Screening and validating genes associated with cuproptosis in systemic lupus erythematosus by expression profiling combined with machine learning.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39388708", "kind": "science-record", "revision": 3, "content_hash": "sha256:634a420875dd223b66c5eca5a1d19b40240f6d30d012d6f88982f44b330099a8", "created_at": "2026-11-01T20:29:36Z", "updated_at": "2026-11-01T22:12:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and validating genes associated with cuproptosis in systemic lupus erythematosus by expression profiling combined with machine learning.", "doi": "10.17305/bb.2024.10996", "pmid": "39388708", "authors": ["Zhongbin Xia", "Ruoying Cheng", "Qi Liu", "Yuxin Zu", "Shilu Liao"], "journal": "Biomolecules & biomedicine", "year": 2025, "abstract": "Cell death has long been a focal point in life sciences research, and recently, scientists have discovered a novel form of cell death induced by copper, termed cuproptosis. This paper aimed to identify genes associated with cuproptosis in systemic lupus erythematosus (SLE) through machine learning, combined with single-cell RNA sequencing (scRNA-seq), to screen and validate related genes. The analytical results were then experimentally verified. Two published microarray gene expression datasets (GSE65391 and GSE61635) from SLE and control peripheral blood samples were downloaded from the GEO database. The GSE65391 dataset was used as the training group, while the GSE61635 dataset served as the validation group. Differentially expressed genes from GSE65391 identified 12 differential genes. Nine diagnostic genes, considered potential biomarkers, were selected using the least absolute shrinkage and selection operator and support vector machine recursive feature elimination analysis. The receiver operating characteristic (ROC) curves for both the training and validation groups were used to calculate the area under the curve to assess discriminatory properties. CIBERSORT was used to assess the relationship between these diagnostic genes and a reference set of infiltrating immune cells. scRNA-seq data (GSE162577) from SLE patients were also obtained from the GEO database and analyzed. Experimental validation of the most important SLE biomarkers was performed. Twelve significantly different cuproptosis-related genes were identified in the GSE65391 training set. Immune cell analysis revealed 12 immune cell types and identified nine signature genes, including PDHB, glutaminase (GLS), DLAT, LIAS, MTF1, DLST, DLD, LIPT1, and FDX1. In the GSE61635 validation set, seven genes were weakly expressed, and two genes were strongly expressed in the treatment group. According to the ROC curves, PDHB and GLS demonstrated significant diagnostic value. Additionally, correlation analysis was conducted on the nine characteristic genes in relation to immune infiltration. The distribution of key genes in immune cells was determined using scRNA-seq data. Finally, the mRNA expression of the nine diagnostic genes was validated using qPCR.", "claims": [{"id": "claim-method", "statement": "ROC curves and AUC were used to determine the diagnostic efficacy of biomarkers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39388708", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "ROC curves and AUC were used to determine the diagnostic efficacy of biomarkers."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39388708", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "According to the ROC curves, PDHB and GLS demonstrated significant diagnostic value.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39388708", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "According to the ROC curves, PDHB and GLS demonstrated significant diagnostic value."