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pmid:37469408
Predicting the immune microenvironment and prognosis with a anoikis - related signature in breast cancer.
Xiuqing Lu · Qi Yuan · Chao Zhang · Sifen Wang · Weidong Wei
Frontiers in oncology · 2023 doi:10.3389/fonc.2023.1149193
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Experiment
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Data
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Analysis
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Execution
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Complete file
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However, there remains an insufficient understanding of the underlying impact of anoikis on the prognosis of BC patients.\nMethods: The researchers utilized the TCGA-BRCA dataset to screen and analyze the differentially expressed genes of anoikis-related genes (ARGs) in BC and normal breast tissue. Prognostic gene signatures were established through univariate, LASSO, and multivariate Cox regression analyses. These signatures were evaluated using Kaplan-Meier curve and receiver operating characteristic (ROC) analyses, resulting in the development of an anoikis-related index (ACI). The training dataset was TCGA-BRCA, while METABRIC and GSE96058 were used for external validation. Additionally, nomograms were developed by combining risk scores and clinical parameters, enabling gene set enrichment analysis (GSEA) and tumor immunoassay. Furthermore, an exploration of small molecule compounds was conducted to identify potential therapeutic benefits.\nResults: A six-gene anoikis-related signature was constructed, which divided BC patients into high- and low-ACI groups based on median ACI scores. The ACI accurately predicted prognosis and acted as an independent prognostic factor for BC patients. Patients in the high-ACI group exhibited poorer overall survival (OS) across all cohorts and showed more severe clinical manifestations compared to the low-ACI group. The study also explored the potential impacts of anoikis on immune cells infiltrating tumors, immune checkpoints, growth factors, and cytokine levels. Additionally, the potential implications of anoikis in BC immunotherapy were discussed, along with highlighting small molecule compounds that could offer therapeutic benefits.\nConclusions: Anoikis was found to hold significant prognostic value in breast cancer, providing a novel approach for managing patients with different prognoses and implementing more precise immunotherapy strategies.", "claims": [{"id": "claim-method", "statement": "Prognostic gene signatures were established through univariate, LASSO, and multivariate Cox regression analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37469408", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Prognostic gene signatures were established through univariate, LASSO, and multivariate Cox regression analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available in the public domain: The TCGA-BRCA dataset can be accessed through the Genomic Data Commons (GDC) data portal at https://portal.gdc.cancer.gov/. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE96058"], "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:GSE96058"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37469408", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2023.1149193", "sha256": "sha256:9575f3906cc1971c621b0abf17d4878f353417f4cacbf3fd24bd8da73a3a2fb1", "bytes": 49407, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2023.1149193", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10353543", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE96058", "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=GSE96058", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE96058", "version": null, "note": "The data that support the findings of this study are available in the public domain: The TCGA-BRCA dataset can be accessed through the Genomic Data Commons (GDC) data portal at https://portal.gdc.cancer.gov/. 