Identification of hub genes and key pathways associated with angioimmunoblastic T-cell lymphoma using weighted gene co-expression network analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31239775", "kind": "science-record", "revision": 8, "content_hash": "sha256:8e3f75c2616ccb6da8e025cce6546ed28cf8788e4da9a18335c8ef2b2bcdab92", "created_at": "2026-11-01T15:40:46Z", "updated_at": "2026-11-01T22:00:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and key pathways associated with angioimmunoblastic T-cell lymphoma using weighted gene co-expression network analysis.", "doi": "10.2147/CMAR.S185030", "pmid": "31239775", "authors": ["Xiaoqian Li", "Zijian Liu", "Mi Mi", "Caijiao Zhang", "Yin Xiao", "Xinxiu Liu", "Gang Wu", "Liling Zhang"], "journal": "Cancer management and research", "year": 2019, "abstract": "Background: Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive subtype of peripheral T-cell lymphoma (PTCL) that has a poor 5-year overall survival rate due to its lack of precise therapeutic targets. Identifying potential prognostic markers of AITL may provide information regarding the development of precision medicine. Methods: RNA sequence data from PTCL and patient clinic traits were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify DEGs between the different PTCL subtypes and investigate the relationship underlying co-expression modules and clinic traits. Gene ontology (GO) and protein-protein interaction (PPI) network analyses based on DAVID and the STRING website, respectively, were utilized to deeply excavate hub genes. Results: After removing the outliers from the GSE65823, GSE58445, GSE19069, and GSE6338 datasets using the results from an unsupervised cluster heatmap, 50 AITL samples and 55 anaplastic large cell lymphoma (ALCL) samples were screened. A total of 677 upregulated DEGs and 237 downregulated DEGs were identified in AITL and used to construct a PPI network complex. Using WGCNA, 12 identified co-expression modules were constructed from the 5468 genes with the top 10% of variance, and 192 genes from the Turquoise and Brown modules were with a Gene Significance (GS) cut-off threshold >0.6. Eleven hub genes (CDH1, LAT, LPAR1, CXCL13, CD27, ICAM2, CD3E, CCL19, CTLA-4, CXCR5, and C3) were identified. Only CTLA-4 overexpressed was found to be a poor prognostic factor according to survival analysis. Gene set enrichment analysis (GSEA) identified and validated the intersection of key pathways (T cell receptor, primary immunodeficiency, and chemokine signaling pathways). Conclusion: Our findings provide the framework for the identification of AITL co-expression gene modules and identify key pathways and driving genes that may be novel treatment targets and helpful for the development of a prognostic evaluation index.", "claims": [{"id": "claim-method", "statement": "The effect of individual parameters on the OS was studied with Kaplan–Meier (KM) survival analysis using dichotomous grouping based on the ROC analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31239775", "locator": "sections[7] \"Survival analysis\" paragraph 2", "quote": "The effect of individual parameters on the OS was studied with Kaplan–Meier (KM) survival analysis using dichotomous grouping based on the ROC analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31239775", "locator": "sections[3] \"Microarray information and DEG identification\" paragraph 2", "quote": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform."}], "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:31239775"], "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:GSE19069"], "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:GSE19069"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31239775", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S185030", "sha256": "sha256:9b27048659966711420154b87af7251e34158288b965173cea83a04fc61871db", "bytes": 43663, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S185030", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6559227", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19069", "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=GSE19069", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19069", "version": null, "note": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM472023", "GSM472024", "GSM472025", "GSM472026", "GSM472027", "GSM472028", "GSM472029", "GSM472030", "GSM472031", "GSM472032", "GSM472033", "GSM472034", "GSM472035", "GSM472036", "GSM472037", "GSM472038", "GSM472039", "GSM472040", "GSM472041", "GSM472042", "GSM472043", "GSM472044", "GSM472045", "GSM472046", "GSM472047", "GSM472048", "GSM472049", "GSM472050", "GSM472051", "GSM472052", "GSM472053", "GSM472054", "GSM472055", "GSM472056", "GSM472057", "GSM472058", "GSM472059", "GSM472060", "GSM472061", "GSM472062", "GSM472063", "GSM472064", "GSM472065", "GSM472066", "GSM472067", "GSM472068", "GSM