Matrix Metalloproteinase 11 Is a Potential Therapeutic Target in Lung Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31024988", "kind": "science-record", "revision": 9, "content_hash": "sha256:f1cab58748beff85cb698ea702dbf70b5ad74bda50300f9ffd61d56f98140820", "created_at": "2026-11-01T15:40:44Z", "updated_at": "2026-11-01T22:43:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Matrix Metalloproteinase 11 Is a Potential Therapeutic Target in Lung Adenocarcinoma.", "doi": "10.1016/j.omto.2019.03.012", "pmid": "31024988", "authors": ["Haoran Yang", "Peng Jiang", "Dongyan Liu", "Hong-Qiang Wang", "Qingmei Deng", "Xiaojie Niu", "Li Lu", "Haiming Dai", "Hongzhi Wang", "Wulin Yang"], "journal": "Molecular therapy oncolytics", "year": 2019, "abstract": "Lung cancer is one of the leading causes of cancer-associated death, with the etiology largely unknown. The aim of this study was to identify key driver genes with therapeutic potentials in lung adenocarcinoma (LUAD). Transcriptome microarray data from four GEO datasets (GEO: GSE7670, GSE10072, GSE68465, and GSE43458) were jointly analyzed for differentially expressed genes (DEGs). Ontologic analysis showed that most of the upregulated DEGs enriched in collagen catabolic and fibril organization processes were regulated by matrix metalloproteinases (MMPs). Matrix metalloproteinase 11 (MMP11), the highest upregulated MMP family member in LUAD-transformed cells, acted in an autocrine manner and was significantly increased in sera of LUAD patients. MMP11 depletion severely impaired LUAD cell proliferation, migration, and invasion in vitro, in line with retarded tumor growth in xenograft models. Treatment of different human LUAD cell lines with anti-MMP11 antibody significantly retarded cell growth and migration. Administration of anti-MMP11 antibody at a dose of 1 μg/g body weight significantly suppressed tumor growth in xenograft models. These findings indicate that MMP11 is a key cancer driver gene in LUAD and is an appealing target for antibody therapy.", "claims": [{"id": "claim-method", "statement": "Comparisons of data were performed with a paired two-tailed Student’s t test with equal variance or one-way ANOVA with Bonferroni’s post hoc test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31024988", "locator": "sections[24] \"Statistical Analysis\" paragraph 2", "quote": "Comparisons of data were performed with a paired two-tailed Student’s t test with equal variance or one-way ANOVA with Bonferroni’s post hoc test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31024988", "locator": "sections[3] \"Bioinformatics Identifies DEGs in LUAD and Non-malignant Tissues\" paragraph 2", "quote": "Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31024988"], "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": "blocked", "blocked_on": "method:student_t", "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": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31024988", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.omto.2019.03.012", "sha256": "sha256:a939c24258c179a2d53d24f5a93c73a480bc4b44724e048f606770946216c615", "bytes": 50033, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.omto.2019.03.012", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6477516", "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": "Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer.", "access_statement_kind": "repository_route_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:GSE68465", "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=GSE68465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68465", "version": null, "note": "Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1672281", "GSM1672282", "GSM1672283", "GSM1672284", "GSM1672285", "GSM1672286", "GSM1672287", "GSM1672288", "GSM1672289", "GSM1672290", "GSM1672291", "GSM1672292", "GSM1672293", "GSM1672294", "GSM1672295", "GSM1672296", "GSM1672297", "GSM1672298", "GSM1672299", "GSM1672300", "GSM1672301", "GSM1672302", "GSM1672303", "GSM1672304", "GSM1672305", "GSM1672306", "GSM1672307", "GSM1672308", "GSM1672309", "GSM1672310", "GSM1672311", "GSM1672312", "GSM1672313", "GSM1672314", "GSM1672315", "GSM1672316", "GSM1672317", "GSM1672318", "GSM1672319", "GSM1672320", "GSM1672321", "GSM1672322", "GSM1672323", "GSM1672324", "GSM1672325", "GSM1672326", "GSM1672327", "GSM1672328", "GSM1672329", "GSM1672330", "GSM1672331", "GSM1672332", "GSM1672333", "GSM1672334", "GSM1672335", "GSM1672336", "GSM1672337", "GSM1672338", "GSM1672339", "GSM1672340", "GSM1672341", "GSM1672342", "GSM1672343", "GSM1672344", "GSM1672345", "GSM1672346", "GSM1672347", "GSM1672348", "GSM1672349", "GSM1672350", "GSM1672351", "GSM1672352", "GSM1672353", "GSM1672354", "GSM1672355", "GSM1672356", "GSM1672357", "GSM1672358", "GSM1672359", "GSM1672360", "GSM1672361", "GSM1672362", "GSM1672363", "GSM1672364", "GSM1672365", "GSM1672366", "GSM1672367", "GSM1672368", "GSM1672369", "GSM1672370", "GSM1672371", "GSM1672372", "GSM1672373", "GSM1672374", "GSM1672375", "GSM1672376", "GSM1672377", "GSM1672378", "GSM1672379", "GSM1672380", "GSM1672381", "GSM1672382", "GSM1672383", "GSM1672384", "GSM1672385", "GSM1672386", "GSM1672387", "GSM1672388", "GSM1672389", "GSM1672390", "GSM1672391", "GSM1672392", "GSM1672393", "GSM1672394", "GSM1672395", "GSM1672396", "GSM1672397", "GSM1672398", "GSM1672399", "GSM1672400", "GSM1672401", "GSM1672402", "GSM1672403", "GSM1672404", "GSM1672405", "GSM1672406", "GSM1672407", "GSM1672408", "GSM1672409", "GSM1672410", "GSM1672411", "GSM1672412", "GSM1672413", "GSM1672414", "GSM1672415", "GSM1672416", "GSM1672417", "GSM1672418", "GSM1672419", "GSM1672420", "GSM1672421", "GSM1672422", "GSM1672423", "GSM1672424", "GSM1672425", "GSM1672426", "GSM1672427", "GSM1672428", "GSM1672429", "GSM1672430", "GSM1672431", "GSM1672432", "GSM1672433", "GSM1672434", "GSM1672435", "GSM1672436", "GSM1672437", "GSM1672438", "GSM1672439", "GSM1672440", "GSM1672441", "GSM1672442", "GSM1672443", "GSM1672444", "GSM1672445", "GSM1672446", "GSM1672447", "GSM1672448", "GSM1672449", "GSM1672450", "GSM1672451", "GSM1672452", "GSM1672453", "GSM1672454", "GSM1672455", "GSM1672456", "GSM1672457", "GSM1672458", "GSM1672459", "GSM1672460", "GSM1672461", "GSM1672462", "GSM1672463", "GSM1672464", "GSM1672465", "GSM1672466", "GSM1672467", "GSM1672468", "GSM1672469", "GSM1672470", "GSM1672471", "GSM1672472", "GSM1672473", "GSM1672474", "GSM1672475", "GSM1672476", "GSM1672477", "GSM1672478", "GSM1672479", "GSM1672480", "GSM1672481", "GSM1672482", "GSM1672483", "GSM1672484", "GSM1672485", "GSM1672486", "GSM1672487", "GSM1672488", "GSM1672489", "GSM1672490", "GSM1672491", "GSM1672492", "GSM1672493", "GSM1672494", "GSM1672495", "GSM1672496", "GSM1672497", "GSM1672498", "GSM1672499", "GSM1672500", "GSM1672501", "GSM1672502", "GSM1672503", "GSM1672504", "GSM1672505", "GSM1672506", "GSM1672507", "GSM1672508", "GSM1672509", "GSM1672510", "GSM1672511", "GSM1672512", "GSM1672513", "GSM1672514", "GSM1672515", "GSM1672516", "GSM1672517", "GSM1672518", "GSM1672519", "GSM1672520", "GSM1672521", "GSM1672522", "GSM1672523", "GSM1672524", "GSM1672525", "GSM1672526", "GSM1672527", "GSM1672528", "GSM1672529", "GSM1672530", "GSM1672531", "GSM1672532", "GSM1672533", "GSM1672534", "GSM1672535", "GSM1672536", "GSM1672537", "GSM1672538", "GSM1672539", "GSM1672540", "GSM1672541", "GSM1672542", "GSM1672543", "GSM1672544", "GSM1672545", "GSM1672546", "GSM1672547", "GSM1672548", "GSM1672549", "GSM1672550", "GSM1672551", "GSM1672552", "GSM1672553", "GSM1672554", "GSM1672555", "GSM1672556", "GSM1672557", "GSM1672558", "GSM1672559", "GSM1672560", "GSM1672561", "GSM1672562", "GSM1672563", "GSM1672564", "GSM1672565", "GSM1672566", "GSM1672567", "GSM1672