Identification of potential core genes in gastric cancer using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34790378", "kind": "science-record", "revision": 4, "content_hash": "sha256:94082f31cca7c0b948ff7022a17d9ca29b1cd21b26f8c673d673a74f8f818363", "created_at": "2026-11-01T17:36:29Z", "updated_at": "2026-11-01T22:05:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential core genes in gastric cancer using bioinformatics analysis.", "doi": "10.21037/jgo-21-628", "pmid": "34790378", "authors": ["Changjiang Shao", "Rong Wang", "Dandan Kong", "Qian Gao", "Chunfang Xu"], "journal": "Journal of gastrointestinal oncology", "year": 2021, "abstract": "BACKGROUND: Gastric cancer is the third leading cause of cancer-related mortality in China. Most patients with gastric cancer have no obvious early symptoms; thus, many of them are in the middle and late stages of gastric cancer at first diagnosis and miss the best treatment opportunity. Molecular targeted therapy is particularly important in changing this status quo.\nMETHODS: Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened using GEO2R. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to analyze the functional features of these DEGs and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. The protein-protein interaction (PPI) of these DEGs was visualized by Cytoscape software. The expressions of hub genes were evaluated based on Gene Expression Profiling Interactive Analysis (GEPIA). Moreover, we used the online Kaplan-Meier plotter survival analysis tool to evaluate the prognostic values of hub genes. The Target Scan database was used to predict microRNAs that could regulate the target gene, collagen type IV alpha 1 chain (COL4A1). The OncomiR database was used to analyze the expression levels of three microRNAs, as well as the relationships with tumor stage, grade, and prognosis.\nRESULTS: We identified 78 DEGs, including 53 upregulated genes and 25 downregulated genes. The DEGs were mainly enriched in extracellular matrix organization, extracellular structure organization, and response to wounding. Moreover, three KEGG pathways were markedly enriched, including focal adhesion, complement and coagulation cascades, and extracellular matrix (ECM)-receptor interaction. Among these 78 genes, we selected 10 hub genes. The overexpression levels of these hub genes were closely related to poor prognosis and the development of gastric cancer (except for COL3A1, LOX, and CXCL8). Moreover, we found that microRNA-29a-3p, miR-29b-3p, and miR-29c-3p were the potential microRNAs that could regulate the target gene, COL4A1.\nCONCLUSIONS: Our results showed that FN1, COL1A1, TIMP1, COL1A2, SPARC, COL4A1, and SERPINE1 could contribute to the development of novel molecular targets and biomarker-driven treatments for gastric cancer.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were screened using GEO2R. Moreover, we used the online Kaplan-Meier plotter survival analysis tool to evaluate the prognostic values of hub genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34790378", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were screened using GEO2R."}, {"asset": "source:pmid:34790378", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Moreover, we used the online Kaplan-Meier plotter survival analysis tool to evaluate the prognostic values of hub genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34790378", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our results showed that FN1, COL1A1, TIMP1, COL1A2, SPARC, COL4A1, and SERPINE1 could contribute to the development of novel molecular targets and biomarker-driven treatments for gastric cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34790378", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our results showed that FN1, COL1A1, TIMP1, COL1A2, SPARC, COL4A1, and SERPINE1 could contribute to the development of novel molecular targets and biomarker-driven treatments for gastric cancer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our results showed that FN1, COL1A1, TIMP1, COL1A2, SPARC, COL4A1, and SERPINE1 could contribute to the development of novel molecular targets and biomarker-driven treatments for gastric cancer.", "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:34790378"], "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:GSE29272"], "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:GSE29272"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34790378", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jgo-21-628", "sha256": "sha256:64fbe5749baa2251ee69aa58956d93c200f4d0d93839c562feda7d76c10a7425", "bytes": 