Long Non-Coding RNA Landscape in Prostate Cancer Molecular Subtypes: A Feature Selection Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33672425", "kind": "science-record", "revision": 4, "content_hash": "sha256:418d51a0a9db41e9eb53120fda0d0bac5a739dbd090165871e3e8143c47e8dea", "created_at": "2026-11-01T15:41:27Z", "updated_at": "2026-11-01T21:24:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Long Non-Coding RNA Landscape in Prostate Cancer Molecular Subtypes: A Feature Selection Approach.", "doi": "10.3390/ijms22042227", "pmid": "33672425", "authors": ["Simona De Summa", "Antonio Palazzo", "Mariapia Caputo", "Rosa Maria Iacobazzi", "Brunella Pilato", "Letizia Porcelli", "Stefania Tommasi", "Angelo Virgilio Paradiso", "Amalia Azzariti"], "journal": "International journal of molecular sciences", "year": 2021, "abstract": "Prostate cancer is one of the most common malignancies in men. It is characterized by a high molecular genomic heterogeneity and, thus, molecular subtypes, that, to date, have not been used in clinical practice. In the present paper, we aimed to better stratify prostate cancer patients through the selection of robust long non-coding RNAs. To fulfill the purpose of the study, a bioinformatic approach focused on feature selection applied to a TCGA dataset was used. In such a way, LINC00668 and long non-coding(lnc)-SAYSD1-1, able to discriminate ERG/not-ERG subtypes, were demonstrated to be positive prognostic biomarkers in ERG-positive patients. Furthermore, we performed a comparison between mutated prostate cancer, identified as \"classified\", and a group of patients with no peculiar genomic alteration, named \"not-classified\". Moreover, LINC00920 lncRNA overexpression has been linked to a better outcome of the hormone regimen. Through the feature selection approach, it was found that the overexpression of lnc-ZMAT3-3 is related to low-grade patients, and three lncRNAs: lnc-SNX10-87, lnc-AP1S2-2, and ADPGK-AS1 showed, through a co-expression analysis, significant correlation values with potentially druggable pathways. In conclusion, the data mining of publicly available data and robust bioinformatic analyses are able to explore the unknown biology of malignancies.", "claims": [{"id": "claim-method", "statement": "To gain accuracy metrics, a Bootstrap resampling strategy was applied to the dataset (number of iterations = 100).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33672425", "locator": "sections[14] \"4.2.2. Feature Selection and Evaluation of Classification Performances\" paragraph 2", "quote": "To gain accuracy metrics, a Bootstrap resampling strategy was applied to the dataset (number of iterations = 100)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available in GDC data portal (https://portal.gdc.cancer.gov/) (accessed on 23 February 2021).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33672425", "locator": "sections[23] \"Data Availability Statement\" paragraph 2", "quote": "Data are available in GDC data portal (https://portal.gdc.cancer.gov/) (accessed on 23 February 2021)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:33672425"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33672425", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms22042227", "sha256": "sha256:2245b34c60d1ef805457054f6b45a5e62d8fa6aebccca13d431f5a3ce2baab6a", "bytes": 58693, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms22042227", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7926489", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33672425:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0f5fe2186fb3a00f559815d875c320b877d0784ad0759570798f488636773cf7", "bytes": 417, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#ijms-22-02227-t001", "version": null, "note": "Distribution