Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32699530", "kind": "science-record", "revision": 7, "content_hash": "sha256:b65a9ccda40b1531f0fd00efaf3a1f7712dd2cc10f24c433839f50bd4dca95fc", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:01:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments.", "doi": "10.1186/s12935-020-01405-6", "pmid": "32699530", "authors": ["Yeda Chen", "Di Gu", "Yaoan Wen", "Shuxin Yang", "Xiaolu Duan", "Yongchang Lai", "Jianan Yang", "Daozhang Yuan", "Aisha Khan", "Wenqi Wu", "Guohua Zeng"], "journal": "Cancer cell international", "year": 2020, "abstract": "BACKGROUND: Although major driver gene have been identified, the complex molecular heterogeneity of renal cell cancer (RCC) remains unclear. Therefore, more relevant genes need to be identified to explain the pathogenesis of renal cancer.\nMETHODS: Microarray datasets GSE781, GSE6344, GSE53000 and GSE68417 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified by employing GEO2R tool, and function enrichment analyses were performed by using DAVID. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using STRING and Cytoscape. Survival analysis was performed using GEPIA. Differential expression was verified in Oncomine. Cell experiments (cell viability assays, transwell migration and invasion assays, wound healing assay, flow cytometry) were utilized to verify the roles of the hub genes on the proliferation of kidney cancer cells (A498 and OSRC-2 cell lines).\nRESULTS: A total of 215 DEGs were identified from four datasets. Six hub gene (SUCLG1, PCK2, GLDC, SLC12A1, ATP1A1, PDHA1) were identified and the overall survival time of patients with RCC were significantly shorter. The expression levels of these six genes were significantly decreased in six RCC cell lines(A498, OSRC-2, 786- O, Caki-1, ACHN, 769-P) compared to 293t cell line. The expression level of both mRNA and protein of these genes were downregulated in RCC samples compared to those in paracancerous normal tissues. Cell viability assays showed that overexpressions of SUCLG1, PCK2, GLDC significantly decreased proliferation of RCC. Transwell migration, invasion, wound healing assay showed overexpression of three genes(SUCLG1, PCK2, GLDC) significantly inhibited the migration, invasion of RCC. Flow cytometry analysis showed that overexpression of three genes(SUCLG1, PCK2, GLDC) induced G1/S/G2 phase arrest of RCC cells.\nCONCLUSION: Based on our current findings, it is concluded that SUCLG1, PCK2, GLDC may serve as a potential prognostic marker of RCC.", "claims": [{"id": "claim-method", "statement": "The DEGs between ccRCC and non-cancerous samples were screened using GEO2R which is an interactive web tool that allows users to compare two or more datasets in a GEO series for identifying DEGs in experimental conditions. The adjusted P-values (adj. P) and Benjamini and Hochberg false discovery rate were applied to provide a balance between discovery of statistically significant genes and limitations of false-positives. Probe sets without corresponding gene symbols or genes with more than one probe set were removed or averaged, respectively. Adj. P-value < 0.01 and logFC (fold change) > 1 were considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32699530", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The DEGs between ccRCC and non-cancerous samples were screened using GEO2R which is an interactive web tool that allows users to compare two or more datasets in a GEO series for identifying DEGs in experimental conditions. The adjusted P-values (adj. P) and Benjamini and Hochberg false discovery rate were applied to provide a balance between discovery of statistically significant genes and limitations of false-positives. Probe sets without corresponding gene symbols or genes with more than one probe set were removed or averaged, respectively. Adj. P-value < 0.01 and logFC (fold change) > 1 were considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32699530", "locator": "sections[34] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32699530"], "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:GSE53000"], "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:GSE53000"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32699530", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-020-01405-6", "sha256": 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the corresponding author on reasonable request", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM146778", "GSM146779", "GSM146780", "GSM146781", "GSM146782", "GSM146783", "GSM146784", "GSM146785", "GSM146786", "GSM146787", "GSM146788", "GSM146789", "GSM146790", "GSM146791", "GSM146792", "GSM146793", "GSM146794", "GSM146795", "GSM146796", "GSM146797", "GSM146798", "GSM146799", "GSM146800", "GSM146801", "GSM146802", "GSM146803", "GSM146804", "GSM146805", "GSM146806", "GSM146807", "GSM146808", "GSM146809", "GSM146810", "GSM146811", "GSM146812", "GSM146813", "GSM146814", "GSM146815", "GSM146816", "GSM146817"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "96;97", "taxon": "Homo sapiens", "title": 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"available", "identifier": "section[20]/table-wrap[1]#Tab1", "version": null, "note": "GO and KEGG pathway enrichment analysis of DEGs in KIRC samples", "structure": {"pmcid": "PMC7372855", "section_index": 5, "section_title": "KEGG and GO enrichment analyses of DEGs", "row_count": 45, "column_count": 4}, "table": {"label": "Table 1", "caption": "GO and KEGG pathway enrichment analysis of DEGs in KIRC samples", "rows": [["Term/pathway ID", "Description", "Count in gene set", "P-value"], ["BP"], ["GO:0019752", "Carboxylic acid metabolic process", "45", "1.07E−16"], ["GO:0006082", "Organic acid metabolic process", "47", "1.23E−16"], ["GO:0043436", "Oxoacid metabolic process", "45", "1.33E−16"], ["GO:0044282", "Small molecule catabolic process", "25", "6.84E−12"], ["GO:0001822", "Kidney development", "22", "1.91E−11"], ["GO:0072001", "Renal system development", "22", "5.72E−11"], ["GO:0055114", "Oxidation–reduction process", "40", "8.91E−11"], ["GO:0016054", "Organic acid catabolic process", "19", "3.42E−10"], ["GO:0001655", "Urogenital system development", "22", "5.53E−10"], ["GO:0006811", "Ion transport", "48", "8.49E−10"], ["CC"], ["GO:0070062", "Extracellular exosome", "101", "9.00E−25"], ["GO:1903561", "Extracellular vesicle", "101", "1.34E−24"], ["GO:0043230", "Extracellular organelle", "101", "1.38E−24"], ["GO:0031988", "Membrane-bounded vesicle", "107", "7.12E−20"], ["GO:0044421", "Extracellular region part", "108", "5.23E−18"], ["GO:0005576", "Extracellular region", "113", "1.48E−14"], ["GO:0045177", "Apical part of cell", "26", "1.04E−11"], ["GO:0016323", "Basolateral plasma membrane", "20", "2.35E−11"], ["GO:0016324", "Apical plasma membrane", "23", "4.15E−11"], ["GO:0098590", "Plasma membrane region", "39", "3.45E−10"], ["MF"], ["GO:0048037", "Cofactor binding", "20", "2.23E−09"], ["GO:0050662", "Coenzyme binding", "14", "7.50E−07"], ["GO:0015291", "Secondary active transmembrane transporter activity", "15", "1.92E−06"], ["GO:0008509", "Anion transmembrane transporter activity", "14", "2.26E−06"], ["GO:0022804", "Active transmembrane transporter activity", "18", "5.05E−06"], ["GO:0016614", "Oxidoreductase activity, acting on CH–OH group of donors", "11", "1.05E−05"], ["GO:1901681", "Sulfur compound binding", "13", "4.69E−05"], ["GO:0015103", "Inorganic anion transmembrane transporter activity", "10", "5.01E−05"], ["GO:0016709", "Oxidoreductase activity, with incorporation or reduction of molecular oxygen", "6", "2.11E−04"], ["GO:0042802", "Identical protein binding", "34", "2.45E−04"], ["KEGG"], ["hsa01100", "Metabolic pathways", "48", "3.79E−09"], ["hsa01130", "Biosynthesis of antibiotics", "18", "6.50E−08"], ["hsa01200", "Carbon metabolism", "12", "2.45E−06"], ["hsa04960", "Aldosterone-regulated sodium