Identification of core genes and outcome in gastric cancer using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29050278", "kind": "science-record", "revision": 8, "content_hash": "sha256:b98076f0dcc033313d4914e310518b2f156f64d2045250d1ea57dd497a9d68f6", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:59:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of core genes and outcome in gastric cancer using bioinformatics analysis.", "doi": "10.18632/oncotarget.20082", "pmid": "29050278", "authors": ["Chenhua Sun", "Qi Yuan", "Dongdong Wu", "Xiaohu Meng", "Baolin Wang"], "journal": "Oncotarget", "year": 2017, "abstract": "Gastric cancer (GC) is a common malignant neoplasm of gastrointestinal tract. We chose gene expression profile of GSE54129 from GEO database aiming to find key genes during the occurrence and development of GC. 132 samples, including 111 cancer and 21 normal gastric mucosa epitheliums, were included in this analysis. Differentially expressed genes (DEGs) between GC patients and health people were picked out using GEO2R tool, then we performed gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using The Database for Annotation, Visualization and Integrated Discovery (DAVID). Moreover, Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING) and Molecular Complex Detection (MCODE) plug-in was utilized to visualize protein-protein interaction (PPI) of these DEGs. There were 971 DEGs, including 468 up-regulated genes enriched in focal adhesion, ECM-receptor interaction and PI3K-Akt signaling pathway, while 503 down-regulated genes enriched in metabolism of xenbiotics and drug by cytochrome P450, chemical carcinogenesis, retinol metabolism and gastric acid secretion. Three important modules were detected from PPI network using MCODE software. Besides, Fifteen hub genes with high degree of connectivity were selected, including BGN, MMP2, COL1A1, and FN1. Moreover, the Kaplan-Meier analysis for overall survival and correlation analysis were applied among those genes. In conclusion, this bioinformatics analysis demonstrated that DEGs and hub genes, such as BGN, might promote the development of gastric cancer, especially in tumor metastasis. In addition, it could be used as a new biomarker for diagnosis and to guide the combination medicine of gastric cancer.", "claims": [{"id": "claim-method", "statement": "Kaplan Meier-plotter (KM plotter, http://kmplot.com/analysis/) could assess the effect of 54675 genes on survival using 10,461 cancer samples, including 5143 breast, 1816 ovarian, 2437 lung and 1,065 gastric cancer patients with a mean follow-up of 69, 40, 49 and 33 months [9].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29050278", "locator": "sections[14] \"Survival analysis of hub genes\" paragraph 2", "quote": "Kaplan Meier-plotter (KM plotter, http://kmplot.com/analysis/) could assess the effect of 54675 genes on survival using 10,461 cancer samples, including 5143 breast, 1816 ovarian, 2437 lung and 1,065 gastric cancer patients with a mean follow-up of 69, 40, 49 and 33 months [9]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. We also downloaded the Series Matrix File of GSE54129 from GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29050278", "locator": "sections[9] \"Microarray data\" paragraph 2", "quote": "We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. We also downloaded the Series Matrix File of GSE54129 from GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GEO2R on GSE54129 from Gene Expression Omnibus, the study identified 971 differentially expressed genes and selected 15 hub genes with high degree of connectivity.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29050278", "locator": "sections[1] \"INTRODUCTION\" paragraph 4", "quote": "In this analysis, we chose GSE54129 from Gene Expression Omnibus (GEO), and used GEO2R online tool to detect the differentially expressed genes (DEGs)."