568", "GSM1672569", "GSM1672570", "GSM1672571", "GSM1672572", "GSM1672573", "GSM1672574", "GSM1672575", "GSM1672576", "GSM1672577", "GSM1672578", "GSM1672579", "GSM1672580", "GSM1672581", "GSM1672582", "GSM1672583", "GSM1672584", "GSM1672585", "GSM1672586", "GSM1672587", "GSM1672588", "GSM1672589", "GSM1672590", "GSM1672591", "GSM1672592", "GSM1672593", "GSM1672594", "GSM1672595", "GSM1672596", "GSM1672597", "GSM1672598", "GSM1672599", "GSM1672600", "GSM1672601", "GSM1672602", "GSM1672603", "GSM1672604", "GSM1672605", "GSM1672606", "GSM1672607", "GSM1672608", "GSM1672609", "GSM1672610", "GSM1672611", "GSM1672612", "GSM1672613", "GSM1672614", "GSM1672615", "GSM1672616", "GSM1672617", "GSM1672618", "GSM1672619", "GSM1672620", "GSM1672621", "GSM1672622", "GSM1672623", "GSM1672624", "GSM1672625", "GSM1672626", "GSM1672627", "GSM1672628", "GSM1672629", "GSM1672630", "GSM1672631", "GSM1672632", "GSM1672633", "GSM1672634", "GSM1672635", "GSM1672636", "GSM1672637", "GSM1672638", "GSM1672639", "GSM1672640", "GSM1672641", "GSM1672642", "GSM1672643", "GSM1672644", "GSM1672645", "GSM1672646", "GSM1672647", "GSM1672648", "GSM1672649", "GSM1672650", "GSM1672651", "GSM1672652", "GSM1672653", "GSM1672654", "GSM1672655", "GSM1672656", "GSM1672657", "GSM1672658", "GSM1672659", "GSM1672660", "GSM1672661", "GSM1672662", "GSM1672663", "GSM1672664", "GSM1672665", "GSM1672666", "GSM1672667", "GSM1672668", "GSM1672669", "GSM1672670", "GSM1672671", "GSM1672672", "GSM1672673", "GSM1672674", "GSM1672675", "GSM1672676", "GSM1672677", "GSM1672678", "GSM1672679", "GSM1672680", "GSM1672681", "GSM1672682", "GSM1672683", "GSM1672684", "GSM1672685", "GSM1672686", "GSM1672687", "GSM1672688", "GSM1672689", "GSM1672690", "GSM1672691", "GSM1672692", "GSM1672693", "GSM1672694", "GSM1672695", "GSM1672696", "GSM1672697", "GSM1672698", "GSM1672699", "GSM1672700", "GSM1672701", "GSM1672702", "GSM1672703", "GSM1672704", "GSM1672705", "GSM1672706", "GSM1672707", "GSM1672708", "GSM1672709", "GSM1672710", "GSM1672711", "GSM1672712", "GSM1672713", "GSM1672714", "GSM1672715", "GSM1672716", "GSM1672717", "GSM1672718", "GSM1672719", "GSM1672720", "GSM1672721", "GSM1672722", "GSM1672723", "GSM1672724", "GSM1672725", "GSM1672726", "GSM1672727", "GSM1672728", "GSM1672729", "GSM1672730", "GSM1672731", "GSM1672732", "GSM1672733", "GSM1672734", "GSM1672735", "GSM1672736", "GSM1672737", "GSM1672738", "GSM1672739", "GSM1672740", "GSM1672741", "GSM1672742"], "sample_count": 462, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "caArray_jacob-00182: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study", "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:GSE7670", "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=GSE7670", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7670", "version": null, "note": "Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM185811", "GSM185812", "GSM185813", "GSM185814", "GSM185815", "GSM185816", "GSM185817", "GSM185818", "GSM185819", "GSM185820", "GSM185821", "GSM185822", "GSM185823", "GSM185824", "GSM185825", "GSM185826", "GSM185827", "GSM185828", "GSM185829", "GSM185830", "GSM185831", "GSM185832", "GSM185833", "GSM185834", "GSM185835", "GSM185836", "GSM185837", "GSM185838", "GSM185839", "GSM185840", "GSM185841", "GSM185842", "GSM185843", "GSM185844", "GSM185845", "GSM185846", "GSM185847", "GSM185848", "GSM185849", "GSM185850", "GSM185851", "GSM185852", "GSM185853", "GSM185854", "GSM185855", "GSM185856", "GSM185857", "GSM185858", "GSM185859", "GSM185860", "GSM185861", "GSM185862", "GSM185863", "GSM185864", "GSM185865", "GSM185866", "GSM185867", "GSM185868", "GSM185869", "GSM185870", "GSM185871", "GSM185872", "GSM185873", "GSM185874", "GSM185875", "GSM185876"], "sample_count": 66, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from Lung