The prognostic value of CXC subfamily ligands in stage I-III patients with colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30973890", "kind": "science-record", "revision": 8, "content_hash": "sha256:980490ddbe3184ee4156e4fdf43a06e5857b1b6e6970e119e2b7b982a60b8c76", "created_at": "2026-11-01T15:40:44Z", "updated_at": "2026-11-01T22:00:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The prognostic value of CXC subfamily ligands in stage I-III patients with colorectal cancer.", "doi": "10.1371/journal.pone.0214611", "pmid": "30973890", "authors": ["Xiangde Li", "Qiulu Zhong", "Danjing Luo", "Qinghua Du", "Wenqi Liu"], "journal": "PloS one", "year": 2019, "abstract": "OBJECTIVE: To investigate the value of CXC subfamily ligands in stage I-III patients with colorectal cancer, in order to find a new predictor for CRC patients.\nMETHODS: We used Gene Expression Omnibus (GEO) database to collect the gene expression of CXC subfamily ligands and corresponding clinical data. The survival analysis was performed by \"survival\" package of Rsoftware. The CRC patients' DFS and the relationship between the expression levels of CXC subfamily ligands were evaluated by the univariate Cox regression analysis.\nRESULTS: By using microarray data, there were 14 CXC subfamily ligands identified from dataset GSE39582. Seven CXC subfamily ligands were significantly correlated with DFS in CRC patients. (p<0.05),including CXCL1, CXCL3, CXCL9, CXCL10, CXCL11, CXCL13, and CXCL14. From multivariate Cox regression analyze, four CXC subfamily ligands (CXCL9, CXCL10, CXCL11, and CXCL13) were significantly associated with CRC patients' DFS (all p<0.05). Three CXC subfamily ligands (CXCL10, CXCL11, and CXCL13) were significantly associated with CRC patients' Overall survival (OS) (all p<0.05). Both CXCL11 and CXCL13 had the similar prediction values for DFS and OS.\nCONCLUSION: There were seven CXC subfamily ligands were significantly correlated with DFS in CRC patients. Different expression level of four CXC subfamily ligands (CXCL9, CXCL10, CXCL11, and CXCL13) and Three CXC subfamily ligands (CXCL10, CXCL11, and CXCL13) were related to CRC patients' DFS and OS. There are still needs more experiments to confirm our conclusions. Next step we will make animal experiment about the genes in order to verified the predictive value of the CXC subfamily ligands.", "claims": [{"id": "claim-method", "statement": "In dataset GSE39582, the association between the expression level of CXC subfamily ligands and CRC patients’ DFS was evaluated using the univariate Cox regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30973890", "locator": "sections[4] \"Statistical analysis\" paragraph 2", "quote": "In dataset GSE39582, the association between the expression level of CXC subfamily ligands and CRC patients’ DFS was evaluated using the univariate Cox regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression of CXC subfamily ligands and corresponding clinical data were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). All log2-transformed expression data of CXC subfamily ligands were obtained from Affymetrix human genome U133 plus 2.0 array (GSE39582, PMID: 23700391, DOI:10.1371/journal.pmed.1001453). The expression values of genes with multiple probes were calculated by using the median values of multiple probes. After filtering out CRC patients without disease-free survival (DFS) and clinical data, there were a total of 491 I-III stage patients with CRC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30973890", "locator": "sections[3] \"Datasets preparation\" paragraph 2", "quote": "Gene expression of CXC subfamily ligands and corresponding clinical data were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). All log2-transformed expression data of CXC subfamily ligands were obtained from Affymetrix human genome U133 plus 2.0 array (GSE39582, PMID: 23700391, DOI:10.1371/journal.pmed.1001453). The expression values of genes with multiple probes were calculated by using the median values of multiple probes. After filtering out CRC patients without disease-free survival (DFS) and clinical data, there were a total of 491 I-III stage patients with CRC."