Identification of Biomarkers Associated With Pathological Stage and Prognosis of Clear Cell Renal Cell Carcinoma by Co-expression Network Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29720944", "kind": "science-record", "revision": 5, "content_hash": "sha256:9335ba9c5f214ee46c2284e743c853f790deee58701f5c4cffb6bcf5fe216057", "created_at": "2026-11-01T15:40:33Z", "updated_at": "2026-11-01T21:21:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Biomarkers Associated With Pathological Stage and Prognosis of Clear Cell Renal Cell Carcinoma by Co-expression Network Analysis.", "doi": "10.3389/fphys.2018.00399", "pmid": "29720944", "authors": ["Liang Chen", "Lushun Yuan", "Kaiyu Qian", "Guofeng Qian", "Yuan Zhu", "Chin-Lee Wu", "Han C Dan", "Yu Xiao", "Xinghuan Wang"], "journal": "Frontiers in physiology", "year": 2018, "abstract": "Clear cell renal cell carcinoma (ccRCC) is the most common subtype among renal cancer whose prognostic is affected by the tumor progression associated with complex gene interactions. However, there is currently no available molecular markers associated with ccRCC progression and used or clinical application. In our study, microarray data of 101 ccRCC samples and 95 normal kidney samples were analyzed and 2,425 differentially expressed genes (DEGs) were screened. Weighted gene co-expression network analysis (WGCNA) was then conducted and 11 co-expressed gene modules were identified. Module preservation analysis revealed that two modules (red and black) were found to be most stable. In addition, Pearson's correlation analysis identified the module most relevant to pathological stage(patho-module) (r = 0.44, p = 3e-07). Functional enrichment analysis showed that biological processes of the patho-module focused on cell cycle and cell division related biological process and pathway. In addition, 29 network hub genes highly related to ccRCC progression were identified from the stage module. These 29 hub genes were subsequently validated using 2 other independent datasets including GSE53757 (n = 72) and TCGA (n = 530), and the results indicated that all hub genes were significantly positive correlated with the 4 stages of ccRCC progression. Kaplan-Meier survival curve showed that patients with higher expression of each hub gene had significantly lower overall survival rate and disease-free survival rate, indicating that all hub genes could act as prognosis and recurrence/progression biomarkers of ccRCC. In summary, we identified 29 molecular markers correlated with different pathological stages of ccRCC. They may have important clinical implications for improving risk stratification, therapeutic decision and prognosis prediction in ccRCC patients.", "claims": [{"id": "claim-method", "statement": "The “WGCNA” (Langfelder and Horvath, 2008) package in R was applied to performed co-expression network using the expression values of 2,425 DEGs from 125 tumor samples and complete clinical data (GSE73731).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29720944", "locator": "sections[5] \"Weighted gene co-expression network construction\" paragraph 2", "quote": "The “WGCNA” (Langfelder and Horvath, 2008) package in R was applied to performed co-expression network using the expression values of 2,425 DEGs from 125 tumor samples and complete clinical data (GSE73731)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29720944", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The headline result was that WGCNA-based analysis identified 29 hub genes associated with pathological stages of ccRCC, which were validated in independent datasets and associated with prognosis: “29 genes with the high connectivity in patho-module were selected as hub genes” and “Patients with higher each hub gene showed significantly shorter overall survival rate and disease-free survival rate, indicating that all hub genes could act as prognosis and recurrence biomarkers of ccRCC”. The statistical route used differential-expression screening followed by weighted co-expression network analysis, module preservation, correlation with clinical traits, one-way ANOVA for stage/grade comparisons, and Kaplan–Meier survival analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29720944", "locator": "sections[14] \"Identification of hub genes\" paragraph 2", "quote": "29 genes with the high connectivity in patho-module were selected as hub genes"}, {"asset": "source:pmid:29720944", "locator": "sections[16] \"Survival analysis\" paragraph 2", "quote": "Patients with higher each hub gene showed significantly shorter overall survival rate and disease-free survival rate, indicating that all hub genes could act as prognosis and recurrence biomarkers of ccRCC"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The headline result was that WGCNA-based analysis identified 29 hub genes associated with pathological stages of ccRCC, which were validated in independent datasets and associated with prognosis: “29 genes with the high connectivity in patho-module were selected as hub genes” and “Patients with higher each hub gene showed significantly shorter overall survival rate and disease-free survival rate, indicating that all hub genes could act as prognosis and recurrence biomarkers of ccRCC”. The statistical route used differential-expression screening followed by weighted co-expression network analysis, module preservation, correlation with clinical traits, one-way ANOVA for stage/grade comparisons, and Kaplan–Meier survival analysis.", "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:29720944"], "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:GSE36895"], "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:GSE36895"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29720944", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fphys.2018.00399", "sha256": "sha256:29ada064d7938ed19cb2332ded99b8baf22741bc2e7a6d979858b3c6364262de", "bytes": 35827, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fphys.2018.00399", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5915556", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE36895", "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=GSE36895", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE36895", "version": null, "note": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM904985", "GSM904986", "GSM904988", "GSM904989", "GSM904990", "GSM904991", "GSM904992", "GSM904994", "GSM904995", "GSM904996", "GSM904998", "GSM904999", "GSM905000", "GSM905002", "GSM905003", "GSM905004", "GSM905006", "GSM905007", "GSM905008", "GSM905009", "GSM905011", "GSM905012", "GSM905013", "GSM905014", "GSM905016", "GSM905017", "GSM905018", "GSM905020", "GSM905021", "GSM905022", "GSM905023", "GSM905024", "GSM905025", "GSM905026", "GSM905027", "GSM905028", "GSM905029", "GSM905030", "GSM905031", "GSM905032", "GSM905033", "GSM905034", "GSM905035", "GSM905036", "GSM905037", "GSM905038", "GSM905039", "GSM905040", "GSM905041", "GSM905042", "GSM905043", "GSM905044", "GSM905045", "GSM905046", "GSM905047", "GSM905048", "GSM905049", "GSM905050", "GSM905051", "GSM905052", "GSM905053", "GSM905054", "GSM905055", "GSM905056", "GSM905057", "GSM905058", "GSM905059", "GSM905060", "GSM905061", "GSM905062", "GSM905063", "GSM905064", "GSM905065", "GSM905066", "GSM905067", "GSM905068"], "sample_count": 76, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular Genetic Classification of clear-cell Renal Cell Carcinoma (ccRCC) based on the Gene Expression Profiling of Tumors and Tumorgrafts deficient for BAP1 or PBRM1", "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:GSE40355", "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=GSE40355", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40355", "version": null, "note": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM881439", "GSM881440", "GSM881441", "GSM881442", "GSM881443", "GSM881444", "GSM881445", "GSM881446", "GSM881447", "GSM881448", "GSM881449", "GSM881450", "GSM881451", "GSM881452", "GSM881453", "GSM881454", "GSM881455", "GSM881456", "GSM881457", "GSM881458", "GSM881459", "GSM881460", "GSM881461", "GSM881462", "GSM991923", "GSM991924", "GSM991925", "GSM991926", "GSM991927", "GSM991928", "GSM991929", "GSM991930", "GSM991931", "GSM991932", "GSM991933", "GSM991934", "GSM991935", "GSM991936", "GSM991937", "GSM991938", "GSM991939", "GSM991940", "GSM991941", "GSM991942", "GSM991943", "GSM991944", "GSM991945", "GSM991946"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "8227;13497", "taxon": "Homo