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "According to the ROC curves, PDHB and GLS demonstrated significant diagnostic value.", "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:39388708"], "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:GSE162577"], "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:GSE162577"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39388708", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.17305/bb.2024.10996", "sha256": "sha256:d092ee0dfed0e09b4c251b85fdf45b2899466ba3d19b8c80139869d1d969b4c5", "bytes": 46710, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.17305/bb.2024.10996", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11959400", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE162577", "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=GSE162577", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE162577", "version": null, "note": "The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4954811", "GSM4954812", "GSM4954813"], "sample_count": 3, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single cell RNA sequencing reveals cellular heterogeneity of PBMC of systemic lupus erythematosus patients", "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:GSE61635", "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=GSE61635", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61635", "version": null, "note": "The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1509610", "GSM1509611", "GSM1509612", "GSM1509613", "GSM1509614", "GSM1509615", "GSM1509616", "GSM1509617", "GSM1509618", "GSM1509619", "GSM1509620", "GSM1509621", "GSM1509622", "GSM1509623", "GSM1509624", "GSM1509625", "GSM1509626", "GSM1509627", "GSM1509628", "GSM1509629", "GSM1509630", "GSM1509631", "GSM1509632", "GSM1509633", "GSM1509634", "GSM1509635", "GSM1509636", "GSM1509637", "GSM1509638", "GSM1509639", "GSM1509640", "GSM1509641", "GSM1509642", "GSM1509643", "GSM1509644", "GSM1509645", "GSM1509646", "GSM1509647", "GSM1509648", "GSM1509649", "GSM1509650", "GSM1509651", "GSM1509652", "GSM1509653", "GSM1509654", "GSM1509655", "GSM1509656", "GSM1509657", "GSM1509658", "GSM1509659", "GSM1509660", "GSM1509661", "GSM1509662", "GSM1509663", "GSM1509664", "GSM1509665", "GSM1509666", "GSM1509667", "GSM1509668", "GSM1509669", "GSM1509670", "GSM1509671", "GSM1509672", "GSM1509673", "GSM1509674", "GSM1509675", "GSM1509676", "GSM1509677", "GSM1509678", "GSM1509679", "GSM1509680", "GSM1509681", "GSM1509682", "GSM1509683", "GSM1509684", "GSM1509685", "GSM1509686", "GSM1509687", "GSM1509688", "GSM1509689", "GSM1509690", "GSM1509691", "GSM1509692", "GSM1509693", "GSM1509694", "GSM1509695", "GSM1509696", "GSM1509697", "GSM1509698", "GSM1509699", "GSM1509700", "GSM1509701", "GSM1509702", "GSM1509703", "GSM1509704", "GSM1509705", "GSM1509706", "GSM1509707", "GSM1509708", "GSM1509709", "GSM1509710", "GSM1509711", "GSM1509712", "GSM1509713", "GSM1509714", "GSM1509715", "GSM1509716", "GSM1509717", "GSM1509718", "GSM1509719", "GSM1509720", "GSM1509721", "GSM1509722", "GSM1509723", "GSM1509724", "GSM1509725", "GSM1509726", "GSM1509727", "GSM1509728", "GSM1509729", "GSM1509730", "GSM1509731", "GSM1509732", "GSM1509733", "GSM1509734", "GSM1509735", "GSM1509736", "GSM1509737", "GSM1509738"], "sample_count": 129, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression in RNP autoantibody+ systemic lupus erythematosus (SLE) patient