc4b965a30ea5836504e31e0b", "bytes": 16671, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000016807", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6831352", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE54514", "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=GSE54514", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54514", "version": null, "note": "Two microarray datasets for sepsis were downloaded from the public Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/): GSE54514[4] and GSE63042.[5]", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Two microarray datasets for sepsis were downloaded from the public Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/): GSE54514[4] and GSE63042.[5]", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1317896", "GSM1317897", "GSM1317898", "GSM1317899", "GSM1317900", "GSM1317901", "GSM1317902", "GSM1317903", "GSM1317904", "GSM1317905", "GSM1317906", "GSM1317907", "GSM1317908", "GSM1317909", "GSM1317910", "GSM1317911", "GSM1317912", "GSM1317913", "GSM1317914", "GSM1317915", "GSM1317916", "GSM1317917", "GSM1317918", "GSM1317919", "GSM1317920", "GSM1317921", "GSM1317922", "GSM1317923", "GSM1317924", "GSM1317925", "GSM1317926", "GSM1317927", "GSM1317928", "GSM1317929", "GSM1317930", "GSM1317931", "GSM1317932", "GSM1317933", "GSM1317934", "GSM1317935", "GSM1317936", "GSM1317937", "GSM1317938", "GSM1317939", "GSM1317940", "GSM1317941", "GSM1317942", "GSM1317943", "GSM1317944", "GSM1317945", "GSM1317946", "GSM1317947", "GSM1317948", "GSM1317949", "GSM1317950", "GSM1317951", "GSM1317952", "GSM1317953", "GSM1317954", "GSM1317955", "GSM1317956", "GSM1317957", "GSM1317958", "GSM1317959", "GSM1317960", "GSM1317961", "GSM1317962", "GSM1317963", "GSM1317964", "GSM1317965", "GSM1317966", "GSM1317967", "GSM1317968", "GSM1317969", "GSM1317970", "GSM1317971", "GSM1317972", "GSM1317973", "GSM1317974", "GSM1317975", "GSM1317976", "GSM1317977", "GSM1317978", "GSM1317979", "GSM1317980", "GSM1317981", "GSM1317982", "GSM1317983", "GSM1317984", "GSM1317985", "GSM1317986", "GSM1317987", "GSM1317988", "GSM1317989", "GSM1317990", "GSM1317991", "GSM1317992", "GSM1317993", "GSM1317994", "GSM1317995", "GSM1317996", "GSM1317997", "GSM1317998", "GSM1317999", "GSM1318000", "GSM1318001", "GSM1318002", "GSM1318003", "GSM1318004", "GSM1318005", "GSM1318006", "GSM1318007", "GSM1318008", "GSM1318009", "GSM1318010", "GSM1318011", "GSM1318012", "GSM1318013", "GSM1318014", "GSM1318015", "GSM1318016", "GSM1318017", "GSM1318018", "GSM1318019", "GSM1318020", "GSM1318021", "GSM1318022", "GSM1318023", "GSM1318024", "GSM1318025", "GSM1318026", "GSM1318027", "GSM1318028", "GSM1318029", "GSM1318030", "GSM1318031", "GSM1318032", "GSM1318033", "GSM1318034", "GSM1318035", "GSM1318036", "GSM1318037", "GSM1318038", "GSM1318039", "GSM1318040", "GSM1318041", "GSM1318042", "GSM1318043", "GSM1318044", "GSM1318045", "GSM1318046", "GSM1318047", "GSM1318048", "GSM1318049", "GSM1318050", "GSM1318051", "GSM1318052", "GSM1318053", "GSM1318054", "GSM1318055", "GSM1318056", "GSM1318057", "GSM1318058"], "sample_count": 163, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Whole blood transcriptome of survivors and nonsurvivors of sepsis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE63042", "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=GSE63042", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63042", "version": null, "note": "Two microarray datasets for sepsis were downloaded from the public Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/): GSE54514[4] and GSE63042.[5]", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Two microarray datasets for sepsis were downloaded from the public Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/): GSE54514[4] and GSE63042.[5]", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1548256", "GSM1548257", "GSM1548258", "GSM1548259", "GSM1548260", "GSM1548261", "GSM1548262", "GSM1548263", "GSM1548264", "GSM1548265", "GSM1548266", "GSM1548267", "GSM1548268", "GSM1548269", "GSM1548270", "GSM1548271", "GSM1548272", "GSM1548273", "GSM1548274", "GSM1548275", "GSM1548276", "GSM1548277", "GSM1548278", "GSM1548279", "GSM1548280", "GSM1548281", "GSM1548282", "GSM1548283", "GSM1548284", "GSM1548285", "GSM1548286", "GSM1548287", "GSM1548288", "GSM1548289", "GSM1548290", "GSM1548291", "GSM1548292", "GSM1548293", "GSM1548294", "GSM1548295", "GSM1548296", "GSM1548297", "GSM1548298", "GSM1548299", "GSM1548300", "GSM1548301", "GSM1548302", "GSM1548303", "GSM1548304", "GSM1548305", "GSM1548306", "GSM1548307", "GSM1548308", "GSM1548309", "GSM1548