{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33632198", "kind": "science-record", "revision": 7, "content_hash": "sha256:5896a911a898fab9bbcb1f14f44dec2b899d846baeb2e723e74a64dd80e15dd3", "created_at": "2026-11-01T15:41:26Z", "updated_at": "2026-11-01T22:03:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes involved in tumor immune cell infiltration and cetuximab resistance in colorectal cancer.", "doi": "10.1186/s12935-021-01829-8", "pmid": "33632198", "authors": ["Li Liang", "Mengling Liu", "Xun Sun", "Yitao Yuan", "Ke Peng", "Khalid Rashid", "Yiyi Yu", "Yuehong Cui", "Yanjie Chen", "Tianshu Liu"], "journal": "Cancer cell international", "year": 2021, "abstract": "BACKGROUND: The anti-epidermal growth factor receptor (EGFR) antibody introduces adaptable variations to the transcriptome and triggers tumor immune infiltration, resulting in colorectal cancer (CRC) treatment resistance. We intended to identify genes that play essential roles in cetuximab resistance and tumor immune cell infiltration.\nMETHODS: A cetuximab-resistant CACO2 cellular model was established, and its transcriptome variations were detected by microarray. Meanwhile, public data from the Gene Expression Omnibus and The Cancer Genome Atlas (TCGA) database were downloaded. Integrated bioinformatics analysis was applied to detect differentially expressed genes (DEGs) between the cetuximab-resistant and the cetuximab-sensitive groups. Then, we investigated correlations between DEGs and immune cell infiltration. The DEGs from bioinformatics analysis were further validated in vitro and in clinical samples.\nRESULTS: We identified 732 upregulated and 1259 downregulated DEGs in the induced cellular model. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses, along with Gene Set Enrichment Analysis and Gene Set Variation Analysis, indicated the functions of the DEGs. Together with GSE59857 and GSE5841, 12 common DEGs (SATB-2, AKR1B10, ADH1A, ADH1C, MYB, ATP10B, CDX-2, FAR2, EPHB2, SLC26A3, ORP-1, VAV3) were identified and their predictive values of cetuximab treatment were validated in GSE56386. In online Genomics of Drug Sensitivity in Cancer (GDSC) database, nine of twelve DEGs were recognized in the protein-protein (PPI) network. Based on the transcriptome profiles of CRC samples in TCGA and using Tumor Immune Estimation Resource Version 2.0, we bioinformatically determined that SATB-2, ORP-1, MYB, and CDX-2 expressions were associated with intensive infiltration of B cell, CD4+ T cell, CD8+ T cell and macrophage, which was then validated the correlation in clinical samples by immunohistochemistry. We found that SATB-2, ORP-1, MYB, and CDX-2 were downregulated in vitro with cetuximab treatment. Clinically, patients with advanced CRC and high ORP-1 expression exhibited a longer progression-free survival time when they were treated with anti-EGFR therapy than those with low ORP-1 expression.\nCONCLUSIONS: SATB-2, ORP-1, MYB, and CDX-2 were related to cetuximab sensitivity as well as enhanced tumor immune cell infiltration in patients with CRC.", "claims": [{"id": "claim-method", "statement": "Kaplan - Meier survival curve and Log - rank test analysis was applied to investigated the predictive valued of identified DEGs for patients with CRC and receiving cetuximab contained therapy.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33632198", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "Kaplan - Meier survival curve and Log - rank test analysis was applied to investigated the predictive valued of identified DEGs for patients with CRC and receiving cetuximab contained therapy."