Immune infiltration landscape on prognosis and therapeutic response and relevant epigenetic and transcriptomic mechanisms in lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36275753", "kind": "science-record", "revision": 4, "content_hash": "sha256:2ad711d03e32644e92ec8917353511d21ec79f9802b01d286293c5fe11613468", "created_at": "2026-11-01T18:15:40Z", "updated_at": "2026-11-01T22:07:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immune infiltration landscape on prognosis and therapeutic response and relevant epigenetic and transcriptomic mechanisms in lung adenocarcinoma.", "doi": "10.3389/fimmu.2022.983570", "pmid": "36275753", "authors": ["Liangming Zhang", "Biwang Jiang", "Zhuxiang Lan", "Chaomian Yang", "Yien Yao", "Jie Lin", "Qiu Wei"], "journal": "Frontiers in immunology", "year": 2022, "abstract": "Objective: Lung adenocarcinoma (LUAD) is the most prevalent lung cancer subtype, but its immune infiltration features are not comprehensively understood. To address the issue, the present study was initiated to describe the immune infiltrations across LUAD from cellular compositional, functional, and mechanism perspectives.\nMethods: We adopted five LUAD datasets (GSE32863, GSE43458, GSE75037, TCGA-LUAD, and GSE72094). Differentially expressed genes between LUAD and controls were selected for co-expression network analysis. Risky immune cell types were determined for classifying LUAD patients as diverse subtypes, followed by a comparison of antitumor immunity and therapeutic response between subtypes. Then, LUAD- and subtype-related key module genes affected by DNA methylation were determined for quantifying a scoring scheme. EXO1 was chosen for functional analysis via in vitro assays.\nResults: Two immune cell infiltration-based subtypes (C1 and C2) were established across LUAD, with poorer prognostic outcomes and lower infiltration of immune cell types in C1. Additionally, C1 presented higher responses to immune checkpoint blockade and targeted agents (JNK inhibitor VIII, BI-D1870, RO-3306, etc.). The scoring system (comprising GAPDH, EXO1, FYN, CFTR, and KLF4) possessed higher accuracy in estimating patients' prognostic outcomes. EXO1 upregulation contributed to the growth, migration, and invasion of LUAD cells. In addition, EXO1 facilitated PD-L1 and sPD-L1 expression in LUAD cells.\nConclusion: Altogether, our findings offer a comprehensive understanding of the immune infiltration landscape on prognosis and therapeutic response of LUAD as well as unveil potential epigenetic and transcriptomic mechanisms, which might assist personalized treatment.", "claims": [{"id": "claim-method", "statement": "The co-expression network of DEGs shared by four datasets was constructed via the weighted gene correlation network analysis (WGCNA) package (17).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36275753", "locator": "sections[5] \"Weighted gene correlation network analysis\" paragraph 2", "quote": "The co-expression network of DEGs shared by four datasets was constructed via the weighted gene correlation network analysis (WGCNA) package (17)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36275753", "locator": "sections[33] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Two immune cell infiltration-based subtypes (C1 and C2) were established across LUAD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36275753", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Two immune cell infiltration-based subtypes (C1 and C2) were established across LUAD, with