reabsorption", "6", "4.38E−04"], ["hsa00010", "Glycolysis/Gluconeogenesis", "7", "8.33E−04"], ["hsa00280", "Valine, leucine and isoleucine degradation", "6", "1.05E−03"], ["hsa00020", "Citrate cycle (TCA cycle)", "5", "1.45E−03"], ["hsa00260", "Glycine, serine and threonine metabolism", "5", "3.88E−03"], ["hsa04610", "Complement and coagulation cascades", "6", "5.74E−03"], ["hsa04966", "Collecting duct acid secretion", "4", "9.94E−03"]], "row_count": 45, "column_count": 4, "numeric_cells": 120, "header_rows": 1, "locator": "section[20]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32699530:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:24ed00b3ac0d3a0e3d196e3ed1d6d183bf9ef2014f52949411c6bc4b342b7c87", "bytes": 1973, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#Tab2", "version": null, "note": "GO and KEGG pathway enrichment analysis of DEGs in the most significant module", "structure": {"pmcid": "PMC7372855", "section_index": 6, "section_title": "PPI network construction and module analysis", "row_count": 33, "column_count": 4}, "table": {"label": "Table 2", "caption": "GO and KEGG pathway enrichment analysis of DEGs in the most significant module", "rows": [["Term/Pathway ID", "Description", "Count in gene set", "P-value"], ["BP"], ["GO:0006813", "Potassium ion transport", "4", "2.29E−04"], ["GO:0055082", "Cellular chemical homeostasis", "5", "5.69E−04"], ["GO:0006732", "Coenzyme metabolic process", "4", "7.29E−04"], ["GO:0019752", "Carboxylic acid metabolic process", "5", "9.93E−04"], ["GO:0043436", "Oxoacid metabolic process", "5", "1.02E−03"], ["GO:0019725", "Cellular homeostasis", "5", "1.02E−03"], ["GO:0051186", "Cofactor metabolic process", "4", "1.30E−03"], ["GO:0006082", "Organic acid metabolic process", "5", "1.41E−03"], ["GO:0035383", "Thioester metabolic process", "3", "1.44E−03"], ["GO:0006637", "Acyl-CoA metabolic process", "3", "1.44E−03"], ["CC"], ["GO:0005759", "Mitochondrial matrix", "4", "1.83E−03"], ["GO:0016324", "Apical plasma membrane", "3", "1.33E−02"], ["GO:0070062", "Extracellular exosome", "6", "1.70E−02"], ["GO:1903561", "Extracellular vesicle", "6", "1.74E−02"], ["GO:0043230", "Extracellular organelle", "6", "1.74E−02"], ["GO:0044429", "Mitochondrial part", "4", "1.94E−02"], ["GO:0045177", "Apical part of cell", "3", "1.98E−02"], ["GO:0030315", "T-tubule", "2", "2.63E−02"], ["GO:0014704", "Intercalated disc", "2", "3.06E−02"], ["GO:0044291", "Cell–cell contact zone", "2", "4.08E−02"], ["MF"], ["GO:0022804", "Active transmembrane transporter activity", "3", "2.22E−02"], ["KEGG"], ["hsa00020", "Citrate cycle (TCA cycle)", "3", "5.07E−04"], ["hsa01130", "Biosynthesis of antibiotics", "4", "1.44E−03"], ["hsa01200", "Carbon metabolism", "3", "7.02E−03"], ["hsa04964", "Proximal tubule bicarbonate reclamation", "2", "2.65E−02"], ["hsa01100", "Metabolic pathways", "5", "3.76E−02"], ["hsa00260", "Glycine, serine and threonine metabolism", "2", "4.45E−02"], ["hsa00620", "Pyruvate metabolism", "2", "4.56E−02"]], "row_count": 33, "column_count": 4, "numeric_cells": 84, 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process", "47", "1.23E−16"], ["GO:0043436", "Oxoacid metabolic process", "45", "1.33E−16"], ["GO:0044282", "Small molecule catabolic process", "25", "6.84E−12"], ["GO:0001822", "Kidney development", "22", "1.91E−11"], ["GO:0072001", "Renal system development", "22", "5.72E−11"], ["GO:0055114", "Oxidation–reduction process", "40", "8.91E−11"], ["GO:0016054", "Organic acid catabolic process", "19", "3.42E−10"], ["GO:0001655", "Urogenital system development", "22", "5.53E−10"], ["GO:0006811", "Ion transport", "48", "8.49E−10"], ["CC"], ["GO:0070062", "Extracellular exosome", "101", "9.00E−25"], ["GO:1903561", "Extracellular vesicle", "101", "1.34E−24"], ["GO:0043230", "Extracellular organelle", "101", "1.38E−24"], ["GO:0031988", "Membrane-bounded vesicle", "107", "7.12E−20"], ["GO:0044421", "Extracellular region part", "108", "5.23E−18"], ["GO:0005576", "Extracellular region", "113", "1.48E−14"], ["GO:0045177", "Apical