}, {"asset": "source:pmid:29050278", "locator": "sections[3] \"Identification of DEGs and hub genes\" paragraph 2", "quote": "A total of 971 differential expressed genes were detected after the analysis of GSE54129; of which, 468 were up-regulated genes and 503 were down-regulated."}, {"asset": "source:pmid:29050278", "locator": "sections[3] \"Identification of DEGs and hub genes\" paragraph 2", "quote": "Besides, 15 hub genes with high degree of connectivity were selected (Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GEO2R on GSE54129 from Gene Expression Omnibus, the study identified 971 differentially expressed genes and selected 15 hub genes with high degree of connectivity.", "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:29050278"], "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:GSE54129"], "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:GSE54129"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29050278", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.20082", "sha256": "sha256:cb4cee10545056021b6a065e85370d53e3e61ae188fe2472d56ab26c5e717c34", "bytes": 19764, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.20082", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5642553", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"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": "We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. We also downloaded the Series Matrix File of GSE54129 from GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. 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"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}}, {"id": "asset:table:pmid:29050278:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:354c239296dea5e02083dec7d8697febff7e18ddc43a35d2ecbf48cd27d5644b", "bytes": 627, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Top 15 hub genes with higher degree of connectivity", "structure": {"pmcid": "PMC5642553", "section_index": 3, "section_title": "Identification of DEGs and hub genes", "row_count": 16, "column_count": 3}, "table": {"label": "Table 1", "caption": "Top 15 hub genes with higher degree of connectivity", "rows": [["Gene", "Degree of connectivity", "Adjusted P value"], ["CTNNB1", "24", "3.13E-22"], ["FN1", "16", "5.13E-21"], ["FYN", "15", "1.98E-34"], ["MMP9", "14", "2.28E-09"], ["COL1A1", "11", "1.47E-33"], ["ITCH", "11", "1.62E-30"], ["TGFB1", "10", "6.43E-42"], ["THBS1", "9", "1.03E-22"], ["MMP2", "9", "3.07E-18"], ["ACTA2", "8", "1.67E-08"], ["ITGA5", "8", "5.44E-20"], ["BMP2", "8", "5.61E-24"], ["BGN", "7", "1.50E-28"], ["HSPA4", "7", "7.44E-32"], ["PIK3R1", "7", "2.29E-37"]], "row_count": 16, "column_count": 3, "numeric_cells": 30, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:29050278:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2bde0162c7e5f76545016eb2d73da5288a278f8d422ab7a36349f944d32a0ae1", "bytes": 3334, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T2", "version": null, "note": "Gene ontology analysis of differentially expressed genes associated with gastric cancer", "structure": {"pmcid": "PMC5642553", "section_index": 4, "section_title": "GO function and KEGG pathway enrichment analysis", "row_count": 31, "column_count": 7}, "table": {"label": "Table 2", "caption": "Gene ontology analysis of differentially expressed genes associated with gastric cancer", "rows": [["Expression", "Category", "Term", "Count", "%", "P-Value", "FDR"], ["Up-regulated", "GOTERM_BP_FAT", "GO:0001944∼vasculature development", "67", "19.65", "7.50E-31", "1.43E-27"], ["GOTERM_BP_FAT", "GO:0001568∼blood vessel development", "62", "18.18", "5.72E-28", "1.09E-24"], ["GOTERM_BP_FAT", "GO:0048514∼blood vessel morphogenesis", "56", "16.42", "2.00E-26", "3.82E-23"], ["GOTERM_BP_FAT", "GO:0072358∼cardiovascular system development", "75", "21.99", "1.28E-25", "2.43E-22"], ["GOTERM_BP_FAT", "GO:0072359∼circulatory