Bioinformatic analysis revealing mitotic spindle assembly regulated NDC80 and MAD2L1 as prognostic biomarkers in non-small cell lung cancer development.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32795325", "kind": "science-record", "revision": 7, "content_hash": "sha256:7bba95a0f90d1ee96f91a018d33bb4c7fcf607b78c73cb3738f8b1a6acec66c6", "created_at": "2026-11-01T15:41:07Z", "updated_at": "2026-11-01T22:02:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis revealing mitotic spindle assembly regulated NDC80 and MAD2L1 as prognostic biomarkers in non-small cell lung cancer development.", "doi": "10.1186/s12920-020-00762-5", "pmid": "32795325", "authors": ["Rong Wei", "Ziyue Wang", "Yaping Zhang", "Bin Wang", "Ningning Shen", "Li E", "Xin Li", "Lifang Shang", "Yangwei Shang", "Wenpeng Yan", "Xiaoqin Zhang", "Wenxia Ma", "Chen Wang"], "journal": "BMC medical genomics", "year": 2020, "abstract": "BACKGROUND: Lung cancer has been the leading cause of tumor related death, and 80% ~ 85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the treatment is still challenging. The study is to identify credible responsible genes during the development of NSCLC using bioinformatic analysis, developing new prognostic biomarkers and potential gene targets to the disease.\nMETHODS: Firstly, three genes expression profiles GSE44077, GSE18842 and GSE33532 were picked from Gene Expression Omnibus (GEO) to analyze the genes with different expression level (GDEs) between NSCLC and normal lung samples, and the cellular location, molecular function and the biology pathways the GDEs enriched in were analyzed. Then, gene function modules of GDEs were explored based on the protein-protein interaction network (PPI), and the top module which contains most genes was identified, followed by containing genes annotation and survival analysis. Moreover, multivariate cox regression analysis was performed in addition to the Kaplan meier survival to narrow down the key genes scale. Further, the clinical pathological features of the picked key genes were explored using TCGA data.\nRESULTS: Three GEO profiles shared a total of 664 GDEs, including 232 up-regulated and 432 down-regulated genes. Based on the GDEs PPI network, the top function module containing a total of 69 genes was identified, and 31 of 69 genes were mitotic cell cycle regulation related. And survival analysis of the 31 genes revealed that 17/31 genes statistical significantly related to NSCLC overall survival, including 4 spindle assembly checkpoints, namely NDC80, BUB1B, MAD2L1 and AURKA. Further, multivariate cox regression analysis identified NDC80 and MAD2L1 as independent prognostic indicators in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) respectively. Interestingly, pearson correlation analysis indicated strong connection between the four genes NDC80, BUB1B, MAD2L1 and AURKA, and their clinical pathological features were addressed.\nCONCLUSIONS: Using bioinformatic analysis of GEO combined with TCGA data, we revealed two independent prognostic indicators in LUAD and LUSC respectively and analyzed their clinical features. However, more detailed experiments and clinical trials are needed to verify their drug targets role in clinical medical use.", "claims": [{"id": "claim-method", "statement": "And then multivariate COX regression analysis was performed using TCGA mRNA transcription data including 223 lung adenocarcinoma and 482 lung squamous cell carcinoma, which were downloaded from TCGA database [24] to identify the independent prognostic indicators from the univariate significant gene lists.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32795325", "locator": "sections[8] \"Survival analysis of module genes to identify key genes\" paragraph 3", "quote": "And then multivariate COX regression analysis was performed using TCGA mRNA transcription data including 223 lung adenocarcinoma and 482 lung squamous cell carcinoma, which were downloaded from TCGA database [24] to identify the independent prognostic indicators from the univariate significant gene lists."