MiR-195 restrains lung adenocarcinoma by regulating CD4+ T cell activation via the CCDC88C/Wnt signaling pathway: a study based on the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31355230", "kind": "science-record", "revision": 3, "content_hash": "sha256:e74a95444a2caf725e4c036b4a261917c2c511c8b8b0786dc00eb8dfc77c84b7", "created_at": "2026-11-01T17:32:58Z", "updated_at": "2026-11-01T21:22:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MiR-195 restrains lung adenocarcinoma by regulating CD4+ T cell activation via the CCDC88C/Wnt signaling pathway: a study based on the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and bioinformatic analysis.", "doi": "10.21037/atm.2019.05.54", "pmid": "31355230", "authors": ["Cheng Yuan", "Liyang Xiang", "Rui Bai", "Kuo Cao", "Yanping Gao", "Xueping Jiang", "Nannan Zhang", "Yan Gong", "Conghua Xie"], "journal": "Annals of translational medicine", "year": 2019, "abstract": "BACKGROUND: To systematically identity microRNA signatures, as well as miRNA-gene axes, for lung adenocarcinoma (LUAD) and to explore the potential biomarkers and mechanisms associated with the LUAD immune responses.\nMETHODS: LUAD-related data were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), and these data were then used to identify the differentially expressed miRNAs that were downregulated in tumor tissues. Summary receiver operating characteristic curve analysis, survival analysis and meta-analysis were applied to evaluate the clinical significance and diagnostic value of the identified miRNAs. The presumed targets of the integrated-signature miRNAs were identified via 3 different target prediction algorithms: TargetScan, miRDB and DIANA-TarBase. Immunologic signature gene sets were enriched by gene set enrichment analysis (GSEA). Tumor-infiltrating lymphocytes were profiled by the Tumor IMmune Estimation Resource (TIMER). After pathway enrichment analysis using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, pathway-gene networks were constructed using Cytoscape software.\nRESULTS: After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker. A total of 287 miR-195 target genes were screened, and 3 functional gene sets (GSE13485, GSE21379 and GSE29164) were enriched. GSE21379 was associated with the upregulation of CD4+ T cells in tumors, and the core genes were validated via the TIMER database. The CCDC88C expression level was significantly correlated with CD4+ T cell activation (partial.cor =0.437, P<0.001). Enrichment analysis revealed that CCDC88C was significantly enriched in the Wnt signaling pathway.\nCONCLUSIONS: MiR-195, as a suppressor of lung adenocarcinoma, regulates CD4+ T cell activation via CCDC88C.", "claims": [{"id": "claim-method", "statement": "Summary receiver operating characteristic curve analysis, survival analysis and meta-analysis were applied to evaluate the clinical significance and diagnostic value of the identified miRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31355230", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Summary receiver operating characteristic curve analysis, survival analysis and meta-analysis were applied to evaluate the clinical significance and diagnostic value of the identified miRNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31355230", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "The CCDC88C expression level was significantly correlated with CD4+ T cell activation (partial.cor =0.437, P<0.001)."}, "evidence": [{"asset": "source:pmid:31355230", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker."