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pmid:34900411
Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer.
Peng Su · Ziqi Peng · Boyang Xu · Bowen Yang · Feng Jin
PeerJ · 2021 doi:10.7717/peerj.12383
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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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With the increase of immunotherapy and its preliminary application in TNBC treatment, the value of immune-related strategies in the treatment of TNBC has been initially reflected. Based thereon, this study plans to classify and further explore TNBC from the perspective of immune cell infiltration.\nMETHOD: The fractions of immune cells of TNBC patients were assessed by six immune component analysis methods in The Cancer Genome Atlas (TCGA) database. Hub genes significantly related to poor prognosis were verified by weighted gene co-expression network analysis (WGCNA) analysis, Lasso analysis, and univariate KM analysis. Two cohorts of TNBC patients with complete prognosis information were collected for validation analysis. Finally, the Genomics of Drug Sensitivity in Cancer (GDSC) database was adopted to ascertain the sensitivity differences of different populations based on hub-gene grouping to different chemotherapy drugs.\nRESULTS: Five hub genes (CD79A, CXCL13, IGLL5, LHFPL2, and PLEKHF1) of the key co-expression gene module could divide TNBC patients into two groups (Cluster A and Cluster B) based on consistency cluster analysis. The patients with Cluster A were responsible for significantly worse prognosis than the patients with Cluster B (P = 0.023). In addition, another classification method, PCoA, and two other datasets (GSE103091 and GSE76124), were used to obtain consistent results with previous findings, which verified the stability of the classification method and dataset in this study. The grouping criteria based on the previous results were developed and the accuracy of the cut-off values was validated. A prognosis model of TNBC patients was then constructed based on the grouping results of five hub genes and N staging as prognostic factors. The results of ROC and decision curve analyses showed that this model had high prediction accuracy and patients could benefit therefrom. Finally, GDSC database analysis proved that patients in Cluster A were more sensitive to Vinorelbine. Separate analysis of the sensitivity of patients in Cluster A to Gemcitabine and Vinorelbine showed that the patients in Cluster A exhibited higher sensitivity to Vinorelbine. We hypothesized that these five genes were related to gemcitabine resistance and they could serve as biomarkers for clinical drug decision-making after anthracene resistance and taxane resistance in patients with advanced TNBC.