{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32775374", "kind": "science-record", "revision": 7, "content_hash": "sha256:5ac741f291fe8a2cae74ea33a40c31ba88c1e6f1271d1c576b98cfbc569ef845", "created_at": "2026-11-01T15:41:07Z", "updated_at": "2026-11-01T22:02:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of APEX2 as an oncogene in liver cancer.", "doi": "10.12998/wjcc.v8.i14.2917", "pmid": "32775374", "authors": ["Ru Zheng", "Heng-Liang Zhu", "Bing-Ren Hu", "Xiao-Jiao Ruan", "Hua-Jie Cai"], "journal": "World journal of clinical cases", "year": 2020, "abstract": "BACKGROUND: DNA damage is one of the critical contributors to the occurrence and development of some cancers. APEX1 and APEX2 are the most important molecules in the DNA damage, and APEX1 has been identified as a diagnostic and prognostic biomarker in liver hepatocellular carcinoma (LIHC). However, the expression of APEX2 and its functional mechanisms in LIHC are still unclear.\nAIM: To examine the expression of APEX2 and the potential mechanism network in LIHC.\nMETHODS: We conducted a pan-cancer analysis of the expression of APEX1 and APEX2 using the interactive TIMER tool. GEO datasets, including GSE14520, GSE22058, and GSE64041, were used to compare the APEX2 expression level in tumor tissues and adjacent non-tumor tissues. Then, we calculated the 5-year survival rate according to the web-based Kaplan-Meier analysis. We included the TCGA liver cancer database in GSEA analysis based on the high and low APEX2 expression, showing the potential mechanisms of APEX2 in LIHC. After that, we conducted Pearson correlation analysis using GEPIA2. Next, we performed quantitative polymerase chain reaction (qPCR) assay to examine the APEX2 levels in normal liver cell line LO2 and several liver cancer cell lines, including HepG2, Huh7, SMMC7721, and HCCLM3. APEX2 in HCCLM3 cells was knocked down using small interfering RNA. The role of APEX2 in cell viability was confirmed using CCK-8. Dual-luciferase reporter assay was performed to examine the promoter activity of CCNB1 and MYC.\nRESULTS: APEX1 and APEX2 are both highly expressed in the tumor tissues of BLCA, BRCA, CHOL, COAD, ESCA, HNSC, LIHC, LUAD, LUSC, READ, and STAD. APEX2 overexpression in LIHC was validated using GSE14520, GSE22058, and GSE64041 datasets. The survival analysis showed that LIHC patients with high expression of APEX2 had a lower overall survival rate, even in the AJCC T1 patients. High level of APEX2 could indicate a lower overall survival rate in patients with or without viral hepatitis. The GSEA analysis identified that kinetochore and spindle microtubules are the two main cellular components of APEX2 in GO Ontology. APEX2 was also positively associated with molecular function regulation of chromosome segregation and DNA replication. The results of KEGG analysis indicated that APEX2 expression was positively correlated with cell cycle pathway and pro-oncogenic MYC signaling. Pearson correlation analysis showed that APEX2 had a significant positive correlation with CCNB1 and MYC. APEX2 level was higher in liver cancer cell lines than in normal liver LO2 cells. Small interfering RNA could knock down the APEX2 expression in HCCLM3 cells. Knockdown of APEX2 resulted in a decrease in the viability of HCCLM3 cells as well as the expression and promoter activity of CCNB1 and MYC.\nCONCLUSION: APEX2 is overexpressed in LIHC, and the higher APEX2 level is associated with a worse prognosis in overall survival. APEX2 is closely involved in the biological processes of chromosome segregation and DNA replication. APEX2 expression is positively correlated with the pro-oncogenic pathways. Knockdown of APEX2 could inhibit the cell viability and CCNB1 and MYC pathways, suggesting that APEX2 is an oncogene in LIHC, which could be a potential pharmaceutic target in the anti-tumor therapy.", "claims": [{"id": "claim-method", "statement": "The Kaplan Meier method was used to analyze the overall survival, and the log-rank P method was applied to show the statistical difference.