Integratively Genomic Analysis Reveals the Prognostic and Immunological Characteristics of Pyroptosis and Ferroptosis in Pancreatic Cancer for Precision Immunotherapy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35242763", "kind": "science-record", "revision": 5, "content_hash": "sha256:b3c00be3fc067856e14d2b762bbc498dd530a99990f032d5cb51ce9abc42216c", "created_at": "2026-11-01T17:37:00Z", "updated_at": "2026-11-01T22:48:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integratively Genomic Analysis Reveals the Prognostic and Immunological Characteristics of Pyroptosis and Ferroptosis in Pancreatic Cancer for Precision Immunotherapy.", "doi": "10.3389/fcell.2022.826879", "pmid": "35242763", "authors": ["Ting Yu", "Huaicheng Tan", "Chunhua Liu", "Wen Nie", "Yang Wang", "Kexun Zhou", "Huashan Shi"], "journal": "Frontiers in cell and developmental biology", "year": 2022, "abstract": "The non-apoptotic cell death processes including pyroptosis and ferroptosis have been implicated in the progression and therapeutic responses of pancreatic adenocarcinoma (PAAD). However, the extent to which pyroptosis and ferroptosis influence tumor biology remains ambiguous, especially in PAAD, which is characterized with \"cold\" immunity. Considering the heterogeneity among different patients, it was more practical to quantify distinct cell death profiles in an individual tumor sample. Herein, we developed a pyroptosis-ferroptosis (P-F) score for PAAD patients in The Cancer Genome Atlas (TCGA) database. A high P-F score was associated with active immune phenotype, decreased genomic alterations, and significantly longer survival. Good accuracy of the P-F score in predicting overall survival (OS) was further confirmed in the TCGA-PAAD, ICGC-PACA-CA, and E-MTAB-6134 cohorts. Besides, one immunotherapy cohort (IMvigor210 dataset) has verified that patients with high P-F scores exhibited significant advantages in therapeutic responses and clinical benefits. The sensitivity to chemotherapeutics was analyzed through the Genomics of Drug Sensitivity in Cancer (GDSC), and patients with low P-F score might be more sensitive to paclitaxel and 5-fluorouracil. Collectively, the P-F score based on the systematic evaluation of cell death profiles could serve as an effective biomarker in predicting the outcomes and responses of PAAD patients to treatments with chemotherapeutic agents or immunotherapies.", "claims": [{"id": "claim-method", "statement": "Comparisons between two groups or more than two groups were conducted through the Wilcoxon test or Kruskal–Wallis test, respectively. Chi-square test was used for analyzing the correlations between categorical variables. The correlation coefficient was calculated through Spearman analysis. Survival analysis for each dataset was conducted using the Kaplan–Meier plotter, where the statistical difference was evaluated through the log rank test. To estimate the predictive efficacy of the variate, time-dependent analysis of the receiver operating characteristic (ROC) curve was performed to calculate the area under the curves (AUCs) through the R package “survivalROC.” The R package “survival” was used for univariate and multivariate Cox regression analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35242763", "locator": "sections[9] \"Statistical Analysis\" paragraph 2", "quote": "Comparisons between two groups or more than two groups were conducted through the Wilcoxon test or Kruskal–Wallis test, respectively. Chi-square test was used for analyzing the correlations between categorical variables. The correlation coefficient was calculated through Spearman analysis. Survival analysis for each dataset was conducted using the Kaplan–Meier plotter, where the statistical difference was evaluated through the log rank test. To estimate the predictive efficacy of the variate, time-dependent analysis of the receiver operating characteristic (ROC) curve was performed to calculate the area under the curves (AUCs) through the R package “survivalROC.” The R package “survival” was used for univariate and multivariate Cox regression analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35242763", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Collectively, the P-F score based on the systematic evaluation of cell death profiles could serve as an effective biomarker in predicting the outcomes and responses of PAAD patients to treatments with chemotherapeutic agents or immunotherapies.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35242763", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Collectively, the P-F score based on the systematic evaluation of cell death profiles could serve as an effective biomarker in predicting the outcomes and responses of PAAD patients to treatments with chemotherapeutic agents or immunotherapies."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Collectively, the P-F score based on the systematic evaluation of cell death profiles could serve as an effective biomarker in predicting the outcomes and responses of PAAD patients to treatments with chemotherapeutic agents or immunotherapies.", "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:35242763"], "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:E-MTAB-6134"], "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:E-MTAB-6134"], "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:35242763", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2022.826879", "sha256": "sha256:01a2836ff50bcd25911325fb330bb50d594a2a7fc72a941152f4e916e78550f0", "bytes": 72191, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcell.2022.826879", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8885993", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:E-MTAB-6134", "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=E-MTAB-6134", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "E-MTAB-6134", "version": null, "note": "Publicly available datasets were analyzed in this study. 