part of cell", "26", "1.04E−11"], ["GO:0016323", "Basolateral plasma membrane", "20", "2.35E−11"], ["GO:0016324", "Apical plasma membrane", "23", "4.15E−11"], ["GO:0098590", "Plasma membrane region", "39", "3.45E−10"], ["MF"], ["GO:0048037", "Cofactor binding", "20", "2.23E−09"], ["GO:0050662", "Coenzyme binding", "14", "7.50E−07"], ["GO:0015291", "Secondary active transmembrane transporter activity", "15", "1.92E−06"], ["GO:0008509", "Anion transmembrane transporter activity", "14", "2.26E−06"], ["GO:0022804", "Active transmembrane transporter activity", "18", "5.05E−06"], ["GO:0016614", "Oxidoreductase activity, acting on CH–OH group of donors", "11", "1.05E−05"], ["GO:1901681", "Sulfur compound binding", "13", "4.69E−05"], ["GO:0015103", "Inorganic anion transmembrane transporter activity", "10", "5.01E−05"], ["GO:0016709", "Oxidoreductase activity, with incorporation or reduction of molecular oxygen", "6", "2.11E−04"], ["GO:0042802", "Identical protein binding", "34", "2.45E−04"], ["KEGG"], ["hsa01100", "Metabolic pathways", "48", "3.79E−09"], ["hsa01130", "Biosynthesis of antibiotics", "18", "6.50E−08"], ["hsa01200", "Carbon metabolism", "12", "2.45E−06"], ["hsa04960", "Aldosterone-regulated sodium reabsorption", "6", "4.38E−04"], ["hsa00010", "Glycolysis/Gluconeogenesis", "7", "8.33E−04"], ["hsa00280", "Valine, leucine and isoleucine degradation", "6", "1.05E−03"], ["hsa00020", "Citrate cycle (TCA cycle)", "5", "1.45E−03"], ["hsa00260", "Glycine, serine and threonine metabolism", "5", "3.88E−03"], ["hsa04610", "Complement and coagulation cascades", "6", "5.74E−03"], ["hsa04966", "Collecting duct acid secretion", "4", "9.94E−03"]], "row_count": 45, "column_count": 4, "numeric_cells": 120, "header_rows": 1, "locator": "section[20]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32699530:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:24ed00b3ac0d3a0e3d196e3ed1d6d183bf9ef2014f52949411c6bc4b342b7c87", "bytes": 1973, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#Tab2", "version": null, "note": "GO and KEGG pathway enrichment analysis of DEGs in the most significant module", "structure": {"pmcid": "PMC7372855", "section_index": 21, "section_title": "PPI network construction and module analysis", "row_count": 33, "column_count": 4}, "table": {"label": "Table 2", "caption": "GO and KEGG pathway enrichment analysis of DEGs in the most significant module", "rows": [["Term/Pathway ID", "Description", "Count in gene set", "P-value"], ["BP"], ["GO:0006813", "Potassium ion transport", "4", "2.29E−04"], ["GO:0055082", "Cellular chemical homeostasis", "5", "5.69E−04"], ["GO:0006732", "Coenzyme metabolic process", "4", "7.29E−04"], ["GO:0019752", "Carboxylic acid metabolic process", "5", "9.93E−04"], ["GO:0043436", "Oxoacid metabolic process", "5", "1.02E−03"], ["GO:0019725", "Cellular homeostasis", "5", "1.02E−03"], ["GO:0051186", "Cofactor metabolic process", "4", "1.30E−03"], ["GO:0006082", "Organic acid metabolic process", "5", "1.41E−03"], ["GO:0035383", "Thioester metabolic process", "3", "1.44E−03"], ["GO:0006637", "Acyl-CoA metabolic process", "3", "1.44E−03"], ["CC"], ["GO:0005759", "Mitochondrial matrix", "4", "1.83E−03"], ["GO:0016324", "Apical plasma membrane", "3", "1.33E−02"], ["GO:0070062", "Extracellular exosome", "6", "1.70E−02"], ["GO:1903561", "Extracellular vesicle", "6", "1.74E−02"], ["GO:0043230", "Extracellular organelle", "6", "1.74E−02"], ["GO:0044429", "Mitochondrial part", "4", "1.94E−02"], ["GO:0045177", "Apical part of cell", "3", "1.98E−02"], ["GO:0030315", "T-tubule", "2", "2.63E−02"], ["GO:0014704", "Intercalated disc", "2", "3.06E−02"], ["GO:0044291", "Cell–cell contact zone", "2", "4.08E−02"], ["MF"], ["GO:0022804", "Active transmembrane transporter activity", "3", "2.22E−02"], ["KEGG"], ["hsa00020", "Citrate cycle (TCA cycle)", "3", "5.07E−04"], ["hsa01130", "Biosynthesis of antibiotics", "4", "1.44E−03"], ["hsa01200", "Carbon metabolism", "3", "7.02E−03"], ["hsa04964", "Proximal