Exploring the therapeutic role of thiabendazole in lung adenocarcinoma via network pharmacology and single-cell analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41130017", "kind": "science-record", "revision": 4, "content_hash": "sha256:6e8c5ae03042be45691da39fb7a05c2b5292cf789e93a6e19556b5f9d908e595", "created_at": "2026-11-01T20:31:11Z", "updated_at": "2026-11-01T22:57:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the therapeutic role of thiabendazole in lung adenocarcinoma via network pharmacology and single-cell analysis.", "doi": "10.1016/j.tranon.2025.102548", "pmid": "41130017", "authors": ["Wanghong Qi", "Guoqiu Xu", "Lang Tang", "Chunlin Ye", "Xi Liu"], "journal": "Translational oncology", "year": 2025, "abstract": "BACKGROUND: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related deaths globally, with over 2.2 million new cases in 2020. Despite advances in targeted therapies, challenges such as drug resistance and severe side effects persist. Thiabendazole, an antiparasitic drug, has shown potential anticancer effects in LUAD.\nMETHODS: This study used network pharmacology, integrating single-cell RNA sequencing (scRNA-seq) data (GSE136103), GEO transcriptome datasets (GSE10072, GSE19188, GSE19804, GSE30219, GSE40791), and bioinformatics tools to explore Thiabendazole's mechanisms in LUAD. Potential targets were predicted through PubChem and SwissTargetPrediction. scRNA-seq data were analyzed using Seurat, and key genes and pathways were identified via Weighted Gene Co-expression Network Analysis (WGCNA) and multi-omics integration. Diagnostic genes were further screened using LASSO regression, Support Vector Machine (SVM), and random forest (RF) models.\nRESULTS: Single-cell analysis revealed macrophages as key targets of Thiabendazole. Transcriptomic analysis identified 2034 downregulated and 2388 upregulated genes. WGCNA found a core gene module (MEred) strongly correlated with Thiabendazole (r = 0.75, p = 2e-07). Four diagnostic genes-ACE, ALDOA, MME, and PMP22-showed high accuracy (0.982). Thiabendazole also modulated immune cell infiltration, particularly affecting macrophage activity. Molecular docking confirmed stable binding to ACE, ALDOA, and MME.\nCONCLUSION: Thiabendazole demonstrates promising anticancer potential in LUAD, influencing key genes and immune pathways. It may serve as an effective therapeutic agent targeting both cancer cells and the tumor microenvironment.", "claims": [{"id": "claim-method", "statement": "The limma package was used to analyze the differentially expressed genes between lung adenocarcinoma patients and control patients in the GEO database, and a volcano plot was drawn to show the distribution of differentially expressed genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41130017", "locator": "sections[6] \"Processing and analysis of transcriptome data\" paragraph 2", "quote": "The limma package was used to analyze the differentially expressed genes between lung adenocarcinoma patients and control patients in the GEO database, and a volcano plot was drawn to show the distribution of differentially expressed genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets utilized or generated during the study are fully available within this article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41130017", "locator": "sections[36] \"Data availability\" paragraph 2", "quote": "All datasets utilized or generated during the study are fully available within this article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Four diagnostic genes—ACE, ALDOA, MME, and PMP22—showed high accuracy (0.982).