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"GSM2528701", "GSM2528702", "GSM2528703", "GSM2528704", "GSM2528705", "GSM2528706", "GSM2528707", "GSM2528708", "GSM2528709", "GSM2528710", "GSM2528711", "GSM2528712", "GSM2528713", "GSM2528714", "GSM2528715", "GSM2528716", "GSM2528717", "GSM2528718", "GSM2528719", "GSM2528720", "GSM2528721", "GSM2528722", "GSM2528723", "GSM2528724", "GSM2528725", "GSM2528726", "GSM2528727", "GSM2528728", "GSM2528729", "GSM2528730", "GSM2528731", "GSM2528732", "GSM2528733", "GSM2528734", "GSM2528735", "GSM2528736", "GSM2528737", "GSM2528738", "GSM2528739", "GSM2528740", "GSM2528741", "GSM2528742", "GSM2528743", "GSM2528744", "GSM2528745", "GSM2528746", "GSM2528747", "GSM2528748", "GSM2528749", "GSM2528750", "GSM2528751", "GSM2528752", "GSM2528753", "GSM2528754", "GSM2528755", "GSM2528756", "GSM2528757", "GSM2528758", "GSM2528759", "GSM2528760", "GSM2528761", "GSM2528762", "GSM2528763", "GSM2528764", "GSM2528765", "GSM2528766", "GSM2528767", "GSM2528768", "GSM2528769", "GSM2528770", "GSM2528771", "GSM2528772", "GSM2528773", "GSM2528774", "GSM2528775", "GSM2528776", "GSM2528777", "GSM2528778", "GSM2528779", "GSM2528780", "GSM2528781", "GSM2528782", "GSM2528783", "GSM2528784", "GSM2528785", "GSM2528786", "GSM2528787", "GSM2528788", "GSM2528789", "GSM2528790", "GSM2528791", "GSM2528792", "GSM2528793", "GSM2528794", "GSM2528795", "GSM2528796", "GSM2528797", "GSM2528798", "GSM2528799", "GSM2528800", "GSM2528801", "GSM2528802", "GSM2528803", "GSM2528804", "GSM2528805", "GSM2528806", "GSM2528807", "GSM2528808", "GSM2528809", "GSM2528810", "GSM2528811", "GSM2528812", "GSM2528813", "GSM2528814", "GSM2528815", "GSM2528816", "GSM2528817", "GSM2528818", "GSM2528819", "GSM2528820", "GSM2528821", "GSM2528822", "GSM2528823", "GSM2528824", "GSM2528825", "GSM2528826", "GSM2528827", "GSM2528828", "GSM2528829", "GSM2528830", "GSM2528831", "GSM2528832", "GSM2528833", "GSM2528834", "GSM2528835", "GSM2528836", "GSM2528837", "GSM2528838", "GSM2528839", "GSM2528840", "GSM2528841", "GSM2528842", "GSM2528843", "GSM2528844", "GSM2528845", "GSM2528846", "GSM2528847", "GSM2528848", "GSM2528849", "GSM2528850", "GSM2528851", "GSM2528852", "GSM2528853", "GSM2528854", "GSM2528855", "GSM2528856", "GSM2528857", "GSM2528858", "GSM2528859", "GSM2528860", "GSM2528861", "GSM2528862", "GSM2528863", "GSM2528864", "GSM2528865", "GSM2528866", "GSM2528867", "GSM2528868", "GSM2528869", "GSM2528870", "GSM2528871", "GSM2528872", "GSM2528873", "GSM2528874", "GSM2528875", "GSM2528876", "GSM2528877", "GSM2528878", "GSM2528879", "GSM2528880", "GSM2528881", "GSM2528882", "GSM2528883", "GSM2528884", "GSM2528885", "GSM2528886", "GSM2528887", "GSM2528888", "GSM2528889", "GSM2528890", "GSM2528891", "GSM2528892", "GSM2528893", "GSM2528894", "GSM2528895", "GSM2528896", "GSM2528897", "GSM2528898", "GSM2528899", "GSM2528900", "GSM2528901", "GSM2528902", "GSM2528903", "GSM2528904", "GSM2528905", "GSM2528906", "GSM2528907", "GSM2528908", "GSM2528909", "GSM2528910", "GSM2528911", "GSM2528912", "GSM2528913", "GSM2528914", "GSM2528915", "GSM2528916", "GSM2528917", "GSM2528918", "GSM2528919", "GSM2528920", "GSM2528921", "GSM2528922", "GSM2528923", "GSM2528924", "GSM2528925", "GSM2528926", "GSM2528927", "GSM2528928", "GSM2528929", "GSM2528930", "GSM2528931", "GSM2528932", "GSM2528933", "GSM2528934", "GSM2528935", "GSM2528936", "GSM2528937", "GSM2528938", "GSM2528939", "GSM2528940", "GSM2528941", "GSM2528942", "GSM2528943", "GSM2528944", "GSM2528945", "GSM2528946", "GSM2528947", "GSM2528948", "GSM2528949", "GSM2528950", "GSM2528951", "GSM2528952", "GSM2528953", "GSM2528954", "GSM2528955", "GSM2528956", "GSM2528957", "GSM2528958", "GSM2528959", "GSM2528960", "GSM2528961", "GSM2528962", "GSM2528963", "GSM2528964", "GSM2528965", "GSM2528966", "GSM2528967", "GSM2528968", "GSM2528969", "GSM2528970", "GSM2528971", "GSM2528972", "GSM2528973", "GSM2528974", "GSM2528975", "GSM2528976", "GSM2528977", "GSM2528978", "GSM2528979", "GSM2528980", "GSM2528981", "GSM2528982", "GSM2528983", "GSM2528984", "GSM2528985", "GSM2528986", "GSM2528987", "GSM2528988", "GSM2528989", "GSM2528990", "GSM2528991", "GSM2528992", "GSM2528993", "GSM2528994", "GSM2528995