blood", "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:GSE65391", "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=GSE65391", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65391", "version": null, "note": "The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1594219", "GSM1594220", "GSM1594221", "GSM1594222", "GSM1594223", "GSM1594224", "GSM1594225", "GSM1594226", "GSM1594227", "GSM1594228", "GSM1594229", "GSM1594230", "GSM1594231", "GSM1594232", "GSM1594233", "GSM1594234", "GSM1594235", "GSM1594236", "GSM1594237", "GSM1594238", "GSM1594239", "GSM1594240", "GSM1594241", "GSM1594244", "GSM1594247", "GSM1594250", "GSM1594253", "GSM1594254", "GSM1594255", "GSM1594256", "GSM1594257", "GSM1594258", "GSM1594259", "GSM1594260", "GSM1594261", "GSM1594262", "GSM1594263", "GSM1594264", "GSM1594265", "GSM1594266", "GSM1594267", "GSM1594268", "GSM1594269", "GSM1594270", "GSM1594271", "GSM1594272", "GSM1594273", "GSM1594274", "GSM1594275", "GSM1594276", "GSM1594277", "GSM1594278", "GSM1594279", "GSM1594280", "GSM1594281", "GSM1594282", "GSM1594283", "GSM1594284", "GSM1594285", "GSM1594286", "GSM1594287", "GSM1594288", "GSM1594289", "GSM1594290", "GSM1594291", "GSM1594292", "GSM1594293", "GSM1594294", "GSM1594295", "GSM1594296", "GSM1594297", "GSM1594298", "GSM1594299", "GSM1594300", "GSM1594301", "GSM1594302", "GSM1594303", "GSM1594304", "GSM1594305", "GSM1594306", "GSM1594307", "GSM1594308", "GSM1594309", "GSM1594310", "GSM1594311", "GSM1594312", "GSM1594313", "GSM1594314", "GSM1594315", "GSM1594316", "GSM1594317", "GSM1594318", "GSM1594319", "GSM1594320", "GSM1594321", "GSM1594322", "GSM1594323", "GSM1594324", "GSM1594325", "GSM1594326", "GSM1594327", "GSM1594328", "GSM1594329", "GSM1594330", "GSM1594331", "GSM1594332", "GSM1594333", "GSM1594334", "GSM1594335", "GSM1594336", "GSM1594337", "GSM1594338", "GSM1594339", "GSM1594340", "GSM1594341", "GSM1594342", "GSM1594343", "GSM1594344", "GSM1594345", "GSM1594346", "GSM1594347", "GSM1594348", "GSM1594349", "GSM1594350", "GSM1594351", "GSM1594352", "GSM1594353", "GSM1594354", "GSM1594355", "GSM1594356", "GSM1594357", "GSM1594358", "GSM1594359", "GSM1594360", "GSM1594361", "GSM1594362", "GSM1594363", "GSM1594364", "GSM1594365", "GSM1594366", "GSM1594367", "GSM1594368", "GSM1594369", "GSM1594370", "GSM1594371", "GSM1594372", "GSM1594373", "GSM1594374", "GSM1594375", "GSM1594376", "GSM1594377", "GSM1594378", "GSM1594379", "GSM1594380", "GSM1594381", "GSM1594382", "GSM1594383", "GSM1594384", "GSM1594385", "GSM1594386", "GSM1594387", "GSM1594388", "GSM1594389", "GSM1594390", "GSM1594391", "GSM1594392", "GSM1594393", "GSM1594394", "GSM1594395", "GSM1594396", "GSM1594397", "GSM1594398", "GSM1594399", "GSM1594400", "GSM1594401", "GSM1594402", "GSM1594403", "GSM1594404", "GSM1594405", "GSM1594406", "GSM1594407", "GSM1594408", "GSM1594409", "GSM1594410", "GSM1594411", "GSM1594412", "GSM1594413", "GSM1594414", "GSM1594415", "GSM1594416", "GSM1594417", "GSM1594418", "GSM1594419", "GSM1594420", "GSM1594421", "GSM1594422", "GSM1594423", "GSM1594424", "GSM1594425", "GSM1594426", "GSM1594427", "GSM1594428", "GSM1594429", "GSM1594430", "GSM1594431", "GSM1594432", "GSM1594433", "GSM1594434", "GSM1594435", "GSM1594436", "GSM1594437", "GSM1594438", "GSM1594439", "GSM1594440", "GSM1594441", "GSM1594442", "GSM1594443", "GSM1594444", "GSM1594445", "GSM1594446", "GSM1594447", "GSM1594448", "GSM1594449", "GSM1594450", "GSM1594451", "GSM1594452", "GSM1594453", "GSM1594454", "GSM1594455", "GSM1594456", "GSM1594457", "GSM1594458", "GSM1594459", "GSM1594460", "GSM1594461", "GSM1594462", "GSM1594463", "GSM1594464", "GSM1594465", "GSM1594466", "GSM1594467", "GSM1594468", "GSM1594469", "GSM1594470", "GSM1594471", "GSM1594472", "GSM1594473", "GSM1594474", "GSM1594475", "GSM1594476", "GSM1594477", "GSM1594478", "GSM1594479", "GSM1594480", "GSM1594481", "GSM1594482", "GSM1594483", "GSM1594484", "GSM1594485", "GSM1594486", "GSM1594487", "GSM1594488", "GSM1594489", "GSM1594490", "GSM1594491", "GSM1594492", "GSM1594493", "GSM1594494", "GSM1594495", "GSM1594496", "GSM1594497