Identification and verification of mitochondria-related genes biomarkers associated with immune infiltration for COPD using WGCNA and machine learning algorithms.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40274954", "kind": "science-record", "revision": 4, "content_hash": "sha256:51f6c01cf070c50c40638904d0539bcc6c4403a192be4cf1db5700bc6b8e1d6b", "created_at": "2026-11-01T20:30:25Z", "updated_at": "2026-11-01T22:56:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and verification of mitochondria-related genes biomarkers associated with immune infiltration for COPD using WGCNA and machine learning algorithms.", "doi": "10.1038/s41598-025-99002-y", "pmid": "40274954", "authors": ["Meijuan Peng", "Chen Jiang", "Ziyu Dai", "Bin Xie", "Qiong Chen", "Jianing Lin"], "journal": "Scientific reports", "year": 2025, "abstract": "Mitochondrial dysfunction plays a pivotal role in the pathogenesis of chronic obstructive pulmonary disease (COPD). This study combines bioinformatics analysis with machine learning to elucidate potential key mitochondrial-related genes associated with COPD and its immune microenvironment. We utilized the limma package and Weighted Gene Co-expression Network Analysis (WGCNA) to analyze datasets from the Gene Expression Omnibus (GEO) database (GSE57148), identifying 12 key differentially expressed mitochondrial genes (MitoDEGs). Using 12 distinct machine learning algorithms (comprising 143 predictive models), we identified the optimal diagnostic model, which includes five pivotal MitoDEGs: ERN1, FASTK, HIGD1B, NDUFA7 and NDUFB7. The diagnostic specificity and sensitivity of each gene, as well as the diagnostic model itself, were evaluated using Receiver operating characteristic (ROC) curves. This model demonstrated high specificity in the validation cohorts (GSE76925, GSE151052, GSE239897). Expression analysis revealed upregulation of ERN1 and downregulation of FASTK, HIGD1B, NDUFA7 and NDUFB7 in COPD patients. Spearman's correlation analysis indicated a significant association between MitoDEGs and immune cell infiltration, with ERN1 expression positively correlated with neutrophil infiltration and the other genes negatively correlated. The GABA receptor modulator androstenol was identified as a potential therapeutic candidate. In vivo studies confirmed reduced mRNA expression of HIGD1B and NDUFB7 in COPD mice. These findings elucidate mitochondrial-immune interactions in COPD and highlight novel diagnostic and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "We utilized the limma package and Weighted Gene Co-expression Network Analysis (WGCNA) to analyze datasets from the Gene Expression Omnibus (GEO) database (GSE57148), identifying 12 key differentially expressed mitochondrial genes (MitoDEGs).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40274954", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We utilized the limma package and Weighted Gene Co-expression Network Analysis (WGCNA) to analyze datasets from the Gene Expression Omnibus (GEO) database (GSE57148), identifying 12 key differentially expressed mitochondrial genes (MitoDEGs)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The limma and WGCNA analysis of GSE57148 identified 12 key differentially expressed mitochondrial genes in COPD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40274954", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We utilized the limma package and Weighted Gene Co-expression Network Analysis (WGCNA) to analyze datasets from the Gene Expression Omnibus (GEO) database (GSE57148), identifying 12 key differentially expressed mitochondrial genes (MitoDEGs)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The limma and WGCNA analysis of GSE57148 identified 12 key differentially expressed mitochondrial genes in