sapiens", "title": "Bladder cancer: analysis of miRNA-mRNA interactions", "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:GSE53757", "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=GSE53757", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53757", "version": null, "note": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1300062", "GSM1300063", "GSM1300064", "GSM1300065", "GSM1300066", "GSM1300067", "GSM1300068", "GSM1300069", "GSM1300070", "GSM1300071", "GSM1300072", "GSM1300073", "GSM1300074", "GSM1300075", "GSM1300076", "GSM1300077", "GSM1300078", "GSM1300079", "GSM1300080", "GSM1300081", "GSM1300082", "GSM1300083", "GSM1300084", "GSM1300085", "GSM1300086", "GSM1300087", "GSM1300088", "GSM1300089", "GSM1300090", "GSM1300091", "GSM1300092", "GSM1300093", "GSM1300094", "GSM1300095", "GSM1300096", "GSM1300097", "GSM1300098", "GSM1300099", "GSM1300100", "GSM1300101", "GSM1300102", "GSM1300103", "GSM1300104", "GSM1300105", "GSM1300106", "GSM1300107", "GSM1300108", "GSM1300109", "GSM1300110", "GSM1300111", "GSM1300112", "GSM1300113", "GSM1300114", "GSM1300115", "GSM1300116", "GSM1300117", "GSM1300118", "GSM1300119", "GSM1300120", "GSM1300121", "GSM1300122", "GSM1300123", "GSM1300124", "GSM1300125", "GSM1300126", "GSM1300127", "GSM1300128", "GSM1300129", "GSM1300130", "GSM1300131", "GSM1300132", "GSM1300133", "GSM1300134", "GSM1300135", "GSM1300136", "GSM1300137", "GSM1300138", "GSM1300139", "GSM1300140", "GSM1300141", "GSM1300142", "GSM1300143", "GSM1300144", "GSM1300145", "GSM1300146", "GSM1300147", "GSM1300148", "GSM1300149", "GSM1300150", "GSM1300151", "GSM1300152", "GSM1300153", "GSM1300154", "GSM1300155", "GSM1300156", "GSM1300157", "GSM1300158", "GSM1300159", "GSM1300160", "GSM1300161", "GSM1300162", "GSM1300163", "GSM1300164", "GSM1300165", "GSM1300166", "GSM1300167", "GSM1300168", "GSM1300169", "GSM1300170", "GSM1300171", "GSM1300172", "GSM1300173", "GSM1300174", "GSM1300175", "GSM1300176", "GSM1300177", "GSM1300178", "GSM1300179", "GSM1300180", "GSM1300181", "GSM1300182", "GSM1300183", "GSM1300184", "GSM1300185", "GSM1300186", "GSM1300187", "GSM1300188", "GSM1300189", "GSM1300190", "GSM1300191", "GSM1300192", "GSM1300193", "GSM1300194", "GSM1300195", "GSM1300196", "GSM1300197", "GSM1300198", "GSM1300199", "GSM1300200", "GSM1300201", "GSM1300202", "GSM1300203", "GSM1300204", "GSM1300205"], "sample_count": 144, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene array analysis of clear cell renal cell carcinoma tissue versus matched normal kidney tissue", "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:GSE73731", "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=GSE73731", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73731", "version": null, "note": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1930996", "GSM1930997", "GSM1930998", "GSM1930999", "GSM1931000", "GSM1931001", "GSM1931002", "GSM1931003", "GSM1931004", "GSM1931005", "GSM1931006", "GSM1931007", "GSM1931008", "GSM1931009", "GSM1931010", "GSM1931011", "GSM1931012", "GSM1931013", "GSM1931014", "GSM1931015", "GSM1931016", "GSM1931017", "GSM1931018", "GSM1931019", "GSM1931020", "GSM1931021", "GSM1931022", "GSM1931023", "GSM1931024", "GSM1931025", "GSM1931026", "GSM1931027", "GSM1931028", "GSM1931029", "GSM1931030", "GSM1931031", "GSM1931032", "GSM1931033", "GSM1931034", "GSM1931035", "GSM1931036", "GSM1931037", "GSM1931038", "GSM1931039", "GSM1931040", "GSM1931041", "GSM1931042", "GSM1931043", "GSM1931044", "GSM1931045", "GSM1931046", "GSM1931047", "GSM1931048", "GSM1931049", "GSM1931050", "GSM1931051", "GSM1931052", "GSM1931053", "GSM1931054", "GSM1931055", "GSM1931056", "GSM1931057", "GSM1931058", "GSM1931059", "GSM1931060", "GSM1931061", "GSM1931062", "GSM1931063", "GSM1931064", "GSM1931065", "GSM1931066", "GSM1931067", "GSM1931068", "GSM1931069", "GSM1931070", "GSM1931071", "GSM1931072", "GSM1931073", "GSM1931074", "GSM1931075", "GSM1931076", "GSM1931077", "GSM1931078", "GSM1931079", "GSM1931080", "GSM1931081", "GSM1931082", "GSM1931083", "GSM1931084", "GSM1931085", "GSM1931086", "GSM1931087", "GSM1931088", "GSM1931089", "GSM1931090", "GSM1931091", "GSM1931092", "GSM1931093", "GSM1931094", "GSM1931095", "GSM1931096", "GSM1931097", "GSM1931098", "GSM1931099", "GSM1931100", "GSM1931101", "GSM1931102", "GSM1931103", "GSM1931104", "GSM1931105", "GSM1931106", "GSM1931107", "GSM1931108", "GSM1931109", "GSM1931110", "GSM1931111", "GSM1931112", "GSM1931113", "GSM1931114", "GSM1931115", "GSM1931116", "GSM1931117", "GSM1931118", "GSM1931119", "GSM1931120", "GSM1931121", "GSM1931122", "GSM1931123", "GSM1931124", "GSM1931125", "GSM1931126", "GSM1931127", "GSM1931128", "GSM1931129", "GSM1931130", "GSM1931131", "GSM1931132", "GSM1931133", "GSM1931134", "GSM1931135", "GSM1931136", "GSM1931137", "GSM1931138", "GSM1931139", "GSM1931140", "GSM1931141", "GSM1931142", "GSM1931143", "GSM1931144", "GSM1931145", "GSM1931146", "GSM1931147", "GSM1931148", "GSM1931149", "GSM1931150", "GSM1931151", "GSM1931152", "GSM1931153", "GSM1931154", "GSM1931155", "GSM1931156", "GSM1931157", "GSM1931158", "GSM1931159", "GSM1931160", "GSM1931161", "GSM1931162", "GSM1931163", "GSM1931164", "GSM1931165", "GSM1931166", "GSM1931167", "GSM1931168", "GSM1931169", "GSM1931170", "GSM1931171", "GSM1931172", "GSM1931173", "GSM1931174", "GSM1931175", "GSM1931176", "GSM1931177", "GSM1931178", "GSM1931179", "GSM1931180", "GSM1931181", "GSM1931182", "GSM1931183", "GSM1931184", "GSM1931185", "GSM1931186", "GSM1931187", "GSM1931188", "GSM1931189", "GSM1931190", "GSM1931191", "GSM1931192", "GSM1931193", "GSM1931194", "GSM1931195", "GSM1931196", "GSM1931197", "GSM1931198", "GSM1931199", "GSM1931200", "GSM1931201", "GSM1931202", "GSM1931203", "GSM1931204", "GSM1931205", "GSM1931206", "GSM1931207", "GSM1931208", "GSM1931209", "GSM1931210", "GSM1931211", "GSM1931212", "GSM1931213", "GSM1931214", "GSM1931215", "GSM1931216", "GSM1931217", "GSM1931218", "GSM1931219", "GSM1931220", "GSM1931221", "GSM1931222", "GSM1931223", "GSM1931224", "GSM1931225", "GSM1931226", "GSM1931227", "GSM1931228", "GSM1931229", "GSM1931230", "GSM1931231", "GSM1931232", "GSM1931233", "GSM1931234", "GSM1931235", "GSM1931236", "GSM1931237", "GSM1931238", "GSM1931239", "GSM1931240", "GSM1931241", "GSM1931242", "GSM1931243", "GSM1931244", "GSM1931245", "GSM1931246", "GSM1931247", "GSM1931248", "GSM1931249", "GSM1931250", "GSM1931251", "GSM1931252", "GSM1931253", "GSM1931254", "GSM1931255", "GSM1931256", "GSM1931257", "GSM1931258", "GSM1931259", "GSM1931260"], "sample_count": 265, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Clear cell renal cell carcinoma (ccRCC) samples", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29720944:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b578cb8b750596fa55f588d8bc9241e2009052b22738d419b650aba64d4290b5", "bytes": 2015, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T1", "version": null, "note": "Hub genes in the modules related with pathological stages.", "structure": {"pmcid": "PMC5915556", "section_index": 14, "section_title": "Identification of hub genes", "row_count": 31, "column_count": 7}, "table": {"label": "Table 1", "caption": "Hub genes in the modules related with pathological stages.", "rows": [["Gene", "Entrez ID", "Probe ID", "Co-expression analysis", "DEG analysis"], ["", "", "", "cor.geneModuleMembership", "cor.gene TraitSignificance", "Fold change", "FDR"], ["ANLN", "54443", "222608_s_at", "0.918", "0.345", "4.33", "0"], ["ASPM", "259266", "219918_s_at", "0.870", "0.383", "4.95", "0"], ["ATAD2", "29028", "222740_at", "0.813", "0.356", "2.57", "0"], ["BUB1B", "701", "203755_at", "0.916", "0.414", "2.61", "0"], ["CCNA2", "890", "213226_at", "0.872", "0.311", "2.57", "0"], ["CCNB1", "891", "214710_s_at", "0.887", "0.415", "2.20", "0"], ["CDK1", "983", "203213_at", "0.850", "0.221", "2.28", "0"], ["CDKN3", "1033", "1555758_a_at", "0.813", "0.266", "2.36", "0"], ["CENPF", "1063", "207828_s_at", "0.861", "0.332", "2.49", "0"], ["CENPK", "64105", "222848_at", "0.840", "0.322", "4.19", "0"], ["CENPW", "387103", "226936_at", "0.805", "0.373", "2.01", "0"], ["CEP55", "55165", "218542_at", "0.935", "0.384", "2.88", "0"], ["DLGAP5", "9787", "203764_at", "0.840", "0.298", "2.63", "0"], ["FOXM1", "2305", "202580_x_at", "0.832", "0.378", "2.03", "0"], ["KIF11", "3832", "204444_at", "0.855", "0.395", "2.61", "0"], ["KIF14", "9928", "236641_at", "0.930", "0.333", "2