", "GSM1594498", "GSM1594499", "GSM1594500", "GSM1594501", "GSM1594502", "GSM1594503", "GSM1594504", "GSM1594505", "GSM1594506", "GSM1594507", "GSM1594508", "GSM1594509", "GSM1594510", "GSM1594511", "GSM1594512", "GSM1594513", "GSM1594514", "GSM1594515", "GSM1594516", "GSM1594517", "GSM1594518", "GSM1594519", "GSM1594520", "GSM1594521", "GSM1594522", "GSM1594523", "GSM1594524", "GSM1594525", "GSM1594526", "GSM1594527", "GSM1594528", "GSM1594529", "GSM1594530", "GSM1594531", "GSM1594532", "GSM1594533", "GSM1594534", "GSM1594535", "GSM1594536", "GSM1594537", "GSM1594538", "GSM1594539", "GSM1594540", "GSM1594541", "GSM1594542", "GSM1594543", "GSM1594544", "GSM1594545", "GSM1594546", "GSM1594547", "GSM1594548", "GSM1594549", "GSM1594550", "GSM1594551", "GSM1594552", "GSM1594553", "GSM1594554", "GSM1594555", "GSM1594556", "GSM1594557", "GSM1594558", "GSM1594559", "GSM1594560", "GSM1594561", "GSM1594562", "GSM1594563", "GSM1594564", "GSM1594565", "GSM1594566", "GSM1594567", "GSM1594568", "GSM1594569", "GSM1594570", "GSM1594571", "GSM1594572", "GSM1594573", "GSM1594574", "GSM1594575", "GSM1594576", "GSM1594577", "GSM1594578", "GSM1594579", "GSM1594580", "GSM1594581", "GSM1594582", "GSM1594583", "GSM1594584", "GSM1594585", "GSM1594586", "GSM1594587", "GSM1594588", "GSM1594589", "GSM1594590", "GSM1594591", "GSM1594592", "GSM1594593", "GSM1594594", "GSM1594595", "GSM1594596", "GSM1594597", "GSM1594598", "GSM1594599", "GSM1594600", "GSM1594601", "GSM1594602", "GSM1594603", "GSM1594604", "GSM1594605", "GSM1594606", "GSM1594607", "GSM1594608", "GSM1594609", "GSM1594610", "GSM1594611", "GSM1594612", "GSM1594613", "GSM1594614", "GSM1594615", "GSM1594616", "GSM1594617", "GSM1594618", "GSM1594619", "GSM1594620", "GSM1594621", "GSM1594622", "GSM1594623", "GSM1594624", "GSM1594625", "GSM1594626", "GSM1594627", "GSM1594628", "GSM1594629", "GSM1594630", "GSM1594631", "GSM1594632", "GSM1594633", "GSM1594634", "GSM1594635", "GSM1594636", "GSM1594637", "GSM1594638", "GSM1594639", "GSM1594640", "GSM1594641", "GSM1594642", "GSM1594643", "GSM1594644", "GSM1594645", "GSM1594646", "GSM1594647", "GSM1594648", "GSM1594649", "GSM1594650", "GSM1594651", "GSM1594652", "GSM1594653", "GSM1594654", "GSM1594655", "GSM1594656", "GSM1594657", "GSM1594658", "GSM1594659", "GSM1594660", "GSM1594661", "GSM1594662", "GSM1594663", "GSM1594664", "GSM1594665", "GSM1594666", "GSM1594667", "GSM1594668", "GSM1594669", "GSM1594670", "GSM1594671", "GSM1594672", "GSM1594673", "GSM1594674", "GSM1594675", "GSM1594676", "GSM1594677", "GSM1594678", "GSM1594679", "GSM1594680", "GSM1594681", "GSM1594682", "GSM1594683", "GSM1594684", "GSM1594685", "GSM1594686", "GSM1594687", "GSM1594688", "GSM1594689", "GSM1594690", "GSM1594691", "GSM1594692", "GSM1594693", "GSM1594694", "GSM1594695", "GSM1594696", "GSM1594697", "GSM1594698", "GSM1594699", "GSM1594700", "GSM1594701", "GSM1594702", "GSM1594703", "GSM1594704", "GSM1594705", "GSM1594706", "GSM1594707", "GSM1594708", "GSM1594709", "GSM1594710", "GSM1594711", "GSM1594712", "GSM1594713", "GSM1594714", "GSM1594715", "GSM1594716", "GSM1594717", "GSM1594718", "GSM1594719", "GSM1594720", "GSM1594721", "GSM1594722", "GSM1594723", "GSM1594724", "GSM1594725", "GSM1594726", "GSM1594727", "GSM1594728", "GSM1594729", "GSM1594730", "GSM1594731", "GSM1594732", "GSM1594733", "GSM1594734", "GSM1594735", "GSM1594736", "GSM1594737", "GSM1594738", "GSM1594739", "GSM1594740", "GSM1594741", "GSM1594742", "GSM1594743", "GSM1594744", "GSM1594745", "GSM1594746", "GSM1594747", "GSM1594748", "GSM1594749", "GSM1594750", "GSM1594751", "GSM1594752", "GSM1594753", "GSM1594754", "GSM1594755", "GSM1594756", "GSM1594757", "GSM1594758", "GSM1594759", "GSM1594760", "GSM1594761", "GSM1594762", "GSM1594763", "GSM1594764", "GSM1594765", "GSM1