Role of CENPL, DARS2, and PAICS in determining the prognosis of patients with lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39507047", "kind": "science-record", "revision": 4, "content_hash": "sha256:1d42fc8544ce82793a2d24634f35e70b5311afb16d6d0be303429a3db88348b9", "created_at": "2026-11-01T20:29:45Z", "updated_at": "2026-11-01T22:55:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Role of CENPL, DARS2, and PAICS in determining the prognosis of patients with lung adenocarcinoma.", "doi": "10.21037/tlcr-24-696", "pmid": "39507047", "authors": ["Rongjian Xu", "Fengyi Han", "Yandong Zhao", "Ao Liu", "Ning An", "Baogang Wang", "Patrick Zardo", "José Sanz-Santos", "Aimée J P M Franssen", "Erik R de Loos", "Min Zhao"], "journal": "Translational lung cancer research", "year": 2024, "abstract": "Background: Non-small cell lung cancer (NSCLC) accounts for about 85% of lung cancers, and is the leading cause of tumor-related death. Lung adenocarcinoma (LUAD) is the most prevalent subtype of NSCLC. Although significant progress of LUAD treatment has been made under multimodal strategies, the prognosis of advanced LUAD is still poor due to recurrence and metastasis. There is still a lack of reliable markers to evaluate the LUAD prognosis. This study aims to explore novel biomarkers and construct a prognostic model to predict the prognosis of LUAD patients.\nMethods: The Genomic Data Commons-The Cancer Genome Atlas-Lung Adenocarcinoma (GDC-TCGA-LUAD) dataset was downloaded from the University of California, Santa Cruz (UCSC) Xena browser. The GSE72094 and GSE13213 datasets and corresponding clinical information were downloaded from the Gene Expression Omnibus (GEO) database. By analyzing these datasets using DESeq2 R package and Limma R package, differentially expressed genes (DEGs) were found. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to analyze possible enrichment pathways. A protein-protein interaction (PPI) network was constructed to explore possible relationship among DEGs by using the STRING database. A survival analysis was performed to identify reliable prognostic genes using the Kaplan-Meier method. A multi-omics analysis was performed using the Gene Set Cancer Analysis (GSCA). The Tumor Immune Estimation Score (TIMER) database was used to analyze the association between prognostic genes and immune infiltration. A Spearman correlation analysis was conducted to examine the correlation between prognostic genes and drug sensitivity. A multivariate Cox regression was used to identify independent prognostic factors. Next, a nomogram was constructed using the rms R package. Finally, the expressions of aspartyl-tRNA synthetase 2 (DARS2) and phosphoribosyl aminoimidazole carboxylase (PAICS) were detected using immunohistochemistry (IHC).\nResults: We screened out 30 DEGs prior to functional enrichment and PPI network analysis revealing potential enrichment pathways and interactions of these DEGs. Then survival analysis revealed the CENPL, DARS2, and PAICS expression was negatively correlated with LUAD prognosis. Additionally, multi-omics analysis showed CENPL, DARS2, and PAICS expressions were significantly higher in LUAD tissues than normal tissues. CENPL, DARS2, and PAICS were all up-regulated in late stage and M1 stage. Correlation analysis indicated CENPL, DARS2, and PAICS may not be associated with activation or suppression of immune cells. Drug sensitivity analysis revealed many potentially effective drugs and small molecule compounds. Moreover, we successfully constructed a robust and stable nomogram by combining the DARS2 and PAICS expression with other clinicopathological variables. Finally, IHC results showed DARS2 and PAICS were significantly up-regulated in LUAD.\nConclusions: The CENPL, DARS2, and PAICS expression was negatively correlated with LUAD prognosis. A prognostic model, which integrated DARS2, PAICS, and other clinicopathological variables, was able to effectively predict LUAD patients prognosis.", "claims": [{"id": "claim-method", "statement": "The Kaplan-Meier method was used for survival analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39507047", "locator": "sections[8] \"Identification of key genes significantly associated with prognosis\" paragraph 2", "quote": "The Kaplan-Meier method was used for survival analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Available at https://tlcr.amegroups.com/article/view/10.21037/tlcr-24-696/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39507047", "locator": "sections[32] \"Data