of the molecular subtypes in the TCGA-PRAD cohort.", "structure": {"pmcid": "PMC7926489", "section_index": 3, "section_title": "2.1. lncRNA Discriminating ERG-Positive Subtype: Feature Selection", "row_count": 9, "column_count": 2}, "table": {"label": "Table 1", "caption": "Distribution of the molecular subtypes in the TCGA-PRAD cohort.", "rows": [["MolecularSubtypes", "n (%)"], ["ERG", "151 (45.6)"], ["ETV1", "27 (8.1)"], ["ETV4", "14 (4.2)"], ["FLI1", "4 (1.2)"], ["SPOP", "38 (11.4)"], ["FOXA1", "9 (2.7)"], ["IDH1", "3 (0.9)"], ["other", "86 (25.9)"]], "row_count": 9, "column_count": 2, "numeric_cells": 8, "header_rows": 1, "locator": "section[3]/table-wrap[1]#ijms-22-02227-t001"}}, {"id": "asset:table:pmid:33672425:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7e2e306ffd4390a8ec4d88e7dcdc721fd29ba71fb0bc674ac4cc48e6283d6cf6", "bytes": 1382, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#ijms-22-02227-t002", "version": null, "note": "Co-expressed long non-coding RNAs(lncRNAs) and coding genes.", "structure": {"pmcid": "PMC7926489", "section_index": 4, "section_title": "2.2. lncRNA-mRNA Coexpression Analysis of lncRNA Discriminating ERG-Positive Subtype", "row_count": 28, "column_count": 4}, "table": {"label": "Table 2", "caption": "Co-expressed long non-coding RNAs(lncRNAs) and coding genes.", "rows": [["lncRNA", "Gene", "r", "p-Value"], ["SLC5A4-AS1", "CPSF1P1", "0.8586", "<0.0001"], ["LINC02418", "ERG", "0.7761", "<0.0001"], ["lnc-PXDN-3", "TPO", "0.6901", "<0.0001"], ["lnc-OR1D5-1", "ERG", "0.6836", "<0.0001"], ["lnc-OR1D5-1", "LINC02418", "0.6693", "<0.0001"], ["LINC02418", "CD8B2", "0.6686", "<0.0001"], ["LINC02418", "DACT2", "0.6676", "<0.0001"], ["LINC02418", "HDAC1", "0.6631", "<0.0001"], ["LINC02418", "ANKRD6", "0.6573", "<0.0001"], ["LINC02418", "OGDHL", "0.6564", "<0.0001"], ["LINC02418", "ALOX15", "0.6530", "<0.0001"], ["LINC02418", "CPNE2", "0.6489", "<0.0001"], ["LINC02418", "SEPTIN9", "0.6437", "<0.0001"], ["LINC02418", "CDH7", "0.6389", "<0.0001"], ["LINC02418", "ITPR3", "0.6339", "<0.0001"], ["lnc-OR1D5-1", "SEPTIN9", "0.6311", "<0.0001"], ["LINC02418", "HLA-DMB", "0.6308", "<0.0001"], ["LINC02418", "VSTM5", "0.6233", "<0.0001"], ["LINC02418", "KCNS3", "0.6211", "<0.0001"], ["LINC02418", "NKAIN1", "0.6202", "<0.0001"], ["LINC02418", "FZD8", "0.6138", "<0.0001"], ["LINC02418", "AMPD3", "0.6120", "<0.0001"], ["lnc-PXDN-3", "ERG", "0.6114", "<0.0001"], ["lnc-OR1D5-1", "ALOX15", "0.6073", "<0.0001"], ["LINC02418", "LAMC2", "0.6065", "<0.0001"], ["LINC02418", "SCYL3", "0.6056", "<0.0001"], ["lnc-OR1D5-1", "CD8B2", "0.6026", "<0.0001"]], "row_count": 28, "column_count": 4, "numeric_cells": 83, "header_rows": 1, "locator": "section[4]/table-wrap[1]#ijms-22-02227-t002"}}, {"id": "asset:table:pmid:33672425:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c47736a8f934b766c9a015510e23dfe8dd3b426bd9f7986877a1a51e79dc8337", "bytes": 2932, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#ijms-22-02227-t003", "version": null, "note": "Functional enrichment of the first subcluster of the protein–protein interaction (PPI) network.", "structure": {"pmcid": "PMC7926489", "section_index": 5, "section_title": "2.3. PPI Network and Identification of Highly Connected Subnetwork in ERG-Positive Subtype", "row_count": 41, "column_count": 3}, "table": {"label": "Table 3", "caption": "Functional enrichment of the first subcluster of the protein–protein interaction (PPI) network.", "rows": [["Category", "Description", "FDR Value"], ["GO Function", "inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity", "4.7 × 10−6"], ["GO Function", "Cation channel activity", "4.7 × 10−6"], ["GO Function", "Ion-gated channel activity", "4.7 × 10−6"], ["GO Function", "metal ion transmembrane