594766", "GSM1594767", "GSM1594768", "GSM1594769", "GSM1594770", "GSM1594771", "GSM1594772", "GSM1594773", "GSM1594774", "GSM1594775", "GSM1594776", "GSM1594777", "GSM1594778", "GSM1594779", "GSM1594780", "GSM1594781", "GSM1594782", "GSM1594783", "GSM1594784", "GSM1594785", "GSM1594786", "GSM1594787", "GSM1594788", "GSM1594789", "GSM1594790", "GSM1594791", "GSM1594792", "GSM1594793", "GSM1594794", "GSM1594795", "GSM1594796", "GSM1594797", "GSM1594798", "GSM1594799", "GSM1594800", "GSM1594801", "GSM1594802", "GSM1594803", "GSM1594804", "GSM1594805", "GSM1594806", "GSM1594807", "GSM1594808", "GSM1594809", "GSM1594810", "GSM1594811", "GSM1594812", "GSM1594813", "GSM1594814", "GSM1594815", "GSM1594816", "GSM1594817", "GSM1594818", "GSM1594819", "GSM1594820", "GSM1594821", "GSM1594822", "GSM1594823", "GSM1594824", "GSM1594825", "GSM1594826", "GSM1594827", "GSM1594828", "GSM1594829", "GSM1594830", "GSM1594831", "GSM1594832", "GSM1594833", "GSM1594834", "GSM1594835", "GSM1594836", "GSM1594837", "GSM1594838", "GSM1594839", "GSM1594840", "GSM1594841", "GSM1594842", "GSM1594843", "GSM1594844", "GSM1594845", "GSM1594846", "GSM1594847", "GSM1594848", "GSM1594849", "GSM1594850", "GSM1594851", "GSM1594852", "GSM1594853", "GSM1594854", "GSM1594855", "GSM1594856", "GSM1594857", "GSM1594858", "GSM1594859", "GSM1594860", "GSM1594861", "GSM1594862", "GSM1594863", "GSM1594864", "GSM1594865", "GSM1594866", "GSM1594867", "GSM1594868", "GSM1594869", "GSM1594870", "GSM1594871", "GSM1594872", "GSM1594873", "GSM1594874", "GSM1594875", "GSM1594876", "GSM1594877", "GSM1594878", "GSM1594879", "GSM1594880", "GSM1594881", "GSM1594882", "GSM1594883", "GSM1594884", "GSM1594885", "GSM1594886", "GSM1594887", "GSM1594888", "GSM1594889", "GSM1594890", "GSM1594891", "GSM1594892", "GSM1594893", "GSM1594894", "GSM1594895", "GSM1594896", "GSM1594897", "GSM1594898", "GSM1594899", "GSM1594900", "GSM1594901", "GSM1594902", "GSM1594903", "GSM1594904", "GSM1594905", "GSM1594906", "GSM1594907", "GSM1594908", "GSM1594909", "GSM1594910", "GSM1594911", "GSM1594912", "GSM1594913", "GSM1594914", "GSM1594915", "GSM1594916", "GSM1594917", "GSM1594918", "GSM1594919", "GSM1594920", "GSM1594921", "GSM1594922", "GSM1594923", "GSM1594924", "GSM1594925", "GSM1594926", "GSM1594927", "GSM1594928", "GSM1594929", "GSM1594930", "GSM1594931", "GSM1594932", "GSM1594933", "GSM1594934", "GSM1594935", "GSM1594936", "GSM1594937", "GSM1594938", "GSM1594939", "GSM1594940", "GSM1594941", "GSM1594942", "GSM1594943", "GSM1594944", "GSM1594945", "GSM1594946", "GSM1594947", "GSM1594948", "GSM1594949", "GSM1594950", "GSM1594951", "GSM1594952", "GSM1594953", "GSM1594954", "GSM1594955", "GSM1594956", "GSM1594957", "GSM1594958", "GSM1594959", "GSM1594960", "GSM1594961", "GSM1594962", "GSM1594963", "GSM1594964", "GSM1594965", "GSM1594966", "GSM1594967", "GSM1594968", "GSM1594969", "GSM1594970", "GSM1594971", "GSM1594972", "GSM1594973", "GSM1594974", "GSM1594975", "GSM1594976", "GSM1594977", "GSM1594978", "GSM1594979", "GSM1594980", "GSM1594981", "GSM1594982", "GSM1594983", "GSM1594984", "GSM1594985", "GSM1594986", "GSM1594987", "GSM1594988", "GSM1594989", "GSM1594990", "GSM1594991", "GSM1594992", "GSM1594993", "GSM1594994", "GSM1594995", "GSM1594996", "GSM1594997", "GSM1594998", "GSM1594999", "GSM1595000", "GSM1595001", "GSM1595002", "GSM1595003", "GSM1595004", "GSM1595005", "GSM1595006", "GSM1595007", "GSM1595008", "GSM1595009", "GSM1595010", "GSM1595011", "GSM1595012", "GSM1595013", "GSM1595014", "GSM1595015", "GSM1595016", "GSM1595017", "GSM1595018", "GSM1595019", "GSM1595020", "GSM1595021", "GSM1595022", "GSM1595023", "GSM1595024", "GSM1595025", "GSM1595026", "GSM1595027", "GSM1595028", "GSM1595029", "GSM1595030", "GSM1595031", "GSM1595032", "GSM1595033", "GSM1595034", "