}], "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:32795325"], "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:32795325", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-020-00762-5", "sha256": "sha256:7b6f953a7422fcd2fb9b3752fa95af79cf2ab091d35b51249d5004fb0a1c5b29", "bytes": 35493, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-020-00762-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7437940", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32795325:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:afdbeb345a707f38396a25b9fca1636390b84af7732c58f5df5e154537d08ee4", "bytes": 1729, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab1", "version": null, "note": "Signaling pathways that Cluster 1 genes mainly enriched in", "structure": {"pmcid": "PMC7437940", "section_index": 13, "section_title": "Function module analysis based on PPI network", "row_count": 10, "column_count": 4}, "table": {"label": "Table 1", "caption": "Signaling pathways that Cluster 1 genes mainly enriched in", "rows": [["pathways", "count", "P value", "Related GDEs in the network"], ["Cell Cycle, Mitotic", "31", "2.76403E-29", "CENPE; KNTC1; KIF18A; TOP2A; MAD2L1; CCNB2; CKS1B; MCM4; CCNB1; PTTG1; NUF2; CDK1; AURKA; PLK1; TYMS; CCNA2; CDC20; NDC80; BUB1; CDC6; GINS2; CDC45; PLK4; CDCA8; KIF20A; RRM2; KIF2C; RFC4; KIF23; CENPF; NEK2;"], ["DNA Replication", "22", "1.71367E-18", "CENPE; KNTC1; KIF18A; MAD2L1; MCM4; NUF2; CDK1; PLK1; CDC20; NDC80; BUB1; CDC6; GINS2; CDC45; PLK4; CDCA8; KIF20A; KIF2C; RFC4; KIF23; CENPF; NEK2;"], ["Mitotic M-M/G1 phases", "20", "1.48601E-16", "CENPE; KNTC1; KIF18A; MAD2L1; MCM4; NUF2; CDK1; PLK1; CDC20; NDC80; BUB1; CDC6; CDC45; PLK4; CDCA8; KIF20A; KIF2C; KIF23; CENPF; NEK2;"], ["M Phase", "17", "5.76137E-16", "CENPE; KNTC1; KIF18A; MAD2L1; NUF2; CDK1; PLK1; CDC20; NDC80; BUB1; PLK4; CDCA8; KIF20A; KIF2C; KIF23; CENPF; NEK2;"], ["Polo-like kinase signaling events in the cell cycle", "14", "2.77681E-14", "CENPE; CCNB1; CDK1; AURKA; TPX2; ECT2; PLK1; PRC1; CDC20; NDC80; BUB1; PLK4; DLGAP5; KIF20A;"], ["PLK1 signaling events", "13", "3.83583E-13", "CENPE; CCNB1; CDK1; AURKA; TPX2; ECT2; PLK1; PRC1; CDC20; NDC80; BUB1; DLGAP5; KIF20A;"], ["Mitotic Prometaphase", "12", "5.11023E-12", "CENPE; KNTC1; KIF18A; MAD2L1; NUF2; PLK1; CDC20; NDC80; BUB1; CDCA8; KIF2C; CENPF;"], ["Cell Cycle Checkpoints", "11", "1.32039E-08", "MAD2L1; CCNB2; MCM4; NDC80; CCNB1; CDK1; CDC20; CDC6; CDC45; RFC4; CHEK1;"], ["Signaling by Aurora kinases", "11", "1.04137E-10", "NCAPH; NCAPG; AURKA; TPX2; NDC80; BUB1; CDCA8; DLGAP5; KIF20A; KIF2C; KIF23;"]], "row_count": 10, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32795325:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:68f06c4db5636237e1968b9d04e73502707129d37bad98d73a719d64cfdcb9f0", "bytes": 549, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab2", "version": null, "note": "Multivariate cox regression analysis on LUAD overall survival", "structure": {"pmcid": "PMC7437940", "section_index": 14, "section_title": "Survival analysis of cluster 1 module genes", "row_count": 10, "column_count": 4}, "table": {"label": "Table 2", "caption": "Multivariate cox regression analysis on LUAD overall survival", "rows": [["Variables", "Lung adenocarcinoma"], ["Hazard ratio", "95% CI", "P value"], ["Age"], ["< 60 years vs ≥60 years", "1.034", "1.006 ~ 1.064", "0.018"], ["Stage"], ["I vs II vs III vs IV", "1.554", "1.213 ~ 1.99", "0.001"], ["M"], ["Mo vs M1", "2.321", "1.172 ~ 4.069", "0.032"], ["NDC80 expression"], ["< median vs > median", "2.480", "1.375 ~ 4.472", "0.003"]], "row_count": 10, "column_count": 4, "numeric_cells": 15, "header_rows": 2, "locator": "section[14]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:32795325:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cd4afa44ea4bedbbab5bcfecf64b0e6b4bae0c04aefc0faa47416e46e2bca44f", "bytes": 485, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#Tab3", "version": null, "note": "Multivariate cox regression analysis on LUSC overall survival", "structure": {"pmcid": "PMC7437940", "section_index": 14, "section_title": "Survival analysis of cluster 1 module genes", "row_count": 8, "column_count": 4}, "table": {"label": "Table 3", "caption": "Multivariate cox regression analysis on LUSC overall survival", "rows": [["Variables", "Lung squamous cell carcinoma"], ["Hazard ratio", "95% CI", "P value"], ["T"], ["T1 vs T2 vs T3 vs T4", "1.305", "1.085 ~ 1.569", "0.005"], ["M"], ["Mo vs M1", "1.701", "1.172 ~ 2.469", "0.005"], ["MAD2L1 expression"], ["< median vs > median", "0.753", "0.567 ~ 0.999", "0.045"]], "row_count": 8, "column_count": 4, "numeric_cells": 10, "header_rows": 2, "locator": "section[14]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:32795325:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6b00a986f2bd1671a376df9c7d9e27a55aef54707a1e1798c3dd99ba65135437", "bytes": 1132, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab4", "version": null, "note": "The association between NDC80 and LUAD clinical pathological features", "structure": {"pmcid": "PMC7437940", "section_index": 15, "section_title": "NDC80 and MAD2L1 association with NSCLC clinical features", "row_count": 29, "column_count": 3}, "table": {"label": "Table 4", "caption": "The association between NDC80 and LUAD clinical pathological features", "rows": [["parameters", "NDC80", "P value"], ["–", "+"], ["Gender", "P = 0.209"], ["male", "45 (45.9%)", "53 (54.1%)"], ["female", "68 (54.4%)", "57 (45.6%)"], ["Age", "P = 0.027"], ["< 60 years old", "24 (39.3%)", "37 (60.7%)"], ["≥ 60 years old", "82 (56.2%)", "64 (43.8%)"], ["Smoke", "P = 0.002"], ["no", "23 (65.7%)", "12 (34.3%)"], ["Current smoker", "15 (32.6%)", "31 (67.4%)"], ["Smoker < 15 years", "31 (44.9%)", "38 (55.1%)"], ["Smoker ≥15 years", "39 (59.1%)", "27 (40.9%)"], ["Stage", "P = 0.032"], ["I", "66 (57.4%)", "49 (42.6%)"], ["II", "23 (48.9%)", "24 (51.1%)"], ["III", "15 (31.9%)", "32 (68.2%)"], ["IV", "5 (55.6%)", "4 (44.4%)"], ["T", "P = 0.199"], ["I", "37 (61.7%)", "23 (38.3%)"], ["II", "63 (47.7%)", "68 (52.3%)"], ["III", "7 (41.2%)", "10 (58.8%)"], ["IV", "6 (40.0%)", "9 (60.0%)"], ["N", "P = 0.053"], ["-", "69 (56.6%)", "53 (43.4%)"], ["+", "44 (43.6%)", "57 (56.4%)"], ["M", "P = 0.497"], ["-", "81 (50.9%)", "78 (49.1%)"], ["+", "27 (45.8%)", "31 (54.2%)"]], "row_count": 29, "column_count": 3, "numeric_cells": 52, "header_rows": 2, "locator": "section[15]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:32795325:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:39ef4c3df65f3735cdad5a92a721a62abb1b17f7f42611f50032fc3f5cdef50d", "bytes": 1107, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#Tab5", "version": null, "note": "The association between MAD2L1 and LUSC clinical pathological features", "structure": {"pmcid": "PMC7437940", "section_index": 15, "section_title": "NDC80 and MAD2L1 association with NSCLC clinical features", "row_count": 28, "column_count": 3}, "table": {"label": "Table 5", "caption": "The association between MAD2L1 and LUSC clinical pathological features", "rows": [["parameters", "MAD2L1", "P value"], ["–", "+"], ["Gender", "P = 0.097"], ["male", "170 (47.8%)", "186 (52.2%)"], ["female", "71 (56.3%)", "55 (43.7%)"], ["Age", "P = 0.100"], ["< 60 years old", "44 (42.7%)", "59 (57.3%)"], ["≥ 60 years old", "192 (51.9%)", "178 (48.1%)"], ["Smoke", "P = 0.973"], ["no", "131 (50.6%)", "128 (49.4%)"], ["Smoker < 15 years", "28 (50.0%)", "28 (50.0%)"], ["Smoker ≥15 years", "82 (49.4%)", "84 (50.6%)"], ["Stage", "P = 0.062"], ["I", "132 (56.2%)", "103 (43.8%)"], ["II", "70 (44.6%)", "87 (55.4%)"], ["III", "35 (42.7%)", "47 (57.3%)"], ["IV", "4 (57.1%)", "3 (42.9%)"], ["T", "P = 0.314"], ["I", "60 (56.1%)", "47 (43.9%)"], ["II", "131 (46.5%)", "151 (53.5%)"], ["III", "38 (54.3%)", "32 (45.7%)"], ["IV", "12 (52.2%)", "11 (47.8%)"], ["N", "P = 0.001"], ["-", "171 (55.9%)", "135 (44.1%)"], ["+", "70 (39.8%)", "106 (60.2%)"], ["M", "P = 0.036"], ["-", "188 (48.0%)", "204 (52.0%)"], ["+", "52 (60.5%)", "34 (39.5%)"]], "row_count": 28, "column_count": 3, "numeric_cells": 49, "header_rows": 2, "locator": "section[15]/table-wrap[2]#Tab5"}}, {"id": "asset:table:pmid:32795325:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b2b2be4b9d5288c2c72b9fbe7ad5a0ad0dce5ae6cddd7be979750d96a2214bdd", "bytes": 776, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#Tab6", "version": null, "note": "Go analysis revealing biological processes centered on NDC80", "structure": {"pmcid": "PMC7437940", "section_index": 16, "section_title": "NDC80 and MAD2L1 centered signaling pathways", "row_count": 6, "column_count": 5}, "table": {"label": "Table 6", "caption": "Go analysis revealing biological processes centered on NDC80", "rows": [["Description", "Gene counts", "Background