}, {"asset": "source:pmid:31355230", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The CCDC88C expression level was significantly correlated with CD4+ T cell activation (partial.cor =0.437, P<0.001)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "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:31355230"], "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:GSE13485"], "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:GSE13485"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31355230", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm.2019.05.54", "sha256": "sha256:72f342ed185be9a7d73b4396357299d731a51f1343190fc7273d2f37bb9d74cc", "bytes": 1893, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm.2019.05.54", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6614311", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13485", "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=GSE13485", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13485", "version": null, "note": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM339820", "GSM339821", "GSM339822", "GSM339823", "GSM339824", "GSM339825", "GSM339826", "GSM339827", "GSM339828", "GSM339829", "GSM339830", "GSM339831", "GSM339832", "GSM339833", "GSM339834", "GSM339835", "GSM339836", "GSM339837", "GSM339838", "GSM339839", "GSM339840", "GSM339841", "GSM339842", "GSM339843", "GSM339844", "GSM339845", "GSM339846", "GSM339847", "GSM339848", "GSM339849", "GSM339850", "GSM339851", "GSM339852", "GSM339853", "GSM339854", "GSM339855", "GSM339856", "GSM339857", "GSM339858", "GSM339859", "GSM339860", "GSM339861", "GSM339862", "GSM339863", "GSM339864", "GSM339865", "GSM339866", "GSM339867", "GSM339868", "GSM339869", "GSM339870", "GSM339871", "GSM339872", "GSM339873", "GSM339874", "GSM339875", "GSM339876", "GSM339877", "GSM339878", "GSM339879", "GSM339880", "GSM339881", "GSM339882", "GSM339883", "GSM339884", "GSM339885", "GSM339886", "GSM339887", "GSM339888", "GSM339889", "GSM339890", "GSM339891", "GSM339892", "GSM339893", "GSM339894", "GSM339895", "GSM339896", "GSM339897", "GSM339898", "GSM339899", "GSM339900", "GSM339901", "GSM339902", "GSM339903", "GSM339904", "GSM339905", "GSM339906"], "sample_count": 87, "group_sizes": null, "group_sizes_basis": null, "platform": "7567", "taxon": "Homo sapiens", "title": "Profiling 20,077 genes in 25 vaccine recipients: U133 Plus 2.0, Custom CDF Version 9", "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:GSE21379", "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=GSE21379", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21379", "version": null, "note": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM418234", "GSM418235", "GSM418236", "GSM418237", "GSM418238", "GSM534245", "GSM534246", "GSM534247", "GSM534248", "GSM534249"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Expression Data from WT and Sh2d1a-/- in vivo follicular helper CD4 T cells (TFH) versus non follicular helper CD4 T cells (non-TFH)", "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:GSE29164", "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=GSE29164", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29164", "version": null, "note": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM721735", "GSM721736", "GSM721737", "GSM721738", "GSM721739", "GSM721740", "GSM721741", "GSM721742", "GSM721743", "GSM721744", "GSM721745", "GSM721746", "GSM721747", "GSM721748", "GSM721749", "GSM721750", "GSM721751", "GSM721752", "GSM721753", "GSM721754", "GSM721755", "GSM721756", "GSM721757", "GSM721758"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6246", "taxon": "Mus musculus", "title": "IL-12 induces myeloid cells in situ to cross-present antigen", "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:GSE48414", "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=GSE48414", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48414", "version": null, "note": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1177525", "GSM1177526", "GSM1177527", "GSM1177528", "GSM1177529", "GSM1177530", "GSM1177531", "GSM1177532", "GSM1177533", "GSM1177534", "GSM1177535", "GSM1177536", "GSM1177537", "GSM1177538", "GSM1177539", "GSM1177540", "GSM1177541", "GSM1177542", "GSM1177543", "GSM1177544", "GSM1177545", "GSM1177546", "GSM1177547", "GSM1177548", "GSM1177549", "GSM1177550", "GSM1177551", "GSM