GSM1595035", "GSM1595036", "GSM1595037", "GSM1595038", "GSM1595039", "GSM1595040", "GSM1595041", "GSM1595042", "GSM1595043", "GSM1595044", "GSM1595045", "GSM1595046", "GSM1595047", "GSM1595048", "GSM1595049", "GSM1595050", "GSM1595051", "GSM1595052", "GSM1595053", "GSM1595054", "GSM1595055", "GSM1595056", "GSM1595057", "GSM1595058", "GSM1595059", "GSM1595060", "GSM1595061", "GSM1595062", "GSM1595063", "GSM1595064", "GSM1595065", "GSM1595066", "GSM1595067", "GSM1595068", "GSM1595069", "GSM1595070", "GSM1595071", "GSM1595072", "GSM1595073", "GSM1595074", "GSM1595075", "GSM1595076", "GSM1595077", "GSM1595078", "GSM1595079", "GSM1595080", "GSM1595081", "GSM1595082", "GSM1595083", "GSM1595084", "GSM1595085", "GSM1595086", "GSM1595087", "GSM1595088", "GSM1595089", "GSM1595090", "GSM1595091", "GSM1595092", "GSM1595093", "GSM1595094", "GSM1595095", "GSM1595096", "GSM1595097", "GSM1595098", "GSM1595099", "GSM1595100", "GSM1595101", "GSM1595102", "GSM1595103", "GSM1595104", "GSM1595105", "GSM1595106", "GSM1595107", "GSM1595108", "GSM1595109", "GSM1595110", "GSM1595111", "GSM1595112", "GSM1595113", "GSM1595114", "GSM1595115", "GSM1595116", "GSM1595117", "GSM1595118", "GSM1595119", "GSM1595120", "GSM1595121", "GSM1595122", "GSM1595123", "GSM1595124", "GSM1595125", "GSM1595126", "GSM1595127", "GSM1595128", "GSM1595129", "GSM1595130", "GSM1595131", "GSM1595132", "GSM1595133", "GSM1595134", "GSM1595135", "GSM1595136", "GSM1595137", "GSM1595138", "GSM1595139", "GSM1595140", "GSM1595141", "GSM1595142", "GSM1595143", "GSM1595144", "GSM1595145", "GSM1595146", "GSM1595147", "GSM1595148", "GSM1595149", "GSM1595150", "GSM1595151", "GSM1595152", "GSM1595153", "GSM1595154", "GSM1595155", "GSM1595156", "GSM1595157", "GSM1595158", "GSM1595159", "GSM1595160", "GSM1595161", "GSM1595162", "GSM1595163", "GSM1595164", "GSM1595165", "GSM1595166", "GSM1595167", "GSM1595168", "GSM1595169", "GSM1595170", "GSM1595171", "GSM1595172", "GSM1595173", "GSM1595174", "GSM1595175", "GSM1595176", "GSM1595177", "GSM1595178", "GSM1595179", "GSM1595180", "GSM1595181", "GSM1595182", "GSM1595183", "GSM1595184", "GSM1595185", "GSM1595186", "GSM1595187", "GSM1595188", "GSM1595189", "GSM1595190", "GSM1595191", "GSM1595192", "GSM1595193", "GSM1595194", "GSM1595195", "GSM1595196", "GSM1595197", "GSM1595198", "GSM1595199", "GSM1595200", "GSM1595201", "GSM1595202", "GSM1595203", "GSM1595204", "GSM1595205", "GSM1595206", "GSM1595207", "GSM1595208", "GSM1595209", "GSM1595210", "GSM1595211", "GSM1595212", "GSM1595213", "GSM1595214", "GSM1595215", "GSM1595216", "GSM1595217", "GSM1595218", "GSM1595219", "GSM1595220", "GSM1595221", "GSM1595222"], "sample_count": 996, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Longitudinal transcriptional pediatric SLE study with clinical parameters", "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:GSE162577 not downloaded", "asset:data:geo:GSE162577 licence not read", "asset:data:geo:GSE61635 not downloaded", "asset:data:geo:GSE61635 licence not read", "asset:data:geo:GSE65391 not downloaded", "asset:data:geo:GSE65391 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "principal component analysis"}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-3", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "support vector machine"}}, {"id": "method-4", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "linear regression"}}, {"id": "method-5", "family": null, "specific": null, "label": "ROC curves and area under the curve", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "ROC curves and AUC were used to determine the diagnostic efficacy of biomarkers."