CGN Correlates With the Prognosis and Tumor Immune Microenvironment in Clear Cell Renal Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35223987", "kind": "science-record", "revision": 4, "content_hash": "sha256:c6a5dc4ed6ee9dc11814a1b223e14e6caca6085e85bea8158fd65604115ab642", "created_at": "2026-11-01T17:36:59Z", "updated_at": "2026-11-01T21:27:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CGN Correlates With the Prognosis and Tumor Immune Microenvironment in Clear Cell Renal Cell Carcinoma.", "doi": "10.3389/fmolb.2022.758974", "pmid": "35223987", "authors": ["Zijian Tian", "Lingfeng Meng", "Xin Wang", "Tongxiang Diao", "Maolin Hu", "Miao Wang", "Yaqun Zhang", "Ming Liu", "Jianye Wang"], "journal": "Frontiers in molecular biosciences", "year": 2022, "abstract": "This study aimed to screen and verify the important prognostic genes related to clear cell renal cell carcinoma (ccRCC) and further analyze their relationship with the immune microenvironment. Gene expression profiles from the TCGA-KIRC, GSE46699, GSE36895, and GSE16449 datasets were utilized to explore differentially co-expressed genes in ccRCC. We screened 124 differentially co-expressed genes using a weighted gene co-expression network and differential gene expression analyses. Univariate and multivariate Cox survival analyses revealed that the expressions of genes CGN, FECH, UCHL1, and WT1 were independently related to the overall survival of ccRCC patients. Kaplan-Meier survival analysis was performed, and CGN was found to have the strongest correlation with the prognosis of ccRCC patients and was consequently selected for further analyses and experimental verification. The results showed that NK cell activation, resting dendritic cells, resting monocytes, and resting mast cells were positively correlated with CGN expression; CD4+ memory activated T cells, regulatory T cells, and M0 macrophages were negatively correlated with CGN expression. Finally, using western blotting and reverse transcription polymerase chain reaction, we verified that the CGN protein level was down-regulated in ccRCC samples, which was consistent with the mRNA levels. CGN was thus identified as diagnosis and prognosis biomarker for ccRCC and is related to the immune microenvironment.", "claims": [{"id": "claim-method", "statement": "Weighted gene co-expression network analysis (WGCNA) is a systems biology method that delineates gene association patterns between different samples and can be used to identify highly coordinated gene sets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35223987", "locator": "sections[1] \"Introduction\" paragraph 3", "quote": "Weighted gene co-expression network analysis (WGCNA) is a systems biology method that delineates gene association patterns between different samples and can be used to identify highly coordinated gene sets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35223987", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CGN was thus identified as diagnosis and prognosis biomarker for ccRCC and is related to the immune microenvironment.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35223987", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "CGN was thus identified as diagnosis and prognosis biomarker for ccRCC and is related to the immune microenvironment."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CGN was thus identified as diagnosis and prognosis biomarker for ccRCC and is related to the immune microenvironment.", "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:35223987"], "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:GSE16449"], "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:GSE16449"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35223987", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmolb.2022.758974", "sha256": "sha256:83af4d3cb52b6a1cb6755d9a847fedcbad51cb472308da49a1a387521d88a773", "bytes": 