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Public datasets of colon adenocarcinoma and rectum adenocarcinoma analyzed during the current study can be retrieved from The Cancer Genome Atlas (TCGA) at https://portal.gdc.cancer.gov/. GSE5851, GSE56368, and GSE59857 datasets can be retrieved from the Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/. Other data that support the findings of this study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33632198", "locator": "sections[29] \"Availability of data and materials\" paragraph 2", "quote": "Public datasets of colon adenocarcinoma and rectum adenocarcinoma analyzed during the current study can be retrieved from The Cancer Genome Atlas (TCGA) at https://portal.gdc.cancer.gov/. GSE5851, GSE56368, and GSE59857 datasets can be retrieved from the Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/. Other data that support the findings of this study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33632198"], "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:GSE56386"], "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:GSE56386"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33632198", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-021-01829-8", "sha256": "sha256:678d56d7692e9406b1527d7d0fddbe67c69b980b717828fbdb5d37c512bd88fa", "bytes": 50326, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-021-01829-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7905896", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE56386", "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=GSE56386", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE56386", "version": null, "note": "Public datasets of colon adenocarcinoma and rectum adenocarcinoma analyzed during the current study can be retrieved from The Cancer Genome Atlas (TCGA) at https://portal.gdc.cancer.gov/. GSE5851, GSE56368, and GSE59857 datasets can be retrieved from the Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/. Other data that support the findings of this study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Public datasets of colon adenocarcinoma and rectum adenocarcinoma analyzed during the current study can be retrieved from The Cancer Genome Atlas (TCGA) at https://portal.gdc.cancer.gov/. GSE5851, GSE56368, and GSE59857 datasets can be retrieved from the Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/. 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"open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab1", "version": null, "note": "The expression of the top 20 upregulated and downregulated genes in the cetuximab resistant CACO2", "structure": {"pmcid": "PMC7905896", "section_index": 15, "section_title": "Model establishment and screening of DEGs", "row_count": 45, "column_count": 10}, "table": {"label": "Table 1", "caption": "The expression of the top 20 upregulated and downregulated genes in the cetuximab resistant CACO2", "rows": [["Gene symbol", "Normalized Signal Value", "Log [fold change]", "P value", "Adjustive p value"], ["Sensitive", "Resistant"], ["Sam.1", "Sam.2", "Sam.3", "Sam.1", "Sam.2", "Sam.3"], ["Top 20 of up-regulated genes"], ["DRD2", "1.253", "1.265", "1.252", "7.414", "7.471", "7.331", "6.149", "2.76E–09", "5.19E–05"], ["SLC2A5", "8.931", "9.006", "9.037", "13.002", "12.996", "12.980", "4.001", "2.62E–08", "9.87E–05"], ["CADM1", "4.659", "4.421", "4.556", "9.133", "9.344", "9.152", "4.664", "4.91E–08", "1.11E–04"], ["RTP3", "1.232", "1.300", "1.161", "4.731", "4.881", "4.823", "3.581", "8.34E–08", "1.14E–04"], ["NPR2", "6.365", "6.349", "6.191", "10.112", "10.297", "10.310", "3.938", "9.25E–08", "1.16E–04"], ["SERPINF1", "10.281", "10.168", "10.135", "13.543", "13.716", "13.685", "3.453", "1.29E–07", "1.26E–04"], ["BASP1", "6.890", "6.446", "6.407", "11.922", "12.156", "12.069", "5.468", "1.33E–07", "1.26E–04"], ["LAMA1", "6.237", "6.392", "6.334", "9.733", "9.873", "9.949", "3.531", "1.42E–07", "1.26E–04"], ["THPO", "1.271", "1.275", "1.418", "4.485", "4.429", "4.562", "3.171", "1.75E–07", "1.26E–04"], ["