.11", "0"], ["KIF20A", "10112", "218755_at", "0.847", "0.368", "3.08", "0"], ["KIF4A", "24137", "218355_at", "0.883", "0.338", "2.42", "0"], ["MELK", "9833", "204825_at", "0.850", "0.323", "2.23", "0"], ["NCAPG", "54892", "218662_s_at", "0.823", "0.317", "2.12", "0"], ["NEK2", "4751", "204641_at", "0.857", "0.345", "2.41", "0"], ["NUF2", "83540", "223381_at", "0.891", "0.416", "2.30", "0"], ["PRC1", "9055", "218009_s_at", "0.909", "0.366", "4.01", "0"], ["PTTG1", "9232", "203554_x_at", "0.829", "0.285", "2.76", "0"], ["RRM2", "6241", "201890_at", "0.888", "0.370", "5.29", "0"], ["TOP2A", "7153", "201291_s_at", "0.917", "0.392", "5.59", "0"], ["TPX2", "22974", "210052_s_at", "0.833", "0.360", "2.91", "0"], ["TTK", "7272", "204822_at", "0.846", "0.443", "2.55", "0"], ["UHRF1", "29128", "225655_at", "0.867", "0.331", "3.65", "0"]], "row_count": 31, "column_count": 7, "numeric_cells": 178, "header_rows": 2, "locator": "section[14]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE36895 not downloaded", "asset:data:geo:GSE36895 licence not read", "asset:data:geo:GSE40355 not downloaded", "asset:data:geo:GSE40355 licence not read", "asset:data:geo:GSE53757 not downloaded", "asset:data:geo:GSE53757 licence not read", "asset:data:geo:GSE73731 not downloaded", "asset:data:geo:GSE73731 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.7, "band": "medium", "quote": "Pearson's correlation"}}, {"id": "method-3", "family": null, "specific": null, "label": "Weighted gene co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The “WGCNA” (Langfelder and Horvath, 2008) package in R was applied to performed co-expression network using the expression values of 2,425 DEGs from 125 tumor samples and complete clinical data (GSE73731)."}}], "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": ["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": ["GSE53757", "GSE36895", "GSE73731", "GSE40355"], "resolved_accessions": ["GSE53757", "GSE36895", "GSE73731", "GSE40355"], "statements": ["Datasets GSE53757 Von Roemeling et al., 2014 and GSE36895 (Peña-Llopis et al., 2012) performed on the same platform Affymetrix Human Genome U133 Plus 2.0 Array (HG U133 Plus 2.0) were combined and analyzed to screen DEGs."], "basis": "The paper names GSE53757, GSE36895, GSE73731, GSE40355 in Gene Expression Omnibus (GEO) database 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:29720944", "data:geo:GSE36895", "asset:table:pmid:29720944:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE36895"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:21Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 74471, "completion_tokens": 5306, "cached_tokens": 10784}}, "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:29720944", "type": "paper", "label": "pmid:29720944"}, {"id": "source:pmid:29720944", "type": "manuscript", "label": "PMID 29720944 full text"}, {"id": "data:geo:GSE36895", "type": "dataset", "label": "GEO GSE36895"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29720944", "type": "paper", "label": "pmid:29720944"}, {"id": "source:pmid:29720944", "type": "manuscript", "label": "PMID 29720944 full text"}, {"id": "data:geo:GSE36895", "type": "dataset", "label": "GEO GSE36895"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29720944", "type": "extraction", "used": ["source:pmid:29720944"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE36895", "type": "accession_resolution", "used": ["data:geo:GSE36895"], "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:29720944", "parent_hash": "sha256:eb0623a8e834333f5834fbafa47ab7d2c251a7eaf418da7514e48dae1e3c3d04", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE36895 licence not read", "asset:data:geo:GSE36895 not downloaded", "asset:data:geo:GSE40355 licence not read", "asset:data:geo:GSE40355 not downloaded", "asset:data:geo:GSE53757 licence not read", "asset:data:geo:GSE53757 not downloaded", "asset:data:geo:GSE73731 licence not read", "asset:data:geo:GSE73731 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": ["used or clinical application. In our study, microarray data of 101 ccRCC samples and 95 normal kidn"], "order_basis": "paper_text_order:428", "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"}]}