transporter activity", "4.7× 10−6"], ["GO Function", "Calcium channel activity", "5.56 × 10−6"], ["GO Process", "Calcium ion transport", "6.31 × 10−6"], ["KEGG Pathways", "cGMP-PKG signaling pathway", "7.6 × 10−6"], ["KEGG Pathways", "Cellular senescence", "7.6 × 10−6"], ["KEGG Pathways", "Vascular smooth muscle contraction", "7.6 × 10−6"], ["KEGG Pathways", "Circadian entrainment", "7.6 × 10−6"], ["KEGG Pathways", "Retrograde endocannabinoid signaling", "7.6 × 10−6"], ["KEGG Pathways", "Glutamatergic synapse", "7.6 × 10−6"], ["KEGG Pathways", "Cholinergic synapse", "7.6 × 10−6"], ["KEGG Pathways", "Serotonergic synapse", "7.6 × 10−6"], ["KEGG Pathways", "Dopaminergic synapse", "7.6 × 10−6"], ["KEGG Pathways", "Insulin secretion", "7.6 × 10−6"], ["KEGG Pathways", "GnRH signaling pathway", "7.6 × 10−6"], ["KEGG Pathways", "Oxytocin signaling pathway", "7.6 × 10−6"], ["KEGG Pathways", "Renin secretion", "7.6 × 10−6"], ["KEGG Pathways", "Aldosterone synthesis and secretion", "7.6 × 10−6"], ["KEGG Pathways", "Cortisol synthesis and secretion", "7.6 × 10−6"], ["KEGG Pathways", "Cushing’s syndrome", "7.6 × 10−6"], ["KEGG Pathways", "Salivary secretion", "7.6 × 10−6"], ["KEGG Pathways", "Alzheimer’s disease", "7.6 × 10−6"], ["KEGG Pathways", "Calcium signaling pathway", "8.6 × 10−6"], ["GO Function", "inositol 1,4,5 trisphosphate binding", "1.36 × 10−6"], ["GO Process", "regulation of protein secretion", "1.43 × 10−5"], ["Reactome Pathways", "Regulation of insulin secretion", "1.58 × 10−5"], ["Reactome Pathways", "Integration of energy metabolism", "1.96 × 10−5"], ["Reactome Pathways", "Cardiac conduction", "2.57 × 10−5"], ["Reactome Pathways", "CLEC7A (Dectin-1) induces NFAT activation", "3.3 × 10−5"], ["GO Process", "Inorganic cation transmembrane transport", "4.36 × 10−5"], ["Reactome Pathways", "Elevation of cytosolic Ca2+ levels", "4.58 × 10−5"], ["Reactome Pathways", "Muscle contraction", "4.58 × 10−5"], ["Reactome Pathways", "VEGFR2-mediated cell proliferation", "4.58 × 10−5"], ["GO Process", "regulation of insulin secretion", "4.82 × 10−5"], ["GO Process", "Calcium ion transmembrane transport", "5.98 × 10−5"], ["GO Process", "regulation of heart contraction", "6.38 × 10−5"], ["Reactome Pathways", "Role of phospholipids in phagocytosis", "7.41 × 10−5"], ["Reactome Pathways", "Effects of PIP2 hydrolysis", "7.62 × 10−5"]], "row_count": 41, "column_count": 3, "numeric_cells": 43, "header_rows": 1, "locator": "section[5]/table-wrap[1]#ijms-22-02227-t003"}}, {"id": "asset:table:pmid:33672425:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2c9e7aac0dbaeb3ca40081650a7f30a3f198cbcbfb281c94d868524be28608a5", "bytes": 734, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#ijms-22-02227-t004", "version": null, "note": "Functional enrichment of the second subcluster of the PPI network.", "structure": {"pmcid": "PMC7926489", "section_index": 5, "section_title": "2.3. PPI Network and Identification of Highly Connected Subnetwork in ERG-Positive Subtype", "row_count": 9, "column_count": 3}, "table": {"label": "Table 4", "caption": "Functional enrichment of the second subcluster of the PPI network.", "rows": [["Category", "Description", "FDR Value"], ["KEGG Pathways", "Purine metabolism", "9.3 × 10−6"], ["Reactome Pathways", "Metabolism of nucleotides", "0.002"], ["GO Process", "purine nucleotide catabolic process", "0.0038"], ["GO Process", "nucleoside metabolic process", "0.0064"], ["GO Process", "carbohydrate derivative catabolic process", "0.0064"], ["GO Process", "purine nucleotide metabolic process", "0.032"], ["GO Function", "Phosphoric ester hydrolase activity", "0.0323"], ["GO Function", "Hydrolase activity", "0.0324"]], "row_count": 9, "column_count": 3, "numeric_cells": 8, "header_rows": 