ACTA1", "4.330", "3.837", "4.273", "9.829", "9.596", "9.503", "5.496", "1.80E–07", "1.26E–04"], ["SERPINF2", "11.096", "11.257", "10.992", "14.287", "14.346", "14.294", "3.194", "2.59E–07", "1.35E–04"], ["ANXA8", "9.699", "9.805", "9.662", "12.950", "13.168", "12.871", "3.274", "3.77E–07", "1.73E–04"], ["DPYSL3", "7.688", "7.165", "7.810", "12.588", "12.744", "12.676", "5.115", "4.15E–07", "1.82E–04"], ["PDGFRA", "1.312", "1.304", "1.231", "5.091", "5.216", "4.782", "3.748", "4.25E–07", "1.82E–04"], ["SDC2", "4.645", "4.510", "4.744", "7.533", "7.547", "7.725", "2.968", "5.37E–07", "2.10E–04"], ["ORM1", "12.007", "12.089", "11.909", "14.634", "14.613", "14.758", "2.667", "5.43E–07", "2.10E–04"], ["ORM2", "12.062", "12.209", "12.006", "14.728", "14.646", "14.739", "2.612", "5.85E–07", "2.10E–04"], ["ADM", "10.696", "10.620", "10.518", "13.201", "13.321", "13.175", "2.621", "5.92E–07", "2.10E–04"], ["ADAM19", "9.666", "9.526", "9.323", "12.874", "12.710", "12.676", "3.248", "6.38E–07", "2.22E–04"], ["CCDC3", "9.139", "9.112", "8.781", "12.448", "12.206", "12.351", "3.324", "9.05E–07", "2.59E–04"], ["Top 20 of down-regulated genes"], ["GC", "6.719", "6.693", "6.902", "1.271", "1.278", "1.263", "–5.500", "8.90E–09", "6.23E–05"], ["SCIN", "6.839", "6.926", "7.093", "1.350", "1.309", "1.335", "–5.621", "9.94E–09", "6.23E–05"], ["ST6GALNAC1", "7.759", "7.546", "7.389", "1.269", "1.309", "1.356", "–6.253", "1.39E–08", "6.51E–05"], ["PADI2", "8.533", "8.655", "8.104", "1.339", "1.256", "1.373", "–7.108", "3.18E–08", "9.95E–05"], ["MUC13", "14.179", "13.905", "14.478", "7.486", "7.521", "7.534", "–6.674", "4.05E–08", "1.09E–04"], ["SULF2", "9.285", "8.985", "9.273", "3.737", "3.522", "3.850", "–5.478", "5.92E–08", "1.11E–04"], ["COL17A1", "8.492", "8.749", "8.525", "2.545", "2.030", "2.235", "–6.319", "6.07E–08", "1.11E–04"], ["FAM83E", "10.754", "10.695", "10.635", "6.944", "7.056", "6.897", "–3.729", "6.48E–08", "1.11E–04"], ["HLA-DMB", "5.666", "5.548", "5.337", "1.177", "1.237", "1.244", "–4.298", "8.23E–08", "1.14E–04"], ["NPAS2", "5.506", "5.310", "5.640", "1.250", "1.186", "1.173", "–4.282", "8.47E–08", "1.14E–04"], ["PNLIPRP2", "9.009", "8.923", "8.898", "4.505", "4.836", "4.560", "–4.310", "1.04E–07", "1.22E–04"], ["LCN2", "11.287", "11.659", "11.027", "4.564", "4.442", "4.834", "–6.711", "1.24E–07", "1.26E–04"], ["SRPX", "9.803", "9.612", "9.507", "5.937", "5.942", "5.842", "–3.734", "1.53E–07", "1.26E–04"], ["HOXB9", "10.762", "10.582", "10.682", "7.503", "7.485", "7.573", "–3.155", "1.66E–07", "1.26E–04"], ["BTNL3", "5.120", "5.170", "5.485", "1.188", "1.231", "1.215", "–4.047", "1.77E–07", "1.26E–04"], ["TMC5", "7.201", "6.746", "7.401", "1.274", "1.203", "1.339", "–5.844", "1.77E–07", "1.26E–04"], ["APOBEC1", "6.060", "5.632", "6.092", "1.210", "1.170", "1.156", "–4.749", "1.78E–07", "1.26E–04"], ["S100A9", "10.469", "10.404", "9.896", "3.540", "3.948", "3.972", "–6.436", "2.00E–07", "1.31E–04"], ["DDIT4L", "6.599", "6.789", "7.249", "1.229", "1.281", "1.306", "–5.607", "2.07E–07", "1.31E–04"], ["PI3", "13.824", "13.941", "13.611", "9.571", "9.226", "9.378", "–4.400", "2.12E–07", "1.31E–04"]], "row_count": 45, "column_count": 10, "numeric_cells": 373, "header_rows": 3, "locator": "section[15]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:33632198:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d78d18b8e9b362d25640960ca3b9ac3c37dbe3ef300da5cee98bcd9e987473e7", "bytes": 6363, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#Tab2", "version": null, "note": "GO term and KEGG pathway enrichment analyses of differentially expressed genes", "structure": {"pmcid": "PMC7905896", "section_index": 15, "section_title": "Model establishment and screening of DEGs", "row_count": 85, "column_count": 6}, "table": {"label": "Table 2", "caption": "GO term and KEGG pathway enrichment