472069", "GSM472070", "GSM472071", "GSM472072", "GSM472073", "GSM472074", "GSM472075", "GSM472076", "GSM472077", "GSM472078", "GSM472079", "GSM472080", "GSM472081", "GSM472082", "GSM472083", "GSM472084", "GSM472085", "GSM472086", "GSM472087", "GSM472088", "GSM472089", "GSM472090", "GSM472091", "GSM472092", "GSM472093", "GSM472094", "GSM472095", "GSM472096", "GSM472097", "GSM472098", "GSM472099", "GSM472100", "GSM472101", "GSM472102", "GSM472103", "GSM472104", "GSM472105", "GSM472106", "GSM472107", "GSM472108", "GSM472109", "GSM472110", "GSM472111", "GSM472112", "GSM472113", "GSM472114", "GSM472115", "GSM472116", "GSM472117", "GSM472118", "GSM472119", "GSM472120", "GSM472121", "GSM472122", "GSM472123", "GSM472124", "GSM472125", "GSM472126", "GSM472127", "GSM472128", "GSM472129", "GSM472130", "GSM472131", "GSM472132", "GSM472133", "GSM472134", "GSM472135", "GSM472136", "GSM472137", "GSM472138", "GSM472139", "GSM472140", "GSM472141", "GSM472142", "GSM472143", "GSM472144", "GSM472145", "GSM472146", "GSM472147", "GSM472148", "GSM472149", "GSM472150", "GSM472151", "GSM472152", "GSM472153", "GSM472154", "GSM472155", "GSM472156", "GSM472157", "GSM472158", "GSM472159", "GSM472160", "GSM472161", "GSM472162", "GSM472163", "GSM472164", "GSM472165", "GSM472166", "GSM472167", "GSM472168", "GSM472169"], "sample_count": 147, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular signatures in peripheral T-cell lymphoma (PTCL)", "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:GSE58445", "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=GSE58445", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58445", "version": null, "note": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1411273", "GSM1411274", "GSM1411275", "GSM1411276", "GSM1411277", "GSM1411278", "GSM1411279", "GSM1411280", "GSM1411281", "GSM1411282", "GSM1411283", "GSM1411284", "GSM1411285", "GSM1411286", "GSM1411287", "GSM1411288", "GSM1411289", "GSM1411290", "GSM1411291", "GSM1411292", "GSM1411293", "GSM1411294", "GSM1411295", "GSM1411296", "GSM1411297", "GSM1411298", "GSM1411299", "GSM1411300", "GSM1411301", "GSM1411302", "GSM1411303", "GSM1411304", "GSM1411305", "GSM1411306", "GSM1411307", "GSM1411308", "GSM1411309", "GSM1411310", "GSM1411311", "GSM1411312", "GSM1411313", "GSM1411314", "GSM1411315", "GSM1411316", "GSM1411317", "GSM1411318", "GSM1411319", "GSM1411320", "GSM1411321", "GSM1411322", "GSM1411323", "GSM1411324", "GSM1411325", "GSM1411326", "GSM1411327", "GSM1411328", "GSM1411329", "GSM1411330", "GSM1411331", "GSM1411332", "GSM1411333", "GSM1411334", "GSM1411335", "GSM1411336", "GSM1411337", "GSM1411338", "GSM1411339", "GSM1411340", "GSM1411341", "GSM1411342", "GSM1411343", "GSM1411344", "GSM1411345", "GSM1411346", "GSM1411347", "GSM1411348", "GSM1411349", "GSM1411350", "GSM1411351", "GSM1411352", "GSM1411353", "GSM1411354", "GSM1411355", "GSM1411356", "GSM1411357", "GSM1411358", "GSM1411359", "GSM1411360", "GSM1411361", "GSM1411362", "GSM1411363", "GSM1411364", "GSM1411365", "GSM1411366", "GSM1411367", "GSM1411368", "GSM1411369", "GSM1411370", "GSM1411371", "GSM1411372", "GSM1411373", "GSM1411374", "GSM1411375", "GSM1411376", "GSM1411377", "GSM1411378", "GSM1411379", "GSM1411380", "GSM1411381", "GSM1411382", "GSM1411383", "GSM1411384", "GSM1411385", "GSM1411386", "GSM1411387", "GSM1411388", "GSM1411389", "GSM1411390", "GSM1411391", "GSM1411392", "GSM1411393", "GSM1411394", "GSM1411395", "GSM1411396", "GSM1411397", "GSM1411398", "GSM1411399", "GSM1411400", "GSM1411401", "GSM1411402", "GSM1411403", "GSM1411404", "GSM1411405", "GSM1411406", "GSM1411407", "GSM1411408", "GSM1411409", "GSM1411410", "GSM1411411", "GSM1411412", "GSM1411413", "GSM1411414", "GSM1411415", "GSM1411416", "GSM1411417", "GSM1411418", "GSM1411419", "GSM1411420", "GSM1411421", "GSM1411422", "GSM1411423", "GSM1411424", "GSM1411425", "GSM1411426", "GSM1411427", "GSM1411428", "GSM1411429", "GSM1411430", "GSM1411431", "GSM1411432", "GSM1411433", "GSM1411434", "GSM1411435", "GSM1411436", "GSM1411437", "GSM1411438", "GSM1411439", "GSM1411440", "GSM1411441", "GSM1411442", "GSM1411443", "GSM1411444", "GSM1411445", "GSM1411446", "GSM1411447", "GSM1411448", "GSM1411449", "GSM1411450", "GSM1411451", "GSM1411452", "GSM1411453", "GSM1411454", "GSM1411455", "GSM1411456", "GSM1411457", "GSM1411458", "GSM1411459", "GSM1411460", "GSM1411461", "GSM1411462", "GSM1411463", "GSM1411464", "GSM1411465"], "sample_count": 193, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression signatures delineate biological and prognostic subgroups in peripheral T-cell