2302, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/jgo-21-628", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8576244", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29272", "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=GSE29272", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29272", "version": null, "note": "Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM723464", "GSM723465", "GSM723466", "GSM723467", "GSM723468", "GSM723469", "GSM723470", "GSM723471", "GSM723472", "GSM723473", "GSM723474", "GSM723475", "GSM723476", "GSM723477", "GSM723478", "GSM723479", "GSM723480", "GSM723481", "GSM723482", "GSM723483", "GSM723484", "GSM723485", "GSM723486", "GSM723487", "GSM723488", "GSM723489", "GSM723490", "GSM723491", "GSM723492", "GSM723493", "GSM723494", "GSM723495", "GSM723496", "GSM723497", "GSM723498", "GSM723499", "GSM723500", "GSM723501", "GSM723502", "GSM723503", "GSM723504", "GSM723505", "GSM723506", "GSM723507", "GSM723508", "GSM723509", "GSM723510", "GSM723511", "GSM723512", "GSM723513", "GSM723514", "GSM723515", "GSM723516", "GSM723517", "GSM723518", "GSM723519", "GSM723520", "GSM723521", "GSM723522", "GSM723523", "GSM723524", "GSM723525", "GSM723526", "GSM723527", "GSM723528", "GSM723529", "GSM723530", "GSM723531", "GSM723532", "GSM723533", "GSM723534", "GSM723535", "GSM723536", "GSM723537", "GSM723538", "GSM723539", "GSM723540", "GSM723541", "GSM723542", "GSM723543", "GSM723544", "GSM723545", "GSM723546", "GSM723547", "GSM723548", "GSM723549", "GSM723550", "GSM723551", "GSM723552", "GSM723553", "GSM723554", "GSM723555", "GSM723556", "GSM723557", "GSM723558", "GSM723559", "GSM723560", "GSM723561", "GSM723562", "GSM723563", "GSM723564", "GSM723565", "GSM723566", "GSM723567", "GSM723568", "GSM723569", "GSM723570", "GSM723571", "GSM723572", "GSM723573", "GSM723574", "GSM723575", "GSM723576", "GSM723577", "GSM723578", "GSM723579", "GSM723580", "GSM723581", "GSM723582", "GSM723583", "GSM723584", "GSM723585", "GSM723586", "GSM723587", "GSM723588", "GSM723589", "GSM723590", "GSM723591", "GSM723592", "GSM723593", "GSM723594", "GSM723595", "GSM723596", "GSM723597", "GSM723598", "GSM723599", "GSM723600", "GSM723601", "GSM723602", "GSM723603", "GSM723604", "GSM723605", "GSM723606", "GSM723607", "GSM723608", "GSM723609", "GSM723610", "GSM723611", "GSM723612", "GSM723613", "GSM723614", "GSM723615", "GSM723616", "GSM723617", "GSM723618", "GSM723619", "GSM723620", "GSM723621", "GSM723622", "GSM723623", "GSM723624", "GSM723625", "GSM723626", "GSM723627", "GSM723628", "GSM723629", "GSM723630", "GSM723631", "GSM723632", "GSM723633", "GSM723634", "GSM723635", "GSM723636", "GSM723637", "GSM723638", "GSM723639", "GSM723640", "GSM723641", "GSM723642", "GSM723643", "GSM723644", "GSM723645", "GSM723646", "GSM723647", "GSM723648", "GSM723649", "GSM723650", "GSM723651", "GSM723652", "GSM723653", "GSM723654", "GSM723655", "GSM723656", "GSM723657", "GSM723658", "GSM723659", "GSM723660", "GSM723661", "GSM723662", "GSM723663", "GSM723664", "GSM723665", "GSM723666", "GSM723667", "GSM723668", "GSM723669", "GSM723670", "GSM723671", "GSM723672", "GSM723673", "GSM723674", "GSM723675", "GSM723676", "GSM723677", "GSM723678", "GSM723679", "GSM723680", "GSM723681", "GSM723682", "GSM723683", "GSM723684", "GSM723685", "GSM723686", "GSM723687", "GSM723688", "GSM723689", "GSM723690", "GSM723691", "GSM723692", "GSM723693", "GSM723694", "GSM723695", "GSM723696", "GSM723697", "GSM723698", "GSM723699", "GSM723700", "GSM723701", "GSM723702", "GSM723703", "GSM723704", "GSM723705", "GSM723706", "GSM723707", "GSM723708", "GSM723709", "GSM723710", "GSM723711", "GSM723712", "GSM723713", "GSM723714", "GSM723715", "GSM723716", "GSM723717", "GSM723718", "GSM723719", "GSM723720", "GSM723721", "GSM723722", "GSM723723", "GSM723724", "GSM723725", "GSM723726", "GSM723727", "GSM723728", "GSM723729", "GSM723730", "GSM723731"], "sample_count": 268, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Affymetrix gene expression array data for cardia and non-cardia gastric cancer  samples", "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:GSE33651", "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=GSE33651", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33651", "version": null, "note": "Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM832257", "GSM832258", "GSM832259", "GSM832260", "GSM832261", "GSM832262", "GSM832263", "GSM832264", "GSM832265", "GSM832266", "GSM832267", "GSM832268", "GSM832269", "GSM832270", "GSM832271", "GSM832272", "GSM832273", "GSM832274", "GSM832275", "GSM832276", "GSM832277", "GSM832278", "GSM832279", "GSM832280", "GSM832281", "GSM832282", "GSM832283", "GSM832284", "GSM832285", "GSM832286", "GSM832287", "GSM832288", "GSM832289", "GSM832290", "GSM832291", "GSM832292", "GSM832293", "GSM832294", "GSM832295", "GSM832296", "GSM832297", "GSM832298", "GSM832299", "GSM832300", "GSM832301", "GSM832302", "GSM832303", "GSM832304", "GSM832305", "GSM832306", "GSM832307", "GSM832308"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "2895", "taxon": "Homo sapiens", "title": "Genome-wide gene expression profile of human gastric cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE54129", "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=GSE54129", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54129", "version": null, "note": "Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1308392", "GSM1308393", "GSM1308394", "GSM1308395", "GSM1308396", "GSM1308397", "GSM1308398", "GSM1308399", "GSM1308400", "GSM1308401", "GSM1308402", "GSM1308403", "GSM1308404", "GSM1308405", "GSM1308406", "GSM1308407", "GSM1308408", "GSM1308409", "GSM1308410", "GSM1308411", "GSM1308412", "GSM1308413", "GSM1308414", "GSM1308415", "GSM1308416", "GSM1308417", "GSM1308418", "GSM1308419", "GSM1308420", "GSM1308421", "GSM1308422", "GSM1308423", "GSM1308424", "GSM1308425", "GSM1308426", "GSM1308427", "GSM1308428", "GSM1308429", "GSM1308430", "GSM1308431", "GSM1308432", "GSM1308433", "GSM1308434", "GSM1308435", "GSM1308436", "GSM1308437", "GSM1308438", "GSM1308439", "GSM1308440", "GSM1308441", "GSM1308442", "GSM1308443", "GSM1308444", "GSM1308445", "GSM1308446", "GSM1308447", "GSM1308448", "GSM1308449", "GSM1308450", "GSM1308451", "GSM1308452", "GSM1308453", "GSM1308454", "GSM1308455", "GSM1308456", "GSM1308457", "GSM1308458", "GSM1308459", "GSM1308460", "GSM1308461", "GSM1308462", "GSM1308463", "GSM1308464", "GSM1308465", "GSM1308466", "GSM1308467", "GSM1308468", "GSM1308469", "GSM1308470", "GSM1308471", "GSM1308472", "GSM1308473", "GSM1308474", "GSM1308475", "GSM1308476", "GSM1308477", "GSM1308478", "GSM1308479", "GSM1308480", "GSM1308481", "GSM1308482", "GSM1308483", "GSM1308484", "GSM1308485", "GSM1308486", "GSM1308487", "GSM1308488", "GSM1308489", "GSM1308490", "GSM1308491", "GSM1308492", "GSM1308493", "GSM1308494", "GSM1308495", "GSM1308496", "GSM1308497", "GSM1308498", "GSM1308499", "GSM1308500", "GSM1308501", "GSM1308502", "GSM1308503", "GSM1308504", "GSM1308505", "GSM1308506", "GSM1308507", "GSM1308508", "GSM1308509", "GSM1308510", "GSM1308511", "GSM1308512", "GSM1308513", "GSM1308514", "GSM1308515", "GSM1308516", "GSM1308517", "GSM1308518", "GSM1308519", "GSM1308520", "GSM1308521", "GSM1308522", "GSM1308523"], "sample_count": 132, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Global gene expression analysis of gastric cancer by oligonucleotide microarrays", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE29272 not downloaded", "asset:data:geo:GSE29272 licence not read", "asset:data:geo:GSE33651 not downloaded", "asset:data:geo:GSE33651 licence not read", "asset:data:geo:GSE54129 not downloaded", "asset:data:geo:GSE54129 licence not read"]}, "analysis": {"state": "complete", "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": "reordered", "quote": "Differentially expressed genes (DEGs) were screened using GEO2R. Moreover, we used the online Kaplan-Meier plotter survival analysis tool to evaluate the prognostic values of hub genes."}}, {"id": "method-2", "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-3", "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": 0.7, "band": "medium", "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": "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": ["GSE29272", "GSE33651", "GSE54129"], "resolved_accessions": ["GSE29272", "GSE33651", "GSE54129"], "statements": ["Three microarray datasets (GSE29272, GSE33651, and GSE54129) were selected from the Gene Expression Omnibus (GEO) database."], "basis": "The paper names GSE29272, GSE33651, GSE54129 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:34790378", "data:geo:GSE29272"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29272"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:07:42Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2131, "completion_tokens": 909, "cached_tokens": 128}}, "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:34790378", "type": "paper", "label": "pmid:34790378"}, {"id": "source:pmid:34790378", "type": "manuscript", "label": "PMID 34790378 full text"}, {"id": "data:geo:GSE29272", "type": "dataset", "label": "GEO GSE29272"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34790378", "type": "paper", "label": "pmid:34790378"}, {"id": "source:pmid:34790378", "type": "manuscript", "label": "PMID 34790378 full text"}, {"id": "data:geo:GSE29272", "type": "dataset", "label": "GEO GSE29272"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34790378", "type": "extraction", "used": ["source:pmid:34790378"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29272", "type": "accession_resolution", "used": ["data:geo:GSE29272"], "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:34790378", "parent_hash": "sha256:f5c4ff95696e1b4b982a5d57225c3a80f0c7111bbae0a32deb87c39cec4c2598", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE29272 licence not read", "asset:data:geo:GSE29272 not downloaded", "asset:data:geo:GSE33651 licence not read", "asset:data:geo:GSE33651 not downloaded", "asset:data:geo:GSE54129 licence not read", "asset:data:geo:GSE54129 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["in changing this status quo. METHODS: Three microarray datasets (GSE29272, GSE33651, and GSE54129)"], "order_basis": "paper_text_order:430", "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": ["Differentially expressed genes (DEGs) were screened using GEO2R. Moreover, we used the online Kaplan-Meier plotter survival analysis tool to evaluate the prognostic values of hub genes."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}