310", "GSM1548311", "GSM1548312", "GSM1548313", "GSM1548314", "GSM1548315", "GSM1548316", "GSM1548317", "GSM1548318", "GSM1548319", "GSM1548320", "GSM1548321", "GSM1548322", "GSM1548323", "GSM1548324", "GSM1548325", "GSM1548326", "GSM1548327", "GSM1548328", "GSM1548329", "GSM1548330", "GSM1548331", "GSM1548332", "GSM1548333", "GSM1548334", "GSM1548335", "GSM1548336", "GSM1548337", "GSM1548338", "GSM1548339", "GSM1548340", "GSM1548341", "GSM1548342", "GSM1548343", "GSM1548344", "GSM1548345", "GSM1548346", "GSM1548347", "GSM1548348", "GSM1548349", "GSM1548350", "GSM1548351", "GSM1548352", "GSM1548353", "GSM1548354", "GSM1548355", "GSM1548356", "GSM1548357", "GSM1548358", "GSM1548359", "GSM1548360", "GSM1548361", "GSM1548362", "GSM1548363", "GSM1548364", "GSM1548365", "GSM1548366", "GSM1548367", "GSM1548368", "GSM1548369", "GSM1548370", "GSM1548371", "GSM1548372", "GSM1548373", "GSM1548374", "GSM1548375", "GSM1548376", "GSM1548377", "GSM1548378", "GSM1548379", "GSM1548380", "GSM1548381", "GSM1548382", "GSM1548383", "GSM1548384"], "sample_count": 129, "group_sizes": null, "group_sizes_basis": null, "platform": "9115", "taxon": "Homo sapiens", "title": "An integrated transcriptome and expressed variant analysis of sepsis survival and death", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31415393:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ec647875c47203c50d51142bd590d2de1f2ad57871f104f8a245107a4987913b", "bytes": 210, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "Clinical and demographic description in GSE54514 and GSE63042.", "structure": {"pmcid": "PMC6831352", "section_index": 10, "section_title": "Demographics of the septic patients", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Clinical and demographic description in GSE54514 and GSE63042.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:31415393:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d7073a12f83743dcf8afdacbb61a39fb36226e0cc8653cadf4e62466bc476af5", "bytes": 196, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T2", "version": null, "note": "Crucial genes located in survival networks (96).", "structure": {"pmcid": "PMC6831352", "section_index": 13, "section_title": "PPI survival network", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Crucial genes located in survival networks (96).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE54514 not downloaded", "asset:data:geo:GSE54514 licence not read", "asset:data:geo:GSE63042 not downloaded", "asset:data:geo:GSE63042 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": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DEGs between survivors and non-survivors were selected by t-test, with a P value <.05 considered the cut-off criteria."}}], "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": ["GSE54514", "GSE63042"], "resolved_accessions": ["GSE54514", "GSE63042"], "statements": ["Two microarray datasets for sepsis were downloaded from the public Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/): GSE54514[4] and GSE63042.[5]"], "basis": "The paper names GSE54514, GSE63042 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:31415393", "data:geo:GSE54514", "asset:table:pmid:31415393:1", "asset:table:pmid:31415393:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE54514"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 12682, "completion_tokens": 1329, "cached_tokens": 4360}}, "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:31415393", "type": "paper", "label": "pmid:31415393"}, {"id": "source:pmid:31415393", "type": "manuscript", "label": "PMID 31415393 full text"}, {"id": "data:geo:GSE54514", "type": "dataset", "label": "GEO GSE54514"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31415393", "type": "paper", "label": "pmid:31415393"}, {"id": "source:pmid:31415393", "type": "manuscript", "label": "PMID 31415393 full text"}, {"id": "data:geo:GSE54514", "type": "dataset", "label": "GEO GSE54514"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31415393", "type": "extraction", "used": ["source:pmid:31415393"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE54514", "type": "accession_resolution", "used": ["data:geo:GSE54514"], "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:31415393", "parent_hash": "sha256:b946057f234f02b9a58ce00dc1e3048a14581b6fbf5c404fadf2208216adaa0f", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE54514 licence not read", "asset:data:geo:GSE54514 not downloaded", "asset:data:geo:GSE63042 licence not read", "asset:data:geo:GSE63042 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"}]}