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32775374", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "The Kaplan Meier method was used to analyze the overall survival, and the log-rank P method was applied to show the statistical difference."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No additional data are available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32775374", "locator": "sections[30] \"Footnotes\" paragraph 2", "quote": "No additional data are available."}], "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:32775374"], "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:GSE14520"], "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:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32775374", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12998/wjcc.v8.i14.2917", "sha256": "sha256:228acbe5f7194b0af6782fb9c799a8bccdf8b16bae39dd9dfb73a558853fb6fd", "bytes": 42521, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12998/wjcc.v8.i14.2917", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7385600", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "No additional data are available.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No additional data are available.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM362947", "GSM362948", "GSM362949", "GSM362950", "GSM362951", "GSM362952", "GSM362953", "GSM362954", "GSM362955", "GSM362956", "GSM362957", "GSM362958", "GSM362959", "GSM362960", "GSM362961", "GSM362962", "GSM362963", "GSM362964", "GSM362965", "GSM362966", "GSM362967", "GSM362968", "GSM362969", "GSM362970", "GSM362971", "GSM362972", "GSM362973", "GSM362974", "GSM362975", "GSM362976", "GSM362977", "GSM362978", "GSM362979", "GSM362980", "GSM362981", "GSM362982", "GSM362983", "GSM362984", "GSM362985", "GSM362986", "GSM362987", "GSM362988", "GSM362989", "GSM362990", "GSM362991", "GSM362992", "GSM362993", "GSM362994", "GSM362995", "GSM362996", "GSM362997", "GSM362998", "GSM362999", "GSM363000", "GSM363001", "GSM363002", "GSM363003", "GSM363004", "GSM363005", "GSM363006", "GSM363007", "GSM363008", "GSM363009", "GSM363010", "GSM363011", "GSM363012", "GSM363013", "GSM363014", "GSM363015", "GSM363016", "GSM363017", "GSM363018", "GSM363019", "GSM363020", "GSM363021", "GSM363022", "GSM363023", "GSM363024", "GSM363025", "GSM363026", "GSM363027", "GSM363028", "GSM363029", "GSM363030", "GSM363031", "GSM363032", "GSM363033", "GSM363034", "GSM363035", "GSM363036", "GSM363037", "GSM363038", "GSM363039", "GSM363040", "GSM363041", "GSM363042", "GSM363043", "GSM363044", "GSM363045", "GSM363046", "GSM363047", "GSM363048", "GSM363049", "GSM363050", "GSM363051", "GSM363052", "GSM363053", "GSM363054", "GSM363055", "GSM363056", "GSM363057", "GSM363058", "GSM363059", "GSM363060", "GSM363061", "GSM363062", "GSM363063", "GSM363064", "GSM363065", "GSM363066", "GSM363067", "GSM363068", "GSM363069", "GSM363070", "GSM363071", "GSM363072", "GSM363073", "GSM363074", "GSM363075", "GSM363076", "GSM363077", "GSM363078", "GSM363079", "GSM363080", "GSM363081", "GSM363082", "GSM363083", "GSM363084", "GSM363085", "GSM363086", "GSM363087", "GSM363088", "GSM363089", "GSM363090", "GSM363091", "GSM363092", "GSM363093", "GSM363094", "GSM363095", "GSM363096", "GSM363097", "GSM363098", "GSM363099", "GSM363100", "GSM363101", "GSM363102", "GSM363103", "GSM363104", "GSM363105", "GSM363106", "GSM363107", "GSM363108", "GSM363109", "GSM363110", "GSM363111", "GSM363112", "GSM363113", "GSM363114", "GSM363115", "GSM363116", "GSM363117", "GSM363118", "GSM363119", "GSM363120", "GSM363121", "GSM363122", "GSM363123", "GSM363124", "GSM363125", "GSM363126", "GSM363127", "GSM363128", "GSM363129", "GSM363130", "GSM363131", "GSM363132", "GSM363133", "GSM363134", "GSM363135", "GSM363136", "GSM363137", "GSM363138", "GSM363139", "GSM363140", "GSM363141", "GSM363142", "GSM363143", "GSM363144", "GSM363145", "GSM363146", "GSM363147", "GSM363148", "GSM363149", "