Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34852788", "kind": "science-record", "revision": 4, "content_hash": "sha256:269a3378211704685b49dd0cd4770a2a90f60d383833aeb7fdc8ecda2f745897", "created_at": "2026-11-01T17:36:32Z", "updated_at": "2026-11-01T22:05:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis.", "doi": "10.1186/s12866-021-02392-y", "pmid": "34852788", "authors": ["Jia-Xin Li", "Xun-Jie Cao", "Yuan-Yi Huang", "Ya-Ping Li", "Zi-Yuan Yu", "Min Lin", "Qiu-Ying Li", "Ji-Chun Chen", "Xu-Guang Guo"], "journal": "BMC microbiology", "year": 2021, "abstract": "INTRODUCTION: Staphylococcus aureus is a gram-positive bacterium that causes serious infection. With the increasing resistance of bacteria to current antibiotics, it is necessary to learn more about the molecular mechanism and cellular pathways involved in the Staphylococcus aureus infection.\nMETHODS: We downloaded the GSE33341 dataset from the GEO database and applied the weighted gene co-expression network analysis (WGCNA), from which we obtained some critical modules. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were applied to illustrate the biological functions of genes in these modules. We constructed the protein-protein interaction (PPI) network by Cytoscape and selected five candidate hub genes. Five potential hub genes were validated in GSE30119 by GraphPad Prism 8.0. The diagnostic values of these genes were calculated and present in the ROC curve based on the GSE13670 dataset. Their gene functions were analyzed by Gene Set Enrichment Analysis (GSEA).\nRESULTS: A co-expression network was built with 5000 genes divided into 11 modules. The genes in green and turquoise modules demonstrated a high correlation. According to the KEGG and GO analyses, genes in the green module were closely related to ubiquitination and autophagy. Subsequently, we picked out the top five hub genes in the green module. And UBB was determined as the hub gene in the GSE30119 dataset. The expression level of UBB, ASB, and MKRN1 could significantly differentiate between Staphylococcus aureus infection and healthy controls based on the ROC curve. The GSEA analysis indicated that lower expression levels of UBB were associated with the P53 signal pathway.\nCONCLUSIONS: We identified some hub genes and significant signal enrichment pathways in Staphylococcus aureus infection via bioinformatics analysis, which may facilitate the development of potential clinical therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "We downloaded the GSE33341 dataset from the GEO database and applied the weighted gene co-expression network analysis (WGCNA), from which we obtained some critical modules.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34852788", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We downloaded the GSE33341 dataset from the GEO database and applied the weighted gene co-expression network analysis (WGCNA), from which we obtained some critical modules."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34852788", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively."}], "state": "complete"}, {"id": "claim-target-result", "statement": "WGCNA of the GSE33341 dataset identified a co-expression network containing 5000 genes divided into 11 modules.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34852788", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A co-expression network was built with 5000 genes divided into 11 modules."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "WGCNA of the GSE33341 dataset identified a co-expression network containing 5000 genes divided into 11 modules.", "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:34852788"], "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:GSE13670"], "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:GSE13670"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34852788", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12866-021-02392-y", "sha256": "sha256:8812d4db5b7136f080268f6df4d854729daf836e3978d94bcad3d18fdf7b9d96", "bytes": 35829, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12866-021-02392-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8633612", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13670", "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=GSE13670", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13670", "version": null, "note": "Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM343802", "GSM343803", "GSM343804", "GSM343805", "GSM343806", "GSM343807", "GSM343808", "GSM343809", "GSM343810", "GSM343811", "GSM343812", "GSM343813", "GSM343814", "GSM343815", "GSM343816", "GSM343817", "GSM343818", "GSM343819", "GSM343820", "GSM343821", "GSM343822", "GSM343823", "GSM343824", "GSM343825", "GSM343826", "GSM343827", "GSM343828", "GSM343829", "GSM343830", "GSM343831"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data from S. aureus-exposed