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41130017", "locator": "sections[0] \"Abstract\" paragraph 9", "quote": "Four diagnostic genes—ACE, ALDOA, MME, and PMP22—showed high accuracy (0.982)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Four diagnostic genes—ACE, ALDOA, MME, and PMP22—showed high accuracy (0.982).", "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:41130017"], "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:GSE10072"], "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:GSE10072"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41130017", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.tranon.2025.102548", "sha256": "sha256:1fd19a8f48e8384def6f3192a46eb01465c158215a3751e5e8b2e5a2b30a7bd5", "bytes": 66795, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.tranon.2025.102548", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12590012", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10072", "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=GSE10072", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10072", "version": null, "note": "All datasets utilized or generated during the study are fully available within this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets utilized or generated during the study are fully available within this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM254625", "GSM254626", "GSM254627", "GSM254628", "GSM254629", "GSM254630", "GSM254631", "GSM254632", "GSM254633", "GSM254634", "GSM254635", "GSM254636", "GSM254637", "GSM254638", "GSM254639", "GSM254640", "GSM254641", "GSM254642", "GSM254643", "GSM254644", "GSM254645", "GSM254646", "GSM254647", "GSM254648", "GSM254649", "GSM254650", "GSM254651", "GSM254652", "GSM254653", "GSM254654", "GSM254655", "GSM254656", "GSM254657", "GSM254658", "GSM254659", "GSM254660", "GSM254661", "GSM254662", "GSM254663", "GSM254664", "GSM254665", "GSM254666", "GSM254667", "GSM254668", "GSM254669", "GSM254670", "GSM254671", "GSM254672", "GSM254673", "GSM254674", "GSM254675", "GSM254676", "GSM254677", "GSM254678", "GSM254679", "GSM254680", "GSM254681", "GSM254682", "GSM254683", "GSM254684", "GSM254685", "GSM254686", "GSM254687", "GSM254688", "GSM254689", "GSM254690", "GSM254691", "GSM254692", "GSM254693", "GSM254694", "GSM254695", "GSM254696", "GSM254697", "GSM254698", "GSM254699", "GSM254700", "GSM254701", "GSM254702", "GSM254703", "GSM254704", "GSM254705", "GSM254706", "GSM254707", "GSM254708", "GSM254709", "GSM254710", "GSM254711", "GSM254712", "GSM254713", "GSM254714", "GSM254715", "GSM254716", "GSM254717", "GSM254718", "GSM254719", "GSM254720", "GSM254721", "GSM254722", "GSM254723", "GSM254724", "GSM254725", "GSM254726", "GSM254727", "GSM254728", "GSM254729", "GSM254730", "GSM254731"], "sample_count": 107, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival", "resolution_checked_at": "2026-11-01T15:30:21Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE136103", "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=GSE136103", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE136103", "version": null, "note": "All datasets utilized or generated during the study are fully available within this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets utilized or generated during the study are fully available within this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4041150", "GSM4041151", "GSM4041152", "GSM4041153", "GSM4041154", "GSM4041155", "GSM4041156", "GSM4041157", "GSM4041158", "GSM4041159", "GSM4041160", "GSM4041161", "GSM4041162", "GSM4041163", "GSM4041164", "GSM4041165", "GSM4041166", "GSM4041167", "GSM4041168", "GSM4041169", "GSM4041170", "GSM4041171", "GSM4041172", "GSM4041173", "GSM4041174", "GSM4041175"], "sample_count": 26, "group_sizes": null, "group_sizes_basis": null, "platform": "20301;21103", "taxon": "Homo sapiens; Mus musculus", "title": "Resolving the fibrotic niche of human liver cirrhosis using single-cell transcriptomics", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE19188", "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=GSE19188", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19188", "version": null, "note": "All datasets utilized or generated during the study are fully available within this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets utilized or generated during the study are fully available within