Prognostic value of GLCE and infiltrating immune cells in Ewing sarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37662777", "kind": "science-record", "revision": 5, "content_hash": "sha256:6759e31ca3688827c652783445037e4412081bebf793125723ee36d3bcc6a70c", "created_at": "2026-11-01T19:02:26Z", "updated_at": "2026-11-01T22:52:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic value of GLCE and infiltrating immune cells in Ewing sarcoma.", "doi": "10.1016/j.heliyon.2023.e19357", "pmid": "37662777", "authors": ["Jian Wen", "Lijun Yi", "Lijia Wan", "Xieping Dong"], "journal": "Heliyon", "year": 2023, "abstract": "Background: The prognostic value of D-glucuronyl C5-epimerase (GLCE) and mast cell infiltration in Ewing sarcoma (ES) has not been well specified and highlighted, which may facilitate survival prediction and treatment.\nMethods: Several qualified datasets were downloaded from the GEO website. Common differentially expressed genes between normal subjects and ES patients in GSE17679, GSE45544, and GSE68776 were identified and screened by multiple algorithms to find hub genes with prognostic value. The prognostic value of 64 infiltrating cells was also explored. A prognostic model was established and then validated with GSE63155 and GSE63156. Finally, functional analysis was performed.\nResults: GLCE and mast cell infiltration were screened as two indicators for a prognostic model. The Kaplan‒Meier analysis showed that patients in the low GLCE expression, mast cell infiltration and risk score groups had poorer outcomes than patients in the high GLCE expression, mast cell infiltration and risk score groups, both in the training and validation sets. Scatter plots and heatmaps also indicated the same results. The concordance indices and calibration analyses indicated a high prediction accuracy of the model in the training and validation sets. The time-dependent receiver operating characteristic analyses suggested high sensitivity and specificity of the model, with area under the curve values between 0.76 and 0.98. The decision curve analyses suggested a significantly higher net benefit by the model than the treat-all and treat-none strategies. Functional analyses suggested that glycosaminoglycan biosynthesis-heparan sulfate/heparin, the cell cycle and microRNAs in cancer were upregulated in ES patients.\nConclusions: GLCE and mast cell infiltration are potential prognostic indicators in ES. GLCE may affect the proliferation, angiogenesis and metastasis of ES by affecting the biosynthesis of heparan sulfate and heparin.", "claims": [{"id": "claim-method", "statement": "DEGs between the normal subjects and ES patients were identified by this package in the GSE17679, GSE68776, and GSE45544 sets (|log2FC| > 1 and adjusted p value < 0.05). Then, common DEGs in the three sets were selected for subsequent screening. Univariate Cox regression analysis with a p value < 0.05 was used to identify genes directly associated with the survival of ES. Kaplan‒Meier analysis was then adopted to screen potential prognostic genes with a p value < 0.05 between the high and low expression groups (stratified by median). Thereafter, least absolute shrinkage and selection operator (LASSO) regression analysis (λ = 1 se) [18,19] and random forest (RF) feature selection [20,21] were used to screen prognostic genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37662777", "locator": "sections[4] \"Identification of common DEGs and prognostic genes\" paragraph 2", "quote": "DEGs between the normal subjects and ES patients were identified by this package in the GSE17679, GSE68776, and GSE45544 sets (|log2FC| > 1 and adjusted p value < 0.05). Then, common DEGs in the three sets were selected for subsequent screening. Univariate Cox regression analysis with a p value < 0.05 was used to identify genes directly associated with the survival of ES. Kaplan‒Meier analysis was then adopted to screen potential prognostic genes with a p value < 0.05 between the high and low expression groups (stratified by median). Thereafter, least absolute shrinkage and selection operator (LASSO) regression analysis (λ = 1 se) [18,19] and random forest (RF) feature selection [20,21] were used to screen prognostic genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available data sets were analyzed in this study. These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37662777", "locator": "sections[24] \"Data availability\" paragraph 2", "quote": "Publicly available data sets were analyzed in this study. These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:37662777"], "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:GSE17679"], "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:GSE17679"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37662777", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2023.e19357", "sha256": "sha256:1c3c4fe1b19d2b94f6cee8e38d0e2434186dda3c36c738860e59b231704f29c8", "bytes": 57377, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2023.e19357", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10474439", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17679", "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=GSE17679", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17679", "version": null, "note": "Publicly available data sets were analyzed in this study. 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These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM439886", "GSM439887", "GSM439888", "GSM439889", "GSM439890", "GSM439891", "GSM439892", "GSM439893", "GSM439894", "GSM439895", "GSM439896", "GSM439897", "GSM439898", "GSM439899", "GSM439900", "GSM439901", "GSM439902", "GSM439903", "GSM439904", "GSM439905", "GSM439906", "GSM439907", "GSM439908", "GSM439909", "GSM439910", "GSM439911", "GSM439912", "GSM439913", "GSM439914", "GSM439915", "GSM439916", "GSM439917", "GSM439918", "GSM439919", "GSM439920", "GSM439921", "GSM439922", "GSM439923", "GSM439924", "GSM439925", "GSM439926", "GSM439927", "GSM439928", "GSM439929", "GSM439930", "GSM439931", "GSM439932", "GSM439933", "GSM439934", "GSM439935", "GSM439936", "GSM439937", "GSM439938", "GSM439939", "GSM439940", "GSM440999", "GSM441000", "GSM441001", "GSM441002", "GSM441003", "GSM441004", "GSM441005", "GSM441006", "GSM441007", "GSM441008", "GSM441009", "GSM441010", "GSM441011", "GSM441012", "GSM441013", "GSM441014", "GSM441015", "GSM441016", "GSM441017", "GSM441018", "GSM441019", "GSM441020", "GSM441021", "GSM441022", "GSM441023", "GSM441024", "GSM441025", "GSM441026", "GSM441027", "GSM441028", "GSM441029", "GSM441030", "GSM441031", "GSM441032", "GSM441033", "GSM441034", "GSM441035", "GSM441036", "GSM441037", "GSM441038", "GSM441039", "GSM441040", "GSM441041", "GSM441042", "GSM441044", "GSM441045", "GSM441046", "GSM441047", "GSM441048", "GSM441049", "GSM441050", "GSM441051", "GSM441052", "GSM441053", "GSM441054", "GSM441055", "GSM441056", "GSM441057", "GSM441058", "GSM441059", "GSM441060", "GSM441061"], "sample_count": 117, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Inflammatory gene profiling of Ewing sarcoma family of tumors", "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:GSE45544", "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=GSE45544", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45544", "version": null, "note": "Publicly available data sets were analyzed in this study. 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These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1108333", "GSM1108334", "GSM1108335", "GSM1108336", "GSM1108337", "GSM1108338", "GSM1108339", "GSM1108340", "GSM1108341", "GSM1108342", "GSM1108343", "GSM1108344", "GSM1108345", "GSM1108346", "GSM1108347", "GSM1108348", "GSM1108349", "GSM1108350", "GSM1108351", "GSM1108352", "GSM1108353", "GSM1108354", "GSM1108355", "GSM1108356", "GSM1108357", "GSM1108358", "GSM1108359", "GSM1108360", "GSM1108361", "GSM1108362", "GSM1108363", "GSM1108364", "GSM1108365", "GSM1108366", "GSM1108367", "GSM1108368", "GSM1108369", "GSM1108370", "GSM1534664", "GSM1534665", "GSM1534666", "GSM1534667", "GSM1534668", "GSM1534669"], "sample_count": 44, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Ewing sarcoma compared to a normal body map", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE63155", "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=GSE63155", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63155", "version": null, "note": "Publicly available