}], "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:30973890"], "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:GSE39582"], "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:GSE39582"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30973890", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0214611", "sha256": "sha256:e4fbe7aaaa815e77832d70737311ac19a9bb9ace43e64cf68c956801e9082a59", "bytes": 17982, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0214611", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6459597", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "Gene expression of CXC subfamily ligands and corresponding clinical data were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). All log2-transformed expression data of CXC subfamily ligands were obtained from Affymetrix human genome U133 plus 2.0 array (GSE39582, PMID: 23700391, DOI:10.1371/journal.pmed.1001453). The expression values of genes with multiple probes were calculated by using the median values of multiple probes. After filtering out CRC patients without disease-free survival (DFS) and clinical data, there were a total of 491 I-III stage patients with CRC.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression of CXC subfamily ligands and corresponding clinical data were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). All log2-transformed expression data of CXC subfamily ligands were obtained from Affymetrix human genome U133 plus 2.0 array (GSE39582, PMID: 23700391, DOI:10.1371/journal.pmed.1001453). The expression values of genes with multiple probes were calculated by using the median values of multiple probes. After filtering out CRC patients without disease-free survival (DFS) and clinical data, there were a total of 491 I-III stage patients with CRC.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1681353", "GSM1681354", "GSM1681355", "GSM1681356", "GSM1681357", "GSM1681358", "GSM1681359", "GSM1681360", "GSM1681361", "GSM1681362", "GSM1681363", "GSM1681364", "GSM1681365", "GSM1681366", "GSM1681367", "GSM1681368", "GSM1681369", "GSM1681370", "GSM1681371", "GSM971957", "GSM971958", "GSM971959", "GSM971960", "GSM971961", "GSM971962", "GSM971963", "GSM971964", "GSM971965", "GSM971966", "GSM971967", "GSM971968", "GSM971969", "GSM971970", "GSM971971", "GSM971972", "GSM971973", "GSM971974", "GSM971975", "GSM971976", "GSM971977", "GSM971978", "GSM971979", "GSM971980", "GSM971981", "GSM971982", "GSM971983", "GSM971984", "GSM971985", "GSM971986", "GSM971987", "GSM971988", "GSM971989", "GSM971990", "GSM971991", "GSM971992", "GSM971993", "GSM971994", "GSM971995", "GSM971996", "GSM971997", "GSM971998", "GSM971999", "GSM972000", "GSM972001", "GSM972002", "GSM972003", "GSM972004", "GSM972005", "GSM972006", "GSM972007", "GSM972008", "GSM972009", "GSM972010", "GSM972011", "GSM972012", "GSM972013", "GSM972014", "GSM972015", "GSM972016", "GSM972017", "GSM972018", "GSM972019", "GSM972020", "GSM972021", "GSM972022", "GSM972023", "GSM972024", "GSM972025", "GSM972026", "GSM972027", "GSM972028", "GSM972029", "GSM972030", "GSM972031", "GSM972032", "GSM972033", "GSM972034", "GSM972035", "GSM972036", "GSM972037", "GSM972038", "GSM972039", "GSM972040", "GSM972041", "GSM972042", "GSM972043", "GSM972044", "GSM972045", "GSM972046", "GSM972047", "GSM972048", "GSM972049", "GSM972050", "GSM972051", "GSM972052", "GSM972053", "GSM972054", "GSM972055", "GSM972056", "GSM972057", "GSM972058", "GSM972059", "GSM972060", "GSM972061", "GSM972062", "GSM972063", "GSM972064", "GSM972065", "GSM972066", "GSM972067", "GSM972068", "GSM972