system development", "75", "21.99", "1.28E-25", "2.43E-22"], ["GOTERM_MF_FAT", "GO:0005539∼glycosaminoglycan binding", "28", "8.21", "3.99E-15", "6.14E-12"], ["GOTERM_MF_FAT", "GO:0008201∼heparin binding", "23", "6.74", "4.66E-13", "7.16E-10"], ["GOTERM_MF_FAT", "GO:1901681∼sulfur compound binding", "26", "7.62", "3.41E-12", "5.23E-09"], ["GOTERM_MF_FAT", "GO:0005102∼receptor binding", "64", "18.77", "6.71E-10", "1.03E-06"], ["GOTERM_MF_FAT", "GO:0032403∼protein complex binding", "42", "12.32", "2.71E-09", "4.17E-06"], ["GOTERM_CC_FAT", "GO:0031012∼extracellular matrix", "66", "19.35", "8.53E-32", "1.23E-28"], ["GOTERM_CC_FAT", "GO:0005578∼proteinaceous extracellular matrix", "52", "15.25", "7.99E-28", "1.16E-24"], ["GOTERM_CC_FAT", "GO:0044421∼extracellular region part", "159", "46.63", "7.12E-21", "1.03E-17"], ["GOTERM_CC_FAT", "GO:0005615∼extracellular space", "87", "25.51", "9.70E-20", "1.40E-16"], ["GOTERM_CC_FAT", "GO:0005576∼extracellular region", "171", "50.15", "4.15E-18", "6.00E-15"], ["Down-regulated", "GOTERM_BP_FAT", "GO:0030855∼epithelial cell differentiation", "42", "10.85", "2.99E-13", "5.61E-10"], ["GOTERM_BP_FAT", "GO:0007586∼digestion", "21", "5.43", "5.83E-11", "1.10E-07"], ["GOTERM_BP_FAT", "GO:0060429∼epithelium development", "49", "12.66", "3.66E-08", "6.88E-05"], ["GOTERM_BP_FAT", "GO:0006805∼xenobiotic metabolic process", "14", "3.62", "5.49E-08", "1.03E-04"], ["GOTERM_BP_FAT", "GO:0006629∼lipid metabolic process", "56", "14.47", "7.06E-08", "1.33E-04"], ["GOTERM_MF_FAT", "GO:0016614∼oxidoreductase activity, acting on CH-OH group of donors", "22", "5.68", "2.20E-13", "3.43E-10"], ["GOTERM_MF_FAT", "GO:0016616∼oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor", "17", "4.39", "9.66E-10", "1.51E-06"], ["GOTERM_MF_FAT", "GO:0004745∼retinol dehydrogenase activity", "8", "2.07", "2.60E-08", "4.05E-05"], ["GOTERM_MF_FAT", "GO:0004033∼aldo-keto reductase (NADP) activity", "7", "1.81", "1.08E-05", "0.016818"], ["GOTERM_MF_FAT", "GO:0016709∼oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen", "7", "1.81", "1.71E-04", "0.266413"], ["GOTERM_CC_FAT", "GO:0044421∼extracellular region part", "124", "32.04", "5.03E-08", "7.04E-05"], ["GOTERM_CC_FAT", "GO:0005576∼extracellular region", "140", "36.18", "1.05E-07", "1.47E-04"], ["GOTERM_CC_FAT", "GO:0045177∼apical part of cell", "26", "6.72", "1.38E-07", "1.93E-04"], ["GOTERM_CC_FAT", "GO:0070062∼extracellular exosome", "92", "23.77", "3.26E-06", "0.004567"], ["GOTERM_CC_FAT", "GO:1903561∼extracellular vesicle", "92", "23.77", "4.04E-06", "0.005651"]], "row_count": 31, "column_count": 7, "numeric_cells": 150, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:29050278:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5952b42f74343482a7548af7123d5b4f7e14ba1a33d6f5960ed221844fd5a63e", "bytes": 2162, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#T3", "version": null, "note": "KEGG pathway analysis of differentially expressed genes associated with gastric cancer", "structure": {"pmcid": "PMC5642553", "section_index": 4, "section_title": "GO function and KEGG pathway enrichment analysis", "row_count": 11, "column_count": 7}, "table": {"label": "Table 3", "caption": "KEGG pathway analysis of differentially expressed genes associated with gastric cancer", "rows": [["Category", "Term", "Count", "%", "P-Value", "Genes", "FDR"], ["Up-regulated DEGs", "hsa04510:Focal adhesion", "25", "7.3", "5.06E-11", "TLN1, TNC, MYL9, COL6A3, COL6A2, COL6A1, ZYX, THBS1, COL11A1, THBS2, PIK3R1, SPP1, THBS4, FN1, COL4A2, COL4A1, IGF1, FLNA, VEGFC, FYN, ITGA5, ITGA7, COL1A2, COL1A1, MYLK", "6.32E-08"], ["hsa04512:ECM-receptor interaction", "16", "4.7", "1.13E-09", "COL4A2, COL4A1, TNC, ITGA5, ITGA7, COL6A3, COL6A2, COL1A2, COL6A1, COL1A1, THBS1, THBS2, COL11A1, SPP1, THBS4, FN1", "1.42E-06"], ["hsa04151:PI3K-Akt signaling