Identification of critical prognosis signature associated with lymph node metastasis of stomach adenocarcinomas.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36823639", "kind": "science-record", "revision": 3, "content_hash": "sha256:5831883699c491f761917ec49774e45b6d97c7416bdcb929277ac208e463dc01", "created_at": "2026-11-01T19:01:26Z", "updated_at": "2026-11-01T22:08:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of critical prognosis signature associated with lymph node metastasis of stomach adenocarcinomas.", "doi": "10.1186/s12957-023-02940-y", "pmid": "36823639", "authors": ["Xiaohui Wang", "Wei Zhang", "Yulin Guo", "Yifei Zhang", "Xiaofeng Bai", "Yibin Xie"], "journal": "World journal of surgical oncology", "year": 2023, "abstract": "Lymph node metastasis (LNM) is an important factor affecting the prognosis of patients with gastric adenocarcinoma (STAD), which is the most common malignancy of the human digestive system. Current detection techniques have limited sensitivity and specificity, and there is a lack of effective biomarkers to screen for LNM. Therefore, it is critical to screen for biomarkers that predict LNM in STAD. Gene expression differential analysis (false discovery rate < 0.05, |log2Fold change| ≥1.5) was performed on 102 LNM samples, 224 non-LNM samples, and 29 normal gastric tissue samples from The Cancer Genome Atlas (TCGA) STAD dataset, and 269 LNM-specific genes (DEGs) were obtained. Enrichment analysis showed that LNM-specific genes functioned mainly in cytokine-cytokine receptor interactions, calcium signaling, and other pathways. Ten DEGs significantly associated with overall survival in STAD patients were screened by multivariate Cox regression, and an LNM-based 10-mRNA prognostic signature was established (Logrank P < 0.0001). This 10-mRNA signature was well predicted in both the TCGA training set and the Gene Expression Omnibus validation dataset (GSE84437) and was associated with survival in patients with LNM or advanced-stage STAD. Using Kaplan-Meier survival, receiver operating characteristic curve, C-index analysis, and decision curve analysis, the 10-mRNA signature was found to be a more effective predictor of prognosis in STAD patients than the other two reported models (P < 0.0005). Protein-protein interaction network and gene set enrichment analysis of the 10-mRNA signature revealed that the signature may affect the expression of multiple biological pathways and related genes. Finally, the expression levels of prognostic genes in STAD tissues and cell lines were verified using qRT-PCR, Western blot, and the Human Protein Atlas database. Taken together, the prognostic signature constructed in this study may become an indicator for clinical prognostic assessment of LNM-STAD and provide a new strategy for future targeted therapy.", "claims": [{"id": "claim-method", "statement": "Then, multivariate COX regression analysis was conducted using a bivariate stepwise regression method to screen out genes associated with the prognosis of STAD patients, and risk scores (RS) were calculated according to the following formula.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36823639", "locator": "sections[5] \"Construction and evaluation of prognostic signature\" paragraph 2", "quote": "Then, multivariate COX regression analysis was conducted using a bivariate stepwise regression method to screen out genes associated with the prognosis of STAD patients, and risk scores (RS) were calculated according to the following formula."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36823639", "locator": "sections[28] \"Availability of data and materials\" paragraph 2", "quote": "The TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A 10-mRNA prognostic signature was well validated in the TCGA training set and the GSE84437 validation dataset and was a more effective predictor of prognosis in STAD patients than two previously reported models (P < 0.0005).", "kind": "quantitative", "target": {"value": 0.0005, "unit": "p-value", "tolerance": null, "source": "Using Kaplan-Meier survival, receiver operating characteristic curve, C-index analysis, and decision curve analysis, the 10-mRNA signature was found to be a more effective predictor of prognosis in STAD patients than the other two reported models (P < 0.0005)."