32696, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmolb.2022.758974", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8865610", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16449", "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=GSE16449", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16449", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM413237", "GSM413238", "GSM413239", "GSM413240", "GSM413241", "GSM413242", "GSM413243", "GSM413244", "GSM413245", "GSM413246", "GSM413247", "GSM413248", "GSM413249", "GSM413250", "GSM413251", "GSM413252", "GSM413253", "GSM413254", "GSM413255", "GSM413256", "GSM413257", "GSM413258", "GSM413259", "GSM413260", "GSM413261", "GSM413262", "GSM413263", "GSM413264", "GSM413265", "GSM413266", "GSM413267", "GSM413268", "GSM413269", "GSM413270", "GSM413514", "GSM413515", "GSM413516", "GSM413517", "GSM413518", "GSM413519", "GSM413520", "GSM413521", "GSM413522", "GSM413523", "GSM413524", "GSM413525", "GSM413526", "GSM413527", "GSM413528", "GSM413529", "GSM413530", "GSM413531", "GSM413532", "GSM413533", "GSM413534", "GSM413535", "GSM413536", "GSM413537", "GSM413538", "GSM413539", "GSM413540", "GSM413541", "GSM413542", "GSM413543", "GSM413544", "GSM413545", "GSM413546", "GSM413547", "GSM413548", "GSM414718"], "sample_count": 70, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Molecular Stratification of Clear Cell Renal Cell Carcinoma Reveals Distinct Subtypes and Survival Patterns", "resolution_checked_at": "2026-11-01T15:30:21Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE22541", "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=GSE22541", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22541", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM359477", "GSM359478", "GSM359479", "GSM359480", "GSM359481", "GSM359482", "GSM359483", "GSM359484", "GSM359485", "GSM359486", "GSM359487", "GSM359488", "GSM359489", "GSM359490", "GSM359491", "GSM359492", "GSM359493", "GSM359494", "GSM359495", "GSM359496", "GSM559577", "GSM559578", "GSM559579", "GSM559580", "GSM559581", "GSM559582", "GSM559583", "GSM559584", "GSM559585", "GSM559586", "GSM559587", "GSM559588", "GSM559589", "GSM559590", "GSM559591", "GSM559592", "GSM559593", "GSM559594", "GSM559595", "GSM559596", "GSM559597", "GSM559598", "GSM559599", "GSM559600", "GSM559705", "GSM559706", "GSM559707", "GSM559708", "GSM559709", "GSM559710", "GSM559711", "GSM559712", "GSM559713", "GSM559714", "GSM559715", "GSM559716", "GSM559717", "GSM559718", "GSM559719", "GSM559720", "GSM559721", "GSM559722", "GSM559723", "GSM559724", "GSM559725", "GSM559726", "GSM559727", "GSM559728"], "sample_count": 68, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from pulmonary metastases and primary tumors of clear-cell renal cell carcinoma (ccRCC) with different disease-free survivals", "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:GSE29609", "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=GSE29609", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29609", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM733579", "GSM733580", "GSM733581", "GSM733582", "GSM733583", "GSM733584", "GSM733585", "GSM733586", "GSM733587", "GSM733588", "GSM733589", "GSM733590", "GSM733591", "GSM733592", "GSM733593", "GSM733594", "GSM733595", "GSM733596", "GSM733597", "GSM733598", "GSM733599", "GSM733600", "GSM733601", "GSM733602", "GSM733603", "GSM733604", "GSM733605", "GSM733606", "GSM733607", "GSM733608", "GSM733609", "GSM733610", "GSM733611", "GSM733612", "GSM733613", "GSM733614", "GSM733615", "GSM733616", "GSM733617"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "1708", "taxon": "Homo sapiens", "title": "Clear-cell renal cell carcinomas tumors", "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:GSE3", "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=GSE3", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM100", "GSM101", "GSM102", "GSM103", "GSM104", "GSM105", "GSM106", "GSM107", "GSM108", "GSM109", "GSM110", "GSM111", "GSM112", "GSM113", "GSM114", "GSM115", "GSM116", "GSM117", "GSM118", "GSM119", "GSM120", "GSM121", "GSM122", "GSM123", "GSM124", "GSM125", "GSM126", "GSM127", "GSM128", "GSM129", "GSM130", "GSM131", "GSM132", "GSM133", "GSM134", "GSM135", "GSM136", "GSM137", "GSM138", "GSM139", "GSM140", "GSM141", "GSM142", "GSM143", "GSM144", "GSM145", "GSM146", "GSM147", "GSM148", "GSM149", "GSM150", "GSM151", "GSM152", "GSM153", "GSM154", "GSM155", "GSM156", "GSM157", "GSM158", "GSM159", "GSM160", "GSM161", "GSM162", "GSM163", "GSM164", "GSM165", "GSM166", "GSM167", "GSM168", "GSM169", "GSM170", "GSM171", "GSM172", "GSM173", "GSM174", "GSM175", "GSM176", "GSM177", "GSM178", "GSM179", "GSM180", "GSM181", "GSM182", "GSM183", "GSM184", "GSM185", "GSM186", "GSM187", "GSM188", "GSM189", "GSM190", "GSM191", "GSM192", "GSM193", "GSM194", "GSM195", "GSM196", "GSM197", "GSM198", "GSM199", "GSM200", "GSM201", "GSM202", "GSM203", "GSM204", "GSM205", "GSM206", "GSM207", "GSM208", "GSM209", "GSM210", "GSM211", "GSM212", "GSM213", "GSM214", "GSM215", "GSM216", "GSM217", "GSM218", "GSM219", "GSM220", "GSM221", "GSM222", "GSM223", "GSM224", "GSM225", "GSM226", "GSM227", "GSM228", "GSM229", "GSM230", "GSM231", "GSM232", "GSM233", "GSM234", "GSM235", "GSM236", "GSM237", "GSM238", "GSM239", "GSM240", "GSM241", "GSM242", "GSM243", "GSM244", "GSM245", "GSM246", "GSM247", "GSM248", "GSM249", "GSM250", "GSM251", "GSM252", "GSM253", "GSM254", "GSM255", "GSM256", "GSM257", "GSM258", "GSM259", "GSM260", "GSM261", "GSM262", "GSM263", "GSM264", "GSM265", "GSM266", "GSM267", "GSM268", "GSM269", "GSM270", "GSM271", "GSM272", "GSM273", "GSM274", "GSM275", "GSM276", "GSM277", "GSM278", "GSM279", "GSM280", "GSM281", "GSM282", "GSM283", "GSM284", "GSM285", "GSM286", "GSM287", "GSM288", "GSM289", "GSM290", "GSM291", "GSM292", "GSM293", "GSM294", "GSM295", "GSM296", "GSM297", "GSM298", "GSM299", "GSM300", "GSM301", "GSM302", "GSM303", "GSM304", "GSM305", "GSM306", "GSM307", "GSM308", "GSM309", "GSM310", "GSM311", "GSM312", "GSM313", "GSM314", "GSM315", "GSM316", "GSM317", "GSM318", "GSM319", "GSM320", "GSM321", "GSM322", "GSM323", "GSM324", "GSM325", "GSM326", "GSM327", "GSM328", "GSM329", "GSM330", "GSM331", "GSM332", "GSM333", "GSM334", "GSM335", "GSM336", "GSM337", "GSM338", "GSM339", "GSM340", "GSM341", "GSM342", "GSM343", "GSM344", "GSM345", "GSM346", "GSM347", "GSM348", "GSM349", "GSM350", "GSM351", "GSM352", "GSM353", "GSM354", "GSM355", "GSM356", "GSM357", "GSM358", "GSM359", "GSM360", "GSM361", "GSM362", "GSM363", "GSM364", "GSM365", "GSM366", "GSM367", "GSM368", "GSM369", "GSM370", "GSM371", "GSM372", "GSM373", "GSM374", "GSM375", "GSM376", "GSM377", "GSM378", "GSM379", "GSM380", "GSM381", "GSM382", "GSM383", "GSM384", "GSM385", "GSM386", "GSM387", "GSM388", "GSM389", "GSM390", "GSM391", "GSM392", "GSM393", "GSM394", "GSM395", "GSM396", "GSM397", "GSM398", "GSM399", "GSM400", "GSM401", "GSM402", "GSM403", "GSM404", "GSM405", "GSM406", "GSM407", "GSM408", "GSM409", "GSM410", "GSM411", "GSM412", "GSM413", "GSM414", "GSM415", "GSM416", "GSM417", "GSM418", "GSM419", "GSM420", "GSM421", "GSM422", "GSM81", "GSM82", "GSM83", "GSM84", "GSM85", "GSM86", "GSM87", "GSM88", "GSM89", "GSM90", "GSM91", "GSM92", "GSM93", "GSM94", "GSM95", "GSM96", "GSM97", "GSM98", "GSM99"], "sample_count": 342, "group_sizes": null, "group_sizes_basis": null, "platform": "10;9", "taxon": "Homo sapiens", "title": "Renal Cell Carcinoma Differential Expression", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"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": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_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:GSE46699", "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=GSE46699", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46699", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1134764", "GSM1134765", "GSM1134766", "GSM1134767", "GSM1134768", "GSM1134769", "GSM1134770", "GSM1134771", "GSM1134772", "GSM1134773", "GSM1134774", "GSM1134775", "GSM1134776", "GSM1134777", "GSM1134778", "GSM1134779", "GSM1134780", "GSM1134781", "GSM1134782", "GSM1134783", "GSM1134784", "GSM1134785", "GSM1134786", "GSM1134787", "GSM1134788", "GSM1134789", "GSM1134790", "GSM1134791", "GSM1134792", "GSM1134793", "GSM1134794", "GSM1134795", "GSM1134796", "GSM1134797", "GSM1134798", "GSM1134799", "GSM1134800", "GSM1134801", "GSM1134802", "GSM1134803", "GSM1134804", "GSM1134805", "GSM1134806", "GSM1134807", "GSM1134808", "GSM1134809", "GSM1134810", "GSM1134811", "GSM1134812", "GSM1134813", "GSM1134814", "GSM1134815", "GSM1134816", "GSM1134817", "GSM1134818", "GSM1134819", "GSM1134820", "GSM1134821", "GSM1134822", "GSM1134823", "GSM1134824", "GSM1134825", "GSM1134826", "GSM1134827", "GSM1134828", "GSM1134829", "GSM1134830", "GSM1134831", "GSM1134832", "GSM1134833", "GSM1134834", "GSM1134835", "GSM1134836", "GSM1134837", "GSM1134838", "GSM1134839", "GSM1134840", "GSM1134841", "GSM1134842", "GSM1134843", "GSM1134844", "GSM1134845", "GSM1134846", "GSM1134847", "GSM1134848", "GSM1134849", "GSM1134850", "GSM1134851", "GSM1134852", "GSM1134853", "GSM1134854", "GSM1134855", "GSM1134856", "GSM1134857", "GSM1134858", "GSM1134859", "GSM1134860", "GSM1134861", "GSM1134862", "GSM1134863", "GSM1134864", "GSM1134865", "GSM1134866", "GSM1134867", "GSM1134868", "GSM1134869", "GSM1134870", "GSM1134871", "GSM1134872", "GSM1134873", "GSM1134874", "GSM1134875", "GSM1134876", "GSM1134877", "GSM1134878", "GSM1134879", "GSM1134880", "GSM1134881", "GSM1134882", "GSM1134883", "GSM1134884", "GSM1134885", "GSM1134886", "GSM1134887", "GSM1134888", "GSM1134889", "GSM1304420", "GSM1304421", "GSM1304422", "GSM1304423"], "sample_count": 130, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Smoking and Obesity Related Molecular Alterations in Clear Cell Renal Cell Carcinoma", "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:GSE16449 not downloaded", "asset:data:geo:GSE16449 licence not read", "asset:data:geo:GSE22541 not downloaded", "asset:data:geo:GSE22541 licence not read", "asset:data:geo:GSE29609 not downloaded", "asset:data:geo:GSE29609 licence not read", "asset:data:geo:GSE3 not downloaded", "asset:data:geo:GSE3 licence not read", "asset:data:geo:GSE36895 not downloaded", "asset:data:geo:GSE36895 licence not read", "asset:data:geo:GSE46699 not downloaded", "asset:data:geo:GSE46699 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": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-4", "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": "Weighted gene co-expression network analysis (WGCNA) is a systems biology method that delineates gene association patterns between different samples and can be used to identify highly coordinated gene sets."}}], "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": ["GSE46699", "GSE36895", "GSE16449", "GSE3", "GSE22541", "GSE29609"], "resolved_accessions": ["GSE46699", "GSE36895", "GSE16449", "GSE3", "GSE22541", "GSE29609"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE46699, GSE36895, GSE16449, GSE3, GSE22541, GSE29609 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:35223987", "data:geo:GSE16449"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16449"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:36:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9801, "completion_tokens": 2255, "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:35223987", "type": "paper", "label": "pmid:35223987"}, {"id": "source:pmid:35223987", "type": "manuscript", "label": "PMID 35223987 full text"}, {"id": "data:geo:GSE16449", "type": "dataset", "label": "GEO GSE16449"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35223987", "type": "paper", "label": "pmid:35223987"}, {"id": "source:pmid:35223987", "type": "manuscript", "label": "PMID 35223987 full text"}, {"id": "data:geo:GSE16449", "type": "dataset", "label": "GEO GSE16449"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35223987", "type": "extraction", "used": ["source:pmid:35223987"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16449", "type": "accession_resolution", "used": ["data:geo:GSE16449"], "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:35223987", "parent_hash": "sha256:0c0d18b558ba1bf6e654098a6346a13dc03306a8fdd44576f57d56ebafe5ef0b", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE16449 licence not read", "asset:data:geo:GSE16449 not downloaded", "asset:data:geo:GSE22541 licence not read", "asset:data:geo:GSE22541 not downloaded", "asset:data:geo:GSE29609 licence not read", "asset:data:geo:GSE29609 not downloaded", "asset:data:geo:GSE3 licence not read", "asset:data:geo:GSE3 not downloaded", "asset:data:geo:GSE36895 licence not read", "asset:data:geo:GSE36895 not downloaded", "asset:data:geo:GSE46699 licence not read", "asset:data:geo:GSE46699 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rrelated with CGN expression. Finally, using western blotting and reverse transcription polymerase chain r", "ption polymerase chain reaction (RT-PCR) and western blotting (WB) were performed on the fresh ccRCC sampl", "sues. (D) Expressed CGN protein confirmed by western blot analysis in normal and tumor tissues. Supple"], "order_basis": "paper_text_order:1239", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Methods Data and Sample Collection RNA sequencing data of 72 normal renal samples and 539 ccRC"], "order_basis": "paper_text_order:1591", "id": "assay:2"}, {"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": [") database (https://cancerg enome.nih.gov/). Microarray data sets (GSE46699 (63 normal renal and 67"], "order_basis": "paper_text_order:1802", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ormal tissues (p < 0.001; Figure 8D). (A, B) Immunohistochemistry of the CGN gene in normal and tumor tissues"], "order_basis": "paper_text_order:7232", "id": "assay:4"}, {"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:5"}]}