1177552", "GSM1177553", "GSM1177554", "GSM1177555", "GSM1177556", "GSM1177557", "GSM1177558", "GSM1177559", "GSM1177560", "GSM1177561", "GSM1177562", "GSM1177563", "GSM1177564", "GSM1177565", "GSM1177566", "GSM1177567", "GSM1177568", "GSM1177569", "GSM1177570", "GSM1177571", "GSM1177572", "GSM1177573", "GSM1177574", "GSM1177575", "GSM1177576", "GSM1177577", "GSM1177578", "GSM1177579", "GSM1177580", "GSM1177581", "GSM1177582", "GSM1177583", "GSM1177584", "GSM1177585", "GSM1177586", "GSM1177587", "GSM1177588", "GSM1177589", "GSM1177590", "GSM1177591", "GSM1177592", "GSM1177593", "GSM1177594", "GSM1177595", "GSM1177596", "GSM1177597", "GSM1177598", "GSM1177599", "GSM1177600", "GSM1177601", "GSM1177602", "GSM1177603", "GSM1177604", "GSM1177605", "GSM1177606", "GSM1177607", "GSM1177608", "GSM1177609", "GSM1177610", "GSM1177611", "GSM1177612", "GSM1177613", "GSM1177614", "GSM1177615", "GSM1177616", "GSM1177617", "GSM1177618", "GSM1177619", "GSM1177620", "GSM1177621", "GSM1177622", "GSM1177623", "GSM1177624", "GSM1177625", "GSM1177626", "GSM1177627", "GSM1177628", "GSM1177629", "GSM1177630", "GSM1177631", "GSM1177632", "GSM1177633", "GSM1177634", "GSM1177635", "GSM1177636", "GSM1177637", "GSM1177638", "GSM1177639", "GSM1177640", "GSM1177641", "GSM1177642", "GSM1177643", "GSM1177644", "GSM1177645", "GSM1177646", "GSM1177647", "GSM1177648", "GSM1177649", "GSM1177650", "GSM1177651", "GSM1177652", "GSM1177653", "GSM1177654", "GSM1177655", "GSM1177656", "GSM1177657", "GSM1177658", "GSM1177659", "GSM1177660", "GSM1177661", "GSM1177662", "GSM1177663", "GSM1177664", "GSM1177665", "GSM1177666", "GSM1177667", "GSM1177668", "GSM1177669", "GSM1177670", "GSM1177671", "GSM1177672", "GSM1177673", "GSM1177674", "GSM1177675", "GSM1177676", "GSM1177677", "GSM1177678", "GSM1177679", "GSM1177680", "GSM1177681", "GSM1177682", "GSM1177683", "GSM1177684", "GSM1177685", "GSM1177686", "GSM1177687", "GSM1177688", "GSM1177689", "GSM1177690", "GSM1177691", "GSM1177692", "GSM1177693", "GSM1177694", "GSM1177695", "GSM1177696", "GSM1177697", "GSM1177698"], "sample_count": 174, "group_sizes": null, "group_sizes_basis": null, "platform": "16770", "taxon": "Homo sapiens", "title": "Unique microRNA profiles in EGFR-mutated lung adenocarcinomas", "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:GSE51853", "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=GSE51853", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51853", "version": null, "note": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1253944", "GSM1253945", "GSM1253946", "GSM1253947", "GSM1253948", "GSM1253949", "GSM1253950", "GSM1253951", "GSM1253952", "GSM1253953", "GSM1253954", "GSM1253955", "GSM1253956", "GSM1253957", "GSM1253958", "GSM1253959", "GSM1253960", "GSM1253961", "GSM1253962", "GSM1253963", "GSM1253964", "GSM1253965", "GSM1253966", "GSM1253967", "GSM1253968", "GSM1253969", "GSM1253970", "GSM1253971", "GSM1253972", "GSM1253973", "GSM1253974", "GSM1253975", "GSM1253976", "GSM1253977", "GSM1253978", "GSM1253979", "GSM1253980", "GSM1253981", "GSM1253982", "GSM1253983", "GSM1253984", "GSM1253985", "GSM1253986", "GSM1253987", "GSM1253988", "GSM1253989", "GSM1253990", "GSM1253991", "GSM1253992", "GSM1253993", "GSM1253994", "GSM1253995", "GSM1253996", "GSM1253997", "GSM1253998", "GSM1253999", "GSM1254000", "GSM1254001", "GSM1254002", "GSM1254003", "GSM1254004", "GSM1254005", "GSM1254006", "GSM1254007", "GSM1254008", "GSM1254009", "GSM1254010", "GSM1254011", "GSM1254012", "GSM1254013", "GSM1254014", "GSM1254015", "GSM1254016", "GSM1254017", "GSM1254018", "GSM1254019", "GSM1254020", "GSM1254021", "GSM1254022", "GSM1254023", "GSM1254024", "GSM1254025", "GSM1254026", "GSM1254027", "GSM1254028", "GSM1254029", "GSM1254030", "GSM1254031", "GSM1254032", "GSM1254033", "GSM1254034", "GSM1254035", "GSM1254036", "GSM1254037", "GSM1254038", "GSM1254039", "GSM1254040", "GSM1254041", "GSM1254042", "GSM1254043", "GSM1254044", "GSM1254045", "GSM1254046", "GSM1254047", "GSM1254048", "GSM1254049", "GSM1254050", "GSM1254051", "GSM1254052", "GSM1254053", "GSM1254054", "GSM1254055", "GSM1254056", "GSM1254057", "GSM1254058", "GSM1254059", "GSM1254060", "GSM1254061", "GSM1254062", "GSM1254063", "GSM1254064", "GSM1254065", "GSM1254066", "GSM1254067", "GSM1254068", "GSM1254069", "GSM1254070", "GSM1254071", "GSM1254072", "GSM1254073", "GSM1254074"], "sample_count": 