069", "GSM972070", "GSM972071", "GSM972072", "GSM972073", "GSM972074", "GSM972075", "GSM972076", "GSM972077", "GSM972078", "GSM972079", "GSM972080", "GSM972081", "GSM972082", "GSM972083", "GSM972084", "GSM972085", "GSM972086", "GSM972087", "GSM972088", "GSM972089", "GSM972090", "GSM972091", "GSM972092", "GSM972093", "GSM972094", "GSM972095", "GSM972096", "GSM972097", "GSM972098", "GSM972099", "GSM972100", "GSM972101", "GSM972102", "GSM972103", "GSM972104", "GSM972105", "GSM972106", "GSM972107", "GSM972108", "GSM972109", "GSM972110", "GSM972111", "GSM972112", "GSM972113", "GSM972114", "GSM972115", "GSM972116", "GSM972117", "GSM972118", "GSM972119", "GSM972120", "GSM972121", "GSM972122", "GSM972123", "GSM972124", "GSM972125", "GSM972126", "GSM972127", "GSM972128", "GSM972129", "GSM972130", "GSM972131", "GSM972132", "GSM972133", "GSM972134", "GSM972135", "GSM972136", "GSM972137", "GSM972138", "GSM972139", "GSM972140", "GSM972141", "GSM972142", "GSM972143", "GSM972144", "GSM972145", "GSM972146", "GSM972147", "GSM972148", "GSM972149", "GSM972150", "GSM972151", "GSM972152", "GSM972153", "GSM972154", "GSM972155", "GSM972156", "GSM972157", "GSM972158", "GSM972159", "GSM972160", "GSM972161", "GSM972162", "GSM972163", "GSM972164", "GSM972165", "GSM972166", "GSM972167", "GSM972168", "GSM972169", "GSM972170", "GSM972171", "GSM972172", "GSM972173", "GSM972174", "GSM972175", "GSM972176", "GSM972177", "GSM972178", "GSM972179", "GSM972180", "GSM972181", "GSM972182", "GSM972183", "GSM972184", "GSM972185", "GSM972186", "GSM972187", "GSM972188", "GSM972189", "GSM972190", "GSM972191", "GSM972192", "GSM972193", "GSM972194", "GSM972195", "GSM972196", "GSM972197", "GSM972198", "GSM972199", "GSM972200", "GSM972201", "GSM972202", "GSM972203", "GSM972204", "GSM972205", "GSM972206", "GSM972207", "GSM972208", "GSM972209", "GSM972210", "GSM972211", "GSM972212", "GSM972213", "GSM972214", "GSM972215", "GSM972216", "GSM972217", "GSM972218", "GSM972219", "GSM972220", "GSM972221", "GSM972222", "GSM972223", "GSM972224", "GSM972225", "GSM972226", "GSM972227", "GSM972228", "GSM972229", "GSM972230", "GSM972231", "GSM972232", "GSM972233", "GSM972234", "GSM972235", "GSM972236", "GSM972237", "GSM972238", "GSM972239", "GSM972240", "GSM972241", "GSM972242", "GSM972243", "GSM972244", "GSM972245", "GSM972246", "GSM972247", "GSM972248", "GSM972249", "GSM972250", "GSM972251", "GSM972252", "GSM972253", "GSM972254", "GSM972255", "GSM972256", "GSM972257", "GSM972258", "GSM972259", "GSM972260", "GSM972261", "GSM972262", "GSM972263", "GSM972264", "GSM972265", "GSM972266", "GSM972267", "GSM972268", "GSM972269", "GSM972270", "GSM972271", "GSM972272", "GSM972273", "GSM972274", "GSM972275", "GSM972276", "GSM972277", "GSM972278", "GSM972279", "GSM972280", "GSM972281", "GSM972282", "GSM972283", "GSM972284", "GSM972285", "GSM972286", "GSM972287", "GSM972288", "GSM972289", "GSM972290", "GSM972291", "GSM972292", "GSM972293", "GSM972294", "GSM972295", "GSM972296", "GSM972297", "GSM972298", "GSM972299", "GSM972300", "GSM972301", "GSM972302", "GSM972303", "GSM972304", "GSM972305", "GSM972306", "GSM972307", "GSM972308", "GSM972309", "GSM972310", "GSM972311", "GSM972312", "GSM972313", "GSM972314", "GSM972315", "GSM972316", "GSM972317", "GSM972318", "GSM972319", "GSM972320", "GSM972321", "GSM972322", "GSM972323", "GSM972324", "GSM972325", "GSM972326", "GSM972327", "GSM972328", "GSM972329", "GSM972330", "GSM972331", "GSM972332", "GSM972333", "GSM972334", "GSM972335", "GSM972336", "GSM972337", "GSM972338", "GSM972339", "GSM972340", "GSM972341", "GSM972342", "GSM972343", "GSM972344", "GSM972345", "GSM972346", "GSM972347", "GSM972348", "GSM972349", "GSM972350", "GSM972351", "GSM972352", "GSM972353", "GSM972354", "GSM972355", "GSM972356", "GSM972357", "GSM972358", "GSM972359", "GSM972360", "GSM972361", "GSM972362", "GSM972363", "GSM972364", "GSM972365", "GSM972366", "GSM972367", "GSM972368", "GSM972369", "GSM972370", "GSM972371", "GSM972372", "GSM972373", "GSM972374", "GSM972375", "GSM972376", "GSM972377", "GSM972378", "GSM972379", "GSM972380", "GSM972381", "GSM972382", "GSM972383", "GSM972384", "GSM972385", "GSM972386", "GSM972387", "GSM972388", "GSM972389", "GSM972390", "GSM972391", "GSM972392", "GSM972393", "GSM972394", "GSM972395", "GSM972396", "GSM972397", "GSM972398", "GSM972399", "GSM972400", "GSM972401", "GSM972402", "GSM972403", "GSM972404", "GSM972405", "GSM972406", "GSM972407", "GSM972408", "GSM972409", "GSM972410", "GSM972411", "GSM972412", "GSM972413", "GSM972414", "GSM972415", "GSM972416", "GSM972417", "GSM972418", "GSM972419", "GSM972420", "GSM972421", "GSM972422", "GSM972423", "GSM972424", "GSM972425", "GSM972426", "GSM972427", "GSM972428", "GSM972429", "GSM972430", "GSM972431", "GSM972432", "GSM972433", "GSM972434", "GSM972435", "GSM972436", "GSM972437", "GSM972438", "GSM972439", "GSM972440", "GSM972441", "GSM972442", "GSM972443", "GSM972444", "GSM972445", "GSM972446", "GSM972447", "GSM972448", "GSM972449", "GSM972450", "GSM972451", "GSM972452", "GSM972453", "GSM972454", "GSM972455", "GSM972456", "GSM972457", "GSM972458", "GSM972459", "GSM972460", "GSM972461", "GSM972462", "GSM972463", "GSM972464", "GSM972465", "GSM972466", "GSM972467", "GSM972468", "GSM972469", "GSM972470", "GSM972471", "GSM972472", "GSM972473", "GSM972474", "GSM972475", "GSM972476", "GSM972477", "GSM972478", "GSM972479", "GSM972480", "GSM972481", "GSM972482", "GSM972483", "GSM972484", "GSM972485", "GSM972486", "GSM972487", "GSM972488", "GSM972489", "GSM972490", "GSM972491", "GSM972492", "GSM972493", "GSM972494", "GSM972495", "GSM972496", "GSM972497", "GSM972498", "GSM972499", "GSM972500", "GSM972501", "GSM972502", "GSM972503", "GSM972504", "GSM972505", "GSM972506", "GSM972507", "GSM972508", "GSM972509", "GSM972510", "GSM972511", "GSM972512", "GSM972513", "GSM972514", "GSM972515", "GSM972516", "GSM972517", "GSM972518", "GSM972519", "GSM972520", "GSM972521", "GSM972522"], "sample_count": 585, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30973890:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fd4d93954c592097a82bb7fc6da45196229e101db0ed9830af23a4d808e85e7b", "bytes": 290, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#pone.0214611.t001", "version": null, "note": "Univariate Cox regression analysis of CXC subfamily ligands associated with disease-free survival in dataset GSE39582 (n = 491).", "structure": {"pmcid": "PMC6459597", "section_index": 7, "section_title": "Identification of survival-related CXC subfamily ligands", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Univariate Cox regression analysis of CXC subfamily ligands associated with disease-free survival in dataset GSE39582 (n = 491).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[7]/table-wrap[1]#pone.0214611.t001"}}, {"id": "asset:table:pmid:30973890:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:806bf3591bcd0905f55e16e345090c0966677e6ab162a883f447dee3c1706eed", "bytes": 317, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#pone.0214611.t002", "version": null, "note": "Multivariate Cox regression analysis of seven CXC subfamily ligands, gender, age, stage, adjuvant chemotherapy, and survival in dataset GSE39582 (n = 492).", "structure": {"pmcid": "PMC6459597", "section_index": 8, "section_title": "Multivariate Cox regression analysis for CXCL1, CXCL3, CXCL9, CXCL10, CXCL11, CXCL13, and CXCL14", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Multivariate Cox regression analysis of seven CXC subfamily ligands, gender, age, stage, adjuvant chemotherapy, and survival in dataset GSE39582 (n = 492).