COPD.", "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:40274954"], "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:GSE151052"], "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:GSE151052"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40274954", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-99002-y", "sha256": "sha256:6ceb15305f723161a597c1a3bce285694fa1c19c87d15c0f412d92ec183129d0", "bytes": 46285, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-99002-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12022275", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE151052", "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=GSE151052", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE151052", "version": null, "note": "The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). 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Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM7676839", "GSM7676840", "GSM7676841", "GSM7676842", "GSM7676843", "GSM7676844", "GSM7676845", "GSM7676846", "GSM7676847", "GSM7676848", "GSM7676849", "GSM7676850", "GSM7676851", "GSM7676852", "GSM7676853", "GSM7676854", "GSM7676855", "GSM7676856", "GSM7676857", "GSM7676858", "GSM7676859", "GSM7676860", "GSM7676861", "GSM7676862", "GSM7676863", "GSM7676864", "GSM7676865", "GSM7676866", "GSM7676867", "GSM7676868", "GSM7676869", "GSM7676870", "GSM7676871", "GSM7676872", "GSM7676873", "GSM7676874", "GSM7676875", "GSM7676876", "GSM7676877", "GSM7676878", "GSM7676879", "GSM7676880", "GSM7676881", "GSM7676882", "GSM7676883", "GSM7676884", "GSM7676885", "GSM7676886", "GSM7676887", "GSM7676888", "GSM7676889", "GSM7676890", "GSM7676891", "GSM7676892", "GSM7676893", "GSM7676894", "GSM7676895", "GSM7676896", "GSM7732798", "GSM7732799", "GSM7732800", "GSM7732801", "GSM7732802", "GSM7732803", "GSM7732804", "GSM7732805", "GSM7732806", "GSM7732807", "GSM7732808", "GSM7732809", "GSM7732810", "GSM7732811", "GSM7732812", "GSM7732813", "GSM7732814", "GSM7732815", "GSM7732816", "GSM7732817", "GSM7732818", "GSM7732819", "GSM7732820", "GSM7732821"], "sample_count": 82, "group_sizes": null, "group_sizes_basis": null, "platform": "17303", "taxon": "Homo sapiens", "title": "Mucosal immune alterations at the early onset of tissue destruction in Chronic Obstructive Pulmonary Disease", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE57148", "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=GSE57148", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57148", "version": null, "note": "The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1375986", "GSM1375987", "GSM1375988", "GSM1375989", "GSM1375990", "GSM1375991", "GSM1375992", "GSM1375993", "GSM1375994", "GSM1375995", "GSM1375996", "GSM1375997", "GSM1375998", "GSM1375999", "GSM1376000", "GSM1376001", "GSM1376002", "GSM1376003", "GSM1376004", "GSM1376005", "GSM1376006", "GSM1376007", "GSM1376008", "GSM1376009", "GSM1376010", "GSM1376011", "GSM1376012", "GSM1376013", "GSM1376014", "GSM1376015", "GSM1376016", "GSM1376017", "GSM1376018", "GSM1376019", "GSM1376020", "GSM1376021", "GSM1376022", "GSM1376023", "GSM1376024", "GSM1376025", "GSM1376026", "GSM1376027", "GSM1376028", "GSM1376029", "GSM1376030", "GSM1376031", "GSM1376032", "GSM1376033", "GSM1376034", "GSM1376035", "GSM1376036", "GSM1376037", "GSM1376038", "GSM1376039", "GSM1376040", "GSM1376041", "GSM1376042", "GSM1376043", "GSM1376044", "GSM1376045", "GSM1376046", "GSM1376047", "GSM1376048", "GSM1376049", "GSM1376050", "GSM1376051", "GSM1376052", "GSM1376053", "GSM1376054", "GSM1376055", "GSM1376056", "GSM1376057", "GSM1376058", "GSM1376059", "GSM1376060", "GSM1376061", "GSM1376062", "GSM1376063", "GSM1376064", "GSM1376065", "GSM1376066", "GSM1376067", "GSM1376068", "GSM1376069", "GSM1376070", "GSM1376071", "GSM1376072", "GSM1376073", "GSM1376074", "GSM1376075", "GSM1376076", "GSM1376077", "GSM1376078", "GSM1376079", "GSM1376080", "GSM1376081", "GSM1376082", "GSM1376083", "GSM1376084", "GSM1376085", "GSM1376086", "GSM1376087", "GSM1376088", "GSM1376089", "GSM1376090", "GSM1376091", "GSM1376092", "GSM1376093", "GSM1376094", "GSM1376095", "GSM1376