poorer prognostic outcomes and lower infiltration of immune cell types in C1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Two immune cell infiltration-based subtypes (C1 and C2) were established across LUAD.", "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:36275753"], "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:GSE32863"], "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:group_comparison_wilcoxon", "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:GSE32863"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36275753", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2022.983570", "sha256": "sha256:e048b618f240dcba8a5a0d1ea2100054f95b82cadfeaa27cd00b8c64f44e4524", "bytes": 41102, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2022.983570", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9582346", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE32863", "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=GSE32863", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32863", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM813411", "GSM813412", "GSM813413", "GSM813414", "GSM813415", "GSM813416", "GSM813417", "GSM813418", "GSM813419", "GSM813420", "GSM813421", "GSM813422", "GSM813423", "GSM813424", "GSM813425", "GSM813426", "GSM813427", "GSM813428", "GSM813429", "GSM813430", "GSM813431", "GSM813432", "GSM813433", "GSM813434", "GSM813435", "GSM813436", "GSM813437", "GSM813438", "GSM813439", "GSM813440", "GSM813441", "GSM813442", "GSM813443", "GSM813444", "GSM813445", "GSM813446", "GSM813447", "GSM813448", "GSM813449", "GSM813450", "GSM813451", "GSM813452", "GSM813453", "GSM813454", "GSM813455", "GSM813456", "GSM813457", "GSM813458", "GSM813459", "GSM813460", "GSM813461", "GSM813462", "GSM813463", "GSM813464", "GSM813465", "GSM813466", "GSM813467", "GSM813468", "GSM813469", "GSM813470", "GSM813471", "GSM813472", "GSM813473", "GSM813474", "GSM813475", "GSM813476", "GSM813477", "GSM813478", "GSM813479", "GSM813480", "GSM813481", "GSM813482", "GSM813483", "GSM813484", "GSM813485", "GSM813486", "GSM813487", "GSM813488", "GSM813489", "GSM813490", "GSM813491", "GSM813492", "GSM813493", "GSM813494", "GSM813495", "GSM813496", "GSM813497", "GSM813498", "GSM813499", "GSM813500", "GSM813501", "GSM813502", "GSM813503", "GSM813504", "GSM813505", "GSM813506", "GSM813507", "GSM813508", "GSM813509", "GSM813510", "GSM813511", "GSM813512", "GSM813513", "GSM813514", "GSM813515", "GSM813516", "GSM813517", "GSM813518", "GSM813519", "GSM813520", "GSM813521", "GSM813522", "GSM813523", "GSM813524", "GSM813525", "GSM813526"], "sample_count": 116, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Gene expression analysis of lung adenocarcinoma and matched adjacent non-tumor lung tissue", "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:GSE43458", "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=GSE43458", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43458", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1062765", "GSM1062766", "GSM1062767", "GSM1062768", "GSM1062769", "GSM1062770", "GSM1062771", "GSM1062772", "GSM1062773", "GSM1062774", "GSM1062775", "GSM1062776", "GSM1062777", "GSM1062778", "GSM1062779", "GSM1062780", "GSM1062781", "GSM1062782", "GSM1062783", "GSM1062784", "GSM1062785", "GSM1062786", "GSM1062787", "GSM1062788", "GSM1062789", "GSM1062790", "GSM1062791", "GSM1062792", "GSM1062793", "GSM1062794", "GSM1062795", "GSM1062796", "GSM1062797", "GSM1062798", "GSM1062799", "GSM1062800", "GSM1062801", "GSM1062802", "