1, "locator": "section[5]/table-wrap[2]#ijms-22-02227-t004"}}, {"id": "asset:table:pmid:33672425:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:31fc34b2ec5f75cf2c88a1715d69fa2cab78e4d44f4d25d35e184804b1710ee6", "bytes": 1923, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[3]#ijms-22-02227-t005", "version": null, "note": "Functional enrichment of the third subcluster of the PPI network.", "structure": {"pmcid": "PMC7926489", "section_index": 5, "section_title": "2.3. PPI Network and Identification of Highly Connected Subnetwork in ERG-Positive Subtype", "row_count": 29, "column_count": 3}, "table": {"label": "Table 5", "caption": "Functional enrichment of the third subcluster of the PPI network.", "rows": [["Category", "Description", "FDR Value"], ["GO Component", "Wnt-Frizzled-LRP5/6 complex", "7.05 × 10−6"], ["ReactomePathways", "RNF mutants show enhanced WNT signaling and proliferation", "1.2 × 10−5"], ["GO Function", "Coreceptor activity involved in Wnt signaling pathway", "2.89 × 10−5"], ["ReactomePathways", "Regulation of FZD by ubiquitination", "3.37 × 10−5"], ["GO Process", "CanonicalWnt signaling pathway", "5.31 × 10−5"], ["ReactomePathways", "Signaling by WNT in cancer", "5.59 × 10−5"], ["GO Function", "Wnt-activated receptor activity", "8.12 × 10−5"], ["GO Function", "Wnt-protein binding", "1.1 × 10−4"], ["GO Process", "Blood vessel development", "0.0013"], ["ReactomePathways", "TCF-dependent signaling in response to WNT", "0.0013"], ["GO Process", "Tube morphogenesis", "0.0018"], ["KEGG Pathways", "mTOR signaling pathway", "0.0023"], ["KEGG Pathways", "Wnt signaling pathway", "0.0023"], ["KEGG Pathways", "Breast cancer", "0.0023"], ["KEGG Pathways", "Hepatocellular carcinoma", "0.0023"], ["KEGG Pathways", "Gastric cancer", "0.0023"], ["ReactomePathways", "Signaling by WNT", "0.0023"], ["ReactomePathways", "Diseases of signal transduction", "0.0029"], ["GO Function", "Signaling receptor activity", "0.0032"], ["GO Process", "Non-canonical Wnt signaling pathway", "0.0032"], ["KEGG Pathways", "Pathways in cancer", "0.0048"], ["GO Process", "Sensory organ morphogenesis", "0.0173"], ["ReactomePathways", "Disease", "0.0191"], ["GO Process", "Epithelial tube morphogenesis", "0.0231"], ["GO Component", "Plasma membrane part", "0.0293"], ["GO Process", "Blood vessel morphogenesis", "0.0328"], ["GO Process", "Regulation of protein serine/threonine kinase activity", "0.0451"], ["GO Process", "Embryonic morphogenesis", "0.0484"]], "row_count": 29, "column_count": 3, "numeric_cells": 29, "header_rows": 1, "locator": "section[5]/table-wrap[3]#ijms-22-02227-t005"}}, {"id": "asset:table:pmid:33672425:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:22f3e4ad419cb4e3a03bb8484350a74ea9dd88bf9088b894e1c15ef8f02fdb7b", "bytes": 1346, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#ijms-22-02227-t006", "version": null, "note": "Co-expressed lncRNAs and genes.", "structure": {"pmcid": "PMC7926489", "section_index": 8, "section_title": "2.6. Co-Expression Network, Functional Enrichment and Prognostic Significance in Classified versus Nonclassified Subtypes", "row_count": 26, "column_count": 4}, "table": {"label": "Table 6", "caption": "Co-expressed lncRNAs and genes.", "rows": [["lncRNA", "Gene", "r", "p-Value"], ["lnc-AP1S2-2", "GRPR", "0.6863", "<0.0001"], ["lnc-SNX10-87", "ALOX15", "0.6841", "<0.0001"], ["lnc-SNX10-87", "SEPTIN9", "0.6841", "<0.0001"], ["lnc-SNX10-87", "ERG", "0.6795", "<0.0001"], ["lnc-SNX10-87", "KCNH8", "0.6795", "<0.0001"], ["lnc-SNX10-87", "CDH7", "0.6555", "<0.0001"], ["lnc-SNX10-87", "CACNA1D", "0.6539", "<0.0001"], ["lnc-SNX10-87", "LAMC2", "0.6372", "<0.0001"], ["lnc-SNX10-87", "TTC7B", "0.6349", "<0.0001"], ["lnc-SNX10-87", "MCOLN3", "0.6330", "<0.0001"], ["lnc-SNX10-87", "KIF16B", "0.6330", "<0.0001"], ["lnc-