gene counts", "FDR", "Matching proteins in the network"], ["Cell division", "11", "483", "7.33E-16", "AURKB,BUB1,BUB1B,CASC5,NUF2,CENPE,MAD2L1,NDC80,SPC24,SPC25,ZWINT"], ["Chromosome segregation", "10", "253", "7.33E-16", "AURKB,BUB1,BUB1B,CASC5,CENPE, MAD2L1,NDC80,NUF2,SPC25,ZWINT"], ["Sister chromatid segregation", "7", "123", "1.31E-11", "AURKB,BUB1,BUB1B,CENPE,MAD2L1, NDC80,ZWINT"], ["Spindle attachment to kinetochore", "4", "20", "1.32E-08", "AURKB,CASC5,CENPE,NDC80"], ["Spindle checkpoint", "4", "23", "2.07E-08", "AURKB,BUB1,BUB1B,MAD2L1"]], "row_count": 6, "column_count": 5, "numeric_cells": 19, "header_rows": 1, "locator": "section[16]/table-wrap[1]#Tab6"}}, {"id": "asset:table:pmid:32795325:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f6f1ca179672d1f2de68cc2c2945362a669d33093fa8130188df9a3f8d18f432", "bytes": 837, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#Tab7", "version": null, "note": "Go analysis revealing biological processes centered on MAD2L1", "structure": {"pmcid": "PMC7437940", "section_index": 16, "section_title": "NDC80 and MAD2L1 centered signaling pathways", "row_count": 6, "column_count": 5}, "table": {"label": "Table 7", "caption": "Go analysis revealing biological processes centered on MAD2L1", "rows": [["Description", "Gene counts", "Background gene counts", "FDR", "Matching proteins in the network"], ["Cell division", "10", "483", "1.09E-15", "ANAPC1,ANAPC4,BUB1,BUB1B,BUB3, CDC16,CDC20,MAD1L1,MAD2L1,NEK2"], ["Nuclear division regulation", "9", "184", "9.05E-15", "ANAPC4,BUB1,NEK2,BUB1B,BUB3, CDC16,CDC20,MAD1L1,MAD2L1"], ["Chromosome organization", "8", "999", "6.17E-08", "BUB1,BUB1B,BUB3,CCNA2,CDC20, MAD1L1,MAD2L1,NEK2"], ["anaphase-promoting complex-dependent catabolic process", "7", "35", "9.05E-15", "ANAPC1,ANAPC4,BUB1B,BUB3,CDC16,CDC20,MAD2L1"], ["Mitotic spindle assembly checkpoint", "5", "21", "4.46E-11", "BUB1,BUB1B,BUB3,MAD1L1,MAD2L1"]], "row_count": 6, "column_count": 5, "numeric_cells": 19, "header_rows": 1, "locator": "section[16]/table-wrap[2]#Tab7"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "And then multivariate COX regression analysis was performed using TCGA mRNA transcription data including 223 lung adenocarcinoma and 482 lung squamous cell carcinoma, which were downloaded from TCGA database [24] to identify the independent prognostic indicators from the univariate significant gene lists."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan meier"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.7, "band": "medium", "quote": "pearson correlation"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"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": "Pathway enrichment"}}], "targets": [], "gaps": []}, "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": "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:32795325", "asset:table:pmid:32795325:1", "asset:table:pmid:32795325:2", "asset:table:pmid:32795325:3", "asset:table:pmid:32795325:4", "asset:table:pmid:32795325:5", "asset:table:pmid:32795325:6", "asset:table:pmid:32795325:7"], "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": "2026-10-31T19:08:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 29493, "completion_tokens": 2845, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32795325", "type": "paper", "label": "pmid:32795325"}, {"id": "source:pmid:32795325", "type": "manuscript", "label": "PMID 32795325 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32795325", "type": "paper", "label": "pmid:32795325"}, {"id": "source:pmid:32795325", "type": "manuscript", "label": "PMID 32795325 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32795325", "type": "extraction", "used": ["source:pmid:32795325"], "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:32795325", "parent_hash": "sha256:41d0c2ec277bec6fa9852cd0665926513fc0c3125cf18010733ec549a080dadf", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["And then multivariate COX regression analysis was performed using TCGA mRNA transcription data including 223 lung adenocarcinoma and 482 lung squamous cell carcinoma, which were downloaded from TCGA database [24] to identify the independent prognostic indicators from the univariate significant gene lists."], "order_basis": "analysis_only", "id": "assay:1"}]}