131, "group_sizes": null, "group_sizes_basis": null, "platform": "7341", "taxon": "Homo sapiens", "title": "Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features [miRNA analysis - miRNA Microarray, pre-commercial version 6.0]", "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:GSE63805", "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=GSE63805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63805", "version": null, "note": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1557646", "GSM1557647", "GSM1557648", "GSM1557649", "GSM1557650", "GSM1557651", "GSM1557652", "GSM1557653", "GSM1557654", "GSM1557655", "GSM1557656", "GSM1557657", "GSM1557658", "GSM1557659", "GSM1557660", "GSM1557661", "GSM1557662", "GSM1557663", "GSM1557664", "GSM1557665", "GSM1557666", "GSM1557667", "GSM1557668", "GSM1557669", "GSM1557670", "GSM1557671", "GSM1557672", "GSM1557673", "GSM1557674", "GSM1557675", "GSM1557676", "GSM1557677", "GSM1557678", "GSM1557679", "GSM1557680", "GSM1557681", "GSM1557682", "GSM1557683", "GSM1557684", "GSM1557685", "GSM1557686", "GSM1557687", "GSM1557688", "GSM1557689", "GSM1557690", "GSM1557691", "GSM1557692", "GSM1557693", "GSM1557694", "GSM1557695", "GSM1557696", "GSM1557697", "GSM1557698", "GSM1557699", "GSM1557700", "GSM1557701", "GSM1557702", "GSM1557703", "GSM1557704", "GSM1557705", "GSM1557706", "GSM1557707"], "sample_count": 62, "group_sizes": null, "group_sizes_basis": null, "platform": "18410", "taxon": "Homo sapiens", "title": "Multi-platform Characterization of Stage I Lung Adenocarcinoma (miRNA profiling)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE74190", "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=GSE74190", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE74190", "version": null, "note": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1913414", "GSM1913415", "GSM1913416", "GSM1913417", "GSM1913418", "GSM1913419", "GSM1913420", "GSM1913421", "GSM1913422", "GSM1913423", "GSM1913424", "GSM1913425", "GSM1913426", "GSM1913427", "GSM1913428", "GSM1913429", "GSM1913430", "GSM1913431", "GSM1913432", "GSM1913433", "GSM1913434", "GSM1913435", "GSM1913436", "GSM1913437", "GSM1913438", "GSM1913439", "GSM1913440", "GSM1913441", "GSM1913442", "GSM1913443", "GSM1913444", "GSM1913445", "GSM1913446", "GSM1913447", "GSM1913448", "GSM1913449", "GSM1913450", "GSM1913451", "GSM1913452", "GSM1913453", "GSM1913454", "GSM1913455", "GSM1913456", "GSM1913457", "GSM1913458", "GSM1913459", "GSM1913460", "GSM1913461", "GSM1913462", "GSM1913463", "GSM1913464", "GSM1913465", "GSM1913466", "GSM1913467", "GSM1913468", "GSM1913469", "GSM1913470", "GSM1913471", "GSM1913472", "GSM1913473", "GSM1913474", "GSM1913475", "GSM1913476", "GSM1913477", "GSM1913478", "GSM1913479", "GSM1913480", "GSM1913481", "GSM1913482", "GSM1913483", "GSM1913484", "GSM1913485", "GSM1913486", "GSM1913487", "GSM1913488", "GSM1913489", "GSM1913490", "GSM1913491", "GSM1913492", "GSM1913493", "GSM1913494", "GSM1913495", "GSM1913496", "GSM1913497", "GSM1913498", "GSM1913499", "GSM1913500", "GSM1913501", "GSM1913502", "GSM1913503", "GSM1913504", "GSM1913505", "GSM1913506", "GSM1913507", "GSM1913508", "GSM1913509", "GSM1913510", "GSM1913511", "GSM1913512", "GSM1913513", "GSM1913514", "GSM1913515", "GSM1913516", "GSM1913517", "GSM1913518", "GSM1913519", "GSM1913520", "GSM1913521", "GSM1913522", "GSM1913523", "GSM1913524", "GSM1913525", "GSM1913526", "GSM1913527", "GSM1913528", "GSM1913529", "GSM1913530", "GSM1913531", "GSM1913532", "GSM1913533", "GSM1913534", "GSM1913535", "GSM1913536", "GSM1913537", "GSM1913538", "GSM1913539", "GSM1913540", "GSM1913541", "GSM1913542", "GSM1913543", "GSM1913544", "GSM1913545", "GSM1913546", "GSM1913547", "GSM1913548", "GSM1913549"], "sample_count": 