this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM475656", "GSM475657", "GSM475658", "GSM475659", "GSM475660", "GSM475661", "GSM475662", "GSM475663", "GSM475664", "GSM475665", "GSM475666", "GSM475667", "GSM475668", "GSM475669", "GSM475670", "GSM475671", "GSM475672", "GSM475673", "GSM475674", "GSM475675", "GSM475676", "GSM475677", "GSM475678", "GSM475679", "GSM475680", "GSM475681", "GSM475682", "GSM475683", "GSM475684", "GSM475685", "GSM475686", "GSM475687", "GSM475688", "GSM475689", "GSM475690", "GSM475691", "GSM475692", "GSM475693", "GSM475694", "GSM475695", "GSM475696", "GSM475697", "GSM475698", "GSM475699", "GSM475700", "GSM475701", "GSM475702", "GSM475703", "GSM475704", "GSM475705", "GSM475706", "GSM475707", "GSM475708", "GSM475709", "GSM475710", "GSM475711", "GSM475712", "GSM475713", "GSM475714", "GSM475715", "GSM475716", "GSM475717", "GSM475718", "GSM475719", "GSM475720", "GSM475721", "GSM475722", "GSM475723", "GSM475724", "GSM475725", "GSM475726", "GSM475727", "GSM475728", "GSM475729", "GSM475730", "GSM475731", "GSM475732", "GSM475733", "GSM475734", "GSM475735", "GSM475736", "GSM475737", "GSM475738", "GSM475739", "GSM475740", "GSM475741", "GSM475742", "GSM475743", "GSM475744", "GSM475745", "GSM475746", "GSM475747", "GSM475748", "GSM475749", "GSM475750", "GSM475751", "GSM475752", "GSM475753", "GSM475754", "GSM475755", "GSM475756", "GSM475757", "GSM475758", "GSM475759", "GSM475760", "GSM475761", "GSM475762", "GSM475763", "GSM475764", "GSM475765", "GSM475766", "GSM475767", "GSM475768", "GSM475769", "GSM475770", "GSM475771", "GSM475772", "GSM475773", "GSM475774", "GSM475775", "GSM475776", "GSM475777", "GSM475778", "GSM475779", "GSM475780", "GSM475781", "GSM475782", "GSM475783", "GSM475784", "GSM475785", "GSM475786", "GSM475787", "GSM475788", "GSM475789", "GSM475790", "GSM475791", "GSM475792", "GSM475793", "GSM475794", "GSM475795", "GSM475796", "GSM475797", "GSM475798", "GSM475799", "GSM475800", "GSM475801", "GSM475802", "GSM475803", "GSM475804", "GSM475805", "GSM475806", "GSM475807", "GSM475808", "GSM475809", "GSM475810", "GSM475811"], "sample_count": 156, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data for early stage NSCLC", "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:GSE19804", "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=GSE19804", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19804", "version": null, "note": "All datasets utilized or generated during the study are fully available within this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets utilized or generated during the study are fully available within this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM494556", "GSM494557", "GSM494558", "GSM494559", "GSM494560", "GSM494561", "GSM494562", "GSM494563", "GSM494564", "GSM494565", "GSM494566", "GSM494567", "GSM494568", "GSM494569", "GSM494570", "GSM494571", "GSM494572", "GSM494573", "GSM494574", "GSM494575", "GSM494576", "GSM494577", "GSM494578", "GSM494579", "GSM494580", "GSM494581", "GSM494582", "GSM494583", "GSM494584", "GSM494585", "GSM494586", "GSM494587", "GSM494588", "GSM494589", "GSM494590", "GSM494591", "GSM494592", "GSM494593", "GSM494594", "GSM494595", "GSM494596", "GSM494597", "GSM494598", "GSM494599", "GSM494600", "GSM494601", "GSM494602", "GSM494603", "GSM494604", "GSM494605", "GSM494606", "GSM494607", "GSM494608", "GSM494609", "GSM494610", "GSM494611", "GSM494612", "GSM494613", "GSM494614", "GSM494615", "GSM494616", "GSM494617", "GSM494618", "GSM494619", "GSM494620", "GSM494621", "GSM494622", "GSM494623", "GSM494624", "GSM494625", "GSM494626", "GSM494627", "GSM494628", "GSM494629", "GSM494630", "GSM494631", "GSM494632", "GSM494633", "GSM494634", "GSM494635", "GSM494636", "GSM494637", "GSM494638", "GSM494639", "GSM494640", "GSM494641", "GSM494642", "GSM494643", "GSM494644", "GSM494645", "GSM494646", "GSM494647", "GSM494648", "GSM494649", "GSM494650", "GSM494651", "GSM494652", "GSM494653", "GSM494654", "GSM494655", "GSM494656", "GSM494657", "GSM494658", "GSM494659", "GSM494660", "GSM494661", "GSM494662", "GSM494663", "GSM494664", "GSM494665", "GSM494666", "GSM494667", "GSM494668", "GSM494669", "GSM494670", "GSM494671", "GSM494672", "GSM494673", "GSM494674", "GSM494675"], "sample_count": 120, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Genome-wide screening of transcriptional modulation in non-smoking female lung cancer in Taiwan", "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:GSE30219", "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=GSE30219", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30219", "version": null, "note": "All