GSM363150", "GSM363151", "GSM363152", "GSM363153", "GSM363154", "GSM363155", "GSM363156", "GSM363157", "GSM363158", "GSM363159", "GSM363160", "GSM363161", "GSM363162", "GSM363163", "GSM363164", "GSM363165", "GSM363166", "GSM363167", "GSM363168", "GSM363169", "GSM363170", "GSM363171", "GSM363172", "GSM363173", "GSM363174", "GSM363175", "GSM363176", "GSM363177", "GSM363178", "GSM363179", "GSM363180", "GSM363181", "GSM363182", "GSM363183", "GSM363184", "GSM363185", "GSM363186", "GSM363187", "GSM363188", "GSM363189", "GSM363190", "GSM363191", "GSM363192", "GSM363193", "GSM363194", "GSM363195", "GSM363196", "GSM363197", "GSM363198", "GSM363199", "GSM363200", "GSM363201", "GSM363202", "GSM363203", "GSM363204", "GSM363205", "GSM363206", "GSM363207", "GSM363208", "GSM363209", "GSM363210", "GSM363211", "GSM363212", "GSM363213", "GSM363214", "GSM363215", "GSM363216", "GSM363217", "GSM363218", "GSM363219", "GSM363220", "GSM363221", "GSM363222", "GSM363223", "GSM363224", "GSM363225", "GSM363226", "GSM363227", "GSM363228", "GSM363229", "GSM363230", "GSM363231", "GSM363232", "GSM363233", "GSM363234", "GSM363235", "GSM363236", "GSM363237", "GSM363238", "GSM363239", "GSM363240", "GSM363241", "GSM363242", "GSM363243", "GSM363244", "GSM363245", "GSM363246", "GSM363247", "GSM363248", "GSM363249", "GSM363250", "GSM363251", "GSM363252", "GSM363253", "GSM363254", "GSM363255", "GSM363256", "GSM363257", "GSM363258", "GSM363259", "GSM363260", "GSM363261", "GSM363262", "GSM363263", "GSM363264", "GSM363265", "GSM363266", "GSM363267", "GSM363268", "GSM363269", "GSM363270", "GSM363271", "GSM363272", "GSM363273", "GSM363274", "GSM363275", "GSM363276", "GSM363277", "GSM363278", "GSM363279", "GSM363280", "GSM363281", "GSM363282", "GSM363283", "GSM363284", "GSM363285", "GSM363286", "GSM363287", "GSM363288", "GSM363289", "GSM363290", "GSM363291", "GSM363292", "GSM363293", "GSM363294", "GSM363295", "GSM363296", "GSM363297", "GSM363298", "GSM363299", "GSM363300", "GSM363301", "GSM363302", "GSM363303", "GSM363304", "GSM363305", "GSM363306", "GSM363307", "GSM363308", "GSM363309", "GSM363310", "GSM363311", "GSM363312", "GSM363313", "GSM363314", "GSM363315", "GSM363316", "GSM363317", "GSM363318", "GSM363319", "GSM363320", "GSM363321", "GSM363322", "GSM363323", "GSM363324", "GSM363325", "GSM363326", "GSM363327", "GSM363328", "GSM363329", "GSM363330", "GSM363331", "GSM363332", "GSM363333", "GSM363334", "GSM363335", "GSM363336", "GSM363337", "GSM363338", "GSM363339", "GSM363340", "GSM363341", "GSM363342", "GSM363343", "GSM363344", "GSM363345", "GSM363346", "GSM363347", "GSM363348", "GSM363349", "GSM363350", "GSM363351", "GSM363352", "GSM363353", "GSM363354", "GSM363355", "GSM363356", "GSM363357", "GSM363358", "GSM363359", "GSM363360", "GSM363361", "GSM363362", "GSM363363", "GSM363364", "GSM363365", "GSM363366", "GSM363367", "GSM363368", "GSM363369", "GSM363370", "GSM363371", "GSM363372", "GSM363373", "GSM363374", "GSM363375", "GSM363376", "GSM363378", "GSM363380", "GSM363381", "GSM363382", "GSM363384", "GSM363386", "GSM363388", "GSM363391", "GSM363393", "GSM363397", "GSM363400", "GSM363402", "GSM363404", "GSM363407", "GSM363417", "GSM363420", "GSM363421", "GSM363422", "GSM363423", "GSM363424", "GSM363425", "GSM363426", "GSM363427", "GSM363428", "GSM363429", "GSM363430", "GSM363431", "GSM363432", "GSM363433", "GSM363434", "GSM363435", "GSM363436", "GSM363437", "GSM363438", "GSM363439", "GSM363440", "GSM363441", "GSM363442", "GSM363443", "GSM363444", "GSM363445", "GSM363446", "GSM363447", "GSM363448", "GSM363449", "GSM363450", "GSM363451", "GSM712532", "GSM712533", "GSM712534", "GSM712535", "GSM712536", "GSM712537", "GSM712538", "GSM712539", "GSM712540", "GSM712541", "GSM712542"], "sample_count": 488, "group_sizes": null, "group_sizes_basis": null, "platform": "3921;571", "taxon": "Homo sapiens", "title": "Gene expression data of human hepatocellular carcinoma (HCC)", "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:GSE22058", "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=GSE22058", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22058", "version": null, "note": "No additional data are available.