analyses of differentially expressed genes", "rows": [["Term", "Description", "Count", "%", "Log10 [p value]", "Log10 [q value]"], ["GO Biological process"], ["GO:0006935", "Chemotaxis", "117", "5.89", "−15.44", "−11.44"], ["GO:0010817", "Regulation of hormone levels", "102", "5.13", "−15.05", "−11.33"], ["GO:1,901,615", "Organic hydroxy compound metabolic process", "100", "5.03", "−13.61", "−10.01"], ["GO:0043062", "Extracellular structure organization", "82", "4.13", "−12.37", "−8.87"], ["GO:0015711", "Organic anion transport", "85", "4.28", "−10.60", "−7.25"], ["GO:0072006", "Nephron development", "37", "1.86", "−9.56", "−6.40"], ["GO:0048514", "Blood vessel morphogenesis", "105", "5.28", "−9.29", "−6.20"], ["GO:0009611", "Response to wounding", "105", "5.28", "−9.25", "−6.20"], ["GO:0051047", "Positive regulation of secretion", "75", "3.77", "−9.14", "−6.11"], ["GO:0006869", "Lipid transport", "66", "3.32", "−9.03", "−6.06"], ["GO:0008285", "Negative regulation of cell proliferation", "113", "5.69", "−8.91", "−6.01"], ["GO:0052548", "Regulation of endopeptidase activity", "73", "3.67", "−8.70", "−5.86"], ["GO:0032787", "Monocarboxylic acid metabolic process", "97", "4.88", "−8.15", "−5.36"], ["GO:0008610", "Lipid biosynthetic process", "103", "5.18", "−7.83", "−5.11"], ["GO:0003013", "Circulatory system process", "83", "4.18", "−7.17", "−4.54"], ["GO:0048598", "Embryonic morphogenesis", "87", "4.38", "−6.84", "−4.26"], ["GO:0030155", "Regulation of cell adhesion", "99", "4.98", "−6.68", "−4.14"], ["GO:0046683", "Response to organophosphorus", "31", "1.56", "−6.68", "−4.14"], ["GO:0035272", "Exocrine system development", "17", "0.86", "−6.62", "−4.11"], ["GO:0015718", "Monocarboxylic acid transport", "35", "1.76", "−6.53", "−4.04"], ["GO molecular function"], ["GO:0008289", "Lipid binding", "104", "5.23", "−6.90", "−3.45"], ["GO:0004857", "Enzyme inhibitor activity", "62", "3.12", "−6.81", "−3.45"], ["GO:0005509", "Calcium ion binding", "97", "4.88", "−6.45", "−3.37"], ["GO:0008201", "Heparin binding", "34", "1.71", "−6.05", "−3.17"], ["GO:0008514", "Organic anion transmembrane transporter activity", "39", "1.96", "−5.75", "−3.06"], ["GO:0048018", "Receptor ligand activity", "70", "3.52", "−5.72", "−3.06"], ["GO:0000987", "Proximal promoter sequence-specific DNA binding", "84", "4.23", "−5.16", "−2.65"], ["GO:0016491", "Oxidoreductase activity", "95", "4.78", "−4.82", "−2.41"], ["GO:0005201", "Extracellular matrix structural constituent", "30", "1.51", "−4.52", "−2.18"], ["GO:0016298", "Lipase activity", "25", "1.26", "−4.46", "−2.16"], ["GO:0033293", "Monocarboxylic acid binding", "18", "0.91", "−4.39", "−2.14"], ["GO:0043178", "Alcohol binding", "19", "0.96", "−4.39", "−2.14"], ["GO:0015144", "Carbohydrate transmembrane transporter activity", "12", "0.60", "−4.35", "−2.12"], ["GO:0033764", "Steroid dehydrogenase activity", "10", "0.50", "−4.05", "−1.90"], ["GO:0030515", "snoRNA binding", "10", "0.50", "−4.05", "−1.90"], ["GO:0042803", "Protein homodimerization activity", "81", "4.08", "−4.04", "−1.90"], ["GO:0008233", "Peptidase activity", "78", "3.93", "−3.82", "−1.73"], ["GO:0004745", "Retinol dehydrogenase activity", "8", "0.40", "−3.80", "−1.73"], ["GO:0019955", "Cytokine binding", "24", "1.21", "−3.69", "−1.63"], ["GO:0015250", "Water channel activity", "6", "0.30", "−3.50", "−1.46"], ["GO cellular component"], ["GO:0031012", "Extracellular matrix", "98", "4.93", "−13.46", "−10.17"], ["GO:0016324", "Apical plasma membrane", "68", "3.42", "−11.60", "−8.79"], ["GO:0044420", "Extracellular matrix component", "17", "0.86", "−6.08", "−3.57"], ["GO:0016323", "Basolateral plasma membrane", "41", "2.06", "−5.91", "−3.52"], ["GO:0031253", "Cell projection membrane", "56", "2.82", "−5.90", "−3.52"], ["GO:0005604", "Basement membrane", "23", "1.16", "−5.55", "−3.21"], ["GO:0031526", "Brush