[Master genes and co-expression network analysis in peripheral blood mononuclear cells of patients with gram-positive and gram-negative sepsis].

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33448176", "kind": "science-record", "revision": 3, "content_hash": "sha256:265380c0ca1e966665430465feb8cfeea6b7d66646015a13f32ba1afa3c1d2b7", "created_at": "2026-11-01T17:34:37Z", "updated_at": "2026-11-01T21:24:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[Master genes and co-expression network analysis in peripheral blood mononuclear cells of patients with gram-positive and gram-negative sepsis].", "doi": "10.3785/j.issn.1008-9292.2020.12.08", "pmid": "33448176", "authors": ["Lu Li", "Junjun Fang", "Zhitao Li", "Leixing Shen", "Guobin Wang", "Shuiqiao Fu"], "journal": "Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences", "year": 2020, "abstract": "OBJECTIVE: To investigate the functional pathways enriched and differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMCs) of patients with gram-positive and gram-negative sepsis.\nMETHODS: Dataset GSE9960 obtained from NCBI GEO database containing PBMC samples from 16 non-infectious systematic inflammatory response syndrome (SIRS) patients, 17 gram-positive septic patients and 18 gram-negative septic patients were included in the study. Functional pathway annotations were conducted by gene set enrichment analysis and weighted gene co-expression network analysis. DEGs were filtered and master DEGs were then validated in PBMCs of gram-positive septic, gram-negative septic and non-infectious SIRS patients.\nRESULTS: The enriched gene sets in gram-positive sepsis and gram-negative sepsis were significantly different. The results indicated the opposite co-expression networks in SIRS and gram-negative sepsis, and the entirely different co-expression networks in gram-positive and gram-negative sepsis. Furthermore, we validated that TYMS was up-regulated in gram-positive sepsis (P<0.05), CD3D was down-regulated in gram-negative sepsis (P<0.01), while IRAK3 was up-regulated in gram-negative sepsis (P<0.05).\nCONCLUSIONS: The results indicate that there are differences in the mechanism and pathogenesis of gram-positive and gram-negative sepsis, which may provide potential markers for sepsis diagnosis and empirical antimicrobial therapy.", "claims": [{"id": "claim-method", "statement": "利用基因集富集分析和加权基因共表达网络分析探索GSE9960基因表达谱芯片中革兰阳性菌感染与革兰阴性菌感染脓毒症富集功能通路与共表达网络模块，并对高度相关模块进行通路注释。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33448176", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "利用基因集富集分析和加权基因共表达网络分析探索GSE9960基因表达谱芯片中革兰阳性菌感染与革兰阴性菌感染脓毒症富集功能通路与共表达网络模块，并对高度相关模块进行通路注释。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "在美国国立生物技术信息中心平台获取GSE9960表达谱芯片，包含16例非感染全身炎症反应综合征（SIRS）患者外周血单个核细胞（PBMC）样本，17例革兰阳性菌感染脓毒症患者PBMC样本，以及18例革兰阴性菌感染脓毒症患者PBMC样本。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33448176", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "在美国国立生物技术信息中心平台获取GSE9960表达谱芯片，包含16例非感染全身炎症反应综合征（SIRS）患者外周血单个核细胞（PBMC）样本，17例革兰阳性菌感染脓毒症患者PBMC样本，以及18例革兰阴性菌感染脓毒症患者PBMC样本。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "进一步在临床样本中验证显示，主要差异表达基因 TYMS在革兰阳性菌感染脓毒症患者PBMC中显著上调（ P< 0.05）； CD3D在革兰阴性菌感染脓毒症中表达下调（ P< 0.01），而 IRAK3则显著上调（ P< 0.05）。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:33448176", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "进一步在临床样本中验证显示，主要差异表达基因 TYMS在革兰阳性菌感染脓毒症患者PBMC中显著上调（ P< 0.05）； CD3D在革兰阴性菌感染脓毒症中表达下调（ P< 0.01），而 IRAK3则显著上调（ P< 0.05）。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "进一步在临床样本中验证显示，主要差异表达基因 TYMS在革兰阳性菌感染脓毒症患者PBMC中显著上调（ P< 0.05）； CD3D在革兰阴性菌感染脓毒症中表达下调（ P< 0.01），而 IRAK3则显著上调（ P< 0.05）。", "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:33448176"], "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:GSE9960"], "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:GSE9960"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33448176", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3785/j.issn.1008-9292.2020.12.08", "sha256": "sha256:19be0bd12c83d5d7403776bd684db567b3b3527272a431771727a6759beade10", "bytes": 627, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3785/j.issn.1008-9292.2020.12.08", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10412950", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE9960", "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=GSE9960", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE9960", "version": null, "note": "在美国国立生物技术信息中心平台获取GSE9960表达谱芯片，包含16例非感染全身炎症反应综合征（SIRS）患者外周血单个核细胞（PBMC）样本，17例革兰阳性菌感染脓毒症患者PBMC样本，以及18例革兰阴性菌感染脓毒症患者PBMC样本。", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "在美国国立生物技术信息中心平台获取GSE9960表达谱芯片，包含16例非感染全身炎症反应综合征（SIRS）患者外周血单个核细胞（PBMC）样本，17例革兰阳性菌感染脓毒症患者PBMC样本，以及18例革兰阴性菌感染脓毒症患者PBMC样本。", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM251887", "GSM251888", "GSM251889", "GSM251890", "GSM251891", "GSM251892", "GSM251893", "GSM251894", "GSM251895", "GSM251896", "GSM251897", "GSM251898", "GSM251899", "GSM251900", "GSM251901", "GSM251902", "GSM251903", "GSM251904", "GSM251905", "GSM251928", "GSM251929", "GSM251930", "GSM251931", "GSM251932", "GSM251933", "GSM251934", "GSM251935", "GSM251936", "GSM251937", "GSM251938", "GSM251939", "GSM251940", "GSM251941", "GSM251942", "GSM251943", "GSM251944", "GSM251945", "GSM251946", "GSM251947", "GSM251948", "GSM251949", "GSM251950", "GSM251951", "GSM251952", "GSM251953", "GSM251982", "GSM251983", "GSM251984", "GSM251985", "GSM251986", "GSM251987", "GSM251988", "GSM251989", "GSM251990", "GSM251991", "GSM251992", "GSM251993", "GSM251994", "GSM251995", "GSM251996", "GSM251997", "GSM251998", "GSM251999", "GSM252000", "GSM252001", "GSM252002", "GSM252003", "GSM252004", "GSM252005", "GSM252006"], "sample_count": 70, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene-expression profiling of peripheral blood mononuclear cells in sepsis", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE9960 not downloaded", "asset:data:geo:GSE9960 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "基因集富集分析和加权基因共表达网络分析", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "利用基因集富集分析和加权基因共表达网络分析探索GSE9960基因表达谱芯片中革兰阳性菌感染与革兰阴性菌感染脓毒症富集功能通路与共表达网络模块，并对高度相关模块进行通路注释。"}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (基因集富集分析和加权基因共表达网络分析), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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