Integrated Analyses of m6A Regulator-Based Signature on Its Clinical Application and Immunogenomic Landscape in Stomach Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36193316", "kind": "science-record", "revision": 4, "content_hash": "sha256:177d0ec7f611ea5a97bc695865c59c5a7acda5c0d8fd2ed4ffae547495ae028e", "created_at": "2026-11-01T18:15:30Z", "updated_at": "2026-11-01T22:07:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Analyses of m6A Regulator-Based Signature on Its Clinical Application and Immunogenomic Landscape in Stomach Adenocarcinoma.", "doi": "10.1155/2022/2053719", "pmid": "36193316", "authors": ["Lan Zhang", "Qing Zhang", "Zebo Huang", "Mingxia Zhu", "Tongshan Wang", "Wei Zhu", "Xiaping Wang", "Xin Zhou"], "journal": "BioMed research international", "year": 2022, "abstract": "Background: The whole tumor microenvironment (TME) infiltration features monitored by integrated roles of different RNA N6-methyladenosine (m6A) regulators remain elusive. Our study is aimed at exploring the association between m6A modification patterns, TME cell-infiltrating levels, and patients' prognosis in stomach adenocarcinoma (STAD) patients.\nMethods: Consensus clustering was performed based on the integrated analyses of 17 m6A regulators and 229 m6A-related hallmark genes in STAD (The Cancer Genome Atlas (TCGA) cohort, n = 443; Gene Expression Omnibus (GEO) GSE57303, n = 70, GSE62254 n = 300, and GSE84437 n = 433). A m6ASig scoring system was calculated by the principal component analysis (PCA), and its prognostic value was validated in an independent dataset GES15459.\nResults: Three m6A clusters were identified among 1246 STAD patients, which had significant overall survival (OS) differences and demonstrated different TME immune cell infiltration and biological behaviors. According to the m6ASig score, which was generated from the m6A-related hallmark genes, STAD patients were divided into the high-m6ASig group (n = 585) and low-m6ASig group (n = 586). Patients in the high-m6ASig group had a notably prolonged OS and higher immune cell infiltration. Moreover, patients with higher m6ASig score were associated with higher microsatellite instability (MSI); higher PD-L1, CTLA4, and ERBB2 expressions; and greater tumor mutation burden (TMB). Patients with higher m6ASig score demonstrated a better immune response and drug sensitivity.\nConclusion: Our m6ASig scoring system could characterize TME immune cell infiltration, thus predict patient's prognosis and immunotherapy and chemotherapy efficacy, offering a novel tool for the individualized therapeutic implications for STAD patients.", "claims": [{"id": "claim-method", "statement": "Additionally, an m6ASig model was constructed with the combination of PC1 and PC2 from PCA analysis of m6A cluster hallmark genes: m6ASig = PC1 + PC2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36193316", "locator": "sections[9] \"2.7. Construction and Evaluation of the m6ASig Model\" paragraph 2", "quote": "Additionally, an m6ASig model was constructed with the combination of PC1 and PC2 from PCA analysis of m6A cluster hallmark genes: m6ASig = PC1 + PC2."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available from the corresponding authors upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36193316", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The data that support the findings of this study are available from the corresponding authors upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The m6ASig score divided 1,171 STAD patients into high- and low-score groups, and the high-m6ASig group had significantly better overall survival.