border membrane", "16", "0.81", "−5.25", "−2.97"], ["GO:0031091", "Platelet alpha granule", "21", "1.06", "−4.93", "−2.72"], ["GO:0030684", "Pre-ribosome", "19", "0.96", "−4.87", "−2.70"], ["GO:0005667", "Transcription factor complex", "53", "2.67", "−4.60", "−2.46"], ["GO:0070161", "Anchoring junction", "71", "3.57", "−3.64", "−1.68"], ["GO:0044452", "Nucleolar part", "29", "1.46", "−3.61", "−1.67"], ["GO:0005911", "Cell-cell junction", "53", "2.67", "−3.49", "−1.60"], ["GO:0005773", "Vacuole", "93", "4.68", "−3.40", "−1.56"], ["GO:0005777", "Peroxisome", "24", "1.21", "−3.40", "−1.56"], ["GO:0034358", "Plasma lipoprotein particle", "10", "0.50", "−3.32", "−1.52"], ["GO:0000940", "Condensed chromosome outer kinetochore", "6", "0.30", "−3.29", "−1.52"], ["GO:0071438", "Invadopodium membrane", "4", "0.20", "−3.22", "−1.48"], ["GO:0048471", "Perinuclear region of cytoplasm", "85", "4.28", "−3.20", "−1.47"], ["GO:0005593", "FACIT collagen trimer", "4", "0.20", "−2.88", "−1.25"], ["KEGG pathway"], ["hsa04974", "Protein digestion and absorption", "23", "1.16", "−6.16", "−3.46"], ["hsa04060", "Cytokine-cytokine receptor interaction", "45", "2.26", "−5.38", "−2.98"], ["hsa00830", "Retinol metabolism", "17", "0.86", "−4.86", "−2.64"], ["hsa04510", "Focal adhesion", "34", "1.71", "−4.45", "−2.36"], ["hsa04918", "Thyroid hormone synthesis", "17", "0.86", "−4.08", "−2.08"], ["hsa04610", "Complement and coagulation cascades", "17", "0.86", "−3.71", "−1.85"], ["hsa04310", "Wnt signaling pathway", "24", "1.21", "−3.21", "−1.49"], ["hsa03320", "PPAR signaling pathway", "15", "0.75", "−3.18", "−1.49"], ["hsa05323", "Rheumatoid arthritis", "17", "0.86", "−3.02", "−1.36"], ["hsa05146", "Amoebiasis", "17", "0.86", "−2.70", "−1.27"], ["hsa04540", "Gap junction", "16", "0.81", "−2.69", "−1.27"], ["hsa00471", "D-Glutamine and D-glutamate metabolism", "3", "0.15", "−2.68", "−1.27"], ["hsa04978", "Mineral absorption", "11", "0.55", "−2.60", "−1.21"], ["hsa04146", "Peroxisome", "15", "0.75", "−2.53", "−1.16"], ["hsa04621", "NOD-like receptor signaling pathway", "25", "1.26", "−2.49", "−1.14"], ["hsa04390", "Hippo signaling pathway", "23", "1.16", "−2.42", "−1.13"], ["hsa00590", "Arachidonic acid metabolism", "12", "0.60", "−2.38", "−1.13"], ["hsa00564", "Glycerophospholipid metabolism", "16", "0.81", "−2.35", "−1.12"], ["hsa04976", "Bile secretion", "13", "0.65", "−2.32", "−1.10"], ["hsa05412", "Arrhythmogenic right ventricular cardiomyopathy", "13", "0.65", "−2.26", "−1.06"]], "row_count": 85, "column_count": 6, "numeric_cells": 402, "header_rows": 1, "locator": "section[15]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:33632198:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3297a1ec256c668469513d721300990d955757ed6ad8d4b9015ebca8cb4f0805", "bytes": 2882, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#Tab3", "version": null, "note": "Gene set enrichment analysis of upregulated and downregulated gene sets in the cetuximab resistant group", "structure": {"pmcid": "PMC7905896", "section_index": 16, "section_title": "Gene set enrichment", "row_count": 37, "column_count": 7}, "table": {"label": "Table 3", "caption": "Gene set enrichment analysis of upregulated and downregulated gene sets in the cetuximab resistant group", "rows": [["Name", "Size", "Es", "Nes", "Non p value", "FDR q value", "FWER p value"], ["Up-regulation in Resistant Group", "", "", "", ""], ["HALLMARK_PEROXISOME", "19", "−0.36", "−1.32", "0.00", "0.49", "0.39"], ["HALLMARK_UV_RESPONSE_UP", "24", "−0.17", "−1.00", "0.38", "1.00", "1.00"], ["HALLMARK_MYOGENESIS", "38", "−0.48", "−0.93", "0.79", "1.00", "1.00"], ["HALLMARK_KRAS_SIGNALING_DN", "27", "−0.24", "−0.92", "0.54", "1.00", "1.00"], ["HALLMARK_ADIPOGENESIS", "24", "−0.17", "−0.80", "0.51", "1.00", "1.00"], ["HALLMARK_INTERFERON_GAMMA_RESPONSE", "31", "−0.21", "−0.77", "0.91", "1.00", "1.00"], ["HALLMARK_INTERFERON_ALPHA_RESPONSE", "24", "−0.28", "−0.76", "0.91", "0.98", "1.00"], ["HALLMARK_P53_PATHWAY", "24", "−0.14", "−0.68", "0.91", "0.92", "1.00"], ["Down-regulation