", "GSM2528996", "GSM2528997", "GSM2528998", "GSM2528999", "GSM2529000", "GSM2529001", "GSM2529002", "GSM2529003", "GSM2529004", "GSM2529005", "GSM2529006", "GSM2529007", "GSM2529008", "GSM2529009", "GSM2529010", "GSM2529011", "GSM2529012", "GSM2529013", "GSM2529014", "GSM2529015", "GSM2529016", "GSM2529017", "GSM2529018", "GSM2529019", "GSM2529020", "GSM2529021", "GSM2529022", "GSM2529023", "GSM2529024", "GSM2529025", "GSM2529026", "GSM2529027", "GSM2529028", "GSM2529029", "GSM2529030", "GSM2529031", "GSM2529032", "GSM2529033", "GSM2529034", "GSM2529035", "GSM2529036", "GSM2529037", "GSM2529038", "GSM2529039", "GSM2529040", "GSM2529041", "GSM2529042", "GSM2529043", "GSM2529044", "GSM2529045", "GSM2529046", "GSM2529047", "GSM2529048", "GSM2529049", "GSM2529050", "GSM2529051", "GSM2529052", "GSM2529053", "GSM2529054", "GSM2529055", "GSM2529056", "GSM2529057", "GSM2529058", "GSM2529059", "GSM2529060", "GSM2529061", "GSM2529062", "GSM2529063", "GSM2529064", "GSM2529065", "GSM2529066", "GSM2529067", "GSM2529068", "GSM2529069", "GSM2529070", "GSM2529071", "GSM2529072", "GSM2529073", "GSM2529074", "GSM2529075", "GSM2529076", "GSM2529077", "GSM2529078", "GSM2529079", "GSM2529080", "GSM2529081", "GSM2529082", "GSM2529083", "GSM2529084", "GSM2529085", "GSM2529086", "GSM2529087", "GSM2529088", "GSM2529089", "GSM2529090", "GSM2529091", "GSM2529092", "GSM2529093", "GSM2529094", "GSM2529095", "GSM2529096", "GSM2529097", "GSM2529098", "GSM2529099", "GSM2529100", "GSM2529101", "GSM2529102", "GSM2529103", "GSM2529104", "GSM2529105", "GSM2529106", "GSM2529107", "GSM2529108", "GSM2529109", "GSM2529110", "GSM2529111", "GSM2529112", "GSM2529113", "GSM2529114", "GSM2529115", "GSM2529116", "GSM2529117", "GSM2529118", "GSM2529119", "GSM2529120", "GSM2529121", "GSM2529122", "GSM2529123", "GSM2529124", "GSM2529125", "GSM2529126", "GSM2529127", "GSM2529128", "GSM2529129", "GSM2529130", "GSM2529131", "GSM2529132", "GSM2529133", "GSM2529134", "GSM2529135", "GSM2529136", "GSM2529137", "GSM2529138", "GSM2529139", "GSM2529140", "GSM2529141", "GSM2529142", "GSM2529143", "GSM2529144", "GSM2529145", "GSM2529146", "GSM2529147", "GSM2529148", "GSM2529149", "GSM2529150", "GSM2529151", "GSM2529152", "GSM2529153", "GSM2529154", "GSM2529155", "GSM2529156", "GSM2529157", "GSM2529158", "GSM2529159", "GSM2529160", "GSM2529161", "GSM2529162", "GSM2529163", "GSM2529164", "GSM2529165", "GSM2529166", "GSM2529167", "GSM2529168", "GSM2529169", "GSM2529170", "GSM2529171", "GSM2529172", "GSM2529173", "GSM2529174", "GSM2529175", "GSM2529176", "GSM2529177", "GSM2529178", "GSM2529179", "GSM2529180", "GSM2529181", "GSM2529182", "GSM2529183", "GSM2529184", "GSM2529185", "GSM2529186", "GSM2529187", "GSM2529188", "GSM2529189", "GSM2529190", "GSM2529191", "GSM2529192", "GSM2529193", "GSM2529194", "GSM2529195", "GSM2529196", "GSM2529197", "GSM2529198", "GSM2529199", "GSM2529200", "GSM2529201", "GSM2529202", "GSM2529203", "GSM2529204", "GSM2529205", "GSM2529206", "GSM2529207", "GSM2529208", "GSM2529209", "GSM2529210", "GSM2529211", "GSM2529212", "GSM2529213", "GSM2529214", "GSM2529215", "GSM2529216", "GSM2529217", "GSM2529218", "GSM2529219", "GSM2529220", "GSM2529221", "GSM2529222", "GSM2529223", "GSM2529224", "GSM2529225", "GSM2529226", "GSM2529227", "GSM2529228", "GSM2529229", "GSM2529230", "GSM2529231", "GSM2529232", "GSM2529233", "GSM2529234", "GSM2529235", "GSM2529236", "GSM2529237", "GSM2529238", "GSM2529239", "GSM2529240", "GSM2529241", "GSM2529242", "GSM2529243", "GSM2529244", "GSM2529245", "GSM2529246", "GSM2529247", "GSM2529248", "GSM2529249", "GSM2529250", "GSM2529251", "GSM2529252", "GSM2529253", "GSM2529254", "GSM2529255", "GSM2529256", "GSM2529257", "GSM2529258", "GSM2529259", "GSM2529260", "GSM2529261", "GSM2529262", "GSM2529263", "GSM2529264", "GSM2529265", "GSM2529266", "GSM2529267", "GSM2529268", "GSM2529269", "GSM2529270", "GSM2529271", "GSM2529272", "GSM2529273", "GSM2529274", "GSM2529275", "GSM2529276", "GSM2529277", "GSM2529278", "GSM2529279", "GSM2529280", "GSM2529281", "GSM2529282", "GSM2529283", "GSM2529284", "GSM2529285", "GSM2529286", "GSM2529287", "GSM2529288", "GSM2529289", "GSM2529290