data sets were analyzed in this study. These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available data sets were analyzed in this study. These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1542334", "GSM1542335", "GSM1542336", "GSM1542337", "GSM1542338", "GSM1542339", "GSM1542340", "GSM1542341", "GSM1542342", "GSM1542343", "GSM1542344", "GSM1542345", "GSM1542346", "GSM1542347", "GSM1542348", "GSM1542349", "GSM1542350", "GSM1542351", "GSM1542352", "GSM1542353", "GSM1542354", "GSM1542355", "GSM1542356", "GSM1542357", "GSM1542358", "GSM1542359", "GSM1542360", "GSM1542361", "GSM1542362", "GSM1542363", "GSM1542364", "GSM1542365", "GSM1542366", "GSM1542367", "GSM1542368", "GSM1542369", "GSM1542370", "GSM1542371", "GSM1542372", "GSM1542373", "GSM1542374", "GSM1542375", "GSM1542376", "GSM1542377", "GSM1542378", "GSM1542379"], "sample_count": 46, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Ewing Sarcoma Tumors Reveals the Prognostic Importance of Tumor-Stromal Interactions [COG]", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE63156", "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=GSE63156", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63156", "version": null, "note": "Publicly available data sets were analyzed in this study. 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These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1542380", "GSM1542381", "GSM1542382", "GSM1542383", "GSM1542384", "GSM1542385", "GSM1542386", "GSM1542387", "GSM1542388", "GSM1542389", "GSM1542390", "GSM1542391", "GSM1542392", "GSM1542393", "GSM1542394", "GSM1542395", "GSM1542396", "GSM1542397", "GSM1542398", "GSM1542399", "GSM1542400", "GSM1542401", "GSM1542402", "GSM1542403", "GSM1542404", "GSM1542405", "GSM1542406", "GSM1542407", "GSM1542408", "GSM1542409", "GSM1542410", "GSM1542411", "GSM1542412", "GSM1542413", "GSM1542414", "GSM1542415", "GSM1542416", "GSM1542417", "GSM1542418"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Ewing Sarcoma Tumors Reveals the Prognostic Importance of Tumor-Stromal Interactions [EuroEwing]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE68776", "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=GSE68776", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68776", "version": null, "note": "Publicly available data sets were analyzed in this study. 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These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1681080", "GSM1681081", "GSM1681082", "GSM1681083", "GSM1681084", "GSM1681085", "GSM1681086", "GSM1681087", "GSM1681088", "GSM1681089", "GSM1681090", "GSM1681091", "GSM1681092", "GSM1681093", "GSM1681094", "GSM1681095", "GSM1681096", "GSM1681097", "GSM1681098", "GSM1681099", "GSM1681100", "GSM1681101", "GSM1681102", "GSM1681103", "GSM1681104", "GSM1681105", "GSM1681106", "GSM1681107", "GSM1681108", "GSM1681109", "GSM1681110", "GSM1681111", "GSM1681112", "GSM1681113", "GSM1681114", "GSM1681115", "GSM1681116", "GSM1681117", "GSM1681118", "GSM1681119", "GSM1681120", "GSM1681121", "GSM1681122", "GSM1681123", "GSM1681124", "GSM1681125", "GSM1681126", "GSM1681127", "GSM1681128", "GSM1681129", "GSM1681130", "GSM1681131", "GSM1681132", "GSM1681133", "GSM1681134", "GSM1681135", "GSM1681136", "GSM1681137", "GSM1681138", "GSM1681139", "GSM1681140", "GSM1681141", "GSM1681142", "GSM1681143", "GSM1681144", "GSM1681145", "GSM1681146", "GSM1681147", "GSM1681148", "GSM1681149", "GSM1681150", "GSM1681151", "GSM1681152", "GSM1681153"], "sample_count": 74, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Exon array profiles of primary human Ewing sarcoma tumors", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE17679 not downloaded", "asset:data:geo:GSE17679 licence not read", "asset:data:geo:GSE45544 not downloaded", "asset:data:geo:GSE45544 licence not read", "asset:data:geo:GSE63155 not downloaded", "asset:data:geo:GSE63155 licence not read", "asset:data:geo:GSE63156 not downloaded", "asset:data:geo:GSE63156 licence not read", "asset:data:geo:GSE68776 not downloaded", "asset:data:geo:GSE68776 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "DEGs between the normal subjects and ES patients were identified by this package in the GSE17679, GSE68776, and GSE45544 sets (|log2FC| > 1 and adjusted p value < 0.05). Then, common DEGs in the three sets were selected for subsequent screening. Univariate Cox regression analysis with a p value < 0.05 was used to identify genes directly associated with the survival of ES. Kaplan‒Meier analysis was then adopted to screen potential prognostic genes with a p value < 0.05 between the high and low expression groups (stratified by median). Thereafter, least absolute shrinkage and selection operator (LASSO) regression analysis (λ = 1 se) [18,19] and random forest (RF) feature selection [20,21] were used to screen prognostic genes."