datasets utilized or generated during the study are fully available within this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets utilized or generated during the study are fully available within this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1465989", "GSM1465990", "GSM1465991", "GSM1465992", "GSM1465993", "GSM1465994", "GSM1465995", "GSM1465996", "GSM1465997", "GSM1465998", "GSM1465999", "GSM748053", "GSM748054", "GSM748055", "GSM748056", "GSM748057", "GSM748058", "GSM748059", "GSM748060", "GSM748061", "GSM748062", "GSM748063", "GSM748064", "GSM748065", "GSM748066", "GSM748067", "GSM748068", "GSM748069", "GSM748070", "GSM748071", "GSM748072", "GSM748073", "GSM748074", "GSM748075", "GSM748076", "GSM748077", "GSM748078", "GSM748079", "GSM748080", "GSM748081", "GSM748083", "GSM748084", "GSM748085", "GSM748086", "GSM748087", "GSM748088", "GSM748089", "GSM748090", "GSM748091", "GSM748092", "GSM748093", "GSM748094", "GSM748095", "GSM748096", "GSM748097", "GSM748098", "GSM748099", "GSM748100", "GSM748101", "GSM748102", "GSM748103", "GSM748104", "GSM748105", "GSM748106", "GSM748107", "GSM748108", "GSM748109", "GSM748110", "GSM748111", "GSM748112", "GSM748113", "GSM748115", "GSM748116", "GSM748117", "GSM748118", "GSM748119", "GSM748120", "GSM748121", "GSM748122", "GSM748123", "GSM748124", "GSM748125", "GSM748126", "GSM748127", "GSM748128", "GSM748129", "GSM748130", "GSM748131", "GSM748132", "GSM748133", "GSM748134", "GSM748135", "GSM748136", "GSM748137", "GSM748138", "GSM748139", "GSM748140", "GSM748141", "GSM748142", "GSM748143", "GSM748144", "GSM748145", "GSM748146", "GSM748147", "GSM748148", "GSM748149", "GSM748150", "GSM748151", "GSM748152", "GSM748153", "GSM748154", "GSM748155", "GSM748156", "GSM748157", "GSM748158", "GSM748159", "GSM748160", "GSM748161", "GSM748162", "GSM748163", "GSM748164", "GSM748165", "GSM748166", "GSM748167", "GSM748168", "GSM748169", "GSM748170", "GSM748171", "GSM748172", "GSM748173", "GSM748174", "GSM748175", "GSM748176", "GSM748177", "GSM748178", "GSM748179", "GSM748180", "GSM748181", "GSM748182", "GSM748183", "GSM748184", "GSM748185", "GSM748186", "GSM748187", "GSM748188", "GSM748189", "GSM748191", "GSM748192", "GSM748193", "GSM748195", "GSM748196", "GSM748197", "GSM748198", "GSM748199", "GSM748200", "GSM748201", "GSM748202", "GSM748203", "GSM748206", "GSM748207", "GSM748209", "GSM748210", "GSM748211", "GSM748212", "GSM748213", "GSM748214", "GSM748215", "GSM748216", "GSM748217", "GSM748218", "GSM748219", "GSM748220", "GSM748221", "GSM748222", "GSM748223", "GSM748224", "GSM748225", "GSM748226", "GSM748227", "GSM748228", "GSM748229", "GSM748232", "GSM748233", "GSM748234", "GSM748235", "GSM748239", "GSM748240", "GSM748242", "GSM748243", "GSM748244", "GSM748245", "GSM748246", "GSM748247", "GSM748248", "GSM748249", "GSM748250", "GSM748251", "GSM748252", "GSM748253", "GSM748254", "GSM748255", "GSM748256", "GSM748257", "GSM748258", "GSM748259", "GSM748260", "GSM748261", "GSM748262", "GSM748263", "GSM748264", "GSM748265", "GSM748266", "GSM748267", "GSM748268", "GSM748269", "GSM748270", "GSM748271", "GSM748272", "GSM748273", "GSM748274", "GSM748275", "GSM748276", "GSM748277", "GSM748278", "GSM748279", "GSM748280", "GSM748281", "GSM748282", "GSM748283", "GSM748284", "GSM748285", "GSM748286", "GSM748287", "GSM748288", "GSM748291", "GSM748292", "GSM748294", "GSM748295", "GSM748296", "GSM748297", "GSM748298", "GSM748299", "GSM748300", "GSM748301", "GSM748302", "GSM748303", "GSM748304", "GSM748305", "GSM748306", "GSM748307", "GSM748308", "GSM748309", "GSM748310", "GSM748311", "GSM748312", "GSM748313", "GSM748314", "GSM748315", "GSM748316", "GSM748317", "GSM748318", "GSM748319", "GSM748320", "GSM748321", "GSM748323", "GSM748324", "GSM748325", "GSM748326", "GSM748327", "GSM748328", "GSM748329", "GSM748330", "GSM748331", "GSM748332", "GSM748333", "GSM748334", "GSM748335", "GSM748336", "GSM748337", "GSM748338", "GSM748339", "GSM748341", "GSM748342", "GSM748343", "GSM748344", "GSM748345", "GSM748346", "GSM748347", "GSM748348", "GSM748349", "GSM748350", "GSM748351", "GSM748352", "GSM748353", "GSM748354", "GSM748355", "GSM748356", "GSM748357", "GSM748358", "GSM748359", "GSM748360", "GSM748361", "GSM748362", "GSM748363", "GSM748364", "GSM748365", "GSM748366"], "sample_count": 307, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "\"Off-context\" gene expression in lung cancer identifies a group of metastatic-prone tumors", "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:GSE40791", "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=GSE40791", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40791", "version": null, "note": "All datasets utilized or generated during the study are fully available within this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets utilized or generated during the study are fully available within this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1001510", "GSM1001511", "GSM1001512", "GSM1001513", "GSM1001514", "GSM1001515", "GSM1001516", "GSM1001517", "GSM1001518", "GSM1001519", "GSM1001520", "GSM1001521", "GSM1001522", "GSM1001523", "GSM1001524", "GSM1001525", "GSM1001526", "GSM1001527", "GSM1001528", "GSM1001529", "GSM1001530", "GSM1001531", "GSM1001532", "GSM1001533", "GSM1001534", "GSM1001535", "GSM1001536", "GSM1001537", "GSM1001538", "GSM1001539", "GSM1001540", "GSM1001541", "GSM1001542", "GSM1001543", "GSM1001544", "GSM1001545", "GSM1001546", "GSM1001547", "GSM1001548", "GSM1001549", "GSM1001550", "GSM1001551", "GSM1001552", "GSM1001553", "GSM1001554", "GSM1001555", "GSM1001556", "GSM1001557", "GSM1001558", "GSM1001559", "GSM1001560", "GSM1001561", "GSM1001562", "GSM1001563", "GSM1001564", "GSM1001565", "GSM1001566", "GSM1001567", "GSM1001568", "GSM1001569", "GSM1001570", "GSM1001571", "GSM1001572", "GSM1001573", "GSM1001574", "GSM1001575", "GSM1001576", "GSM1001577", "GSM1001578", "GSM1001579", "GSM1001580", "GSM1001581", "GSM1001582", "GSM1001583", "GSM1001584", "GSM1001585", "GSM1001586", "GSM1001587", "GSM1001588", "GSM1001589", "GSM1001590", "GSM1001591", "GSM1001592", "GSM1001593", "GSM1001594", "GSM1001595", "GSM1001596", "GSM1001597", "GSM1001598", "GSM1001599", "GSM1001600", "GSM1001601", "GSM1001602", "GSM1001603", "GSM1001604", "GSM1001605", "GSM1001606", "GSM1001607", "GSM1001608", "GSM1001609", "GSM1001610", "GSM1001611", "GSM1001612", "GSM1001613", "GSM1001614", "GSM1001615", "GSM1001616", "GSM1001617", "GSM1001618", "GSM1001619", "GSM1001620", "GSM1001621", "GSM1001622", "GSM1001623", "GSM1001624", "GSM1001625", "GSM1001626", "GSM1001627", "GSM1001628", "GSM1001629", "GSM1001630", "GSM1001631", "GSM1001632", "GSM1001633", "GSM1001634", "GSM1001635", "GSM1001636", "GSM1001637", "GSM1001638", "GSM1001639", "GSM1001640", "GSM1001641", "GSM1001642", "GSM1001643", "GSM1001644", "GSM1001645", "GSM1001646", "GSM1001647", "GSM1001648", "GSM1001649", "GSM1001650", "GSM1001651", "GSM1001652", "GSM1001653", "GSM1001654", "GSM1001655", "GSM1001656", "GSM1001657", "GSM1001658", "GSM1001659", "GSM1001660", "GSM1001661", "GSM1001662", "GSM1001663", "GSM1001664", "GSM1001665", "GSM1001666", "GSM1001667", "GSM1001668", "GSM1001669", "GSM1001670", "GSM1001671", "GSM1001672", "GSM1001673", "GSM1001674", "GSM1001675", "GSM1001676", "GSM1001677", "GSM1001678", "GSM1001679", "GSM1001680", "GSM1001681", "GSM1001682", "GSM1001683", "GSM1001684", "GSM1001685", "GSM1001686", "GSM1001687", "GSM1001688", "GSM1001689", "GSM1001690", "GSM1001691", "GSM1001692", "GSM1001693", "GSM1001694", "GSM1001695", "GSM1001696", "GSM1001697", "GSM1001698", "GSM1001699", "GSM1001700", "GSM1001701", "GSM1001702", "GSM1001703"], "sample_count": 194, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Usp44 binds centrin to regulate centrosome positioning and suppress tumorigenesis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE10072 not downloaded", "asset:data:geo:GSE10072 licence not read", "asset:data:geo:GSE136103 not downloaded", "asset:data:geo:GSE136103 licence not read", "asset:data:geo:GSE19188 not downloaded", "asset:data:geo:GSE19188 licence not read", "asset:data:geo:GSE19804 not downloaded", "asset:data:geo:GSE19804 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE40791 not downloaded", "asset:data:geo:GSE40791 licence not read"]}, "analysis": {"state": "partial", "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": "The limma package was used to analyze the differentially expressed genes between lung adenocarcinoma patients and control patients in the GEO database, and a volcano plot was drawn to show the distribution of differentially expressed genes."