cancer", "resolution_checked_at": "2026-11-01T15:14:33Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31024988:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1d3e0649dc808985757c208aca8bb2927ee74ede4d9ff5da9ecaa555bc637da7", "bytes": 618, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl1", "version": null, "note": "Common DEGs Identified in Lung Adenocarcinoma", "structure": {"pmcid": "PMC6477516", "section_index": 3, "section_title": "Bioinformatics Identifies DEGs in LUAD and Non-malignant Tissues", "row_count": 3, "column_count": 2}, "table": {"label": "Table 1", "caption": "Common DEGs Identified in Lung Adenocarcinoma", "rows": [["Regulation", "Gene Symbol"], ["DEGs upregulated", "COL11A1, SPINK1, MMP12, S100A2, CDH3, COL10A1, COL3A1, MMP9, AGR2, GREM1, CXCL13, TOX3, MMP7, WFDC2, COL1A1, CST1, CXCL14, TMPRSS4, COMP, SULF1, GOLM1, ABCC3, MMP11, LCN2, PPP1R14(D) FAP, ADAMDEC1, MXRA5, CEACAM5, LGSN"], ["DEGs downregulated", "CDH13, CTNNAL1, HL(F) SEMA5(A) NRN1, ITM2(A) GPM6(B) CX3CR1, SRPX, TSPAN7, GPC3, ADAMTS1, SOCS2, BCH(E) EDNR(B) FHL1, CPB2, CAV1"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl1"}}], "gaps": ["asset:data:geo:GSE10072 not downloaded", "asset:data:geo:GSE10072 licence not read", "asset:data:geo:GSE68465 not downloaded", "asset:data:geo:GSE68465 licence not read", "asset:data:geo:GSE7670 not downloaded", "asset:data:geo:GSE7670 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Comparisons of data were performed with a paired two-tailed Student’s t test with equal variance or one-way ANOVA with Bonferroni’s post hoc test."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE7670", "GSE10072", "GSE68465", "and GSE43458"], "resolved_accessions": ["GSE7670", "GSE10072", "GSE68465"], "statements": ["Four gene expression datasets of LUAD in the GEO database, including GSE7670, GSE10072, GSE68465, and GSE43458, were used for identification of genes differentially expressed in lung cancer."], "basis": "The paper names GSE7670, GSE10072, GSE68465 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31024988", "data:geo:GSE10072", "asset:table:pmid:31024988:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "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": "2026-10-31T18:14:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 39572, "completion_tokens": 1417, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31024988", "type": "paper", "label": "pmid:31024988"}, {"id": "source:pmid:31024988", "type": "manuscript", "label": "PMID 31024988 full text"}, {"id": "data:geo:GSE10072", "type": "dataset", "label": "GEO GSE10072"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31024988", "type": "paper", "label": "pmid:31024988"}, {"id": "source:pmid:31024988", "type": "manuscript", "label": "PMID 31024988 full text"}, {"id": "data:geo:GSE10072", "type": "dataset", "label": "GEO GSE10072"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31024988", "type": "extraction", "used": ["source:pmid:31024988"], "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:31024988", "parent_hash": "sha256:30bc9d14ad79a6116133a5bacc23765748f3fd573a51ce31d680c550c74acb3c", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE10072 licence not read", "asset:data:geo:GSE10072 not downloaded", "asset:data:geo:GSE68465 licence not read", "asset:data:geo:GSE68465 not downloaded", "asset:data:geo:GSE7670 licence not read", "asset:data:geo:GSE7670 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"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": ["in lung adenocarcinoma (LUAD). Transcriptome microarray data from four GEO datasets (GEO: GSE7670, G"], "order_basis": "paper_text_order:273", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Comparisons of data were performed with a paired two-tailed Student’s t test with equal variance or one-way ANOVA with Bonferroni’s post hoc test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}