", "GSM2529291", "GSM2529292", "GSM2529293", "GSM2529294", "GSM2529295", "GSM2529296", "GSM2529297", "GSM2529298", "GSM2529299", "GSM2529300", "GSM2529301", "GSM2529302", "GSM2529303", "GSM2529304", "GSM2529305", "GSM2529306", "GSM2529307", "GSM2529308", "GSM2529309", "GSM2529310", "GSM2529311", "GSM2529312", "GSM2529313", "GSM2529314", "GSM2529315", "GSM2529316", "GSM2529317", "GSM2529318", "GSM2529319", "GSM2529320", "GSM2529321", "GSM2529322", "GSM2529323", "GSM2529324", "GSM2529325", "GSM2529326", "GSM2529327", "GSM2529328", "GSM2529329", "GSM2529330", "GSM2529331", "GSM2529332", "GSM2529333", "GSM2529334", "GSM2529335", "GSM2529336", "GSM2529337", "GSM2529338", "GSM2529339", "GSM2529340", "GSM2529341", "GSM2529342", "GSM2529343", "GSM2529344", "GSM2529345", "GSM2529346", "GSM2529347", "GSM2529348", "GSM2529349", "GSM2529350", "GSM2529351", "GSM2529352", "GSM2529353", "GSM2529354", "GSM2529355", "GSM2529356", "GSM2529357", "GSM2529358", "GSM2529359", "GSM2529360", "GSM2529361", "GSM2529362", "GSM2529363", "GSM2529364", "GSM2529365", "GSM2529366", "GSM2529367", "GSM2529368", "GSM2529369", "GSM2529370", "GSM2529371", "GSM2529372", "GSM2529373", "GSM2529374", "GSM2529375", "GSM2529376", "GSM2529377", "GSM2529378", "GSM2529379", "GSM2529380", "GSM2529381", "GSM2529382", "GSM2529383", "GSM2529384", "GSM2529385", "GSM2529386", "GSM2529387", "GSM2529388", "GSM2529389", "GSM2529390", "GSM2529391", "GSM2529392", "GSM2529393", "GSM2529394", "GSM2529395", "GSM2529396", "GSM2529397", "GSM2529398", "GSM2529399", "GSM2529400", "GSM2529401", "GSM2529402", "GSM2529403", "GSM2529404", "GSM2529405", "GSM2529406", "GSM2529407", "GSM2529408", "GSM2529409", "GSM2529410", "GSM2529411", "GSM2529412", "GSM2529413", "GSM2529414", "GSM2529415", "GSM2529416", "GSM2529417", "GSM2529418", "GSM2529419", "GSM2529420", "GSM2529421", "GSM2529422", "GSM2529423", "GSM2529424", "GSM2529425", "GSM2529426", "GSM2529427", "GSM2529428", "GSM2529429", "GSM2529430", "GSM2529431", "GSM2529432", "GSM2529433", "GSM2529434", "GSM2529435", "GSM2529436", "GSM2529437", "GSM2529438", "GSM2529439", "GSM2529440", "GSM2529441", "GSM2529442", "GSM2529443", "GSM2529444", "GSM2529445", "GSM2529446", "GSM2529447", "GSM2529448", "GSM2529449", "GSM2529450", "GSM2529451", "GSM2529452", "GSM2529453", "GSM2529454", "GSM2529455", "GSM2529456", "GSM2529457", "GSM2529458", "GSM2529459", "GSM2529460", "GSM2529461", "GSM2529462", "GSM2529463", "GSM2529464", "GSM2529465", "GSM2529466", "GSM2529467", "GSM2529468", "GSM2529469", "GSM2529470", "GSM2529471", "GSM2529472", "GSM2529473", "GSM2529474", "GSM2529475", "GSM2529476", "GSM2529477", "GSM2529478", "GSM2529479", "GSM2529480", "GSM2529481", "GSM2529482", "GSM2529483", "GSM2529484", "GSM2529485", "GSM2529486", "GSM2529487", "GSM2529488", "GSM2529489", "GSM2529490", "GSM2529491", "GSM2529492", "GSM2529493", "GSM2529494", "GSM2529495", "GSM2529496", "GSM2529497", "GSM2529498", "GSM2529499", "GSM2529500", "GSM2529501", "GSM2529502", "GSM2529503", "GSM2529504", "GSM2529505", "GSM2529506", "GSM2529507", "GSM2529508", "GSM2529509", "GSM2529510", "GSM2529511", "GSM2529512", "GSM2529513", "GSM2529514", "GSM2529515", "GSM2529516", "GSM2529517", "GSM2529518", "GSM2529519", "GSM2529520", "GSM2529521", "GSM2529522", "GSM2529523", "GSM2529524", "GSM2529525", "GSM2529526", "GSM2529527", "GSM2529528", "GSM2529529", "GSM2529530", "GSM2529531", "GSM2529532", "GSM2529533", "GSM2529534", "GSM2529535", "GSM2529536", "GSM2529537", "GSM2529538", "GSM2529539", "GSM2529540", "GSM2529541", "GSM2529542", "GSM2529543", "GSM2529544", "GSM2529545", "GSM2529546", "GSM2529547", "GSM2529548", "GSM2529549", "GSM2529550", "GSM2529551", "GSM2529552", "GSM2529553", "GSM2529554", "GSM2529555", "GSM2529556", "GSM2529557", "GSM2529558", "GSM2529559", "GSM2529560", "GSM2529561", "GSM2529562", "GSM2529563", "GSM2529564", "GSM2529565", "GSM2529566", "GSM2529567", "GSM2529568", "GSM2529569", "GSM2529570", "GSM2529571", "GSM2529572", "GSM2529573", "GSM2529574", "GSM2529575", "GSM2529576", "GSM2529577", "GSM2529578", "GSM2529579", "GSM2529580", "GSM2529581", "GSM2529582", "GSM2529583", "GSM2529584", "GSM2529