tubule bicarbonate reclamation", "2", "2.65E−02"], ["hsa01100", "Metabolic pathways", "5", "3.76E−02"], ["hsa00260", "Glycine, serine and threonine metabolism", "2", "4.45E−02"], ["hsa00620", "Pyruvate metabolism", "2", "4.56E−02"]], "row_count": 33, "column_count": 4, "numeric_cells": 84, "header_rows": 1, "locator": "section[21]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:32699530:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bc7d9e20be376092692a84cf316b78e76f003670d875f63e8f9761ab93995434", "bytes": 2338, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#Tab3", "version": null, "note": "Functional roles of 11 hub genes with betweenness degrees ≥ 10", "structure": {"pmcid": "PMC7372855", "section_index": 22, "section_title": "Hub gene selection and analysis", "row_count": 12, "column_count": 4}, "table": {"label": "Table 3", "caption": "Functional roles of 11 hub genes with betweenness degrees ≥ 10", "rows": [["No.", "Gene symbol", "Full name", "Function"], ["1", "ANK2", "Ankyrin 2", "Attaches integral membrane proteins to cytoskeletal elements.Also binds to cytoskeletal proteins. Plays a role in endocytosis and intracellular protein transport"], ["2", "SUCLG1", "Succinate-CoA Ligase Alpha Subunit", "Succinyl-CoA synthetase functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP"], ["3", "GLDC", "Glycine Decarboxylase", "The P protein (GLDC) binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (GCSH)"], ["4", "SLC12A1", "Solute Carrier Family 12 Member 1", "Mediates sodium and chloride reabsorption. Plays a vital role in the regulation of ionic balance and cell volume"], ["5", "PIPOX", "Pipecolic Acid And Sarcosine Oxidase", "Metabolizes sarcosine, L-pipecolic acid and l-proline"], ["6", "KNG1", "Kininogen 1", "Kininogens 1 is inhibitors of thiol proteases; plays an important role in blood coagulation; inhibits the thrombin- and plasmin-induced aggregation of thrombocytes"], ["7", "SLC9A2", "Solute Carrier Family 9 Member A2", "Involved in pH regulation to eliminate acids generated by active metabolism or to counter adverse environmental conditions"], ["8", "PCK2", "Phosphoenolpyruvate Carboxykinase 2", "Catalyzes the conversion of oxaloacetate to phosphoenolpyruvate"], ["9", "XPNPEP2", "X-Prolyl Aminopeptidase 2", "Membrane-bound metalloprotease which catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides. May play a role in the metabolism of the vasodilator bradykinin"], ["10", "ATP1A1", "ATPase Na+/K+ Transporting Subunit Alpha 1", "This action creates the electrochemical gradient of sodium and potassium ions, providing the energy for active transport of various nutrients"], ["11", "PDHA1", "Pyruvate Dehydrogenase E1 Alpha 1 Subunit", "The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2, and thereby links the glycolytic pathway to the tricarboxylic cycle."]], "row_count": 12, "column_count": 4, "numeric_cells": 21, "header_rows": 1, "locator": "section[22]/table-wrap[1]#Tab3"}}], "gaps": ["asset:data:geo:GSE53000 not downloaded", "asset:data:geo:GSE53000 licence not read", "asset:data:geo:GSE6344 not downloaded", "asset:data:geo:GSE6344 licence not read", "asset:data:geo:GSE68417 not downloaded", "asset:data:geo:GSE68417 licence not read", "asset:data:geo:GSE781 not downloaded", "asset:data:geo:GSE781 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"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": null, "specific": null, "label": "GEO2R, using adjusted P-values with Benjamini–Hochberg false discovery rate, with a significance threshold of adjusted P-value < 0.01 and logFC > 1; source data were obtained from the GEO datasets GSE781, GSE6344, GSE53000 and GSE68417.