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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": ["GSE65391", "GSE61635", "GSE162577"], "resolved_accessions": ["GSE65391", "GSE61635", "GSE162577"], "statements": ["The data that support the findings of this study are available in Gene Expression Omnibus (datasets with identifiers: GSE65391, GSE61635, and GSE162577), which were downloaded from http://www.ncbi.nlm.nih.gov/geo/."], "basis": "The paper names GSE65391, GSE61635, GSE162577 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pca_fit"], "assets": ["source:pmid:39388708", "data:geo:GSE162577"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE162577"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:34:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14089, "completion_tokens": 1087, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:39388708", "type": "paper", "label": "pmid:39388708"}, {"id": "source:pmid:39388708", "type": "manuscript", "label": "PMID 39388708 full text"}, {"id": "data:geo:GSE162577", "type": "dataset", "label": "GEO GSE162577"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39388708", "type": "paper", "label": "pmid:39388708"}, {"id": "source:pmid:39388708", "type": "manuscript", "label": "PMID 39388708 full text"}, {"id": "data:geo:GSE162577", "type": "dataset", "label": "GEO GSE162577"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39388708", "type": "extraction", "used": ["source:pmid:39388708"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE162577", "type": "accession_resolution", "used": ["data:geo:GSE162577"], "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:39388708", "parent_hash": "sha256:23268862dd2bd87424c5cf757575adeb4d04a4f7ce0332c521506e20e610b6a5", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE162577 licence not read", "asset:data:geo:GSE162577 not downloaded", "asset:data:geo:GSE61635 licence not read", "asset:data:geo:GSE61635 not downloaded", "asset:data:geo:GSE65391 licence not read", "asset:data:geo:GSE65391 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["SLE) through machine learning, combined with single-cell RNA sequencing (scRNA-seq), to screen and validate related", "g, combined with single-cell RNA sequencing (scRNA-seq), to screen and validate related genes. The", "reference set of infiltrating immune cells. scRNA-seq data (GSE162577) from SLE patients were also", "y genes in immune cells was determined using scRNA-seq data. Finally, the mRNA expression of the ni"], "order_basis": "paper_text_order:416", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["machine learning, combined with single-cell RNA sequencing (scRNA-seq), to screen and validate related", "single-cell sequencing data. The single-cell RNA sequencing data were obtained from the GSE162577 datase"], "order_basis": "paper_text_order:429", "id": "assay:2"}, {"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": ["then experimentally verified. Two published microarray gene expression datasets (GSE65391 and GSE61"], "order_basis": "paper_text_order:567", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["he nine diagnostic genes was validated using qPCR."], "order_basis": "paper_text_order:2345", "id": "assay:4"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["y-old MRL/lymphocyte proliferation (lpr) SLE mice were purchased from Cyagen Research Centre for Mo", "gsu, China). Thirty female -week-old C57BL/6 mice were purchased from GemPharmatech Co., Ltd. (Jian", "sms and potential treatments of SLE. All the mice were euthanized using CO2 inhalation, with death", "ing blood samples from the mice. MRL/lpr SLE mice were used as the SLE group, while C57BL/6 mice se"], "order_basis": "paper_text_order:5036", "id": "assay:5"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["principal component analysis"], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}