585", "GSM2529586", "GSM2529587", "GSM2529588", "GSM2529589", "GSM2529590", "GSM2529591", "GSM2529592", "GSM2529593", "GSM2529594", "GSM2529595", "GSM2529596", "GSM2529597", "GSM2529598", "GSM2529599", "GSM2529600", "GSM2529601", "GSM2529602", "GSM2529603", "GSM2529604", "GSM2529605", "GSM2529606", "GSM2529607", "GSM2529608", "GSM2529609", "GSM2529610", "GSM2529611", "GSM2529612", "GSM2529613", "GSM2529614", "GSM2529615", "GSM2529616", "GSM2529617", "GSM2529618", "GSM2529619", "GSM2529620", "GSM2529621", "GSM2529622", "GSM2529623", "GSM2529624", "GSM2529625", "GSM2529626", "GSM2529627", "GSM2529628", "GSM2529629", "GSM2529630", "GSM2529631", "GSM2529632", "GSM2529633", "GSM2529634", "GSM2529635", "GSM2529636", "GSM2529637", "GSM2529638", "GSM2529639", "GSM2529640", "GSM2529641", "GSM2529642", "GSM2529643", "GSM2529644", "GSM2529645", "GSM2529646", "GSM2529647", "GSM2529648", "GSM2529649", "GSM2529650", "GSM2529651", "GSM2529652", "GSM2529653", "GSM2529654", "GSM2529655", "GSM2529656", "GSM2529657", "GSM2529658", "GSM2529659", "GSM2529660", "GSM2529661", "GSM2529662", "GSM2529663", "GSM2529664", "GSM2529665", "GSM2529666", "GSM2529667", "GSM2529668", "GSM2529669", "GSM2529670", "GSM2529671", "GSM2529672", "GSM2529673", "GSM2529674", "GSM2529675", "GSM2529676", "GSM2529677", "GSM2529678", "GSM2529679", "GSM2529680", "GSM2529681", "GSM2529682", "GSM2529683", "GSM2529684", "GSM2529685", "GSM2529686", "GSM2529687", "GSM2529688", "GSM2529689", "GSM2529690", "GSM2529691", "GSM2529692", "GSM2529693", "GSM2529694", "GSM2529695", "GSM2529696", "GSM2529697", "GSM2529698", "GSM2529699", "GSM2529700", "GSM2529701", "GSM2529702", "GSM2529703", "GSM2529704", "GSM2529705", "GSM2529706", "GSM2529707", "GSM2529708", "GSM2529709", "GSM2529710", "GSM2529711", "GSM2529712", "GSM2529713", "GSM2529714", "GSM2529715", "GSM2529716", "GSM2529717", "GSM2529718", "GSM2529719", "GSM2529720", "GSM2529721", "GSM2529722", "GSM2529723", "GSM2529724", "GSM2529725", "GSM2529726", "GSM2529727", "GSM2529728", "GSM2529729", "GSM2529730", "GSM2529731", "GSM2529732", "GSM2529733", "GSM2529734", "GSM2529735", "GSM2529736", "GSM2529737", "GSM2529738", "GSM2529739", "GSM2529740", "GSM2529741", "GSM2529742", "GSM2529743", "GSM2529744", "GSM2529745", "GSM2529746", "GSM2529747", "GSM2529748", "GSM2529749", "GSM2529750", "GSM2529751", "GSM2529752", "GSM2529753", "GSM2529754", "GSM2529755", "GSM2529756", "GSM2529757", "GSM2529758", "GSM2529759", "GSM2529760", "GSM2529761", "GSM2529762", "GSM2529763", "GSM2529764", "GSM2529765", "GSM2529766", "GSM2529767", "GSM2529768", "GSM2529769", "GSM2529770", "GSM2529771", "GSM2529772", "GSM2529773", "GSM2529774", "GSM2529775", "GSM2529776", "GSM2529777", "GSM2529778", "GSM2529779", "GSM2529780", "GSM2529781", "GSM2529782", "GSM2529783", "GSM2529784", "GSM2529785", "GSM2529786", "GSM2529787", "GSM2529788", "GSM2529789", "GSM2529790", "GSM2529791", "GSM2529792", "GSM2529793", "GSM2529794", "GSM2529795", "GSM2529796", "GSM2529797", "GSM2529798", "GSM2529799", "GSM2529800", "GSM2529801", "GSM2529802", "GSM2529803", "GSM2529804", "GSM2529805", "GSM2529806", "GSM2529807", "GSM2529808", "GSM2529809", "GSM2529810", "GSM2529811", "GSM2529812", "GSM2529813", "GSM2529814", "GSM2529815", "GSM2529816", "GSM2529817", "GSM2529818", "GSM2529819", "GSM2529820", "GSM2529821", "GSM2529822", "GSM2529823", "GSM2529824", "GSM2529825", "GSM2529826", "GSM2529827", "GSM2529828", "GSM2529829", "GSM2529830", "GSM2529831", "GSM2529832", "GSM2529833", "GSM2529834", "GSM2529835", "GSM2529836", "GSM2529837", "GSM2529838", "GSM2529839", "GSM2529840", "GSM2529841", "GSM2529842", "GSM2529843", "GSM2529844", "GSM2529845", "GSM2529846", "GSM2529847", "GSM2529848", "GSM2529849", "GSM2529850", "GSM2529851", "GSM2529852", "GSM2529853", "GSM2529854", "GSM2529855", "GSM2529856", "GSM2529857", "GSM2529858", "GSM2529859", "GSM2529860", "GSM2529861", "GSM2529862", "GSM2529863", "GSM2529864", "GSM2529865", "GSM2529866", "GSM2529867", "GSM2529868", "GSM2529869", "GSM2529870", "GSM2529871", "GSM2529872", "GSM2529873", "GSM2529874", "GSM2529875", "GSM2529876", "GSM2529877", "GSM2529878", "GSM2529879", "GSM2529