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "K-M curves showed that patients in the high-m6ASig score group had a notably better OS than the low-m6ASig score group (Figure 5(a), P < 0.001)."}, "evidence": [{"asset": "source:pmid:36193316", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "According to the m6ASig score, which was generated from the m6A-related hallmark genes, STAD patients were divided into the high-m6ASig group (n = 585) and low-m6ASig group (n = 586)."}, {"asset": "source:pmid:36193316", "locator": "sections[19] \"3.6. Construction and Validation of a Novel Signature m6ASig Based on DEGs\" paragraph 2", "quote": "K-M curves showed that patients in the high-m6ASig score group had a notably better OS than the low-m6ASig score group (Figure 5(a), P < 0.001)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The m6ASig score divided 1,171 STAD patients into high- and low-score groups, and the high-m6ASig group had significantly better overall survival.", "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:36193316"], "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:GSE57303"], "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:GSE57303"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36193316", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/2053719", "sha256": "sha256:4efb97cfc894b6dd38693926c384d479a7465a180c4e3d4d3970a5e1b3739e1a", "bytes": 37272, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/2053719", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9526603", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE57303", "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=GSE57303", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57303", "version": null, "note": "The data that support the findings of this study are available from the corresponding authors upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available from the corresponding authors upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1379261", "GSM1379262", "GSM1379263", "GSM1379264", "GSM1379265", "GSM1379266", "GSM1379267", "GSM1379268", "GSM1379269", "GSM1379270", "GSM1379271", "GSM1379272", "GSM1379273", "GSM1379274", "GSM1379275", "GSM1379276", "GSM1379277", "GSM1379278", "GSM1379279", "GSM1379280", "GSM1379281", "GSM1379282", "GSM1379283", "GSM1379284", "GSM1379285", "GSM1379286", "GSM1379287", "GSM1379288", "GSM1379289", "GSM1379290", "GSM1379291", "GSM1379292", "GSM1379293", "GSM1379294", "GSM1379295", "GSM1379296", "GSM1379297", "GSM1379298", "GSM1379299", "GSM1379300", "GSM1379301", "GSM1379302", "GSM1379303", "GSM1379304", "GSM1379305", "GSM1379306", "GSM1379307", "GSM1379308", "GSM1379309", "GSM1379310", "GSM1379311", "GSM1379312", "GSM1379313", "GSM1379314", "GSM1379315", "GSM1379316", "GSM1379317", "GSM1379318", "GSM1379319", "GSM1379320", "GSM1379321", "GSM1379322", "GSM1379323", "GSM1379324", "GSM1379325", "GSM1379326", "GSM1379327", "GSM1379328", "GSM1379329", "GSM1379330"], "sample_count": 70, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from 70 gastric cancer patients", "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:GSE62254", "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=GSE62254", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62254", "version": null, "note": "The data that support the findings of this study are available from the corresponding authors upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available from the corresponding authors upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1523727", "GSM1523728", "GSM1523729", "GSM1523744", "GSM1523745", "GSM1523746", "GSM1523747", "GSM1523748", "GSM1523765", "GSM1523768", "GSM1523769", "GSM1523770", "GSM1523771", "GSM1523772", "GSM1523773", "GSM1523774", "GSM1523775", "GSM1523776", "GSM1523777", "GSM1523778", "GSM1523779", "GSM1523780", "GSM1523781", "GSM1523782", "GSM1523783", "GSM1523784", "GSM1523785", "GSM1523786", "GSM1523787", "GSM1523788", "GSM1523789", "GSM1523790", "GSM1523791", "GSM1523792", "GSM1523793", "GSM1523794", "GSM1523795", "GSM1523796", "GSM1523797", "GSM1523798", "GSM1523799", "GSM1523800", "GSM1523801", "GSM1523802", "GSM1523803", "GSM1523804", "GSM1523805", "GSM1523806", "GSM1523807", "GSM1523808", "GSM1523809", "GSM1523810", "GSM1523811", "GSM1523812", "GSM1523813", "GSM1523814", "GSM1523815", "GSM1523816", "GSM1523817", "GSM1523818", "GSM1523819", "GSM1523820", "GSM1523821", "GSM1523822", "GSM1523823", "GSM1523824", "GSM1523825", "GSM1523826", "GSM1523827", "GSM1523828", "GSM1523829", "GSM1523830", "GSM1523831", "GSM1523832", "GSM1523833", "GSM1523834", "GSM1523835", "GSM1523836", "GSM1523837", "GSM1523838", "GSM1523839", "GSM1523840", "GSM1523841", "GSM1523842", "GSM1523843", "GSM1523844", "GSM1523845", "GSM1523846", "GSM1523847", "GSM1523848", "GSM1523849", "GSM1523850", "GSM1523851", "GSM1523852", "GSM1523853", "GSM1523854", "GSM1523855", "GSM1523856", "GSM1523857", "GSM1523858", "GSM1523859", "GSM1523860", "GSM1523861", "GSM1523862", "GSM1523863", "GSM1523864", "GSM1523865", "GSM1523866", "GSM1523867", "GSM1523868", "GSM1523869", "GSM1523870", "GSM1523871", "GSM1523872", "GSM1523873", "GSM1523874", "GSM1523875", "GSM1523876", "GSM1523877", "GSM1523878", "GSM1523879", "GSM1523880", "GSM1523881", "GSM1523882", "GSM1523883", "GSM1523884", "GSM1523885", "GSM1523886", "GSM1523887", "GSM1523888", "GSM1523889", "GSM1523890", "GSM1523891", "GSM1523892", "GSM1523893", "GSM1523894", "GSM1523895", "GSM1523896", "GSM1523897", "GSM1523898", "GSM1523899", "GSM1523901", "GSM1523903", "GSM1523904", "GSM1523905", "GSM1523906", "GSM1523908", "GSM1523909", "GSM1523910", "GSM1523911", "GSM1523918", "GSM1523919", "GSM1523920", "GSM1523921", "GSM1523922", "GSM1523923", "GSM1523924", "GSM1523925", "GSM1523926", "GSM1523927", "GSM1523928", "GSM1523929", "GSM1523930", "GSM1523931", "GSM1523932", "GSM1523933", "GSM1523934", "GSM1523935", "GSM1523936", "GSM1523937", "GSM1523938", "GSM1523939", "GSM1523940", "GSM1523941", "GSM1523942", "GSM1523943", "GSM1523944", "GSM1523945", "GSM1523946", "GSM1523947", "GSM1523948", "GSM1523949", "GSM1523950", "GSM1523951", "GSM1523952", "GSM1523953", "GSM1523954", "GSM1523955", "GSM1523956", "GSM1523957", "GSM1523958", "GSM1523959", "GSM1523960", "GSM1523961", "GSM1523962", "GSM1523963", "GSM1523964", "GSM1523965", "GSM1523966", "GSM1523967", "GSM1523968", "GSM1523969", "GSM1523970", "GSM1523971", "GSM1523972", "GSM1523973", "GSM1523974", "GSM1523975", "GSM1523976", "GSM1523977", "GSM1523978", "GSM1523979", "GSM1523980", "GSM1523981", "GSM1523982", "GSM1523983", "GSM1523984", "GSM1523985", "GSM1523986", "GSM1523987", "GSM1523988", "GSM1523989", "GSM1523990", "GSM1523991", "GSM1523992", "GSM1523993", "GSM1523994", "GSM1523995", "GSM1523996", "GSM1523997", "GSM1523998", "GSM1523999", "GSM1524000", "GSM1524001", "GSM1524002", "GSM1524003", "GSM1524004", "GSM1524005", "GSM1524006", "GSM1524007", "GSM1524008", "GSM1524009", "GSM1524010", "GSM1524011", "GSM1524012", "GSM1524013", "GSM1524014", "GSM1524015", "GSM1524016", "GSM1524017", "GSM1524018", "GSM1524019", "GSM1524020", "GSM1524021", "GSM1524022", "GSM1524023", "GSM1524024", "GSM1524025", "GSM1524026", "GSM1524027", "GSM1524028", "GSM1524029", "GSM1524030", "GSM1524031", "GSM1524032", "GSM1524033", "GSM1524034", "GSM1524035", "GSM1524036", "GSM1524037", "GSM1524038", "GSM1524039", "GSM1524040", "GSM1524041", "GSM1524042", "GSM1524043", "GSM1524044", "GSM1524045", "GSM1524046", "GSM1524047", "GSM1524048", "GSM1524049", "GSM1524050", "GSM1524051", "GSM1524052", "GSM1524053", "GSM1524054", "GSM1524055", "GSM1524056", "GSM1524057", "GSM1524058", "GSM1524059", "GSM1524060", "GSM1524061", "GSM1524062", "GSM1524068", "GSM1524069", "GSM1524070", "GSM1524071", "GSM1524072"], "sample_count": 300, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study [gastric tumors]", "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:GSE84437", "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=GSE84437", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84437", "version": null, "note": "The data that support the findings of this study are available from the corresponding authors upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available from the corresponding authors upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2235556", "GSM2235557", "GSM2235558", "GSM2235559", "GSM2235560", "GSM2235561", "GSM2235562", "GSM2235563", "GSM2235564", "GSM2235565", "GSM2235566", "GSM2235567", "GSM2235568", "GSM2235569", "GSM2235570", "GSM2235571", "GSM2235572", "GSM2235573", "GSM2235574", "GSM2235575", "GSM2235576", "GSM2235577", "GSM2235578", "GSM2235579", "GSM2235580", "GSM2235582", "GSM2235584", "GSM2235585", "GSM2235586", "GSM2235587", "GSM2235588", "GSM2235589", "GSM2235593", "GSM2235595", "GSM2235596", "GSM2235597", "GSM2235598", "GSM2235599", "GSM2235600", "GSM2235601", "GSM2235602", "GSM2235603", "GSM2235604", "GSM2235605", "GSM2235606", "GSM2235607", "GSM2235608", "GSM2235609", "GSM2235610", "GSM2235611", "GSM2235612", "GSM2235613", "GSM2235614", "GSM2235615", "GSM2235616", "GSM2235617", "GSM2235618", "GSM2235619", "GSM2235620", "GSM2235621", "GSM2235622", "GSM2235623", "GSM2235624", "GSM2235625", "GSM2235626", "GSM2235627", "GSM2235628", "GSM2235629", "GSM2235630", "GSM2235631", "GSM2235632", "GSM2235633", "GSM2235634", "GSM2235635", "GSM2235636", "GSM2235637", "GSM2235695", "GSM2235696", "GSM2235697", "GSM2235698", "GSM2235699", "GSM2235700", "GSM2235701", "GSM2235702", "GSM2235703", "GSM2235704", "GSM2235705", "GSM2235706", "GSM2235707", "GSM2235708", "GSM2235709", "GSM2235710", "GSM2235711", "GSM2235712", "GSM2235713", "GSM2235714", "GSM2235715", "GSM2235716", "GSM2235717", "GSM2235718", "GSM2235719", "GSM2235720", "GSM2235721", "GSM2235722", "GSM2235723", "GSM2235724", "GSM2235725", "GSM2235726", "GSM2235727", "GSM2235728", "GSM2235729", "GSM2235730", "GSM2235731", "GSM2235732", "GSM2235733", "GSM2235734", "GSM2235735", "GSM2235736", "GSM2235737", "GSM2235738", "GSM2235739", "GSM2235740", "GSM2235741", "GSM2235742", "GSM2235743", "GSM2235744", "GSM2235745", "GSM2235746", "GSM2235747", "GSM2235748", "GSM2235749", "GSM2235750", "GSM2235751", "GSM2235752", "GSM2235753", "GSM2235754", "GSM2235755", "GSM2235756", "GSM2235757", "GSM2235758", "GSM2235759", "GSM2235760", "GSM2235761", "GSM2235762", "GSM2235763", "GSM2235764", "GSM2235765", "GSM2235766", "GSM2235767", "GSM2235768", "GSM2235769", "GSM2235770", "GSM2235771", "GSM2235772", "GSM2235773", "GSM2235774", "GSM2235775", "GSM2235776", "GSM2235777", "GSM2235778", "GSM2235779", "GSM2235780", "GSM2235781", "GSM2235782", "GSM2235783", "GSM2235784", "GSM2235785", "GSM2235786", "GSM2235787", "GSM2235788", "GSM2235789", "GSM2235790", "GSM2235791", "GSM2235792", "GSM2235793", "GSM2235794", "GSM2235795", "GSM2235796", "GSM2235797", "GSM2235798", "GSM2235799", "GSM2235800", "GSM2235801", "GSM2235802", "GSM2235803", "GSM2235804", "GSM2235805", "GSM2235806", "GSM2235807", "GSM2235808", "GSM2235809", "GSM2235810", "GSM2235811", "GSM2235812", "GSM2235813", "GSM2235814", "GSM2235815", "GSM2235816", "GSM2235817", "GSM2235818", "GSM2235819", "GSM2235820", "GSM2235821", "GSM2235822", "GSM2235823", "GSM2235824", "GSM2235825", "GSM2235826", "GSM2235827", "GSM2235828", "GSM2235829", "GSM2235830", "GSM2235831", "GSM2235837", "GSM2235838", "GSM2235839", "GSM2235840", "GSM2235841", "GSM2235842", "GSM2235843", "GSM2235844", "GSM2235845", "GSM2235846", "GSM2235847", "GSM2235848", "GSM2235849", "GSM2235850", "GSM2235851", "GSM2235852", "GSM2235853", "GSM2235854", "GSM2235855", "GSM2235862", "GSM2235863", "GSM2235864", "GSM2235865", "GSM2235866", "GSM2235867", "GSM2235878", "GSM2235879", "GSM2235880", "GSM2235881", "GSM2235882", "GSM2235883", "GSM2235884", "GSM2235885", "GSM2235886", "GSM2235887", "GSM2235888", "GSM2235889", "GSM2235899", "GSM2235900", "GSM2235901", "GSM2235902", "GSM2235903", "GSM2235904", "GSM2235905", "GSM2235906", "GSM2235907", "GSM2235908", "GSM2235909", "GSM2235910", "GSM2235921", "GSM2235922", "GSM2235923", "GSM2235924", "GSM2235925", "GSM2235926", "GSM2235927", "GSM2235928", "GSM2235929", "GSM2235930", "GSM2235931", "GSM2235932", "GSM2235933", "GSM2235934", "GSM2235935", "GSM2235936", "GSM2235937", "GSM2235938", "GSM2235939", "GSM2235940", "GSM2235941", "GSM2235942", "GSM2235943", "GSM2235944", "GSM2235945", "GSM2235946", "GSM2235947", "GSM2235948", "GSM2235949", "GSM2235950", "GSM2235951", "GSM2235952", "GSM2235953", "GSM2235954", "GSM2235955", "GSM2235956", "GSM2235957", "GSM2235958", "GSM2235959", "GSM2235960", "GSM2235961", "GSM2235962", "GSM2235963", "GSM2235964", "GSM2235965", "GSM2235966", "GSM2235967", "GSM2235968", "GSM2235969", "GSM2235970", "GSM2235971", "GSM2235972", "GSM2235973", "GSM2235974", "GSM2235975", "GSM2235976", "GSM2235977", "GSM2235978", "GSM2235979", "GSM2235980", "GSM2235981", "GSM2235982", "GSM2235983", "GSM2235984", "GSM2235985", "GSM2235986", "GSM2235987", "GSM2235988", "GSM2235991", "GSM2235992", "GSM2235993", "GSM2235994", "GSM2235995", "GSM2235996", "GSM2235997", "GSM2235998", "GSM2235999", "GSM2236000", "GSM2236001", "GSM2236002", "GSM2236003", "GSM2236004", "GSM2236005", "GSM2236006", "GSM2236007", "GSM2236008", "GSM2236009", "GSM2236010", "GSM2236011", "GSM2236012", "GSM2236013", "GSM2236014", "GSM2236015", "GSM2236016", "GSM2236017", "GSM2236018", "GSM2236019", "GSM2236020", "GSM2236021", "GSM2236022", "GSM2236023", "GSM2236024", "GSM2236025", "GSM2236026", "GSM2236027", "GSM2236028", "GSM2236029", "GSM2236030", "GSM2236031", "GSM2236032", "GSM2236033", "GSM2236034", "GSM2236036", "GSM2236037", "GSM2236038", "GSM2236039", "GSM2236040", "GSM2236041", "GSM2236042", "GSM2236043", "GSM2236044", "GSM2236045", "GSM2236046", "GSM2236047", "GSM2236048", "GSM2236049", "GSM2236050", "GSM2236051", "GSM2236052", "GSM2236053", "GSM2236054", "GSM2236055", "GSM2236056", "GSM2236057", "GSM2236058", "GSM2236059", "GSM2236060", "GSM2236061", "GSM2236062", "GSM2236063", "GSM2236064", "GSM2236065", "GSM2236066", "GSM2236067", "GSM2236068", "GSM2236069", "GSM2236070", "GSM2236071", "GSM2236072", "GSM2236073", "GSM2236074", "GSM2236075", "GSM2236076", "GSM2236077", "GSM2236078", "GSM2236079", "GSM2236080", "GSM2236082", "GSM2236083", "GSM2236084", "GSM2236085", "GSM2236086", "GSM2236087", "GSM2236088", "GSM2236089", "GSM2236090", "GSM2236091", "GSM2236092", "GSM2236093", "GSM2236094", "GSM2236095", "GSM4419484", "GSM4419485", "GSM4419486", "GSM4419487", "GSM4419488", "GSM4419489", "GSM4419490", "GSM4419491", "GSM4419492", "GSM4419493", "GSM4419494", "GSM4419495", "GSM4419496", "GSM4419497", "GSM4419498", "GSM4419499", "GSM4419500", "GSM4419501", "GSM4419502", "GSM4419503", "GSM4419504", "GSM4419505", "GSM4419506", "GSM4419507", "GSM4419508", "GSM4419509", "GSM4419510", "GSM4419511", "GSM4419512", "GSM4419513", "GSM4419514", "GSM4419515", "GSM4419516", "GSM4419517", "GSM4419518", "GSM4419519", "GSM4419520", "GSM4419521", "GSM4419522", "GSM4419523", "GSM4419524", "GSM4419525", "GSM4419526", "GSM4419527", "GSM4419528", "GSM4419529", "GSM4419530", "GSM4419531", "GSM4419532", "GSM4419533"], "sample_count": 483, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer.", "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:GSE57303 not downloaded", "asset:data:geo:GSE57303 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE84437 not downloaded", "asset:data:geo:GSE84437 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Additionally, an m6ASig model was constructed with the combination of PC1 and PC2 from PCA analysis of m6A cluster hallmark genes: m6ASig = PC1 + PC2."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "cox regression"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-5", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-6", "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"}}, {"id": "method-7", "family": "contingency_analysis", "specific": "fisher_exact", "label": "Categorical (contingency table) analysis", "dsl_operations": ["contingency_table", "chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Fisher's exact"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "chi_square_test", "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_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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE57303", "GSE62254", "GSE84437"], "resolved_accessions": ["GSE57303", "GSE62254", "GSE84437"], "statements": ["The data that support the findings of this study are available from the corresponding authors upon reasonable request."], "basis": "The paper names GSE57303, GSE62254, GSE84437 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": ["pca_fit"], "assets": ["source:pmid:36193316", "data:geo:GSE57303"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE57303"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:08:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11587, "completion_tokens": 2409, "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:36193316", "type": "paper", "label": "pmid:36193316"}, {"id": "source:pmid:36193316", "type": "manuscript", "label": "PMID 36193316 full text"}, {"id": "data:geo:GSE57303", "type": "dataset", "label": "GEO GSE57303"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36193316", "type": "paper", "label": "pmid:36193316"}, {"id": "source:pmid:36193316", "type": "manuscript", "label": "PMID 36193316 full text"}, {"id": "data:geo:GSE57303", "type": "dataset", "label": "GEO GSE57303"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36193316", "type": "extraction", "used": ["source:pmid:36193316"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE57303", "type": "accession_resolution", "used": ["data:geo:GSE57303"], "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:36193316", "parent_hash": "sha256:febbbde4f66f36d86cfb6cf2ee6162870cde967b10ff39a89e304da4879dfd89", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE57303 licence not read", "asset:data:geo:GSE57303 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Additionally, an m6ASig model was constructed with the combination of PC1 and PC2 from PCA analysis of m6A cluster hallmark genes: m6ASig = PC1 + PC2."], "order_basis": "analysis_only", "id": "assay:1"}]}