GSM1062803", "GSM1062804", "GSM1062805", "GSM1062806", "GSM1062807", "GSM1062808", "GSM1062809", "GSM1062810", "GSM1062811", "GSM1062812", "GSM1062813", "GSM1062814", "GSM1062815", "GSM1062816", "GSM1062817", "GSM1062818", "GSM1062819", "GSM1062820", "GSM1062821", "GSM1062822", "GSM1062823", "GSM1062824", "GSM1062825", "GSM1062826", "GSM1062827", "GSM1062828", "GSM1062829", "GSM1062830", "GSM1062831", "GSM1062832", "GSM1062833", "GSM1062834", "GSM1062835", "GSM1062836", "GSM1062837", "GSM1062838", "GSM1062839", "GSM1062840", "GSM1062841", "GSM1062842", "GSM1062843", "GSM1062844", "GSM1062845", "GSM1062846", "GSM1062847", "GSM1062848", "GSM1062849", "GSM1062850", "GSM1062851", "GSM1062852", "GSM1062853", "GSM1062854", "GSM1062855", "GSM1062856", "GSM1062857", "GSM1062858", "GSM1062859", "GSM1062860", "GSM1062861", "GSM1062862", "GSM1062863", "GSM1062864", "GSM1062865", "GSM1062866", "GSM1062867", "GSM1062868", "GSM1062869", "GSM1062870", "GSM1062871", "GSM1062872", "GSM1062873", "GSM1062874"], "sample_count": 110, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profiling of lung adenocarcinomas and normal lung tissue", "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:GSE72094", "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=GSE72094", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72094", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1854797", "GSM1854798", "GSM1854799", "GSM1854800", "GSM1854801", "GSM1854802", "GSM1854803", "GSM1854804", "GSM1854805", "GSM1854806", "GSM1854807", "GSM1854808", "GSM1854809", "GSM1854810", "GSM1854811", "GSM1854812", "GSM1854813", "GSM1854814", "GSM1854815", "GSM1854816", "GSM1854817", "GSM1854818", "GSM1854819", "GSM1854820", "GSM1854821", "GSM1854822", "GSM1854823", "GSM1854824", "GSM1854825", "GSM1854826", "GSM1854827", "GSM1854828", "GSM1854829", "GSM1854830", "GSM1854831", "GSM1854832", "GSM1854833", "GSM1854834", "GSM1854835", "GSM1854836", "GSM1854837", "GSM1854838", "GSM1854839", "GSM1854840", "GSM1854841", "GSM1854842", "GSM1854843", "GSM1854844", "GSM1854845", "GSM1854846", "GSM1854847", "GSM1854848", "GSM1854849", "GSM1854850", "GSM1854851", "GSM1854852", "GSM1854853", "GSM1854854", "GSM1854855", "GSM1854856", "GSM1854857", "GSM1854858", "GSM1854859", "GSM1854860", "GSM1854861", "GSM1854862", "GSM1854863", "GSM1854864", "GSM1854865", "GSM1854866", "GSM1854867", "GSM1854868", "GSM1854869", "GSM1854870", "GSM1854871", "GSM1854872", "GSM1854873", "GSM1854874", "GSM1854875", "GSM1854876", "GSM1854877", "GSM1854878", "GSM1854879", "GSM1854880", "GSM1854881", "GSM1854882", "GSM1854883", "GSM1854884", "GSM1854885", "GSM1854886", "GSM1854887", "GSM1854888", "GSM1854889", "GSM1854890", "GSM1854891", "GSM1854892", "GSM1854893", "GSM1854894", "GSM1854895", "GSM1854896", "GSM1854897", "GSM1854898", "GSM1854899", "GSM1854900", "GSM1854901", "GSM1854902", "GSM1854903", "GSM1854904", "GSM1854905", "GSM1854906", "GSM1854907", "GSM1854908", "GSM1854909", "GSM1854910", "GSM1854911", "GSM1854912", "GSM1854913", "GSM1854914", "GSM1854915", "GSM1854916", "GSM1854917", "GSM1854918", "GSM1854919", "GSM1854920", "GSM1854921", "GSM1854922", "GSM1854923", "GSM1854924", "GSM1854925", "GSM1854926", "GSM1854927", "GSM1854928", "GSM1854929", "GSM1854930", "GSM1854931", "GSM1854932", "GSM1854933", "GSM1854934", "GSM1854935", "GSM1854936", "GSM1854937", "GSM1854938", "GSM1854939", "GSM1854940", "GSM1854941", "GSM1854942", "GSM1854943", "GSM1854944", "GSM1854945", "GSM1854946", "GSM1854947", "GSM1854948", "GSM1854949", "GSM1854950", "GSM1854