880", "GSM2529881", "GSM2529882", "GSM2529883", "GSM2529884", "GSM2529885", "GSM2529886", "GSM2529887", "GSM2529888", "GSM2529889", "GSM2529890", "GSM2529891", "GSM2529892", "GSM2529893", "GSM2529894", "GSM2529895", "GSM2529896", "GSM2529897", "GSM2529898", "GSM2529899", "GSM2529900", "GSM2529901", "GSM2529902", "GSM2529903", "GSM2529904", "GSM2529905", "GSM2529906", "GSM2529907", "GSM2529908", "GSM2529909", "GSM2529910", "GSM2529911", "GSM2529912", "GSM2529913", "GSM2529914", "GSM2529915", "GSM2529916", "GSM2529917", "GSM2529918", "GSM2529919", "GSM2529920", "GSM2529921", "GSM2529922", "GSM2529923", "GSM2529924", "GSM2529925", "GSM2529926", "GSM2529927", "GSM2529928", "GSM2529929", "GSM2529930", "GSM2529931", "GSM2529932", "GSM2529933", "GSM2529934", "GSM2529935", "GSM2529936", "GSM2529937", "GSM2529938", "GSM2529939", "GSM2529940", "GSM2529941", "GSM2529942", "GSM2529943", "GSM2529944", "GSM2529945", "GSM2529946", "GSM2529947", "GSM2529948", "GSM2529949", "GSM2529950", "GSM2529951", "GSM2529952", "GSM2529953", "GSM2529954", "GSM2529955", "GSM2529956", "GSM2529957", "GSM2529958", "GSM2529959", "GSM2529960", "GSM2529961", "GSM2529962", "GSM2529963", "GSM2529964", "GSM2529965", "GSM2529966", "GSM2529967", "GSM2529968", "GSM2529969", "GSM2529970", "GSM2529971", "GSM2529972", "GSM2529973", "GSM2529974", "GSM2529975", "GSM2529976", "GSM2529977", "GSM2529978", "GSM2529979", "GSM2529980", "GSM2529981", "GSM2529982", "GSM2529983", "GSM2529984", "GSM2529985", "GSM2529986", "GSM2529987", "GSM2529988", "GSM2529989", "GSM2529990", "GSM2529991", "GSM2529992", "GSM2529993", "GSM2529994", "GSM2529995", "GSM2529996", "GSM2529997", "GSM2529998", "GSM2529999", "GSM2530000", "GSM2530001", "GSM2530002", "GSM2530003", "GSM2530004", "GSM2530005", "GSM2530006", "GSM2530007", "GSM2530008", "GSM2530009", "GSM2530010", "GSM2530011", "GSM2530012", "GSM2530013", "GSM2530014", "GSM2530015", "GSM2530016", "GSM2530017", "GSM2530018", "GSM2530019", "GSM2530020", "GSM2530021", "GSM2530022", "GSM2530023", "GSM2530024", "GSM2530025", "GSM2530026", "GSM2530027", "GSM2530028", "GSM2530029", "GSM2530030", "GSM2530031", "GSM2530032", "GSM2530033", "GSM2530034", "GSM2530035", "GSM2530036", "GSM2530037", "GSM2530038", "GSM2530039", "GSM2530040", "GSM2530041", "GSM2530042", "GSM2530043", "GSM2530044", "GSM2530045", "GSM2530046", "GSM2530047", "GSM2530048", "GSM2530049", "GSM2530050", "GSM2530051", "GSM2530052", "GSM2530053", "GSM2530054", "GSM2530055", "GSM2530056", "GSM2530057", "GSM2530058", "GSM2530059", "GSM2530060", "GSM2530061", "GSM2530062", "GSM2530063", "GSM2530064", "GSM2530065", "GSM2530066", "GSM2530067", "GSM2530068", "GSM2530069", "GSM2530070", "GSM2530071", "GSM2530072", "GSM2530073", "GSM2530074", "GSM2530075", "GSM2530076", "GSM2530077", "GSM2530078", "GSM2530079", "GSM2530080", "GSM2530081", "GSM2530082", "GSM2530083", "GSM2530084", "GSM2530085", "GSM2530086", "GSM2530087", "GSM2530088", "GSM2530089", "GSM2530090", "GSM2530091", "GSM2530092", "GSM2530093", "GSM2530094", "GSM2530095", "GSM2530096", "GSM2530097", "GSM2530098", "GSM2530099", "GSM2530100", "GSM2530101", "GSM2530102", "GSM2530103", "GSM2530104", "GSM2530105", "GSM2530106", "GSM2530107", "GSM2530108", "GSM2530109", "GSM2530110", "GSM2530111", "GSM2530112", "GSM2530113", "GSM2530114", "GSM2530115", "GSM2530116", "GSM2530117", "GSM2530118", "GSM2530119", "GSM2530120", "GSM2530121", "GSM2530122", "GSM2530123", "GSM2530124", "GSM2530125", "GSM2530126", "GSM2530127", "GSM2530128", "GSM2530129", "GSM2530130", "GSM2530131", "GSM2530132", "GSM2530133", "GSM2530134", "GSM2530135", "GSM2530136", "GSM2530137", "GSM2530138", "GSM2530139", "GSM2530140", "GSM2530141", "GSM2530142", "GSM2530143", "GSM2530144", "GSM2530145", "GSM2530146", "GSM2530147", "GSM2530148", "GSM2530149", "GSM2530150", "GSM2530151", "GSM2530152", "GSM2530153", "GSM2530154", "GSM2530155", "GSM2530156", "GSM2530157", "GSM2530158", "GSM2530159", "GSM2530160", "GSM2530161", "GSM2530162", "GSM2530163", "GSM2530164", "GSM2530165", "GSM2530166", "GSM2530167", "GSM2530168", "GSM2530169", "GSM2530170", "GSM2530171", "GSM2530172", "GSM2530173", "GSM2530174", "GSM2530