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No additional data are available.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM548033", "GSM548034", "GSM548035", "GSM548036", "GSM548037", "GSM548038", "GSM548039", "GSM548040", "GSM548041", "GSM548042", "GSM548043", "GSM548044", "GSM548045", "GSM548046", "GSM548047", "GSM548048", "GSM548049", "GSM548050", "GSM548051", "GSM548052", "GSM548053", "GSM548054", "GSM548055", "GSM548056", "GSM548057", "GSM548058", "GSM548059", "GSM548060", "GSM548061", "GSM548062", "GSM548063", "GSM548064", "GSM548065", "GSM548066", "GSM548067", "GSM548068", "GSM548069", "GSM548070", "GSM548071", "GSM548072", "GSM548073", "GSM548074", "GSM548077", "GSM548078", "GSM548079", "GSM548080", "GSM548081", "GSM548082", "GSM548083", "GSM548084", "GSM548085", "GSM548086", "GSM548087", "GSM548088", "GSM548089", "GSM548090", "GSM548091", "GSM548092", "GSM548093", "GSM548094", "GSM548095", "GSM548096", "GSM548097", "GSM548098", "GSM548099", "GSM548100", "GSM548101", "GSM548102", "GSM548103", "GSM548104", "GSM548105", "GSM548106", "GSM548107", "GSM548108", "GSM548109", "GSM548110", "GSM548111", "GSM548112", "GSM548113", "GSM548114", "GSM548115", "GSM548116", "GSM548117", "GSM548118", "GSM548119", "GSM548120", "GSM548121", "GSM548122", "GSM548123", "GSM548124", "GSM548125", "GSM548126", "GSM548127", "GSM548128", "GSM548129", "GSM548130", "GSM548131", "GSM548132", "GSM548133", "GSM548134", "GSM548135", "GSM548136", "GSM548137", "GSM548138", "GSM548139", "GSM548140", "GSM548141", "GSM548142", "GSM548143", "GSM548144", "GSM548145", "GSM548146", "GSM548147", "GSM548148", "GSM548149", "GSM548150", "GSM548151", "GSM548152", "GSM548153", "GSM548154", "GSM548155", "GSM548156", "GSM548157", "GSM548158", "GSM548159", "GSM548160", "GSM548161", "GSM548162", "GSM548163", "GSM548164", "GSM548165", "GSM548166", "GSM548167", "GSM548168", "GSM548169", "GSM548170", "GSM548171", "GSM548172", "GSM548173", "GSM548174", "GSM548175", "GSM548176", "GSM548177", "GSM548178", "GSM548179", "GSM548180", "GSM548181", "GSM548182", "GSM548183", "GSM548184", "GSM548185", "GSM548186", "GSM548187", "GSM548188", "GSM548189", "GSM548190", "GSM548191", "GSM548192", "GSM548193", "GSM548194", "GSM548195", "GSM548196", "GSM548197", "GSM548198", "GSM548199", "GSM548200", "GSM548201", "GSM548202", "GSM548203", "GSM548204", "GSM548205", "GSM548206", "GSM548207", "GSM548208", "GSM548209", "GSM548210", "GSM548211", "GSM548212", "GSM548213", "GSM548214", "GSM548215", "GSM548216", "GSM548217", "GSM548218", "GSM548219", "GSM548220", "GSM548221", "GSM548222", "GSM548223", "GSM548224", "GSM548225", "GSM548226", "GSM548227", "GSM548228", "GSM548229", "GSM548230", "GSM548231", "GSM548232", "GSM548338", "GSM548339", "GSM548340", "GSM548341", "GSM548342", "GSM548343", "GSM548344", "GSM548345", "GSM548346", "GSM548347", "GSM548348", "GSM548349", "GSM548350", "GSM548351", "GSM548352", "GSM548353", "GSM548354", "GSM548355", "GSM548356", "GSM548357", "GSM548358", "GSM548359", "GSM548360", "GSM548361", "GSM548362", "GSM548363", "GSM548364", "GSM548365", "GSM548366", "GSM548367", "GSM548368", "GSM548369", "GSM548370", "GSM548371", "GSM548372", "GSM548373", "GSM548374", "GSM548375", "GSM548376", "GSM548377", "GSM548378", "GSM548379", "GSM548380", "GSM548381", "GSM548382", "GSM548383", "GSM548384", "GSM548385", "GSM548386", "GSM548387", "GSM548388", "GSM548389", "GSM548390", "GSM548391", "GSM548392", "GSM548393", "GSM548394", "GSM548395", "GSM548396", "GSM548397", "GSM548398", "GSM548399", "GSM548400", "GSM548401", "GSM548402", "GSM548403", "GSM548404", "GSM548405", "GSM548406", "GSM548407", "GSM548408", "GSM548409", "GSM548410", "GSM548411", "GSM548412", "GSM548413", "GSM548414", "GSM548415", "GSM548416", "GSM548417", "GSM548418", "GSM548419", "GSM548420", "GSM548421", "GSM548422", "GSM548423", "GSM548424", "GSM548425", "GSM548426", "GSM548427", "GSM548428", "GSM548429", "GSM548430", "GSM548431", "GSM548432", "GSM548433", "GSM548434", "GSM548435", "GSM548436", "GSM548437", "GSM548438", "GSM548439", "GSM548440", "GSM548441", "GSM548442", "GSM548443", "GSM548444", "GSM548445", "GSM548446", "GSM548447", "GSM548448", "GSM548449", "GSM548450", "GSM548451", "GSM548452", "GSM548453", "GSM548454", "GSM548455", "GSM548456", "GSM548457", "GSM548458", "GSM548459", "GSM548460", "GSM548461", "GSM548462", "GSM548463", "GSM548464", "GSM548465", "GSM548466", "GSM548467", "GSM548468", "GSM548469", "GSM548470", "GSM548471", "GSM548472", "GSM548473", "GSM548474", "GSM548475", "GSM548476", "GSM548477", "GSM548478", "GSM548479", "GSM548480", "GSM548481", "GSM548482", "GSM548483", "GSM548484", "GSM548485", "GSM548486", "GSM548487", "GSM548488", "GSM548489", "GSM548490", "GSM548491", "GSM548492", "GSM548493", "GSM548494", "GSM548495", "GSM548496", "GSM548497", "GSM548498", "GSM548499", "GSM548500", "GSM548501", "GSM548502", "GSM548503", "GSM548504", "GSM548505", "GSM548506", "GSM548507", "GSM548508", "GSM548509", "GSM548510", "GSM548511", "GSM548512", "GSM548513", "GSM548514", "GSM548515", "GSM548516", "GSM548517", "GSM548518", "GSM548519", "GSM548520", "GSM548521", "GSM548522", "GSM548523", "GSM548524", "GSM548525", "GSM548526", "GSM548527", "GSM548530", "GSM548531", "GSM548532", "GSM548533", "GSM548534", "GSM548535", "GSM548536", "GSM548537", "GSM548538"], "sample_count": 397, "group_sizes": null, "group_sizes_basis": null, "platform": "9733;10457;6793", "taxon": "Homo sapiens; Mus musculus", "title": "miR-122 as a Regulator of Mitochondrial Metabolic Gene Network in Hepatocellular Carcinoma", "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:GSE64041", "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=GSE64041", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64041", "version": null, "note": "No additional data are available.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No additional data are available.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2052455", "GSM2052456", "GSM2052457", "GSM2052458", "GSM2052459", "GSM2052460", "GSM2052461", "GSM2052462", "GSM2052463", "GSM2052464", "GSM2052465", "GSM2052466", "GSM2052467", "GSM2052468", "GSM2052469", "GSM2052470", "GSM2052471", "GSM2052472", "GSM2052473", "GSM2052474", "GSM2052475", "GSM2052476", "GSM2052477", "GSM2052478", "GSM2052479", "GSM2052480", "GSM2052481", "GSM2052482", "GSM2052483", "GSM2052484", "GSM2052485", "GSM2052486", "GSM2052487", "GSM2052488", "GSM2052489", "GSM2052490", "GSM2052491", "GSM2052492", "GSM2052493", "GSM2052494", "GSM2052495", "GSM2052496", "GSM2052497", "GSM2052498", "GSM2052499", "GSM2052500", "GSM2052501", "GSM2052502", "GSM2052503", "GSM2052504", "GSM2052505", "GSM2052506", "GSM2052507", "GSM2052508", "GSM2052509", "GSM2052510", "GSM2052511", "GSM2052512", "GSM2052513", "GSM2052514", "GSM2052515", "GSM2052516", "GSM2052517", "GSM2052518", "GSM2052519", "GSM2052520", "GSM2052521", "GSM2052522", "GSM2052523", "GSM2052524", "GSM2052525", "GSM2052526", "GSM2052527", "GSM2052528", "GSM2052529", "GSM2052530", "GSM2052531", "GSM2052532", "GSM2052533", "GSM2052534", "GSM2052535", "GSM2052536", "GSM2052537", "GSM2052538", "GSM2052539", "GSM2052540", "GSM2052541", "GSM2052542", "GSM2052543", "GSM2052544", "GSM2052545", "GSM2052546", "GSM2052547", "GSM2052548", "GSM2052549", "GSM2052550", "GSM2052551", "GSM2052552", "GSM2052553", "GSM2052554", "GSM2052555", "GSM2052556", "GSM2052557", "GSM2052558", "GSM2052559", "GSM2052560", "GSM2052561", "GSM2052562", "GSM2052563", "GSM2052564", "GSM2052565", "GSM2052566", "GSM2052567", "GSM2052568", "GSM2052569", "GSM2052570", "GSM2052571", "GSM2052572", "GSM2052573", "GSM2052574", "GSM2052575", "GSM2052576", "GSM2052577", "GSM2052578", "GSM2052579"], "sample_count": 125, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profiling in paired human hepatocellular carcinoma and liver parenchyma biopsies and normal liver biopsies.