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-4", "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-5", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE10072", "GSE19188", "GSE19804", "GSE30219", "GSE40791", "GSE136103"], "resolved_accessions": ["GSE10072", "GSE19188", "GSE19804", "GSE30219", "GSE40791", "GSE136103"], "statements": ["All datasets utilized or generated during the study are fully available within this article."], "basis": "The paper names GSE10072, GSE19188, GSE19804, GSE30219, GSE40791, GSE136103 in 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:41130017", "data:geo:GSE10072"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10072"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:03:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 17681, "completion_tokens": 1724, "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:41130017", "type": "paper", "label": "pmid:41130017"}, {"id": "source:pmid:41130017", "type": "manuscript", "label": "PMID 41130017 full text"}, {"id": "data:geo:GSE10072", "type": "dataset", "label": "GEO GSE10072"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41130017", "type": "paper", "label": "pmid:41130017"}, {"id": "source:pmid:41130017", "type": "manuscript", "label": "PMID 41130017 full text"}, {"id": "data:geo:GSE10072", "type": "dataset", "label": "GEO GSE10072"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41130017", "type": "extraction", "used": ["source:pmid:41130017"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10072", "type": "accession_resolution", "used": ["data:geo:GSE10072"], "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:41130017", "parent_hash": "sha256:a7b8b8a37c1109d89f94912da257c4379aa0be736e3cf18e74c3b9728e9c2eba", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE10072 licence not read", "asset:data:geo:GSE10072 not downloaded", "asset:data:geo:GSE136103 licence not read", "asset:data:geo:GSE136103 not downloaded", "asset:data:geo:GSE19188 licence not read", "asset:data:geo:GSE19188 not downloaded", "asset:data:geo:GSE19804 licence not read", "asset:data:geo:GSE19804 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE40791 licence not read", "asset:data:geo:GSE40791 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": ["study used network pharmacology, integrating single-cell RNA sequencing (scRNA-seq) data (GSE136103), GEO transcript", "ogy, integrating single-cell RNA sequencing (scRNA-seq) data (GSE136103), GEO transcriptome dataset", "d through PubChem and SwissTargetPrediction. scRNA-seq data were analyzed using Seurat, and key gen", "of lung adenocarcinoma single-cell data The single-cell RNA sequencing data for lung adenocarcinoma were obtained f"], "order_basis": "paper_text_order:466", "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": ["etwork pharmacology, integrating single-cell RNA sequencing (scRNA-seq) data (GSE136103), GEO transcript", "nocarcinoma single-cell data The single-cell RNA sequencing data for lung adenocarcinoma were obtained f", "ol tissues (PMID: 34663877). The single-cell RNA sequencing data were analyzed using R software (version", "EO differential genes (GEOdiff), single-cell RNA sequencing differential genes (scRNA), WGCNA module gen"], "order_basis": "paper_text_order:478", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ive for mycoplasma contamination. Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibc", "aracterization Human lung cancer cell lines (A549, HCC827, Calu-3, NCI-H2228, NCI-H1975) and t"], "order_basis": "paper_text_order:5504", "id": "assay:3"}, {"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": ["The limma package was used to analyze the differentially expressed genes between lung adenocarcinoma patients and control patients in the GEO database, and a volcano plot was drawn to show the distribution of differentially expressed genes."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}