Sharing Statement\" paragraph 2", "quote": "Available at https://tlcr.amegroups.com/article/view/10.21037/tlcr-24-696/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "A prognostic model integrating DARS2, PAICS, and other clinicopathological variables effectively predicted prognosis in LUAD patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39507047", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "A prognostic model, which integrated DARS2, PAICS, and other clinicopathological variables, was able to effectively predict LUAD patients prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A prognostic model integrating DARS2, PAICS, and other clinicopathological variables effectively predicted prognosis in LUAD patients.", "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:39507047"], "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:GSE13213"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13213"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39507047", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tlcr-24-696", "sha256": "sha256:146a61fd5c24c088c362b5a8b70a795459c75841a2673f1aa3df767f3258be32", "bytes": 45139, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tlcr-24-696", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11535832", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13213", "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=GSE13213", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13213", "version": null, "note": "Available at https://tlcr.amegroups.com/article/view/10.21037/tlcr-24-696/dss", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Available at https://tlcr.amegroups.com/article/view/10.21037/tlcr-24-696/dss", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM333673", "GSM333674", "GSM333675", "GSM333676", "GSM333677", "GSM333678", "GSM333679", "GSM333680", "GSM333681", "GSM333682", "GSM333683", "GSM333684", "GSM333685", "GSM333686", "GSM333687", "GSM333688", "GSM333689", "GSM333690", "GSM333691", "GSM333692", "GSM333693", "GSM333694", "GSM333695", "GSM333696", "GSM333697", "GSM333698", "GSM333699", "GSM333700", "GSM333701", "GSM333702", "GSM333703", "GSM333704", "GSM333705", "GSM333706", "GSM333707", "GSM333708", "GSM333709", "GSM333710", "GSM333711", "GSM333712", "GSM333713", "GSM333714", "GSM333715", "GSM333716", "GSM333717", "GSM333718", "GSM333719", "GSM333720", "GSM333721", "GSM333722", "GSM333723", "GSM333724", "GSM333725", "GSM333726", "GSM333727", "GSM333728", "GSM333729", "GSM333730", "GSM333731", "GSM333732", "GSM333733", "GSM333734", "GSM333735", "GSM333736", "GSM333737", "GSM333738", "GSM333739", "GSM333740", "GSM333741", "GSM333742", "GSM333743", "GSM333744", "GSM333745", "GSM333746", "GSM333747", "GSM333748", "GSM333749", "GSM333750", "GSM333751", "GSM333752", "GSM333753", "GSM333754", "GSM333755", "GSM333756", "GSM333757", "GSM333758", "GSM333759", "GSM333760", "GSM333761", "GSM333762", "GSM333763", "GSM333764", "GSM333765", "GSM333766", "GSM333767", "GSM333768", "GSM333769", "GSM333770", "GSM333771", "GSM333772", "GSM333773", "GSM333774", "GSM333775", "GSM333776", "GSM333777", "GSM333778", "GSM333779", "GSM333780", "GSM333781", "GSM333782", "GSM333783", "GSM333784", "GSM333785", "GSM333786", "GSM333787", "GSM333788", "GSM333789"], "sample_count": 117, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis", "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:GSE72094", "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=GSE72094", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72094", "version": null, "note": "Available at https://tlcr.amegroups.com/article/view/10.21037/tlcr-24-696/dss", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Available at https://tlcr.amegroups.com/article/view/10.21037/tlcr-24-696/dss", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1854797", "GSM1854798", "GSM1854799", "GSM1854800", "GSM1854801", "GSM1854802", "GSM1854803", "GSM1854804", "GSM1854805", "GSM1854806", "GSM1854807", "GSM1854808", "GSM1854809", "GSM1854810", "GSM1854811", "GSM1854812", "GSM1854813", "GSM1854814", "GSM1854815", "GSM1854816", "GSM1854817", "GSM1854818", "GSM1854819", "GSM1854820", "GSM1854821", "GSM1854822", "GSM1854823", "GSM1854824", "GSM1854825", "GSM1854826", "GSM1854827", "GSM1854828", "GSM1854829", "GSM1854830", "GSM1854831", "GSM1854832", "GSM1854833", "GSM1854834", "GSM1854835", "GSM1854836", "GSM1854837", "GSM1854838", "GSM1854839", "GSM1854840", "GSM1854841", "GSM1854842", "GSM1854843", "GSM1854844", "GSM1854845", "GSM1854846", "GSM1854847", "GSM1854848", "GSM1854849", "GSM1854850", "GSM1854851", "GSM1854852", "GSM1854853", "GSM1854854", "GSM1854855", "GSM1854856", "GSM1854857", "GSM1854858", "GSM1854859", "GSM1854860", "GSM1854861", "GSM1854862", "GSM1854863", "GSM1854864", "GSM1854865", "GSM1854866", "GSM1854867", "GSM1854868", "GSM1854869", "GSM1854870", "GSM1854871", "GSM1854872", "GSM1854873", "GSM1854874", "GSM1854875", "GSM1854876", "GSM1854877", "GSM1854878", "GSM1854879", "GSM1854880", "GSM1854881", "GSM1854882", "GSM1854883", "GSM1854884", "GSM1854885", "GSM1854886", "GSM1854887", "GSM1854888", "GSM1854889", "GSM1854890", "GSM1854891", "GSM1854892", "GSM1854893", "GSM1854894", "GSM1854895", "GSM1854896", "GSM1854897", "GSM1854898", "GSM1854899", "GSM1854900", "GSM1854901", "GSM1854902", "GSM1854903", "GSM1854904", "GSM1854905", "GSM1854906", "GSM1854907", "GSM1854908", "GSM1854909", "GSM1854910", "GSM1854911", "GSM1854912", "GSM1854913", "GSM1854914", "GSM1854915", "GSM1854916", "GSM1854917", "GSM1854918", "GSM1854919", "GSM1854920", "GSM1854921", "GSM1854922", "GSM1854923", "GSM1854924", "GSM1854925", "GSM1854926", "GSM1854927", "GSM1854928", "GSM1854929", "GSM1854930", "GSM1854931", "GSM1854932", "GSM1854933", "GSM1854934", "GSM1854935", "GSM1854936", "GSM1854937", "GSM1854938", "GSM1854939", "GSM1854940", "GSM1854941", "GSM1854942", "GSM1854943", "GSM1854944", "GSM1854945", "GSM1854946", "GSM1854947", "GSM1854948", "GSM1854949", "GSM1854950", "GSM1854951", "GSM1854952", "GSM1854953", "GSM1854954", "GSM1854955", "GSM1854956", "GSM1854957", "GSM1854958", "GSM1854959", "GSM1854960", "GSM1854961", "GSM1854962", "GSM1854963", "GSM1854964", "GSM1854965", "GSM1854966", "GSM1854967", "GSM1854968", "GSM1854969", "GSM1854970", "GSM1854971", "GSM1854972", "GSM1854973", "GSM1854974", "GSM1854975", "GSM1854976", "GSM1854977", "GSM1854978", "GSM1854979", "GSM1854980", "GSM1854981", "GSM1854982", "GSM1854983", "GSM1854984", "GSM1854985", "GSM1854986", "GSM1854987", "GSM1854988", "GSM1854989", "GSM1854990", "GSM1854991", "GSM1854992", "GSM1854993", "GSM1854994", "GSM1854995", "GSM1854996", "GSM1854997", "GSM1854998", "GSM1854999", "GSM1855000", "GSM1855001", "GSM1855002", "GSM1855003", "GSM1855004", "GSM1855005", "GSM1855006", "GSM1855007", "GSM1855008", "GSM1855009", "GSM1855010", "GSM1855011", "GSM1855012", "GSM1855013", "GSM1855014", "GSM1855015", "GSM1855016", "GSM1855017", "GSM1855018", "GSM1855019", "GSM1855020", "GSM1855021", "GSM1855022", "GSM1855023", "GSM1855024", "GSM1855025", "GSM1855026", "GSM1855027", "GSM1855028", "GSM1855029", "GSM1855030", "GSM1855031", "GSM1855032", "GSM1855033", "GSM1855034", "GSM1855035", "GSM1855036", "GSM1855037", "GSM1855038", "GSM1855039", "GSM1855040", "GSM1855041", "GSM1855042", "GSM1855043", "GSM1855044", "GSM1855045", "GSM1855046", "GSM1855047", "GSM1855048", "GSM1855049", "GSM1855050", "GSM1855051", "GSM1855052", "GSM1855053", "GSM1855054", "GSM1855055", "GSM1855056", "GSM1855057", "GSM1855058", "GSM1855059", "GSM1855060", "GSM1855061", "GSM1855062", "GSM1855063", "GSM1855064", "GSM1855065", "GSM1855066", "GSM1855067", "GSM1855068", "GSM1855069", "GSM1855070", "GSM1855071", "GSM1855072", "GSM1855073", "GSM1855074", "GSM1855075", "GSM1855076", "GSM1855077", "GSM1855078", "GSM1855079", "GSM1855080", "GSM1855081", "GSM1855082", "GSM1855083", "GSM1855084", "GSM1855085", "GSM1855086", "GSM1855087", "GSM1855088", "GSM1855089", "GSM1855090", "GSM1855091", "GSM1855092", "GSM1855093", "GSM1855094", "GSM1855095", "GSM1855096", "GSM1855097", "GSM1855098", "GSM1855099", "GSM1855100", "GSM1855101", "GSM1855102", "GSM1855103", "GSM1855104", "GSM1855105", "GSM1855106", "GSM1855107", "GSM1855108", "GSM1855109", "GSM1855110", "GSM1855111", "GSM1855112", "GSM1855113", "GSM1855114", "GSM1855115", "GSM1855116", "GSM1855117", "GSM1855118", "GSM1855119", "GSM1855120", "GSM1855121", "GSM1855122", "GSM1855123", "GSM1855124", "GSM1855125", "GSM1855126", "GSM1855127", "GSM1855128", "GSM1855129", "GSM1855130", "GSM1855131", "GSM1855132", "GSM1855133", "GSM1855134", "GSM1855135", "GSM1855136", "GSM1855137", "GSM1855138", "GSM1855139", "GSM1855140", "GSM1855141", "GSM1855142", "GSM1855143", "GSM1855144", "GSM1855145", "GSM1855146", "GSM1855147", "GSM1855148", "GSM1855149", "GSM1855150", "GSM1855151", "GSM1855152", "GSM1855153", "GSM1855154", "GSM1855155", "GSM1855156", "GSM1855157", "GSM1855158", "GSM1855159", "GSM1855160", "GSM1855161", "GSM1855162", "GSM1855163", "GSM1855164", "GSM1855165", "GSM1