pathway", "25", "7.3", "1.34E-06", "MCL1, OSMR, TNC, BCL2L1, IL7R, COL6A3, COL6A2, COL6A1, IL2RG, THBS1, COL11A1, THBS2, PIK3R1, SPP1, THBS4, FN1, COL4A2, COL4A1, IGF1, YWHAE, VEGFC, ITGA5, ITGA7, COL1A2, COL1A1", "0.001667"], ["hsa04974:Protein digestion and absorption", "12", "3.5", "5.64E-06", "COL4A2, COL14A1, COL4A1, COL6A3, ELN, COL1A2, COL6A2, COL12A1, COL6A1, COL1A1, COL11A1, COL10A1", "0.007038"], ["hsa04270:Vascular smooth muscle contraction", "12", "3.5", "9.93E-05", "EDNRA, GNA13, ACTG2, ACTA2, CALD1, PLA2G2A, GUCY1A3, GUCY1B3, CALCRL, MYLK, KCNMB1, MYL9", "0.123856"], ["Down-regulated DEGs", "hsa00980:Metabolism of xenobiotics by cytochrome P450", "12", "3.1", "2.08E-07", "GSTA1, CYP3A4, CYP3A5, CBR1, CYP2C9, ADH1C, AKR7A3, ADH1A, ADH7, UGT2B15, AKR1C1, ALDH3A1", "2.56E-04"], ["hsa05204:Chemical carcinogenesis", "12", "3.1", "4.70E-07", "GSTA1, CYP3A4, CYP3A5, CBR1, CYP2C19, CYP2C9, CYP2C18, ADH1C, ADH1A, ADH7, UGT2B15, ALDH3A1", "5.78E-04"], ["hsa00830:Retinol metabolism", "11", "2.8", "5.47E-07", "CYP3A4, RDH12, CYP3A5, CYP2C9, CYP2C18, ADH1C, DHRS9, SDR16C5, ADH1A, ADH7, UGT2B15", "6.72E-04"], ["hsa00982:Drug metabolism - cytochrome P450", "11", "2.8", "8.44E-07", "GSTA1, CYP3A4, FMO5, CYP3A5, CYP2C19, CYP2C9, ADH1C, ADH1A, ADH7, UGT2B15, ALDH3A1", "0.001037"], ["hsa04971:Gastric acid secretion", "11", "2.8", "1.66E-06", "KCNJ16, KCNJ15, ATP4A, GNAQ, ATP4B, SLC26A7, KCNE2, GAST, CA2, SST, KCNK10", "0.002035"]], "row_count": 11, "column_count": 7, "numeric_cells": 60, "header_rows": 1, "locator": "section[4]/table-wrap[2]#T3"}}], "gaps": ["asset:data:geo:GSE54129 not downloaded", "asset:data:geo:GSE54129 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE54129"], "resolved_accessions": ["GSE54129"], "statements": ["We chose gene expression profile of GSE54129 from GEO database, which was a public and freely available database. GSE54129, which was based on agilent GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array). The GSE54129 dataset included 132 samples, containing 111 gastric cancer samples and 21 normal gastric mucosa epithelium. We also downloaded the Series Matrix File of GSE54129 from GEO database."], "basis": "The paper names 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:29050278", "data:geo:GSE54129", "asset:table:pmid:29050278:1", "asset:table:pmid:29050278:2", "asset:table:pmid:29050278:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE54129"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:28Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 40669, "completion_tokens": 5202, "cached_tokens": 10624}}, "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:29050278", "type": "paper", "label": "pmid:29050278"}, {"id": "source:pmid:29050278", "type": "manuscript", "label": "PMID 29050278 full text"}, {"id": "data:geo:GSE54129", "type": "dataset", "label": "GEO GSE54129"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29050278", "type": "paper", "label": "pmid:29050278"}, {"id": "source:pmid:29050278", "type": "manuscript", "label": "PMID 29050278 full text"}, {"id": "data:geo:GSE54129", "type": "dataset", "label": "GEO GSE54129"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29050278", "type": "extraction", "used": ["source:pmid:29050278"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE54129", "type": "accession_resolution", "used": ["data:geo:GSE54129"], "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:29050278", "parent_hash": "sha256:2dc6e667ea94da0495383238553a4a4648997d44ea47535909df723f33ba79dc", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE54129 licence not read", "asset:data:geo:GSE54129 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.77, "evidence": ["rall survival information were based on GEO (Affymetrix microarrays only), EGA and TCGA database. Th"], "order_basis": "paper_text_order:3764", "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": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}