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[8]/table-wrap[1]#pone.0214611.t002"}}, {"id": "asset:table:pmid:30973890:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:93a1afbf5e65fdc159412e62338f179c9b6bb8f5a3e0bee0ad89ba7b6b30d947", "bytes": 310, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#pone.0214611.t003", "version": null, "note": "Log-rank test of disease-free survival and overall survival according to CXCL9, CXCL10, CXCL11, and CXCL13 expression in dataset GSE39582 (n = 491).", "structure": {"pmcid": "PMC6459597", "section_index": 9, "section_title": "Survival comparisons for CXCL9, CXCL10, CXCL11, and CXCL13 between high-expression and low-expression in dataset GSE39582", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "Log-rank test of disease-free survival and overall survival according to CXCL9, CXCL10, CXCL11, and CXCL13 expression in dataset GSE39582 (n = 491).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[9]/table-wrap[1]#pone.0214611.t003"}}], "gaps": ["asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 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": "In dataset GSE39582, the association between the expression level of CXC subfamily ligands and CRC patients’ DFS was evaluated using the univariate Cox regression analysis."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "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": 0.8, "band": "high", "quote": "ROC analysis"}}], "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": ["GSE39582"], "resolved_accessions": ["GSE39582"], "statements": ["Gene expression of CXC subfamily ligands and corresponding clinical data were obtained from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/). All log2-transformed expression data of CXC subfamily ligands were obtained from Affymetrix human genome U133 plus 2.0 array (GSE39582, PMID: 23700391, DOI:10.1371/journal.pmed.1001453). The expression values of genes with multiple probes were calculated by using the median values of multiple probes. After filtering out CRC patients without disease-free survival (DFS) and clinical data, there were a total of 491 I-III stage patients with CRC."], "basis": "The paper names GSE39582 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:30973890", "data:geo:GSE39582", "asset:table:pmid:30973890:1", "asset:table:pmid:30973890:2", "asset:table:pmid:30973890:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE39582"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:26Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 14635, "completion_tokens": 1307, "cached_tokens": 784}}, "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:30973890", "type": "paper", "label": "pmid:30973890"}, {"id": "source:pmid:30973890", "type": "manuscript", "label": "PMID 30973890 full text"}, {"id": "data:geo:GSE39582", "type": "dataset", "label": "GEO GSE39582"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30973890", "type": "paper", "label": "pmid:30973890"}, {"id": "source:pmid:30973890", "type": "manuscript", "label": "PMID 30973890 full text"}, {"id": "data:geo:GSE39582", "type": "dataset", "label": "GEO GSE39582"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30973890", "type": "extraction", "used": ["source:pmid:30973890"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE39582", "type": "accession_resolution", "used": ["data:geo:GSE39582"], "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:30973890", "parent_hash": "sha256:04c44f30fa7b5fde21b5368e28c94b901379125128ff3085c63e0cfdd865c408", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "execution.not_run", "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": ["e Cox regression analysis. RESULTS: By using microarray data, there were 14 CXC subfamily ligands id"], "order_basis": "paper_text_order:600", "id": "assay:1"}, {"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": ["In dataset GSE39582, the association between the expression level of CXC subfamily ligands and CRC patients’ DFS was evaluated using the univariate Cox regression analysis."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}