855166", "GSM1855167", "GSM1855168", "GSM1855169", "GSM1855170", "GSM1855171", "GSM1855172", "GSM1855173", "GSM1855174", "GSM1855175", "GSM1855176", "GSM1855177", "GSM1855178", "GSM1855179", "GSM1855180", "GSM1855181", "GSM1855182", "GSM1855183", "GSM1855184", "GSM1855185", "GSM1855186", "GSM1855187", "GSM1855188", "GSM1855189", "GSM1855190", "GSM1855191", "GSM1855192", "GSM1855193", "GSM1855194", "GSM1855195", "GSM1855196", "GSM1855197", "GSM1855198", "GSM1855199", "GSM1855200", "GSM1855201", "GSM1855202", "GSM1855203", "GSM1855204", "GSM1855205", "GSM1855206", "GSM1855207", "GSM1855208", "GSM1855209", "GSM1855210", "GSM1855211", "GSM1855212", "GSM1855213", "GSM1855214", "GSM1855215", "GSM1855216", "GSM1855217", "GSM1855218", "GSM1855219", "GSM1855220", "GSM1855221", "GSM1855222", "GSM1855223", "GSM1855224", "GSM1855225", "GSM1855226", "GSM1855227", "GSM1855228", "GSM1855229", "GSM1855230", "GSM1855231", "GSM1855232", "GSM1855233", "GSM1855234", "GSM1855235", "GSM1855236", "GSM1855237", "GSM1855238"], "sample_count": 442, "group_sizes": null, "group_sizes_basis": null, "platform": "15048", "taxon": "Homo sapiens", "title": "KRAS mutation-associated gene expression, p53 and STK11 mutations, proliferation and immune surveillance in lung adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE13213 not downloaded", "asset:data:geo:GSE13213 licence not read", "asset:data:geo:GSE72094 not downloaded", "asset:data:geo:GSE72094 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The Kaplan-Meier method was used for survival analysis."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-3", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-4", "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": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-5", "family": "differential_expression", "specific": "deseq2", "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": 0.7, "band": "medium", "quote": "DESeq2"}}, {"id": "method-6", "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": 0.7, "band": "medium", "quote": "Limma"}}, {"id": "method-7", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.7, "band": "medium", "quote": "Spearman correlation"}}, {"id": "method-8", "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"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE72094", "GSE13213"], "resolved_accessions": ["GSE72094", "GSE13213"], "statements": ["Available at https://tlcr.amegroups.com/article/view/10.21037/tlcr-24-696/dss"], "basis": "The paper names GSE72094, GSE13213 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:39507047", "data:geo:GSE13213"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13213"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:37:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13225, "completion_tokens": 2602, "cached_tokens": 256}}, "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:39507047", "type": "paper", "label": "pmid:39507047"}, {"id": "source:pmid:39507047", "type": "manuscript", "label": "PMID 39507047 full text"}, {"id": "data:geo:GSE13213", "type": "dataset", "label": "GEO GSE13213"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39507047", "type": "paper", "label": "pmid:39507047"}, {"id": "source:pmid:39507047", "type": "manuscript", "label": "PMID 39507047 full text"}, {"id": "data:geo:GSE13213", "type": "dataset", "label": "GEO GSE13213"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39507047", "type": "extraction", "used": ["source:pmid:39507047"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13213", "type": "accession_resolution", "used": ["data:geo:GSE13213"], "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:39507047", "parent_hash": "sha256:6f23c922ad81806ac1643ac6cafd11ab9c60fbc8ebbb4c04a0417ca9dbcc8637", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE13213 licence not read", "asset:data:geo:GSE13213 not downloaded", "asset:data:geo:GSE72094 licence not read", "asset:data:geo:GSE72094 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["zole carboxylase (PAICS) were detected using immunohistochemistry (IHC). Results: We screened out 30 DEGs prio", "S) were detected using immunohistochemistry (IHC). Results: We screened out 30 DEGs prior to", "ther clinicopathological variables. Finally, IHC results showed DARS2 and PAICS were signific"], "order_basis": "paper_text_order:2048", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Kaplan-Meier method was used for survival analysis."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}