\nCONCLUSION: This study found five hub prognostic genes associated with macrophages, and a prognostic model was established to predict the survival of TNBC patients. Finally, these five genes were related to gemcitabine resistance in TNBC patients.", "claims": [{"id": "claim-method", "statement": "Time-dependent ROC curves were used to study the predictive power of the prognostic model", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34900411", "locator": "sections[19] \"Construction and test of prognosis model based on hub genes\" paragraph 2", "quote": "Time-dependent ROC curves were used to study the predictive power of the prognostic model"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34900411", "locator": "sections[34] \"Data Availability Statement\" paragraphs 1-5", "quote": "The following information was supplied regarding data availability:\nThe data is available at TCGA-BRCA (https://portal.gdc.cancer.gov/ and NCBI GEO: GSE103091, GSE76124.\nThe analysis code is available at GitHub:\nhttps://github.com/HopeStar2018/Macrophages-Related-Gene-Signature-to-Predict-Overall-Survival-in-Patients-with-TNBC.git"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Time-dependent ROC curves were used to study the predictive power of the prognostic model, and the AUC values at one year, three years, five years, seven years, and ten years were 0.77, 0.58, 0.71, 0.75, and 0.96 (Fig. 7B).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34900411", "locator": "sections[19] \"Construction and test of prognosis model based on hub genes\" paragraph 2", "quote": "Time-dependent ROC curves were used to study the predictive power of the prognostic model, and the AUC values at one year, three years, five years, seven years, and ten years were 0.77, 0.58, 0.71, 0.75, and 0.96 (Fig. 7B)."}, {"asset": "source:pmid:34900411", "locator": "sections[19] \"Construction and test of prognosis model based on hub genes\" paragraph 2", "quote": "The prediction results of the model proposed in this study closely matched the real value without statistically significant differences, showing that this prognostic model had high prediction accuracy."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Time-dependent ROC curves were used to study the predictive power of the prognostic model, and the AUC values at one year, three years, five years, seven years, and ten years were 0.77, 0.58, 0.71, 0.75, and 0.96 (Fig. 7B).", "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:34900411"], "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. 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"GSM3326408", "GSM3326409", "GSM3326410", "GSM3326411", "GSM3326412", "GSM3326413", "GSM3326414", "GSM3326415", "GSM3326416", "GSM3326417", "GSM3326418", "GSM3326419", "GSM3326420", "GSM3326421", "GSM3326422", "GSM3326423", "GSM3326424", "GSM3326425", "GSM3326426", "GSM3326427", "GSM3326428", "GSM3326429", "GSM3326430", "GSM3326431", "GSM3326432", "GSM3326433", "GSM3326434", "GSM3326435", "GSM3326436", "GSM3326437", "GSM3326438", "GSM3326439", "GSM3326440", "GSM3326441", "GSM3326442", "GSM3326443", "GSM3326444", "GSM3326445", "GSM3326446", "GSM3326447", "GSM3326448", "GSM3326449", "GSM3326450", "GSM3326451", "GSM3326452", "GSM3326453", "GSM3326454", "GSM3326455", "GSM3326456", "GSM3326457", "GSM3326458", "GSM3326459", "GSM3326460", "GSM3326461", "GSM3326462", "GSM3326463", "GSM3326464", "GSM3326465", "GSM3326466", "GSM3326467", "GSM3326468", "GSM3326469", "GSM3326470", "GSM3326471", "GSM3326472", "GSM3326473", "GSM3326474", "GSM3326475", "GSM3326476", "GSM3326477", "GSM3326478", "GSM3326479", "GSM3326480", "GSM3326481", "GSM3326482", "GSM3326483", "GSM3326484", "GSM3326485", "GSM3326486", "GSM3326487", "GSM3326488", "GSM3326489", "GSM3326490", "GSM3326491", "GSM3326492", "GSM3326493", "GSM3326494", "GSM3326495", "GSM3326496", "GSM3326497", "GSM3326498", "GSM3326499", "GSM3326500", "GSM3326501", "GSM3326502", "GSM3326503", "GSM3326504", "GSM3326505", "GSM3326506", "GSM3326507", "GSM3326508", "GSM3326509", "GSM3326510", "GSM3326511", "GSM3326512", "GSM3326513", "GSM3326514", "GSM3326515", "GSM3326516", "GSM3326517", "GSM3326518", "GSM3326519", "GSM3326520", "GSM3326521", "GSM3326522", "GSM3326523", "GSM3326524", "GSM3326525", "GSM3326526", "GSM3326527", "GSM3326528", "GSM3326529", "GSM3326530", "GSM3326531", "GSM3326532", "GSM3326533", "GSM3326534", "GSM3326535", "GSM3326536", "GSM3326537", "GSM3326538", "GSM3326539", "GSM3326540", "GSM3326541", "GSM3326542", "GSM3326543", "GSM3326544", "GSM3326545", "GSM3326546", "GSM3326547", "GSM3326548", "GSM3326549", "GSM3326550", "GSM3326551", "GSM3326552", "GSM3326553", "GSM3326554", "GSM3326555", "GSM3326556", "GSM3326557", "GSM3326558", "GSM3326559", "GSM3326560", "GSM3326561", "GSM3326562", "GSM3326563", "GSM3326564", "GSM3326565", "GSM3326566", "GSM3326567", "GSM3326568", "GSM3326569", "GSM3326570", "GSM3326571", "GSM3326572", "GSM3326573", "GSM3326574", "GSM3326575", "GSM3326576", "GSM3326577", "GSM3326578", "GSM3326579", "GSM3326580", "GSM3326581", "GSM3326582", "GSM3326583", "GSM3326584", "GSM3326585", "GSM3326586", "GSM3326587", "GSM3326588", "GSM3326589", "GSM3326590", "GSM3326591", "GSM3326592", "GSM3326593", "GSM3326594", "GSM3326595", "GSM3326596", "GSM3326597", "GSM3326598", "GSM3326599", "GSM3326600", "GSM3326601", "GSM3326602", "GSM3326603", "GSM3326604", "GSM3326605", "GSM3326606", "GSM3326607", "GSM3326608", "GSM3326609", "GSM3326610", "GSM3326611", "GSM3326612", "GSM3326613", "GSM3326614", "GSM3326615", "GSM3326616", "GSM3326617", "GSM3326618", "GSM3326619", "GSM3326620", "GSM3326621", "GSM3326622", "GSM3326623", "GSM3326624", "GSM3326625", "GSM3326626", "GSM3326627", "GSM3326628", "GSM3326629", "GSM3326630", "GSM3326631", "GSM3326632", "GSM3326633", "GSM3326634", "GSM3326635", "GSM3326636", "GSM3326637", "GSM3326638", "GSM3326639", "GSM3326640", "GSM3326641", "GSM3326642", "GSM3326643", "GSM3326644", "GSM3326645", "GSM3326646", "GSM3326647", "GSM3326648", "GSM3326649", "GSM3326650", "GSM3326651", "GSM3326652", "GSM3326653", "GSM3326654", "GSM3326655", "GSM3326656", "GSM3326657", "GSM3326658", "GSM3326659", "GSM3326660", "GSM3326661", "GSM3326662", "GSM3326663", "GSM3326664", "GSM3326665", "GSM3326666", "GSM3326667", "GSM3326668", "GSM3326669", "GSM3326670", "GSM3326671", "GSM3326672", "GSM3326673", "GSM3326674", "GSM3326675", "GSM3326676", "GSM3326677", "GSM3326678", "GSM3326679", "GSM3326680", "GSM3326681", "GSM3326682", "GSM3326683", "GSM3326684", "GSM3326685", "GSM3326686", "GSM3326687", "GSM3326688", "GSM3326689", "GSM3326690", "GSM3326691", "GSM3326692", "GSM3326693", "GSM3326694", "GSM3326695", "GSM3326696", "GSM3326697", "GSM3326698", "GSM3326699", "GSM3326700", "GSM3326701", "GSM3326702", "GSM3326703", "GSM3326704", "GSM3326705", "GSM3326706", "GSM3326707", "GSM3326708", "GSM3326709", "GSM3326710", "GSM3326711", "GSM3326712", "GSM3326713", "GSM3326714", "GSM3326715", "GSM3326716", "GSM3326717", "GSM3326718", "GSM3326719", "GSM3326720", "GSM3326721", "GSM3326722", "GSM3326723", "GSM3326724", "GSM3326725", "GSM3326726", "GSM3326727", "GSM3326728", "GSM3326729", "GSM3326730", "GSM3326731", "GSM3326732", "GSM3326733", "GSM3326734", "GSM3326735", "GSM3326736", "GSM3326737", "GSM3326738", "GSM3326739", "GSM3326740", "GSM3326741", "GSM3326742", "GSM3326743", "GSM3326744", "GSM3326745", "GSM3326746", "GSM3326747", "GSM3326748", "GSM3326749", "GSM3326750", "GSM3326751", "GSM3326752", "GSM3326753", "GSM3326754", "GSM3326755", "GSM3326756", "GSM3326757", "GSM3326758", "GSM3326759", "GSM3326760", "GSM3326761", "GSM3326762", "GSM3326763", "GSM3326764", "GSM3326765", "GSM3326766", "GSM3326767", "GSM3326768", "GSM3326769", "GSM3326770", "GSM3326771", "GSM3326772", "GSM3326773", "GSM3326774", "GSM3326775", "GSM3326776", "GSM3326777", "GSM3326778", "GSM3326779", "GSM3326780", "GSM3326781", "GSM3326782", "GSM3326783", "GSM3326784", "GSM3326785", "GSM3326786", "GSM3326787", "GSM3326788", "GSM3326789", "GSM3326790", "GSM3326791", "GSM3326792", "GSM3326793", "GSM3326794", "GSM3326795", "GSM3326796", "GSM3326797", "GSM3326798", "GSM3326799", "GSM3326800", "GSM3326801", "GSM3326802", "GSM3326803", "GSM3326804", "GSM3326805", "GSM3326806", "GSM3326807", "GSM3326808", "GSM3326809", "GSM3326810", "GSM3326811", "GSM3326812", "GSM3326813", "GSM3326814", "GSM3326815", "GSM3326816", "GSM3326817", "GSM3326818", "GSM3326819", "GSM3326820", "GSM3326821", "GSM3326822", "GSM3326823", "GSM3326824", "GSM3326825", "GSM3326826", "GSM3326827", "GSM3326828", "GSM3326829", "GSM3326830", "GSM3326831", "GSM3326832", "GSM3326833", "GSM3326834", "GSM3326835", "GSM3326836", "GSM3326837", "GSM3326838", "GSM3326839", "GSM3326840", "GSM3326841", "GSM3326842", "GSM3326843", "GSM3326844", "GSM3326845", "GSM3326846", "GSM3326847", "GSM3326848", "GSM3326849", "GSM3326850", "GSM3326851", "GSM3326852", "GSM3326853", "GSM3326854", "GSM3326855", "GSM3326856", "GSM3326857", "GSM3326858", "GSM3326859", "GSM3326860", "GSM3326861", "GSM3326862", "GSM3326863", "GSM3326864", "GSM3326865", "GSM3326866", "GSM3326867", "GSM3326868", "GSM3326869", "GSM3326870", "GSM3326871", "GSM3326872", "GSM3326873", "GSM3326874", "GSM3326875", "GSM3326876", "GSM3326877", "GSM3326878", "GSM3326879", "GSM3326880", "GSM3326881", "GSM3326882", "GSM3326883", "GSM3326884", "GSM3326885", "GSM3326886", "GSM3326887", "GSM3326888", "GSM3326889", "GSM3326890", "GSM3326891", "GSM3326892", "GSM3326893", "GSM3326894", "GSM3326895", "GSM3326896", "GSM3326897", "GSM3326898", "GSM3326899", "GSM3326900", "GSM3326901", "GSM3326902", "GSM3326903", "GSM3326904", "GSM3326905", "GSM3326906", "GSM3326907", "GSM3326908", "GSM3326909", "GSM3326910", "GSM3326911", "GSM3326912", "GSM3326913", "GSM3326914", "GSM3326915", "GSM3326916", "GSM3326917", "GSM3326918", "GSM3326919", "GSM3326920", "GSM3326921", "GSM3326922", "GSM3326923", "GSM3326924", "GSM3326925", "GSM3326926", "GSM3326927", "GSM3326928", "GSM3326929", "GSM3326930", "GSM3326931", "GSM3326932", "GSM3326933", "GSM3326934", "GSM3326935", "GSM3326936", "GSM3326937", "GSM3326938", "GSM3326939", "GSM3326940", "GSM3326941", "GSM3326942", "GSM3326943", "GSM3326944", "GSM3326945", "GSM3326946", "GSM3326947", "GSM3326948", "GSM3326949", "GSM3326950", "GSM3326951", "GSM3326952", "GSM3326953", "GSM3326954", "GSM3326955", "GSM3326956", "GSM3326957", "GSM3326958", "GSM3326959", "GSM3326960", "GSM3326961", "GSM3326962", "GSM3326963", "GSM3326964", "GSM3326965", "GSM3326966", "GSM3326967", "GSM3326968", "GSM3326969", "GSM3326970", "GSM3326971", "GSM3326972", "GSM3326973", "GSM3326974", "GSM3326975", "GSM3326976", "GSM3326977", "GSM3326978", "GSM3326979", "GSM3326980", "GSM3326981", "GSM3326982", "GSM3326983", "GSM3326984", "GSM3326985", "GSM3326986", "GSM3326987", "GSM3326988", "GSM3326989", "GSM3326990", "GSM3326991", "GSM3326992", "GSM3326993", "GSM3326994", "GSM3326995", "GSM3326996", "GSM3326997", "GSM3326998", "GSM3326999", "GSM3327000", "GSM3327001", "GSM3327002", "GSM3327003", "GSM3327004", "GSM3327005", "GSM3327006", "GSM3327007", "GSM3327008", "GSM3327009", "GSM3327010", "GSM3327011", "GSM3327012", "GSM3327013", "GSM3327014", "GSM3327015", "GSM3327016", "GSM3327017", "GSM3327018", "GSM3327019", "GSM3327020", "GSM3327021", "GSM3327022", "GSM3327023", "GSM3327024", "GSM3327025", "GSM3327026", "GSM3327027", "GSM3327028", "GSM3327029", "GSM3327030", "GSM3327031", "GSM3327032", "GSM3327033", "GSM3327034", "GSM3327035", "GSM3327036", "GSM3327037", "GSM3327038", "GSM3327039", "GSM3327040", "GSM3327041", "GSM3327042", "GSM3327043", "GSM3327044", "GSM3327045", "GSM3327046", "GSM3327047", "GSM3327048", "GSM3327049", "GSM3327050", "GSM3327051", "GSM3327052", "GSM3327053", "GSM3327054", "GSM3327055", "GSM3327056", "GSM3327057", "GSM3327058", "GSM3327059", "GSM3327060", "GSM3327061", "GSM3327062", "GSM3327063", "GSM3327064", "GSM3327065", "GSM3327066", "GSM3327067", "GSM3327068", "GSM3327069", "GSM3327070", "GSM3327071", "GSM3327072", "GSM3327073", "GSM3327074", "GSM3327075", "GSM3327076", "GSM3327077", "GSM3327078", "GSM3327079", "GSM3327080", "GSM3327081", "GSM3327082", "GSM3327083", "GSM3327084", "GSM3327085", "GSM3327086", "GSM3327087", "GSM3327088", "GSM3327089", "GSM3327090", "GSM3327091", "GSM3327092", "GSM3327093", "GSM3327094", "GSM3327095", "GSM3327096", "GSM3327097", "GSM3327098", "GSM3327099", "GSM3327100", "GSM3327101", "GSM3327102", "GSM3327103", "GSM3327104", "GSM3327105", "GSM3327106", "GSM3327107", "GSM3327108", "GSM3327109", "GSM3327110", "GSM3327111", "GSM3327112", "GSM3327113", "GSM3327114", "GSM3327115", "GSM3327116", "GSM3327117", "GSM3327118", "GSM3327119", "GSM3327120", "GSM3327121", "GSM3327122", "GSM3327123", "GSM3327124", "GSM3327125", "GSM3327126", "GSM3327127", "GSM3327128", "GSM3327129", "GSM3327130", "GSM3327131", "GSM3327132", "GSM3327133", "GSM3327134", "GSM3327135", "GSM3327136", "GSM3327137", "GSM3327138", "GSM3327139", "GSM3327140", "GSM3327141", "GSM3327142", "GSM3327143", "GSM3327144", "GSM3327145", "GSM3327146", "GSM3327147", "GSM3327148", "GSM3327149", "GSM3327150", "GSM3327151", "GSM3327152", "GSM3327153", "GSM3327154", "GSM3327155", "GSM3327156", "GSM3327157", "GSM3327158", "GSM3327159", "GSM3327160", "GSM3327161", "GSM3327162", "GSM3327163", "GSM3327164", "GSM3327165", "GSM3327166", "GSM3327167", "GSM3327168", "GSM3327169", "GSM3327170", "GSM3327171", "GSM3327172", "GSM3327173", "GSM3327174", "GSM3327175", "GSM3327176", "GSM3327177", "GSM3327178", "GSM3327179", "GSM3327180", "GSM3327181", "GSM3327182", "GSM3327183", "GSM3327184", "GSM3327185", "GSM3327186", "GSM3327187", "GSM3327188", "GSM3327189", "GSM3327190", "GSM3327191", "GSM3327192", "GSM3327193", "GSM3327194", "GSM3327195", "GSM3327196", "GSM3327197", "GSM3327198", "GSM3327199", "GSM3327200", "GSM3327201", "GSM3327202", "GSM3327203", "GSM3327204", "GSM3327205", "GSM3327206", "GSM3327207", "GSM3327208", "GSM3327209", "GSM3327210", "GSM3327211", "GSM3327212", "GSM3327213", "GSM3327214", "GSM3327215", "GSM3327216", "GSM3327217", "GSM3327218", "GSM3327219", "GSM3327220", "GSM3327221", "GSM3327222", "GSM3327223", "GSM3327224", "GSM3327225", "GSM3327226", "GSM3327227", "GSM3327228", "GSM3327229", "GSM3327230", "GSM3327231", "GSM3327232", "GSM3327233", "GSM3327234", "GSM3327235", "GSM3327236", "GSM3327237", "GSM3327238", "GSM3327239", "GSM3327240", "GSM3327241", "GSM3327242", "GSM3327243", "GSM3327244", "GSM3327245", "GSM3327246", "GSM3327247", "GSM3327248", "GSM3327249", "GSM3327250", "GSM3327251", "GSM3327252", "GSM3327253", "GSM3327254", "GSM3327255", "GSM3327256", "GSM3327257", "GSM3327258", "GSM3327259", "GSM3327260", "GSM3327261", "GSM3327262", "GSM3327263", "GSM3327264", "GSM3327265", "GSM3327266", "GSM3327267", "GSM3327268", "GSM3327269", "GSM3327270", "GSM3327271", "GSM3327272", "GSM3327273", "GSM3327274", "GSM3327275", "GSM3327276", "GSM3327277", "GSM3327278", "GSM3327279", "GSM3327280", "GSM3327281", "GSM3327282", "GSM3327283", "GSM3327284", "GSM3327285", "GSM3327286", "GSM3327287", "GSM3327288", "GSM3327289", "GSM3327290", "GSM3327291", "GSM3327292", "GSM3327293", "GSM3327294", "GSM3327295", "GSM3327296", "GSM3327297", "GSM3327298", "GSM3327299", "GSM3327300", "GSM3327301", "GSM3327302", "GSM3327303", "GSM3327304", "GSM3327305", "GSM3327306", "GSM3327307", "GSM3327308", "GSM3327309", "GSM3327310", "GSM3327311", "GSM3327312", "GSM3327313", "GSM3327314", "GSM3327315", "GSM3327316", "GSM3327317", "GSM3327318", "GSM3327319", "GSM3327320", "GSM3327321", "GSM3327322", "GSM3327323", "GSM3327324", "GSM3327325", "GSM3327326", "GSM3327327", "GSM3327328", "GSM3327329", "GSM3327330", "GSM3327331", "GSM3327332", "GSM3327333", "GSM3327334", "GSM3327335", "GSM3327336", "GSM3327337", "GSM3327338", "GSM3327339", "GSM3327340", "GSM3327341", "GSM3327342", "GSM3327343", "GSM3327344", "GSM3327345", "GSM3327346", "GSM3327347", "GSM3327348", "GSM3327349", "GSM3327350", "GSM3327351", "GSM3327352", "GSM3327353", "GSM3327354", "GSM3327355", "GSM3327356", "GSM3327357", "GSM3327358", "GSM3327359", "GSM3327360", "GSM3327361", "GSM3327362", "GSM3327363", "GSM3327364", "GSM3327365", "GSM3327366", "GSM3327367", "GSM3327368", "GSM3327369", "GSM3327370", "GSM3327371", "GSM3327372", "GSM3327373", "GSM3327374", "GSM3327375", "GSM3327376", "GSM3327377", "GSM3327378", "GSM3327379", "GSM3327380", "GSM3327381", "GSM3327382", "GSM3327383", "GSM3327384", "GSM3327385", "GSM3327386", "GSM3327387", "GSM3327388", "GSM3327389", "GSM3327390", "GSM3327391", "GSM3327392", "GSM3327393", "GSM3327394", "GSM3327395", "GSM3327396", "GSM3327397", "GSM3327398", "GSM3327399", "GSM3327400", "GSM3327401", 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"parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "KM"}}, {"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": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.8, "band": "high", "quote": "Decision Curve Analysis"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": 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