175", "GSM2530176", "GSM2530177", "GSM2530178", "GSM2530179", "GSM2530180", "GSM2530181", "GSM2530182", "GSM2530183", "GSM2530184", "GSM2530185", "GSM2530186", "GSM2530187", "GSM2530188", "GSM2530189", "GSM2530190", "GSM2530191", "GSM2530192", "GSM2530193", "GSM2530194", "GSM2530195", "GSM2530196", "GSM2530197", "GSM2530198", "GSM2530199", "GSM2530200", "GSM2530201", "GSM2530202", "GSM2530203", "GSM2530204", "GSM2530205", "GSM2530206", "GSM2530207", "GSM2530208", "GSM2530209", "GSM2530210", "GSM2530211", "GSM2530212", "GSM2530213", "GSM2530214", "GSM2530215", "GSM2530216", "GSM2530217", "GSM2530218", "GSM2530219", "GSM2530220", "GSM2530221", "GSM2530222", "GSM2530223", "GSM2530224", "GSM2530225", "GSM2530226", "GSM2530227", "GSM2530228", "GSM2530229", "GSM2530230", "GSM2530231", "GSM2530232", "GSM2530233", "GSM2530234", "GSM2530235", "GSM2530236", "GSM2530237", "GSM2530238", "GSM2530239", "GSM2530240", "GSM2530241", "GSM2530242", "GSM2530243", "GSM2530244", "GSM2530245", "GSM2530246", "GSM2530247", "GSM2530248", "GSM2530249", "GSM2530250", "GSM2530251", "GSM2530252", "GSM2530253", "GSM2530254", "GSM2530255", "GSM2530256", "GSM2530257", "GSM2530258", "GSM2530259", "GSM2530260", "GSM2530261", "GSM2530262", "GSM2530263", "GSM2530264", "GSM2530265", "GSM2530266", "GSM2530267", "GSM2530268", "GSM2530269", "GSM2530270", "GSM2530271", "GSM2530272", "GSM2530273", "GSM2530274", "GSM2530275", "GSM2530276", "GSM2530277", "GSM2530278", "GSM2530279", "GSM2530280", "GSM2530281", "GSM2530282", "GSM2530283", "GSM2530284", "GSM2530285", "GSM2530286", "GSM2530287", "GSM2530288", "GSM2530289", "GSM2530290", "GSM2530291", "GSM2530292", "GSM2530293", "GSM2530294", "GSM2530295", "GSM2530296", "GSM2530297", "GSM2530298", "GSM2530299", "GSM2530300", "GSM2530301", "GSM2530302", "GSM2530303", "GSM2530304", "GSM2530305", "GSM2530306", "GSM2530307", "GSM2530308", "GSM2530309", "GSM2530310", "GSM2530311", "GSM2530312", "GSM2530313", "GSM2530314", "GSM2530315", "GSM2530316", "GSM2530317", "GSM2530318", "GSM2530319", "GSM2530320", "GSM2530321", "GSM2530322", "GSM2530323", "GSM2530324", "GSM2530325", "GSM2530326", "GSM2530327", "GSM2530328", "GSM2530329", "GSM2530330", "GSM2530331", "GSM2530332", "GSM2530333", "GSM2530334", "GSM2530335", "GSM2530336", "GSM2530337", "GSM2530338", "GSM2530339", "GSM2530340", "GSM2530341", "GSM2530342", "GSM2530343", "GSM2530344", "GSM2530345", "GSM2530346", "GSM2530347", "GSM2530348", "GSM2530349", "GSM2530350", "GSM2530351", "GSM2530352", "GSM2530353", "GSM2530354", "GSM2530355", "GSM2530356", "GSM2530357", "GSM2530358", "GSM2530359", "GSM2530360", "GSM2530361", "GSM2530362", "GSM2530363", "GSM2530364", "GSM2530365", "GSM2530366", "GSM2530367", "GSM2530368", "GSM2530369", "GSM2530370", "GSM2530371", "GSM2530372", "GSM2530373", "GSM2530374", "GSM2530375", "GSM2530376", "GSM2530377", "GSM2530378", "GSM2530379", "GSM2530380", "GSM2530381", "GSM2530382", "GSM2530383", "GSM2530384", "GSM2530385", "GSM2530386", "GSM2530387", "GSM2530388", "GSM2530389", "GSM2530390", "GSM2530391", "GSM2530392", "GSM2530393", "GSM2530394", "GSM2530395", "GSM2530396", "GSM2530397", "GSM2530398", "GSM2530399", "GSM2530400", "GSM2530401", "GSM2530402", "GSM2530403", "GSM2530404", "GSM2530405", "GSM2530406", "GSM2530407", "GSM2530408", "GSM2530409", "GSM2530410", "GSM2530411", "GSM2530412", "GSM2530413", "GSM2530414", "GSM2530415", "GSM2530416", "GSM2530417", "GSM2530418", "GSM2530419", "GSM2530420", "GSM2530421", "GSM2530422", "GSM2530423", "GSM2530424", "GSM2530425", "GSM2530426", "GSM2530427", "GSM2530428", "GSM2530429", "GSM2530430", "GSM2530431", "GSM2530432", "GSM2530433", "GSM2530434", "GSM2530435", "GSM2530436", "GSM2530437", "GSM2530438", "GSM2530439", "GSM2530440", "GSM2530441", "GSM2530442", "GSM2530443", "GSM2530444", "GSM2530445", "GSM2530446", "GSM2530447", "GSM2530448", "GSM2530449", "GSM2530450", "GSM2530451", "GSM2530452", "GSM2530453", "GSM2530454", "GSM2530455", "GSM2530456", "GSM2530457", "GSM2530458", "GSM2530459", "GSM2530460", "GSM2530461", "GSM2530462", "GSM2530463", "GSM2530464", "GSM2530465", "GSM2530466", "GSM2530467", "GSM2530468", "GSM2530469", "GSM2