}}, {"id": "method-2", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "random forest"}}, {"id": "method-3", "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": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-4", "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-5", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.7, "band": "medium", "quote": "net benefit"}}], "targets": [], "gaps": []}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE17679", "GSE68776", "GSE45544", "GSE63155", "GSE63156"], "resolved_accessions": ["GSE17679", "GSE68776", "GSE45544", "GSE63155", "GSE63156"], "statements": ["Publicly available data sets were analyzed in this study. These data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17679, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68776, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45544, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63155, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63156."], "basis": "The paper names GSE17679, GSE68776, GSE45544, GSE63155, GSE63156 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": ["cox_ph"], "assets": ["source:pmid:37662777", "data:geo:GSE17679"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17679"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:52:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15403, "completion_tokens": 2743, "cached_tokens": 128}}, "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:37662777", "type": "paper", "label": "pmid:37662777"}, {"id": "source:pmid:37662777", "type": "manuscript", "label": "PMID 37662777 full text"}, {"id": "data:geo:GSE17679", "type": "dataset", "label": "GEO GSE17679"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37662777", "type": "paper", "label": "pmid:37662777"}, {"id": "source:pmid:37662777", "type": "manuscript", "label": "PMID 37662777 full text"}, {"id": "data:geo:GSE17679", "type": "dataset", "label": "GEO GSE17679"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37662777", "type": "extraction", "used": ["source:pmid:37662777"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17679", "type": "accession_resolution", "used": ["data:geo:GSE17679"], "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:37662777", "parent_hash": "sha256:f9a289831f2c67999a53c5b18f3b94376899f2e6152ac6e6d8aecd9d30b603df", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE17679 licence not read", "asset:data:geo:GSE17679 not downloaded", "asset:data:geo:GSE45544 licence not read", "asset:data:geo:GSE45544 not downloaded", "asset:data:geo:GSE63155 licence not read", "asset:data:geo:GSE63155 not downloaded", "asset:data:geo:GSE63156 licence not read", "asset:data:geo:GSE63156 not downloaded", "asset:data:geo:GSE68776 licence not read", "asset:data:geo:GSE68776 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["DEGs between the normal subjects and ES patients were identified by this package in the GSE17679, GSE68776, and GSE45544 sets (|log2FC| > 1 and adjusted p value < 0.05). Then, common DEGs in the three sets were selected for subsequent screening. Univariate Cox regression analysis with a p value < 0.05 was used to identify genes directly associated with the survival of ES. Kaplan‒Meier analysis was then adopted to screen potential prognostic genes with a p value < 0.05 between the high and low expression groups (stratified by median). Thereafter, least absolute shrinkage and selection operator (LASSO) regression analysis (λ = 1 se) [18,19] and random forest (RF) feature selection [20,21] were used to screen prognostic genes."], "order_basis": "analysis_only", "id": "assay:1"}]}