}, "evidence": [{"asset": "source:pmid:36823639", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This 10-mRNA signature was well predicted in both the TCGA training set and the Gene Expression Omnibus validation dataset (GSE84437) and was associated with survival in patients with LNM or advanced-stage STAD."}, {"asset": "source:pmid:36823639", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using Kaplan-Meier survival, receiver operating characteristic curve, C-index analysis, and decision curve analysis, the 10-mRNA signature was found to be a more effective predictor of prognosis in STAD patients than the other two reported models (P < 0.0005)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A 10-mRNA prognostic signature was well validated in the TCGA training set and the GSE84437 validation dataset and was a more effective predictor of prognosis in STAD patients than two previously reported models (P < 0.0005).", "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:36823639"], "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:GSE84437"], "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:GSE84437"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36823639", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12957-023-02940-y", "sha256": "sha256:09c1675b4c3fa7c144b361a6850611ad2b4f9858214dba4a98dfd0d300c6d3d4", "bytes": 49425, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12957-023-02940-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9948474", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84437", "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=GSE84437", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84437", "version": null, "note": "The TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2235556", "GSM2235557", "GSM2235558", "GSM2235559", "GSM2235560", "GSM2235561", "GSM2235562", "GSM2235563", "GSM2235564", "GSM2235565", "GSM2235566", "GSM2235567", "GSM2235568", "GSM2235569", "GSM2235570", "GSM2235571", "GSM2235572", "GSM2235573", "GSM2235574", "GSM2235575", "GSM2235576", "GSM2235577", "GSM2235578", "GSM2235579", "GSM2235580", "GSM2235582", "GSM2235584", "GSM2235585", "GSM2235586", "GSM2235587", "GSM2235588", "GSM2235589", "GSM2235593", "GSM2235595", "GSM2235596", "GSM2235597", "GSM2235598", "GSM2235599", "GSM2235600", "GSM2235601", "GSM2235602", "GSM2235603", "GSM2235604", "GSM2235605", "GSM2235606", "GSM2235607", "GSM2235608", "GSM2235609", "GSM2235610", "GSM2235611", "GSM2235612", "GSM2235613", "GSM2235614", "GSM2235615", "GSM2235616", "GSM2235617", "GSM2235618", "GSM2235619", "GSM2235620", "GSM2235621", "GSM2235622", "GSM2235623", "GSM2235624", "GSM2235625", "GSM2235626", "GSM2235627", "GSM2235628", "GSM2235629", "GSM2235630", "GSM2235631", "GSM2235632", "GSM2235633", "GSM2235634", "GSM2235635", "GSM2235636", "GSM2235637", "GSM2235695", "GSM2235696", "GSM2235697", "GSM2235698", "GSM2235699", "GSM2235700", "GSM2235701", "GSM2235702", "GSM2235703", "GSM2235704", "GSM2235705", "GSM2235706", "GSM2235707", "GSM2235708", "GSM2235709", "GSM2235710", "GSM2235711", "GSM2235712", "GSM2235713", "GSM2235714", "GSM2235715", "GSM2235716", "GSM2235717", "GSM2235718", "GSM2235719", "GSM2235720", "GSM2235721", "GSM2235722", "GSM2235723", "GSM2235724", "GSM2235725", "GSM2235726", "GSM2235727", "GSM2235728", "GSM2235729", "GSM2235730", "GSM2235731", "GSM2235732", "GSM2235733", "GSM2235734", "GSM2235735", "GSM2235736", "GSM2235737", "GSM2235738", "GSM2235739", "GSM2235740", "GSM2235741", "GSM2235742", "GSM2235743", "GSM2235744", "GSM2235745", "GSM2235746", "GSM2235747", "GSM2235748", "GSM2235749", "GSM2235750", "GSM2235751", "GSM2235752", "GSM2235753", "GSM2235754", "GSM2235755", "GSM2235756", "GSM2235757", "GSM2235758", "GSM2235759", "GSM2235760", "GSM2235761", "GSM2235762", "GSM2235763", "GSM2235764", "GSM2235765", "GSM2235766", "GSM2235767", "GSM2235768", "GSM2235769", "GSM2235770", "GSM2235771", "GSM2235772", "GSM2235773", "GSM2235774", "GSM2235775", "GSM2235776", "GSM2235777", "GSM2235778", "GSM2235779", "GSM2235780", "GSM2235781", "GSM2235782", "GSM2235783", "GSM2235784", "GSM2235785", "GSM2235786", "GSM2235787", "GSM2235788", "GSM2235789", "GSM2235790", "GSM2235791", "GSM2235792", "GSM2235793", "GSM2235794", "GSM2235795", "GSM2235796", "GSM2235797", "GSM2235798", "GSM2235799", "GSM2235800", "GSM2235801", "GSM2235802", "GSM2235803", "GSM2235804", "GSM2235805", "GSM2235806", "GSM2235807", "GSM2235808", "GSM2235809", "GSM2235810", "GSM2235811", "GSM2235812", "GSM2235813", "GSM2235814", "GSM2235815", "GSM2235816", "GSM2235817", "GSM2235818", "GSM2235819", "GSM2235820", "GSM2235821", "GSM2235822", "GSM2235823", "GSM2235824", "GSM2235825", "GSM2235826", "GSM2235827", "GSM2235828", "GSM2235829", "GSM2235830", "GSM2235831", "GSM2235837", "GSM2235838", "GSM2235839", "GSM2235840", "GSM2235841", "GSM2235842", "GSM2235843", "GSM2235844", "GSM2235845", "GSM2235846", "GSM2235847", "GSM2235848", "GSM2235849", "GSM2235850", "GSM2235851", "GSM2235852", "GSM2235853", "GSM2235854", "GSM2235855", "GSM2235862", "GSM2235863", "GSM2235864", "GSM2235865", "GSM2235866", "GSM2235867", "GSM2235878", "GSM2235879", "GSM2235880", "GSM2235881", "GSM2235882", "GSM2235883", "GSM2235884", "GSM2235885", "GSM2235886", "GSM2235887", "GSM2235888", "GSM2235889", "GSM2235899", "GSM2235900", "GSM2235901", "GSM2235902", "GSM2235903", "GSM2235904", "GSM2235905", "GSM2235906", "GSM2235907", "GSM2235908", "GSM2235909", "GSM2235910", "GSM2235921", "GSM2235922", "GSM2235923", "GSM2235924", "GSM2235925", "GSM2235926", "GSM2235927", "GSM2235928", "GSM2235929", "GSM2235930", "GSM2235931", "GSM2235932", "GSM2235933", "GSM2235934", "GSM2235935", "GSM2235936", "GSM2235937", "GSM2235938", "GSM2235939", "GSM2235940", "GSM2235941", "GSM2235942", "GSM2235943", "GSM2235944", "GSM2235945", "GSM2235946", "GSM2235947", "GSM2235948", "GSM2235949", "GSM2235950", "GSM2235951", "GSM2235952", "GSM2235953", "GSM2235954", "GSM2235955", "GSM2235956", "GSM2235957", "GSM2235958", "GSM2235959", "GSM2235960", "GSM2235961", "GSM2235962", "GSM2235963", "GSM2235964", "GSM2235965", "GSM2235966", "GSM2235967", "GSM2235968", "GSM2235969", "GSM2235970", "GSM2235971", "GSM2235972", "GSM2235973", "GSM2235974", "GSM2235975", "GSM2235976", "GSM2235977", "GSM2235978", "GSM2235979", "GSM2235980", "GSM2235981", "GSM2235982", "GSM2235983", "GSM2235984", "GSM2235985", "GSM2235986", "GSM2235987", "GSM2235988", "GSM2235991", "GSM2235992", "GSM2235993", "GSM2235994", "GSM2235995", "GSM2235996", "GSM2235997", "GSM2235998", "GSM2235999", "GSM2236000", "GSM2236001", "GSM2236002", "GSM2236003", "GSM2236004", "GSM2236005", "GSM2236006", "GSM2236007", "GSM2236008", "GSM2236009", "GSM2236010", "GSM2236011", "GSM2236012", "GSM2236013", "GSM2236014", "GSM2236015", "GSM2236016", "GSM2236017", "GSM2236018", "GSM2236019", "GSM2236020", "GSM2236021", "GSM2236022", "GSM2236023", "GSM2236024", "GSM2236025", "GSM2236026", "GSM2236027", "GSM2236028", "GSM2236029", "GSM2236030", "GSM2236031", "GSM2236032", "GSM2236033", "GSM2236034", "GSM2236036", "GSM2236037", "GSM2236038", "GSM2236039", "GSM2236040", "GSM2236041", "GSM2236042", "GSM2236043", "GSM2236044", "GSM2236045", "GSM2236046", "GSM2236047", "GSM2236048", "GSM2236049", "GSM2236050", "GSM2236051", "GSM2236052", "GSM2236053", "GSM2236054", "GSM2236055", "GSM2236056", "GSM2236057", "GSM2236058", "GSM2236059", "GSM2236060", "GSM2236061", "GSM2236062", "GSM2236063", "GSM2236064", "GSM2236065", "GSM2236066", "GSM2236067", "GSM2236068", "GSM2236069", "GSM2236070", "GSM2236071", "GSM2236072", "GSM2236073", "GSM2236074", "GSM2236075", "GSM2236076", "GSM2236077", "GSM2236078", "GSM2236079", "GSM2236080", "GSM2236082", "GSM2236083", "GSM2236084", "GSM2236085", "GSM2236086", "GSM2236087", "GSM2236088", "GSM2236089", "GSM2236090", "GSM2236091", "GSM2236092", "GSM2236093", "GSM2236094", "GSM2236095", "GSM4419484", "GSM4419485", "GSM4419486", "GSM4419487", "GSM4419488", "GSM4419489", "GSM4419490", "GSM4419491", "GSM4419492", "GSM4419493", "GSM4419494", "GSM4419495", "GSM4419496", "GSM4419497", "GSM4419498", "GSM4419499", "GSM4419500", "GSM4419501", "GSM4419502", "GSM4419503", "GSM4419504", "GSM4419505", "GSM4419506", "GSM4419507", "GSM4419508", "GSM4419509", "GSM4419510", "GSM4419511", "GSM4419512", "GSM4419513", "GSM4419514", "GSM4419515", "GSM4419516", "GSM4419517", "GSM4419518", "GSM4419519", "GSM4419520", "GSM4419521", "GSM4419522", "GSM4419523", "GSM4419524", "GSM4419525", "GSM4419526", "GSM4419527", "GSM4419528", "GSM4419529", "GSM4419530", "GSM4419531", "GSM4419532", "GSM4419533"], "sample_count": 483, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer.", "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:GSE84437 not downloaded", "asset:data:geo:GSE84437 licence not read"]}, "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": "Then, multivariate COX regression analysis was conducted using a bivariate stepwise regression method to screen out genes associated with the prognosis of STAD patients, and risk scores (RS) were calculated according to the following formula."}}, {"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": "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": 0.7, "band": "medium", "quote": "Logrank"}}, {"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"}}, {"id": "method-6", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.7, "band": "medium", "quote": "decision curve analysis"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.0005, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "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": "R1", "reachable": true, "accessions": ["GSE84437"], "resolved_accessions": ["GSE84437"], "statements": ["The TCGA and GEO belong to public databases. The patients involved in the database have obtained ethical approval. Users can download relevant data for free for research and publish relevant articles. Our study is based on open-source data, so there are no ethical issues and other conflicts of interest."], "basis": "The paper names GSE84437 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": ["cox_ph"], "assets": ["source:pmid:36823639", "data:geo:GSE84437"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE84437"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:28:47Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14620, "completion_tokens": 1244, "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:36823639", "type": "paper", "label": "pmid:36823639"}, {"id": "source:pmid:36823639", "type": "manuscript", "label": "PMID 36823639 full text"}, {"id": "data:geo:GSE84437", "type": "dataset", "label": "GEO GSE84437"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36823639", "type": "paper", "label": "pmid:36823639"}, {"id": "source:pmid:36823639", "type": "manuscript", "label": "PMID 36823639 full text"}, {"id": "data:geo:GSE84437", "type": "dataset", "label": "GEO GSE84437"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36823639", "type": "extraction", "used": ["source:pmid:36823639"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE84437", "type": "accession_resolution", "used": ["data:geo:GSE84437"], "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:36823639", "parent_hash": "sha256:067239c6d2e1e91908e625ee115cabbc2113b2a0e71137d5f45e4f6fa43288e0", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["and cell lines were verified using qRT-PCR, Western blot, and the Human Protein Atlas database. Taken"], "order_basis": "paper_text_order:1891", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ll Biology, Chinese Academy of Sciences. The cell lines were cultured in Dulbecco’s modified Eagle medium (DMEM; I", "ese Academy of Sciences. The cell lines were cultured in Dulbecco’s modified Eagle medium (DMEM; Invi"], "order_basis": "paper_text_order:2914", "id": "assay:2"}, {"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": ["Then, multivariate COX regression analysis was conducted using a bivariate stepwise regression method to screen out genes associated with the prognosis of STAD patients, and risk scores (RS) were calculated according to the following formula."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}