SNX10-87", "FZD8", "0.6286", "<0.0001"], ["lnc-SNX10-87", "OGDHL", "0.6286", "<0.0001"], ["lnc-SNX10-87", "DACT2", "0.6272", "<0.0001"], ["lnc-SNX10-87", "CPNE2", "0.6244", "<0.0001"], ["lnc-SNX10-87", "ANKRD6", "0.6234", "<0.0001"], ["lnc-SNX10-87", "EML6", "0.6161", "<0.0001"], ["lnc-SNX10-87", "ABCC8", "0.6059", "<0.0001"], ["lnc-SNX10-87", "NKAIN1", "0.6059", "<0.0001"], ["ADPGK-AS1", "ADPGK", "−0.6047", "<0.0001"], ["lnc-SNX10-87", "HDAC1", "−0.6154", "<0.0001"], ["lnc-SNX10-87", "KCNS3", "−0.6166", "<0.0001"], ["lnc-SNX10-87", "CD8B2", "−0.6204", "<0.0001"], ["lnc-SNX10-87", "HLA-DMB", "−0.6444", "<0.0001"], ["lnc-SNX10-87", "ITPR3", "−0.6802", "<0.0001"]], "row_count": 26, "column_count": 4, "numeric_cells": 76, "header_rows": 1, "locator": "section[8]/table-wrap[1]#ijms-22-02227-t006"}}, {"id": "asset:table:pmid:33672425:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:389c79865e27f0aa520e3e1c4a950a70c49a44ea81bfb6bae224cc372a6ac9f1", "bytes": 822, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#array1", "version": null, "note": null, "structure": {"pmcid": "PMC7926489", "section_index": 18, "section_title": "Abbreviations", "row_count": 19, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["PCa", "Prostate cancer"], ["PSA", "Prostate Specific Antigen"], ["lncRNA", "Long non-coding RNA"], ["CRPC", "Castration resistant prostate cancer"], ["ADT", "Deprivation Androgenic"], ["MDS plot", "Multidimensional scaling plot"], ["RF", "Random Forest"], ["SVM", "Support Vector Machine"], ["NB", "Naïve Bayes classifiers"], ["LDA", "Latent Dirichlet allocation"], ["LR", "Linear Regression"], ["kNN", "k-nearest neighbors algorithm"], ["PPI", "protein–protein interaction"], ["PFS", "Progression-Free Survival"], ["CRC", "colorectal cancer"], ["CKIs", "protein kinase inhibitors"], ["vst", "Variance stabilizing transformation"], ["sv", "Surrogate variables"], ["fve", "Fraction of Explained Variance"]], "row_count": 19, "column_count": 2, "numeric_cells": 0, "header_rows": 0, "locator": "section[18]/table-wrap[1]#array1"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Bootstrap resampling", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To gain accuracy metrics, a Bootstrap resampling strategy was applied to the dataset (number of iterations = 100)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Bootstrap resampling), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["Data are available in GDC data portal (https://portal.gdc.cancer.gov/) (accessed on 23 February 2021)."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33672425", "asset:table:pmid:33672425:1", "asset:table:pmid:33672425:2", "asset:table:pmid:33672425:3", "asset:table:pmid:33672425:4", "asset:table:pmid:33672425:5", "asset:table:pmid:33672425:6", "asset:table:pmid:33672425:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 48522, "completion_tokens": 1041, "cached_tokens": 784}}, "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:33672425", "type": "paper", "label": "pmid:33672425"}, {"id": "source:pmid:33672425", "type": "manuscript", "label": "PMID 33672425 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33672425", "type": "paper", "label": "pmid:33672425"}, {"id": "source:pmid:33672425", "type": "manuscript", "label": "PMID 33672425 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33672425", "type": "extraction", "used": ["source:pmid:33672425"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:33672425", "parent_hash": "sha256:b3bc418d9e3ab00af135aa510f1532960c6b15b09d7ad7cfc272f79e309be6d7", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": [", identified as \"classified\", and a group of patients with no peculiar genomic alteration, named \"not-c"], "order_basis": "paper_text_order:821", "id": "assay:1"}]}