530470", "GSM2530471", "GSM2530472", "GSM2530473", "GSM2530474", "GSM2530475", "GSM2530476", "GSM2530477", "GSM2530478", "GSM2530479", "GSM2530480", "GSM2530481", "GSM2530482", "GSM2530483", "GSM2530484", "GSM2530485", "GSM2530486", "GSM2530487", "GSM2530488", "GSM2530489", "GSM2530490", "GSM2530491", "GSM2530492", "GSM2530493", "GSM2530494", "GSM2530495", "GSM2530496", "GSM2530497", "GSM2530498", "GSM2530499", "GSM2530500", "GSM2530501", "GSM2530502", "GSM2530503", "GSM2530504", "GSM2530505", "GSM2530506", "GSM2530507", "GSM2530508", "GSM2530509", "GSM2530510", "GSM2530511", "GSM2530512", "GSM2530513", "GSM2530514", "GSM2530515", "GSM2530516", "GSM2530517", "GSM2530518", "GSM2530519", "GSM2530520", "GSM2530521", "GSM2530522", "GSM2530523", "GSM2530524", "GSM2530525", "GSM2530526", "GSM2530527", "GSM2530528", "GSM2530529", "GSM2530530", "GSM2530531", "GSM2530532", "GSM2530533", "GSM2530534", "GSM2530535", "GSM2530536", "GSM2530537", "GSM2530538", "GSM2530539", "GSM2530540", "GSM2530541", "GSM2530542", "GSM2530543", "GSM2530544", "GSM2530545", "GSM2530546", "GSM2530547", "GSM2530548", "GSM2530549", "GSM2530550", "GSM2530551", "GSM2530552", "GSM2530553", "GSM2530554", "GSM2530555", "GSM2530556", "GSM2530557", "GSM2530558", "GSM2530559", "GSM2530560", "GSM2530561", "GSM2530562", "GSM2530563", "GSM2530564", "GSM2530565", "GSM2530566", "GSM2530567", "GSM2530568", "GSM2530569", "GSM2530570", "GSM2530571", "GSM2530572", "GSM2530573", "GSM2530574", "GSM2530575", "GSM2530576", "GSM2530577", "GSM2530578", "GSM2530579", "GSM2530580", "GSM2530581", "GSM2530582", "GSM2530583", "GSM2530584", "GSM2530585", "GSM2530586", "GSM2530587", "GSM2530588", "GSM2530589", "GSM2530590", "GSM2530591", "GSM2530592", "GSM2530593", "GSM2530594", "GSM2530595", "GSM2530596", "GSM2530597", "GSM2530598", "GSM2530599", "GSM2530600", "GSM2530601", "GSM2530602", "GSM2530603", "GSM2530604", "GSM2530605", "GSM2530606", "GSM2530607", "GSM2530608", "GSM2530609", "GSM2530610", "GSM2530611", "GSM2530612", "GSM2530613", "GSM2530614", "GSM2530615", "GSM2530616", "GSM2530617", "GSM2530618", "GSM2530619", "GSM2530620", "GSM2530621", "GSM2530622", "GSM2530623", "GSM2530624", "GSM2530625", "GSM2530626", "GSM2530627", "GSM2530628", "GSM2530629", "GSM2530630", "GSM2530631", "GSM2530632", "GSM2530633", "GSM2530634", "GSM2530635", "GSM2530636", "GSM2530637", "GSM2530638", "GSM2530639", "GSM2530640", "GSM2530641", "GSM2530642", "GSM2530643", "GSM2530644", "GSM2530645", "GSM2530646", "GSM2530647", "GSM2530648", "GSM2530649", "GSM2530650", "GSM2530651", "GSM2530652", "GSM2530653", "GSM2530654", "GSM2530655", "GSM2530656", "GSM2530657", "GSM2530658", "GSM2530659", "GSM2530660", "GSM2530661", "GSM2530662", "GSM2530663", "GSM2530664", "GSM2530665", "GSM2530666", "GSM2530667", "GSM2530668", "GSM2530669", "GSM2530670", "GSM2530671", "GSM2530672", "GSM2530673", "GSM2530674", "GSM2530675", "GSM2530676", "GSM2530677", "GSM2530678", "GSM2530679", "GSM2530680", "GSM2530681", "GSM2530682", "GSM2530683", "GSM2530684", "GSM2530685", "GSM2530686", "GSM2530687", "GSM2530688", 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"cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Prognostic gene signatures were established through univariate, LASSO, and multivariate Cox regression analyses."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"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": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE96058"], "resolved_accessions": ["GSE96058"], "statements": ["The data that support the findings of this study are available in the public domain: The TCGA-BRCA dataset can be accessed through the Genomic Data Commons (GDC) data portal at https://portal.gdc.cancer.gov/. METABRIC project can be accessed through the European Genome-phenome Archive (EGA) at https://ega-archive.org/. The GSE96058 dataset can be accessed through the in the Gene Expression Omnibus (GEO) database at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96058."], "basis": "The paper names GSE96058 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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