096", "GSM1376097", "GSM1376098", "GSM1376099", "GSM1376100", "GSM1376101", "GSM1376102", "GSM1376103", "GSM1376104", "GSM1376105", "GSM1376106", "GSM1376107", "GSM1376108", "GSM1376109", "GSM1376110", "GSM1376111", "GSM1376112", "GSM1376113", "GSM1376114", "GSM1376115", "GSM1376116", "GSM1376117", "GSM1376118", "GSM1376119", "GSM1376120", "GSM1376121", "GSM1376122", "GSM1376123", "GSM1376124", "GSM1376125", "GSM1376126", "GSM1376127", "GSM1376128", "GSM1376129", "GSM1376130", "GSM1376131", "GSM1376132", "GSM1376133", "GSM1376134", "GSM1376135", "GSM1376136", "GSM1376137", "GSM1376138", "GSM1376139", "GSM1376140", "GSM1376141", "GSM1376142", "GSM1376143", "GSM1376144", "GSM1376145", "GSM1376146", "GSM1376147", "GSM1376148", "GSM1376149", "GSM1376150", "GSM1376151", "GSM1376152", "GSM1376153", "GSM1376154", "GSM1376155", "GSM1376156", "GSM1376157", "GSM1376158", "GSM1376159", "GSM1376160", "GSM1376161", "GSM1376162", "GSM1376163", "GSM1376164", "GSM1376165", "GSM1376166", "GSM1376167", "GSM1376168", "GSM1376169", "GSM1376170", "GSM1376171", "GSM1376172", "GSM1376173", "GSM1376174"], "sample_count": 189, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Characterizing gene expression in lung tissue of COPD subjects using RNA-seq", "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:GSE76925", "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=GSE76925", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76925", "version": null, "note": "The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2040792", "GSM2040793", "GSM2040794", "GSM2040795", "GSM2040796", "GSM2040797", "GSM2040798", "GSM2040799", "GSM2040800", "GSM2040801", "GSM2040802", "GSM2040803", "GSM2040804", "GSM2040805", "GSM2040806", "GSM2040807", "GSM2040808", "GSM2040809", "GSM2040810", "GSM2040811", "GSM2040812", "GSM2040813", "GSM2040814", "GSM2040815", "GSM2040816", "GSM2040817", "GSM2040818", "GSM2040819", "GSM2040820", "GSM2040821", "GSM2040822", "GSM2040823", "GSM2040824", "GSM2040825", "GSM2040826", "GSM2040827", "GSM2040828", "GSM2040829", "GSM2040830", "GSM2040831", "GSM2040832", "GSM2040833", "GSM2040834", "GSM2040835", "GSM2040836", "GSM2040837", "GSM2040838", "GSM2040839", "GSM2040840", "GSM2040841", "GSM2040842", "GSM2040843", "GSM2040844", "GSM2040845", "GSM2040846", "GSM2040847", "GSM2040848", "GSM2040849", "GSM2040850", "GSM2040851", "GSM2040852", "GSM2040853", "GSM2040854", "GSM2040855", "GSM2040856", "GSM2040857", "GSM2040858", "GSM2040859", "GSM2040860", "GSM2040861", "GSM2040862", "GSM2040863", "GSM2040864", "GSM2040865", "GSM2040866", "GSM2040867", "GSM2040868", "GSM2040869", "GSM2040870", "GSM2040871", "GSM2040872", "GSM2040873", "GSM2040874", "GSM2040875", "GSM2040876", "GSM2040877", "GSM2040878", "GSM2040879", "GSM2040880", "GSM2040881", "GSM2040882", "GSM2040883", "GSM2040884", "GSM2040885", "GSM2040886", "GSM2040887", "GSM2040888", "GSM2040889", "GSM2040890", "GSM2040891", "GSM2040892", "GSM2040893", "GSM2040894", "GSM2040895", "GSM2040896", "GSM2040897", "GSM2040898", "GSM2040899", "GSM2040900", "GSM2040901", "GSM2040902", "GSM2040903", "GSM2040904", "GSM2040905", "GSM2040906", "GSM2040907", "GSM2040908", "GSM2040909", "GSM2040910", "GSM2040911", "GSM2040912", "GSM2040913", "GSM2040914", "GSM2040915", "GSM2040916", "GSM2040917", "GSM2040918", "GSM2040919", "GSM2040920", "GSM2040921", "GSM2040922", "GSM2040923", "GSM2040924", "GSM2040925", "GSM2040926", "GSM2040927", "GSM2040928", "GSM2040929", "GSM2040930", "GSM2040931", "GSM2040932", "GSM2040933", "GSM2040934", "GSM2040935", "GSM2040936", "GSM2040937", "GSM2040938", "GSM2040939", "GSM2040940", "GSM2040941", "GSM2040942"], "sample_count": 151, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Functional interactors of genomewide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue", "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:GSE151052 not downloaded", "asset:data:geo:GSE151052 licence not read", "asset:data:geo:GSE239897 not downloaded", "asset:data:geo:GSE239897 licence not read", "asset:data:geo:GSE57148 not downloaded", "asset:data:geo:GSE57148 licence not read", "asset:data:geo:GSE76925 not downloaded", "asset:data:geo:GSE76925 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We utilized the limma package and Weighted Gene Co-expression Network Analysis (WGCNA) to analyze datasets from the Gene Expression Omnibus (GEO) database (GSE57148), identifying 12 key differentially expressed mitochondrial genes (MitoDEGs)."