in Resistant Group", "", "", "", ""], ["HALLMARK_COMPLEMENT", "30", "0.34", "1.59", "0.00", "0.27", "0.09"], ["HALLMARK_BILE_ACID_METABOLISM", "21", "0.38", "1.57", "0.00", "0.19", "0.19"], ["HALLMARK_IL2_STAT5_SIGNALING", "31", "0.38", "1.50", "0.00", "0.16", "0.25"], ["HALLMARK_UV_RESPONSE_DN", "24", "0.42", "1.47", "0.00", "0.13", "0.25"], ["HALLMARK_ESTROGEN_RESPONSE_EARLY", "39", "0.30", "1.43", "0.00", "0.12", "0.25"], ["HALLMARK_HYPOXIA", "38", "0.30", "1.41", "0.09", "0.10", "0.25"], ["HALLMARK_APOPTOSIS", "30", "0.28", "1.35", "0.00", "0.19", "0.43"], ["HALLMARK_INFLAMMATORY_RESPONSE", "29", "0.44", "1.29", "0.00", "0.25", "0.56"], ["HALLMARK_GLYCOLYSIS", "16", "0.39", "1.22", "0.32", "0.34", "0.56"], ["HALLMARK_ESTROGEN_RESPONSE_LATE", "34", "0.40", "1.21", "0.00", "0.31", "0.56"], ["HALLMARK_XENOBIOTIC_METABOLISM", "30", "0.25", "1.20", "0.09", "0.31", "0.62"], ["HALLMARK_KRAS_SIGNALING_UP", "41", "0.48", "1.13", "0.32", "0.48", "0.67"], ["HALLMARK_TNFA_SIGNALING_VIA_NFKB", "30", "0.32", "1.13", "0.34", "0.45", "0.67"], ["HALLMARK_HEME_METABOLISM", "21", "0.29", "1.08", "0.29", "0.59", "0.95"], ["HALLMARK_APICAL_JUNCTION", "26", "0.28", "0.99", "0.44", "0.88", "1.00"], ["HALLMARK_COAGULATION", "30", "0.26", "0.99", "0.45", "0.85", "1.00"], ["HALLMARK_G2M_CHECKPOINT", "19", "0.40", "0.98", "0.54", "0.82", "1.00"], ["HALLMARK_E2F_TARGETS", "21", "0.37", "0.97", "0.69", "0.79", "1.00"], ["HALLMARK_MITOTIC_SPINDLE", "15", "0.29", "0.95", "0.66", "0.80", "1.00"], ["HALLMARK_MYC_TARGETS_V1", "21", "0.37", "0.93", "0.79", "0.80", "1.00"], ["HALLMARK_OXIDATIVE_PHOSPHORYLATION", "17", "0.32", "0.91", "0.82", "0.83", "1.00"], ["HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION", "44", "0.29", "0.91", "0.59", "0.80", "1.00"], ["HALLMARK_IL6_JAK_STAT3_SIGNALING", "16", "0.27", "0.87", "0.53", "0.84", "1.00"], ["HALLMARK_ALLOGRAFT_REJECTION", "22", "0.23", "0.81", "0.75", "0.89", "1.00"], ["HALLMARK_MTORC1_SIGNALING", "19", "0.19", "0.67", "0.91", "0.96", "1.00"], ["HALLMARK_FATTY_ACID_METABOLISM", "31", "0.14", "0.61", "0.91", "0.95", "1.00"]], "row_count": 37, "column_count": 7, "numeric_cells": 205, "header_rows": 1, "locator": 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["HALLMARK_INTERFERON_ALPHA_RESPONSE", "1.115", "3.21E−05", "3.89E−04"], ["HALLMARK_MYC_TARGETS_V1", "−1.096", "3.89E−05", "3.89E−04"], ["HALLMARK_MYC_TARGETS_V2", "−1.134", "2.88E−05", "3.89E−04"], ["HALLMARK_ANGIOGENESIS", "1.229", "1.43E−05", "3.89E−04"], ["HALLMARK_TGF_BETA_SIGNALING", "1.078", "9.87E−05", "6.17E−04"], ["HALLMARK_INTERFERON_GAMMA_RESPONSE", "0.909", "9.74E−05", "6.17E−04"], ["HALLMARK_UNFOLDED_PROTEIN_RESPONSE", "−0.978", "7.86E−05", "6.17E−04"], ["HALLMARK_E2F_TARGETS", "−0.915", "2.91E−04", "1.45E−03"], ["HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION", "0.741", "2.72E−04", "1.45E−03"], ["HALLMARK_APICAL_JUNCTION", "0.820", "3.21E−04", "1.46E−03"], ["HALLMARK_G2M_CHECKPOINT", "−0.926", "7.41E−04", "3.09E−03"], ["HALLMARK_APOPTOSIS", "0.574", "1.13E−03", "4.13E−03"], ["HALLMARK_HEME_METABOLISM", "0.610", "1.16E−03", "4.13E−03"], ["HALLMARK_KRAS_SIGNALING_UP", "−0.622", "1.24E−03", "4.13E−03"], ["HALLMARK_ESTROGEN_RESPONSE_EARLY", "0.572", "1.41E−03", "4.16E−03"], ["HALLMARK_PEROXISOME", "0.676", "1.38E−03", "4.16E−03"], ["HALLMARK_UV_RESPONSE_DN", "0.624", "1.95E−03", "5.42E−03"], ["HALLMARK_HEDGEHOG_SIGNALING", "0.742", "1.96E−02", "4.97E−02"], ["HALLMARK_OXIDATIVE_PHOSPHORYLATION", "−0.599", "2.09E−02", "4.97E−02"], ["HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY", "0.706", "2.03E−02", "4.97E−02"]], "row_count": 22, "column_count": 4, "numeric_cells": 