macrophages", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE30119", "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=GSE30119", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30119", "version": null, "note": "Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM745660", "GSM745661", "GSM745662", "GSM745663", "GSM745664", "GSM745665", "GSM745666", "GSM745667", "GSM745668", "GSM745669", "GSM745670", "GSM745671", "GSM745672", "GSM745673", "GSM745674", "GSM745675", "GSM745676", "GSM745677", "GSM745678", "GSM745679", "GSM745680", "GSM745681", "GSM745682", "GSM745683", "GSM745684", "GSM745685", "GSM745686", "GSM745687", "GSM745688", "GSM745689", "GSM745690", "GSM745691", "GSM745692", "GSM745693", "GSM745694", "GSM745695", "GSM745696", "GSM745697", "GSM745698", "GSM745699", "GSM745700", "GSM745701", "GSM745702", "GSM745703", "GSM745704", "GSM745705", "GSM745706", "GSM745707", "GSM745708", "GSM745709", "GSM745710", "GSM745711", "GSM745712", "GSM745713", "GSM745714", "GSM745715", "GSM745716", "GSM745717", "GSM745718", "GSM745719", "GSM745720", "GSM745721", "GSM745722", "GSM745723", "GSM745724", "GSM745725", "GSM745726", "GSM745727", "GSM745728", "GSM745729", "GSM745730", "GSM745731", "GSM745732", "GSM745733", "GSM745734", "GSM745735", "GSM745736", "GSM745737", "GSM745738", "GSM745739", "GSM745740", "GSM745741", "GSM745742", "GSM745743", "GSM745744", "GSM745745", "GSM745746", "GSM745747", "GSM745748", "GSM745749", "GSM745750", "GSM745751", "GSM745752", "GSM745753", "GSM745754", "GSM745755", "GSM745756", "GSM745757", "GSM745758", "GSM745759", "GSM745760", "GSM745761", "GSM745762", "GSM745763", "GSM745764", "GSM745765", "GSM745766", "GSM745767", "GSM745768", "GSM745769", "GSM745770", "GSM745771", "GSM745772", "GSM745773", "GSM745774", "GSM745775", "GSM745776", "GSM745777", "GSM745778", "GSM745779", "GSM745780", "GSM745781", "GSM745782", "GSM745783", "GSM745784", "GSM745785", "GSM745786", "GSM745787", "GSM745788", "GSM745789", "GSM745790", "GSM745791", "GSM745792", "GSM745793", "GSM745794", "GSM745795", "GSM745796", "GSM745797", "GSM745798", "GSM745799", "GSM745800", "GSM745801", "GSM745802"], "sample_count": 143, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Genome-wide analysis of whole blood transcriptional response to community-acquired Staphylococcus aureus infection in vivo", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE33341", "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=GSE33341", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33341", "version": null, "note": "Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM824455", "GSM824456", "GSM824457", "GSM824458", "GSM824459", "GSM824460", "GSM824461", "GSM824462", "GSM824463", "GSM824464", "GSM824465", "GSM824466", "GSM824467", "GSM824468", "GSM824469", "GSM824470", "GSM824471", "GSM824472", "GSM824473", "GSM824474", "GSM824475", "GSM824476", "GSM824477", "GSM824478", "GSM824479", "GSM824480", "GSM824481", "GSM824482", "GSM824483", "GSM824484", "GSM824485", "GSM824486", "GSM824487", "GSM824488", "GSM824489", "GSM824490", "GSM824491", "GSM824492", "GSM824493", "GSM824494", "GSM824495", "GSM824496", "GSM824497", "GSM824498", "GSM824499", "GSM824500", "GSM824501", "GSM824502", "GSM824503", "GSM824504", "GSM824505", "GSM824506", "GSM824507", "GSM824508", "GSM824509", "GSM824510", "GSM824511", "GSM824512", "GSM824513", "GSM824514", "GSM824515", "GSM824516", "GSM824517", "GSM824518", "GSM824519", "GSM824520", "GSM824521", "GSM824522", "GSM824523", "GSM824524", "GSM824525", "GSM824526", "GSM824527", "GSM824528", "GSM824529", "GSM824530", "GSM824531", "GSM824532", "GSM824533", "GSM824534", "GSM824535", "GSM824536", "GSM824537", "GSM824538", "GSM824539", "GSM824540", "GSM824541", "GSM824542", "GSM824543", "GSM824544", "GSM824545", "GSM824546", "GSM824547", "GSM824548", "GSM824549", "GSM824550", "GSM824551", "GSM824552", "GSM824553", "GSM824554", "GSM824555", "GSM824556", "GSM824557", "GSM824558", "GSM824559", "GSM824560", "GSM824561", "GSM824562", "GSM824563", "GSM824564", "GSM824565", "GSM824566", "GSM824567", "GSM824568", "GSM824569", "GSM824570", "GSM824571", "GSM824572", "GSM824573", "GSM824574", "GSM824575", "GSM824576", "GSM824577", "GSM824578", "GSM824579", "GSM824580", "GSM824581", "GSM824582", "GSM824583", "GSM824584", "GSM824585", "GSM824586", "GSM824587", "GSM824588", "GSM824589", "GSM824590", "GSM824591", "GSM824592", "GSM824593", "GSM824594", "GSM824595", "GSM824596", "GSM824597", "GSM824598", "GSM824599", "GSM824600", "GSM824601", "GSM824602", "GSM824603", "GSM824604", "GSM824605", "GSM824606", "GSM824607", "GSM824608", "GSM824609", "GSM824610", "GSM824611", "GSM824612", "GSM824613", "GSM824614", "GSM824615", "GSM824616", "GSM824617", "GSM824618", "GSM824619", "GSM824620", "GSM824621", "GSM824622", "GSM824623", "GSM824624", "GSM824625", "GSM824626", "GSM824627", "GSM824628", "GSM824629", "GSM824630", "GSM824631", "GSM824632", "GSM824633", "GSM824634", "GSM824635", "GSM824636", "GSM824637", "GSM824638", "GSM824639", "GSM824640", "GSM824641", "GSM824642", "GSM824643", "GSM824644", "GSM824645", "GSM824646", "GSM824647", "GSM824648", "GSM824649", "