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.7, "band": "medium", "quote": "Spearman's correlation"}}, {"id": "method-3", "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": "Pathway enrichment"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE57148", "GSE76925", "GSE151052", "GSE239897"], "resolved_accessions": ["GSE57148", "GSE76925", "GSE151052", "GSE239897"], "statements": ["The transcriptome datasets analyzed during the current study are available in the public NCBI GEO database (https://www.ncbi.nlm.nih.gov/geo/). Accession numbers and link URL are GSE57148 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57148), GSE76925 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76925), GSE151052 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151052) and GSE239897 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239897). To ensure the reproducibility of our results, the complete ML code and all R code used in the research are available and provided as a separate document in the Supplementary Material."], "basis": "The paper names GSE57148, GSE76925, GSE151052, GSE239897 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40274954", "data:geo:GSE151052"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE151052"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:51:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13282, "completion_tokens": 1765, "cached_tokens": 256}}, "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:40274954", "type": "paper", "label": "pmid:40274954"}, {"id": "source:pmid:40274954", "type": "manuscript", "label": "PMID 40274954 full text"}, {"id": "data:geo:GSE151052", "type": "dataset", "label": "GEO GSE151052"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40274954", "type": "paper", "label": "pmid:40274954"}, {"id": "source:pmid:40274954", "type": "manuscript", "label": "PMID 40274954 full text"}, {"id": "data:geo:GSE151052", "type": "dataset", "label": "GEO GSE151052"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40274954", "type": "extraction", "used": ["source:pmid:40274954"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE151052", "type": "accession_resolution", "used": ["data:geo:GSE151052"], "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:40274954", "parent_hash": "sha256:60559498d0f1a2bddc066533836d5c45408b19fa4d8f826f10f8626f9ea38f02", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE151052 licence not read", "asset:data:geo:GSE151052 not downloaded", "asset:data:geo:GSE239897 licence not read", "asset:data:geo:GSE239897 not downloaded", "asset:data:geo:GSE57148 licence not read", "asset:data:geo:GSE57148 not downloaded", "asset:data:geo:GSE76925 licence not read", "asset:data:geo:GSE76925 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["tified as a potential therapeutic candidate. In vivo studies confirmed reduced mRNA expression of"], "order_basis": "paper_text_order:1569", "id": "assay:1"}, {"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": ["Materials and methods Microarray data collection and analysis of differential"], "order_basis": "paper_text_order:1822", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We utilized the limma package and Weighted Gene Co-expression Network Analysis (WGCNA) to analyze datasets from the Gene Expression Omnibus (GEO) database (GSE57148), identifying 12 key differentially expressed mitochondrial genes (MitoDEGs)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}