63, "header_rows": 1, "locator": "section[16]/table-wrap[2]#Tab4"}}, {"id": "asset:table:pmid:33632198:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d6a056fc0c1071e23a19075b5ab469d959d19c7c257556e421cd969ec2814fee", "bytes": 1385, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab5", "version": null, "note": "Cetuximab resistance-related genes from the Genomics of Drug Sensitivity in Cancer database", "structure": {"pmcid": "PMC7905896", "section_index": 17, "section_title": "Common DEGs and PPI network construction", "row_count": 21, "column_count": 6}, "table": {"label": "Table 5", "caption": "Cetuximab resistance-related genes from the Genomics of Drug Sensitivity in Cancer database", "rows": [["Cancer feature", "Effect size", "p value", "FDR%", "No. of altered cell lines", "Tissue analysis"], ["SRGAP3_mut", "−1.310", "0.0382", "99.7", "3", "COREAD"], ["PBRM1_mut", "−0.971", "0.0791", "99.7", "4", "COREAD"], ["B2M_mut", "−0.722", "0.0879", "99.7", "7", "COREAD"], ["FBXW7_mut", "−0.575", "0.0998", "99.7", "13", "COREAD"], ["BRAF_mut", "0.580", "0.109", "99.7", "10", "COREAD"], ["cnaCOREAD47", "0.737", "0.111", "99.7", "6", "COREAD"], ["cnaCOREAD18", "0.611", "0.124", "99.7", "8", "COREAD"], ["MGA_mut", "−0.688", "0.132", "99.7", "6", "COREAD"], ["cnaCOREAD14", "0.892", "0.147", "99.7", "3", "COREAD"], ["CTCF_mut", "−0.560", "0.17", "99.7", "7", "COREAD"], ["cnaCOREAD37", "0.634", "0.172", "99.7", "6", "COREAD"], ["CDH1_mut", "−0.819", "0.195", "99.7", "3", "COREAD"], ["CTNNB1_mut", "−0.577", "0.199", "99.7", "6", "COREAD"], ["CREBBP_mut", "0.530", "0.213", "99.7", "6", "COREAD"], ["CHD9_mut", "−0.468", "0.231", "99.7", "9", "COREAD"], ["BRWD1_mut", "−0.740", "0.231", "99.7", "3", "COREAD"], ["CHD4_mut", "0.518", "0.285", "99.7", "3", "COREAD"], ["APC_mut", "−0.285", "0.313", "99.7", "31", "COREAD"], ["AKAP9_mut", "−0.412", "0.316", "99.7", "8", "COREAD"], ["cnaCOREAD32", "−0.372", "0.347", "99.7", "6", "COREAD"]], "row_count": 21, "column_count": 6, "numeric_cells": 85, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab5"}}, {"id": "asset:table:pmid:33632198:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:58cadb7ebb4137f94bf7f28b312a9f5e30e854d41b212e4c81f6a4f85d489d31", "bytes": 1463, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#Tab6", "version": null, "note": "Spearman correlation analysis of differentially expressed genes and tumor-infiltrating immune cell markers in clinical samples", "structure": {"pmcid": "PMC7905896", "section_index": 18, "section_title": "Core DEGs and tumor immune cell infiltration", "row_count": 30, "column_count": 4}, "table": {"label": "Table 6", "caption": "Spearman correlation analysis of differentially expressed genes and tumor-infiltrating immune cell markers in clinical samples", "rows": [["Tumor-infiltrating immune cells marks", "Gene expression level"], ["Spearman correlation", "95% CI", "p value"], ["SATB-"], ["CD4", "0.22", "0.00 to 0.42", "0.047"], ["CD8", "0.15", "-0.07 to 0.35", "0.184"], ["CD19", "0.36", "0.16 to 0.54", "< 0.001"], ["CD68", "0.34", "0.14 to 0.52", "0.002"], ["CD4 and CD8", "0.22", "0.07 to 0.42", "0.044"], ["CD4, CD8, CD19, CD68", "0.40", "0.20 to 0.57", "< 0.001"], ["ORP-1"], ["CD4", "0.28", "0.07 to 0.46", "0.010"], ["CD8", "0.24", "0.03 to 0.43", "0.030"], ["CD19", "0.36", "0.16 to 0.53", "< 0.001"], ["CD68", "0.31", "0.11 to 0.50", "0.003"], ["CD4 and CD8", "0.29", "0.08 to 0.48", "0.007"], ["CD4, CD8, CD19, CD68", "0.42", "0.23 to 0.58", "< 0.001"], ["MYB"], ["CD4", "0.22", "0.01 to 0.42", "0.040"], ["CD8", "0.20", "-0.01 to 0.40", "0.070"], ["CD19", "0.09", "-0.13 to 0.30", "0.450"], ["CD68", "0.28", "0.07 to 0.47", "0.009"], ["CD4 and CD8", "0.26", "0.05 to 0.45", "0.020"], ["CD4, CD8, CD19, CD68", "0.25", "0.04 to 0.44", "0.020"], ["CDX-2"], ["CD4", "0.66", "0.52 to 0.77", "< 0.001"], ["CD8", "0.35", "0.14 