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE22058 not downloaded", "asset:data:geo:GSE22058 licence not read", "asset:data:geo:GSE64041 not downloaded", "asset:data:geo:GSE64041 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Kaplan Meier method was used to analyze the overall survival, and the log-rank P method was applied to show the statistical difference."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "student t-test"}}, {"id": "method-3", "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-4", "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 correlation"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE14520", "GSE22058", "GSE64041"], "resolved_accessions": ["GSE14520", "GSE22058", "GSE64041"], "statements": ["No additional data are available."], "basis": "The paper names GSE14520, GSE22058, GSE64041 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": ["logrank_test"], "assets": ["source:pmid:32775374", "data:geo:GSE14520"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14520"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34842, "completion_tokens": 2556, "cached_tokens": 784}}, "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:32775374", "type": "paper", "label": "pmid:32775374"}, {"id": "source:pmid:32775374", "type": "manuscript", "label": "PMID 32775374 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32775374", "type": "paper", "label": "pmid:32775374"}, {"id": "source:pmid:32775374", "type": "manuscript", "label": "PMID 32775374 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32775374", "type": "extraction", "used": ["source:pmid:32775374"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14520", "type": "accession_resolution", "used": ["data:geo:GSE14520"], "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:32775374", "parent_hash": "sha256:1973d2d23427c2dc6aeb82f8c787e828075a750919908e00d7eea339cb55e43f", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE22058 licence not read", "asset:data:geo:GSE22058 not downloaded", "asset:data:geo:GSE64041 licence not read", "asset:data:geo:GSE64041 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["rmed quantitative polymerase chain reaction (qPCR) assay to examine the APEX2 levels in normal", "IA2 tool. For in vitro studies, we performed qPCR to analyze the level of relative gene expres"], "order_basis": "paper_text_order:1124", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d several liver cancer cell lines, including HepG2, Huh7, SMMC7721, and HCCLM3. APEX2 in HCCLM3", "pe Culture Collection (ATCC). LO2 cells were cultured in RMPI-1640, and HepG2, SMMC7721, Huh7, and HC", "HepG2, SMMC7721, Huh7, and HCCLM3 cells were cultured in DMEM, supplemented with 10% FBS and 100 U/mL", "demy of Science. The liver cancer cell lines HepG2 and Huh7 were acquired from American Type Cu"], "order_basis": "paper_text_order:1241", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["APEX2 in cell viability was confirmed using CCK-8. Dual-luciferase reporter assay was performe", "ring RNA. The cell viability was tested with CCK-8. The promoter activity was detected by dual-"], "order_basis": "paper_text_order:1401", "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": ["k down the APEX2 expression in HCCLM3 cells. Knockdown of APEX2 resulted in a decrease in the viabi", "correlated with the pro-oncogenic pathways. Knockdown of APEX2 could inhibit the cell viability an", "MATERIALS AND METHODS Cell culture and transfection The normal liver cell line LO2 and liver can", "streptomycin. Small interfering RNA (siRNA) transfection was conducted with Lipofectamine 2000 accord"], "order_basis": "paper_text_order:2654", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Kaplan Meier method was used to analyze the overall survival, and the log-rank P method was applied to show the statistical difference."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T03:17:22+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}