951", "GSM1854952", "GSM1854953", "GSM1854954", "GSM1854955", "GSM1854956", "GSM1854957", "GSM1854958", "GSM1854959", "GSM1854960", "GSM1854961", "GSM1854962", "GSM1854963", "GSM1854964", "GSM1854965", "GSM1854966", "GSM1854967", "GSM1854968", "GSM1854969", "GSM1854970", "GSM1854971", "GSM1854972", "GSM1854973", "GSM1854974", "GSM1854975", "GSM1854976", "GSM1854977", "GSM1854978", "GSM1854979", "GSM1854980", "GSM1854981", "GSM1854982", "GSM1854983", "GSM1854984", "GSM1854985", "GSM1854986", "GSM1854987", "GSM1854988", "GSM1854989", "GSM1854990", "GSM1854991", "GSM1854992", "GSM1854993", "GSM1854994", "GSM1854995", "GSM1854996", "GSM1854997", "GSM1854998", "GSM1854999", "GSM1855000", "GSM1855001", "GSM1855002", "GSM1855003", "GSM1855004", "GSM1855005", "GSM1855006", "GSM1855007", "GSM1855008", "GSM1855009", "GSM1855010", "GSM1855011", "GSM1855012", "GSM1855013", "GSM1855014", "GSM1855015", "GSM1855016", "GSM1855017", "GSM1855018", "GSM1855019", "GSM1855020", "GSM1855021", "GSM1855022", "GSM1855023", "GSM1855024", "GSM1855025", "GSM1855026", "GSM1855027", "GSM1855028", "GSM1855029", "GSM1855030", "GSM1855031", "GSM1855032", "GSM1855033", "GSM1855034", "GSM1855035", "GSM1855036", "GSM1855037", "GSM1855038", "GSM1855039", "GSM1855040", "GSM1855041", "GSM1855042", "GSM1855043", "GSM1855044", "GSM1855045", "GSM1855046", "GSM1855047", "GSM1855048", "GSM1855049", "GSM1855050", "GSM1855051", "GSM1855052", "GSM1855053", "GSM1855054", "GSM1855055", "GSM1855056", "GSM1855057", "GSM1855058", "GSM1855059", "GSM1855060", "GSM1855061", "GSM1855062", "GSM1855063", "GSM1855064", "GSM1855065", "GSM1855066", "GSM1855067", "GSM1855068", "GSM1855069", "GSM1855070", "GSM1855071", "GSM1855072", "GSM1855073", "GSM1855074", "GSM1855075", "GSM1855076", "GSM1855077", "GSM1855078", "GSM1855079", "GSM1855080", "GSM1855081", "GSM1855082", "GSM1855083", "GSM1855084", "GSM1855085", "GSM1855086", "GSM1855087", "GSM1855088", "GSM1855089", "GSM1855090", "GSM1855091", "GSM1855092", "GSM1855093", "GSM1855094", "GSM1855095", "GSM1855096", "GSM1855097", "GSM1855098", "GSM1855099", "GSM1855100", "GSM1855101", "GSM1855102", "GSM1855103", "GSM1855104", "GSM1855105", "GSM1855106", "GSM1855107", "GSM1855108", "GSM1855109", "GSM1855110", "GSM1855111", "GSM1855112", "GSM1855113", "GSM1855114", "GSM1855115", "GSM1855116", "GSM1855117", "GSM1855118", "GSM1855119", "GSM1855120", "GSM1855121", "GSM1855122", "GSM1855123", "GSM1855124", "GSM1855125", "GSM1855126", "GSM1855127", "GSM1855128", "GSM1855129", "GSM1855130", "GSM1855131", "GSM1855132", "GSM1855133", "GSM1855134", "GSM1855135", "GSM1855136", "GSM1855137", "GSM1855138", "GSM1855139", "GSM1855140", "GSM1855141", "GSM1855142", "GSM1855143", "GSM1855144", "GSM1855145", "GSM1855146", "GSM1855147", "GSM1855148", "GSM1855149", "GSM1855150", "GSM1855151", "GSM1855152", "GSM1855153", "GSM1855154", "GSM1855155", "GSM1855156", "GSM1855157", "GSM1855158", "GSM1855159", "GSM1855160", "GSM1855161", "GSM1855162", "GSM1855163", "GSM1855164", "GSM1855165", "GSM1855166", "GSM1855167", "GSM1855168", "GSM1855169", "GSM1855170", "GSM1855171", "GSM1855172", "GSM1855173", "GSM1855174", "GSM1855175", "GSM1855176", "GSM1855177", "GSM1855178", "GSM1855179", "GSM1855180", "GSM1855181", "GSM1855182", "GSM1855183", "GSM1855184", "GSM1855185", "GSM1855186", "GSM1855187", "GSM1855188", "GSM1855189", "GSM1855190", "GSM1855191", "GSM1855192", "GSM1855193", "GSM1855194", "GSM1855195", "GSM1855196", "GSM1855197", "GSM1855198", "GSM1855199", "GSM1855200", "GSM1855201", "GSM1855202", "GSM1855203", "GSM1855204", "GSM1855205", "GSM1855206", "GSM1855207", "GSM1855208", "GSM1855209", "GSM1855210", "GSM1855211", "GSM1855212", "GSM1855213", "GSM1855214", "GSM1855215", "GSM1855216", "GSM1855217", "GSM1855218", "GSM1855219", "GSM1855220", "GSM1855221", "GSM1855222", "GSM1855223", "GSM1855224", "GSM1855225", "GSM1855226", "GSM1855227", "GSM1855228", "GSM1855229", "GSM1855230", "GSM1855231", "GSM1855232", "GSM1855233", "GSM1855234", "GSM1855235", "GSM1855236", "GSM1855237", "GSM1855238"], "sample_count": 442, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "KRAS mutation-associated gene expression, p53 and STK11 mutations, proliferation and immune surveillance in lung adenocarcinoma", "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:GSE75037", "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=GSE75037", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75037", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1941120", "GSM1941121", "GSM1941122", "GSM1941123", "GSM1941124", "GSM1941125", "GSM1941126", "GSM1941127", "GSM1941128", "GSM1941129", "GSM1941130", "GSM1941131", "GSM1941132", "GSM1941133", "GSM1941134", "GSM1941135", "GSM1941136", "GSM1941137", "GSM1941138", "GSM1941139", "GSM1941140", "GSM1941141", "GSM1941142", "GSM1941143", "GSM1941144", "GSM1941145", "GSM1941146", "GSM1941147", "GSM1941148", "GSM1941149", "GSM1941150", "GSM1941151", "GSM1941152", "GSM1941153", "GSM1941154", "GSM1941155", "GSM1941156", "GSM1941157", "GSM1941158", "GSM1941159", "GSM1941160", "GSM1941161", "GSM1941162", "GSM1941163", "GSM1941164", "GSM1941165", "GSM1941166", "GSM1941167", "GSM1941168", "GSM1941169", "GSM1941170", "GSM1941171", "GSM1941172", "GSM1941173", "GSM1941174", "GSM1941175", "GSM1941176", "GSM1941177", "GSM1941178", "GSM1941179", "GSM1941180", "GSM1941181", "GSM1941182", "GSM1941183", "GSM1941184", "GSM1941185", "GSM1941186", "GSM1941187", "GSM1941188", "GSM1941189", "GSM1941190", "GSM1941191", "GSM1941192", "GSM1941193", "GSM1941194", "GSM1941195", "GSM1941196", "GSM1941197", "GSM1941198", "GSM1941199", "GSM1941200", "GSM1941201", "GSM1941202", "GSM1941203", "GSM1941204", "GSM1941205", "GSM1941206", "GSM1941207", "GSM1941208", "GSM1941209", "GSM1941210", "GSM1941211", "GSM1941212", "GSM1941213", "GSM1941214", "GSM1941215", "GSM1941216", "GSM1941217", "GSM1941218", "GSM1941219", "GSM1941220", "GSM1941221", "GSM1941222", "GSM1941223", "GSM1941224", "GSM1941225", "GSM1941226", "GSM1941227", "GSM1941228", "GSM1941229", "GSM1941230", "GSM1941231", "GSM1941232", "GSM1941233", "GSM1941234", "GSM1941235", "GSM1941236", "GSM1941237", "GSM1941238", "GSM1941239", "GSM1941240", "GSM1941241", "GSM1941242", "GSM1941243", "GSM1941244", "GSM1941245", "GSM1941246", "GSM1941247", "GSM1941248", "GSM1941249", "GSM1941250", "GSM1941251", "GSM1941252", "GSM1941253", "GSM1941254", "GSM1941255", "GSM1941256", "GSM1941257", "GSM1941258", "GSM1941259", "GSM1941260", "GSM1941261", "GSM1941262", "GSM1941263", "GSM1941264", "GSM1941265", "GSM1941266", "GSM1941267", "GSM1941268", "GSM1941269", "GSM1941270", "GSM1941271", "GSM1941272", "GSM1941273", "GSM1941274", "GSM1941275", "GSM1941276", "GSM1941277", "GSM1941278", "GSM1941279", "GSM1941280", "GSM1941281", "GSM1941282", "GSM1941283", "GSM1941284", "GSM1941285"], "sample_count": 166, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Expression profiling of 83 matched pairs of lung adenocarcinomas and non-malignant adjacent tissue", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE32863 not downloaded", "asset:data:geo:GSE32863 licence not