lymphoma", "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:GSE6338", "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=GSE6338", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6338", "version": null, "note": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM146142", "GSM146143", "GSM146144", "GSM146145", "GSM146146", "GSM146147", "GSM146148", "GSM146149", "GSM146150", "GSM146151", "GSM146152", "GSM146153", "GSM146154", "GSM146155", "GSM146156", "GSM146157", "GSM146158", "GSM146159", "GSM146160", "GSM146161", "GSM146162", "GSM146163", "GSM146164", "GSM146165", "GSM146166", "GSM146167", "GSM146168", "GSM146169", "GSM146170", "GSM146171", "GSM146172", "GSM146173", "GSM146174", "GSM146175", "GSM146176", "GSM146177", "GSM146178", "GSM146179", "GSM146180", "GSM146181", "GSM146182", "GSM146183", "GSM146184", "GSM146185", "GSM146186", "GSM146187", "GSM146188", "GSM146189", "GSM146190", "GSM146191", "GSM146192", "GSM146193", "GSM146194", "GSM146195", "GSM146196", "GSM146197", "GSM146198", "GSM146199", "GSM146200", "GSM146201"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression analysis of Peripheral T-cell Lymphoma/Unspecified", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65823", "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=GSE65823", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65823", "version": null, "note": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1607007", "GSM1607008", "GSM1607009", "GSM1607010", "GSM1607011", "GSM1607012", "GSM1607013", "GSM1607014", "GSM1607015", "GSM1607016", "GSM1607017", "GSM1607018", "GSM1607019", "GSM1607020", "GSM1607021", "GSM1607022", "GSM1607023", "GSM1607024", "GSM1607025", "GSM1607026", "GSM1607027", "GSM1607028", "GSM1607029", "GSM1607030", "GSM1607031", "GSM1607032", "GSM1607033", "GSM1607034", "GSM1607035", "GSM1607036", "GSM1607037"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Identification of a new subclass of ALK negative ALCL expressing aberrant levels of ERBB4 transcripts", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE19069 not downloaded", "asset:data:geo:GSE19069 licence not read", "asset:data:geo:GSE58445 not downloaded", "asset:data:geo:GSE58445 licence not read", "asset:data:geo:GSE6338 not downloaded", "asset:data:geo:GSE6338 licence not read", "asset:data:geo:GSE65823 not downloaded", "asset:data:geo:GSE65823 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The effect of individual parameters on the OS was studied with Kaplan–Meier (KM) survival analysis using dichotomous grouping based on the ROC analysis."}}, {"id": "method-2", "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-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": 0.8, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE65823", "GSE58445", "GSE19069", "GSE6338"], "resolved_accessions": ["GSE65823", "GSE58445", "GSE19069", "GSE6338"], "statements": ["We obtained four series (GSE65823, GSE58445, GSE19069, and GSE6338), which were based on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA). A total of 55 ALCL cases and 50 AITL cases were included in these datasets. We chose these four datasets for our integrated analysis in this study because these datasets, which include both AITL and ALCL subtypes, were generated from the same sequencing platform."], "basis": "The paper names GSE65823, GSE58445, GSE19069, GSE6338 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": ["survival_km"], "assets": ["source:pmid:31239775", "data:geo:GSE19069"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19069"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 34519, "completion_tokens": 2275, "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:31239775", "type": "paper", "label": "pmid:31239775"}, {"id": "source:pmid:31239775", "type": "manuscript", "label": "PMID 31239775 full text"}, {"id": "data:geo:GSE19069", "type": "dataset", "label": "GEO GSE19069"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31239775", "type": "paper", "label": "pmid:31239775"}, {"id": "source:pmid:31239775", "type": "manuscript", "label": "PMID 31239775 full text"}, {"id": "data:geo:GSE19069", "type": "dataset", "label": "GEO GSE19069"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31239775", "type": "extraction", "used": ["source:pmid:31239775"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19069", "type": "accession_resolution", "used": ["data:geo:GSE19069"], "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:31239775", "parent_hash": "sha256:6ad0363df38a843c92b74a8e7733904eaecafd78daf615f2b0e8fbd81db1b7a1", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE19069 licence not read", "asset:data:geo:GSE19069 not downloaded", "asset:data:geo:GSE58445 licence not read", "asset:data:geo:GSE58445 not downloaded", "asset:data:geo:GSE6338 licence not read", "asset:data:geo:GSE6338 not downloaded", "asset:data:geo:GSE65823 licence not read", "asset:data:geo:GSE65823 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": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The effect of individual parameters on the OS was studied with Kaplan–Meier (KM) survival analysis using dichotomous grouping based on the ROC analysis."], "order_basis": "analysis_only", "id": "assay:1"}]}