GSM824650", "GSM824651", "GSM824652", "GSM824653", "GSM824654", "GSM824655", "GSM824656", "GSM824657", "GSM824658", "GSM824659", "GSM824660", "GSM824661", "GSM824662", "GSM824663", "GSM824664", "GSM824665", "GSM824666", "GSM824667", "GSM824668", "GSM824669", "GSM824670", "GSM824671", "GSM824672", "GSM824673", "GSM824674", "GSM824675", "GSM824676", "GSM824677", "GSM824678", "GSM824679", "GSM824680", "GSM824681", "GSM824707", "GSM824708", "GSM824709", "GSM824710", "GSM824711", "GSM824712", "GSM824713", "GSM824714", "GSM824715", "GSM824716", "GSM824717", "GSM824718", "GSM824719", "GSM824720", "GSM824721", "GSM824722", "GSM824723", "GSM824724", "GSM824725", "GSM824726", "GSM824727", "GSM824728", "GSM824729", "GSM824730", "GSM824731", "GSM824732", "GSM824733", "GSM824734", "GSM824735", "GSM824736", "GSM824737", "GSM824738", "GSM824739", "GSM824740", "GSM824741", "GSM824742", "GSM824743", "GSM824744", "GSM824745", "GSM824746", "GSM824747", "GSM824748", "GSM824749", "GSM824750", "GSM824751", "GSM824752", "GSM824753", "GSM824754", "GSM824755", "GSM824756", "GSM824757", "GSM824758", "GSM824759", "GSM824760", "GSM824761", "GSM824762", "GSM824763", "GSM824764", "GSM824765", "GSM824766", "GSM824767", "GSM824768", "GSM824769", "GSM824770", "GSM824771", "GSM824772", "GSM824773", "GSM824774", "GSM824775", "GSM824776", "GSM824777", "GSM824778", "GSM824779", "GSM824780", "GSM824781", "GSM824782", "GSM824783", "GSM824784", "GSM824785", "GSM824786", "GSM824787", "GSM824788", "GSM824790", "GSM932374", "GSM932375", "GSM932376", "GSM932377", "GSM932378", "GSM932379", "GSM932380", "GSM932381", "GSM932382", "GSM932383", "GSM932384"], "sample_count": 321, "group_sizes": null, "group_sizes_basis": null, "platform": "1261;571", "taxon": "Mus musculus; Homo sapiens", "title": "Gene Expression-Based Classifiers Identify Staphylococcus aureus Infection in Mice and Humans", "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:GSE13670 not downloaded", "asset:data:geo:GSE13670 licence not read", "asset:data:geo:GSE30119 not downloaded", "asset:data:geo:GSE30119 licence not read", "asset:data:geo:GSE33341 not downloaded", "asset:data:geo:GSE33341 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": "GO enrichment"}}, {"id": "method-3", "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 curve"}}, {"id": "method-4", "family": null, "specific": null, "label": "weighted gene co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We downloaded the GSE33341 dataset from the GEO database and applied the weighted gene co-expression network analysis (WGCNA), from which we obtained some critical modules."}}], "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": ["GSE33341", "GSE30119", "GSE13670"], "resolved_accessions": ["GSE33341", "GSE30119", "GSE13670"], "statements": ["Microarray datasets (GSE33341, GSE13670 and GSE30119) for this study are openly available in Gene Expression Omnibus database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33341, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13670, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30119, respectively."], "basis": "The paper names GSE33341, GSE30119, GSE13670 in Gene Expression Omnibus 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:34852788", "data:geo:GSE13670"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13670"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:09:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10934, "completion_tokens": 1797, "cached_tokens": 264}}, "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:34852788", "type": "paper", "label": "pmid:34852788"}, {"id": "source:pmid:34852788", "type": "manuscript", "label": "PMID 34852788 full text"}, {"id": "data:geo:GSE13670", "type": "dataset", "label": "GEO GSE13670"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34852788", "type": "paper", "label": "pmid:34852788"}, {"id": "source:pmid:34852788", "type": "manuscript", "label": "PMID 34852788 full text"}, {"id": "data:geo:GSE13670", "type": "dataset", "label": "GEO GSE13670"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34852788", "type": "extraction", "used": ["source:pmid:34852788"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13670", "type": "accession_resolution", "used": ["data:geo:GSE13670"], "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:34852788", "parent_hash": "sha256:d284bbbf522241b3d7db42aebd2b209dfa278e7a10acfb5056c7d36b609908a3", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE13670 licence not read", "asset:data:geo:GSE13670 not downloaded", "asset:data:geo:GSE30119 licence not read", "asset:data:geo:GSE30119 not downloaded", "asset:data:geo:GSE33341 licence not read", "asset:data:geo:GSE33341 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["d P-value Availability of data and materials Microarray datasets (GSE33341, GSE13670 and GSE30119) f"], "order_basis": "paper_text_order:3350", "id": "assay:1"}, {"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": "consumes_earlier_output", "id": "assay:2"}]}