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The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. 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These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM535948", "GSM535949", "GSM535950", "GSM535951", "GSM536032", "GSM536033", "GSM536034", "GSM536035", "GSM536036", "GSM536037", "GSM536038", "GSM536039", "GSM536040", "GSM536041", "GSM536042", "GSM536043", "GSM536044", "GSM536045", "GSM536046", "GSM536443", "GSM536444", "GSM536445", "GSM536446", "GSM536447", "GSM536448", "GSM536449", "GSM536450", "GSM536451", "GSM536452", "GSM536453", "GSM536454", "GSM536455", "GSM536456", "GSM536457", "GSM536458", "GSM536459", "GSM536460", "GSM536461", "GSM536462", "GSM536463", "GSM536464", "GSM536465", "GSM536466", "GSM536467", "GSM536468", "GSM536469", "GSM536470", "GSM536471", "GSM536472", "GSM536473", "GSM536474", "GSM536475", "GSM536476", "GSM536477", "GSM536478", "GSM536479", "GSM536480", "GSM536481", "GSM536482", "GSM536483", "GSM536484", "GSM536485", "GSM536486", "GSM536487", "GSM536488", "GSM536489", "GSM536490", "GSM536491", "GSM536492", "GSM536882", "GSM536883", "GSM536884", "GSM536885", "GSM536886", "GSM536887", "GSM536888", "GSM536889", "GSM536890", "GSM536891", "GSM536892", "GSM536893", "GSM536894", "GSM536895", "GSM536896", "GSM536897", "GSM536898", "GSM536899", "GSM536900", "GSM536901", "GSM536902", "GSM536903", "GSM536904", "GSM536905", "GSM536906", "GSM536907", "GSM536908", "GSM536909", "GSM536910", "GSM536911", "GSM536917", "GSM536918", "GSM536919", "GSM536920", "GSM536921", "GSM536922", "GSM536923", "GSM536924", "GSM536925", "GSM536926", "GSM536927", "GSM536928", "GSM536929", "GSM536930", "GSM536931", "GSM536932", "GSM536933", "GSM536934", "GSM536935", "GSM536936", "GSM536937", "GSM536938", "GSM536939", "GSM536940", "GSM536941", "GSM536942", "GSM536943", "GSM536944", "GSM536945", "GSM536946", "GSM536947", "GSM536948", "GSM536949"], "sample_count": 132, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma", "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:GSE57495", "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=GSE57495", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57495", "version": null, "note": "Publicly available datasets were analyzed in this study. These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1383778", "GSM1383779", "GSM1383780", "GSM1383781", "GSM1383782", "GSM1383783", "GSM1383784", "GSM1383785", "GSM1383786", "GSM1383787", "GSM1383788", "GSM1383789", "GSM1383790", "GSM1383791", "GSM1383792", "GSM1383793", "GSM1383794", "GSM1383795", "GSM1383796", "GSM1383797", "GSM1383798", "GSM1383799", "GSM1383800", "GSM1383801", "GSM1383802", "GSM1383803", "GSM1383804", "GSM1383805", "GSM1383806", "GSM1383807", "GSM1383808", "GSM1383809", "GSM1383810", "GSM1383811", "GSM1383812", "GSM1383813", "GSM1383814", "GSM1383815", "GSM1383816", "GSM1383817", "GSM1383818", "GSM1383819", "GSM1383820", "GSM1383821", "GSM1383822", "GSM1383823", "GSM1383824", "GSM1383825", "GSM1383826", "GSM1383827", "GSM1383828", "GSM1383829", "GSM1383830", "GSM1383831", "GSM1383832", "GSM1383833", "GSM1383834", "GSM1383835", "GSM1383836", "GSM1383837", "GSM1383838", "GSM1383839", "GSM1383840"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "Development of a prognostic gene signature in pancreatic cancer", "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:GSE85916", "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=GSE85916", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE85916", "version": null, "note": "Publicly available datasets were analyzed in this study. These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. These data can be found here: The RNA-sequence (RNA-Seq) data with matched clinical information of all available PAAD patients were extracted from The Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga) (n = 176) and International Cancer Genome Consortium (ICGC) (https://daco.icgc.org/) (n = 165) databases. Additionally, the E-MTAB-6134 dataset with completely clinical information of 288 PAAD patients and datasets without detailed clinical information including GSE57495, GSE21501, and GSE85916 were all extracted from the Array Express database (https://www.ebi.ac.uk/arrayexpress). The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. 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To estimate the predictive efficacy of the variate, time-dependent analysis of the receiver operating characteristic (ROC) curve was performed to calculate the area under the curves (AUCs) through the R package “survivalROC.” The R package “survival” was used for univariate and multivariate Cox regression analyses."}}, {"id": "method-2", "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-3", "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-4", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"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"}}, {"id": "method-6", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}], "targets": [], "gaps": ["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. 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The TCGA dataset was utilized as the training cohort, and the other datasets were set as validation cohorts. Based on the Creative Commons 3.0 license downloaded from http://research-pub.gene.com/IMvigor210CoreBiologie, the IMvigor210 dataset was extracted from a freely available data package. The IMvigor210 dataset containing 298 patients of urothelial cancer who had received immunotherapy was performed to validate the prediction value of the P-F score. The corresponding information of somatic mutations in TCGA-PAAD patients was extracted from UCSC Xena (https://xena.ucsc.edu/)."], "basis": "The paper names E-MTAB-6134, GSE57495, GSE21501, GSE85916 in Array Express database and the accession resolves in the repository. 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