read", "asset:data:geo:GSE43458 not downloaded", "asset:data:geo:GSE43458 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE75037 not downloaded", "asset:data:geo:GSE75037 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-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": "analysis of variance"}}, {"id": "method-3", "family": null, "specific": null, "label": "weighted gene correlation network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The co-expression network of DEGs shared by four datasets was constructed via the weighted gene correlation network analysis (WGCNA) package (17)."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE32863", "GSE43458", "GSE75037", "GSE72094"], "resolved_accessions": ["GSE32863", "GSE43458", "GSE75037", "GSE72094"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."], "basis": "The paper names GSE32863, GSE43458, GSE75037, GSE72094 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": [], "assets": ["source:pmid:36275753", "data:geo:GSE32863"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE32863"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:12:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11879, "completion_tokens": 2115, "cached_tokens": 128}}, "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:36275753", "type": "paper", "label": "pmid:36275753"}, {"id": "source:pmid:36275753", "type": "manuscript", "label": "PMID 36275753 full text"}, {"id": "data:geo:GSE32863", "type": "dataset", "label": "GEO GSE32863"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36275753", "type": "paper", "label": "pmid:36275753"}, {"id": "source:pmid:36275753", "type": "manuscript", "label": "PMID 36275753 full text"}, {"id": "data:geo:GSE32863", "type": "dataset", "label": "GEO GSE32863"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36275753", "type": "extraction", "used": ["source:pmid:36275753"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE32863", "type": "accession_resolution", "used": ["data:geo:GSE32863"], "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:36275753", "parent_hash": "sha256:2b470d0039e4dfba96bb23e3c2fa3727dd659ad8f3b45e1dc082fe354640aa5a", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE32863 licence not read", "asset:data:geo:GSE32863 not downloaded", "asset:data:geo:GSE43458 licence not read", "asset:data:geo:GSE43458 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:GSE75037 licence not read", "asset:data:geo:GSE75037 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Materials and methods Cell culture and transfection Human lung normal epithelial cell line (BEAS", "of polybrene for 12 h. NCI-H1975 cells were transfected with 10 nmol/L short interfering RNAs (siRNA", "was adopted to examine EXO1 expression after transfection. Statistical analysis Data were expressed as", "ghai, China) or a scrambled negative control siRNA (siRNA NC; Hanyin) via Lipofectamine 2000 (I"], "order_basis": "paper_text_order:1925", "id": "assay:1"}, {"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": [") and LUAD cell lines (NCI-H1975, NCI-H1395, A549, and PC9) were cultivated in Roswell Park Me", ") following the manufacturer’s instructions. A549 cells were treated with pLenti-CMV-GFP-Puro-"], "order_basis": "paper_text_order:2024", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["NA5, 5′-CCATTTCACCACCCACTTT-3′. Quantitative real-time PCR was adopted to examine EXO1 expression after"], "order_basis": "paper_text_order:3061", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}