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DEGs between ccRCC and non-cancerous samples were screened using GEO2R which is an interactive web tool that allows users to compare two or more datasets in a GEO series for identifying DEGs in experimental conditions. The adjusted P-values (adj. P) and Benjamini and Hochberg false discovery rate were applied to provide a balance between discovery of statistically significant genes and limitations of false-positives. Probe sets without corresponding gene symbols or genes with more than one probe set were removed or averaged, respectively. Adj. P-value < 0.01 and logFC (fold change) > 1 were considered statistically significant."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE781", "GSE6344", "GSE53000", "GSE68417"], "resolved_accessions": ["GSE781", "GSE6344", "GSE53000", "GSE68417"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request"], "basis": "The paper names GSE781, GSE6344, GSE53000, GSE68417 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:32699530", "data:geo:GSE53000", "asset:table:pmid:32699530:1", "asset:table:pmid:32699530:2", "asset:table:pmid:32699530:3", "asset:table:pmid:32699530:4", "asset:table:pmid:32699530:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE53000"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34132, "completion_tokens": 1968, "cached_tokens": 785}}, "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:32699530", "type": "paper", "label": "pmid:32699530"}, {"id": "source:pmid:32699530", "type": "manuscript", "label": "PMID 32699530 full text"}, {"id": "data:geo:GSE53000", "type": "dataset", "label": "GEO GSE53000"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32699530", "type": "paper", "label": "pmid:32699530"}, {"id": "source:pmid:32699530", "type": "manuscript", "label": "PMID 32699530 full text"}, {"id": "data:geo:GSE53000", "type": "dataset", "label": "GEO GSE53000"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32699530", "type": "extraction", "used": ["source:pmid:32699530"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE53000", "type": "accession_resolution", "used": ["data:geo:GSE53000"], "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:32699530", "parent_hash": "sha256:9f1e2296bcd42c82e8277d44a24df34739598772bb84d3334967d391fc30b57f", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE53000 licence not read", "asset:data:geo:GSE53000 not downloaded", "asset:data:geo:GSE6344 licence not read", "asset:data:geo:GSE6344 not downloaded", "asset:data:geo:GSE68417 licence not read", "asset:data:geo:GSE68417 not downloaded", "asset:data:geo:GSE781 licence not read", "asset:data:geo:GSE781 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": 0.93, "evidence": ["n the pathogenesis of renal cancer. METHODS: Microarray datasets GSE781, GSE6344, GSE53000 and GSE68"], "order_basis": "paper_text_order:308", "id": "assay:1"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on and invasion assays, wound healing assay, flow cytometry) were utilized to verify the roles of the hu", "ly inhibited the migration, invasion of RCC. Flow cytometry analysis showed that overexpression of three"], "order_basis": "paper_text_order:901", "id": "assay:2"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["identified and the overall survival time of patients with RCC were significantly shorter. The expressi"], "order_basis": "paper_text_order:1215", "id": "assay:3"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Materials and methods Cell culture and transfection Human renal carcinoma cell lines OSRC-2 and", "in 6-well plates or 60 mm2 medium dishes and transfected with over expressed plasmids and negative co", "ghai GenePharma Co., Ltd. (Shanghai, China). Transfection was conducted using Lipofectamine® 3000 (The", "nc.). 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OS-RC-2 and A498 cells were cultured in 6-well plates or 60 mm2 medium dishes and tr"], "order_basis": "paper_text_order:2300", "id": "assay:5"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tion-quantitative polymerase chain reaction (RT-qPCR) analysis. Statistical analysis All data wer", "n-quantitative polymerase chain reaction (RT-qPCR) analysis. 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