136, "group_sizes": null, "group_sizes_basis": null, "platform": "19622", "taxon": "Homo sapiens", "title": "The miRNA expression profiles in three subtypes of lung carcinomas", "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:GSE13485 not downloaded", "asset:data:geo:GSE13485 licence not read", "asset:data:geo:GSE21379 not downloaded", "asset:data:geo:GSE21379 licence not read", "asset:data:geo:GSE29164 not downloaded", "asset:data:geo:GSE29164 licence not read", "asset:data:geo:GSE48414 not downloaded", "asset:data:geo:GSE48414 licence not read", "asset:data:geo:GSE51853 not downloaded", "asset:data:geo:GSE51853 licence not read", "asset:data:geo:GSE63805 not downloaded", "asset:data:geo:GSE63805 licence not read", "asset:data:geo:GSE74190 not downloaded", "asset:data:geo:GSE74190 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-2", "family": null, "specific": null, "label": "Summary receiver operating characteristic curve analysis, survival analysis and meta-analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Summary receiver operating characteristic curve analysis, survival analysis and meta-analysis were applied to evaluate the clinical significance and diagnostic value of the identified miRNAs."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "pathway_enrich", "expected_value": 0.001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE48414", "GSE51853", "GSE63805", "GSE74190", "GSE13485", "GSE21379", "GSE29164"], "resolved_accessions": ["GSE48414", "GSE51853", "GSE63805", "GSE74190", "GSE13485", "GSE21379", "GSE29164"], "statements": ["After integrated analysis of 4 GEO data sets (GSE48414, GSE51853, GSE63805 and GSE74190) and TCGA databases, miR-195 was identified as a potential clinical diagnostic marker."], "basis": "The paper names GSE48414, GSE51853, GSE63805, GSE74190, GSE13485, GSE21379, GSE29164 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:31355230", "data:geo:GSE13485"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13485"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T16:58:51Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2035, "completion_tokens": 2832, "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:31355230", "type": "paper", "label": "pmid:31355230"}, {"id": "source:pmid:31355230", "type": "manuscript", "label": "PMID 31355230 full text"}, {"id": "data:geo:GSE13485", "type": "dataset", "label": "GEO GSE13485"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31355230", "type": "paper", "label": "pmid:31355230"}, {"id": "source:pmid:31355230", "type": "manuscript", "label": "PMID 31355230 full text"}, {"id": "data:geo:GSE13485", "type": "dataset", "label": "GEO GSE13485"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31355230", "type": "extraction", "used": ["source:pmid:31355230"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13485", "type": "accession_resolution", "used": ["data:geo:GSE13485"], "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:31355230", "parent_hash": "sha256:e325ed4783914d8ec050ec823b2d9d467a8ec3ceec73ee49f853c19054686851", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE13485 licence not read", "asset:data:geo:GSE13485 not downloaded", "asset:data:geo:GSE21379 licence not read", "asset:data:geo:GSE21379 not downloaded", "asset:data:geo:GSE29164 licence not read", "asset:data:geo:GSE29164 not downloaded", "asset:data:geo:GSE48414 licence not read", "asset:data:geo:GSE48414 not downloaded", "asset:data:geo:GSE51853 licence not read", "asset:data:geo:GSE51853 not downloaded", "asset:data:geo:GSE63805 licence not read", "asset:data:geo:GSE63805 not downloaded", "asset:data:geo:GSE74190 licence not read", "asset:data:geo:GSE74190 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["pathway enrichment"], "order_basis": "analysis_only", "id": "assay:1"}]}