to 0.53", "0.001"], ["CD19", "0.20", "-0.02 to 0.40", "0.070"], ["CD68", "0.23", "0.01 to 0.43", "0.030"], ["CD4 and CD8", "0.65", "0.50 to 0.76", "< 0.001"], ["CD4, CD8, CD19, CD68", "0.46", "0.27 to 0.62", "< 0.001"]], "row_count": 30, "column_count": 4, "numeric_cells": 87, "header_rows": 2, "locator": "section[18]/table-wrap[1]#Tab6"}}], "gaps": ["asset:data:geo:GSE56386 not downloaded", "asset:data:geo:GSE56386 licence not read", "asset:data:geo:GSE5851 not downloaded", "asset:data:geo:GSE5851 licence not read", "asset:data:geo:GSE59857 not downloaded", "asset:data:geo:GSE59857 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": "Kaplan - Meier survival curve and Log - rank test analysis was applied to investigated the predictive valued of identified DEGs for patients with CRC and receiving cetuximab contained therapy."}}, {"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": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "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": ["GSE59857", "GSE5851", "GSE56386"], "resolved_accessions": ["GSE59857", "GSE5851", "GSE56386"], "statements": ["Public datasets of colon adenocarcinoma and rectum adenocarcinoma analyzed during the current study can be retrieved from The Cancer Genome Atlas (TCGA) at https://portal.gdc.cancer.gov/. GSE5851, GSE56368, and GSE59857 datasets can be retrieved from the Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/. Other data that support the findings of this study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE59857, GSE5851, GSE56386 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:33632198", "data:geo:GSE56386", "asset:table:pmid:33632198:1", "asset:table:pmid:33632198:2", "asset:table:pmid:33632198:3", "asset:table:pmid:33632198:4", "asset:table:pmid:33632198:5", "asset:table:pmid:33632198:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE56386"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:17Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 42217, "completion_tokens": 1264, "cached_tokens": 792}}, "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:33632198", "type": "paper", "label": "pmid:33632198"}, {"id": "source:pmid:33632198", "type": "manuscript", "label": "PMID 33632198 full text"}, {"id": "data:geo:GSE56386", "type": "dataset", "label": "GEO GSE56386"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33632198", "type": "paper", "label": "pmid:33632198"}, {"id": "source:pmid:33632198", "type": "manuscript", "label": "PMID 33632198 full text"}, {"id": "data:geo:GSE56386", "type": "dataset", "label": "GEO GSE56386"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33632198", "type": "extraction", "used": ["source:pmid:33632198"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE56386", "type": "accession_resolution", "used": ["data:geo:GSE56386"], "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:33632198", "parent_hash": "sha256:656a2355ebf4181070aebb91e3a99f5b23fc03aee4a7b4024e67af3d206f34b4", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE56386 licence not read", "asset:data:geo:GSE56386 not downloaded", "asset:data:geo:GSE5851 licence not read", "asset:data:geo:GSE5851 not downloaded", "asset:data:geo:GSE59857 licence not read", "asset:data:geo:GSE59857 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": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ts transcriptome variations were detected by microarray. Meanwhile, public data from the Gene Expres", "atients with colorectal cancer in the tissue microarray. Additional file 4: Figure S2. SATB-2, ORP-1"], "order_basis": "paper_text_order:530", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["dated the correlation in clinical samples by immunohistochemistry. We found that SATB-2, ORP-1, MYB, and CDX-2", "Methods Validation in clinical samples by immunohistochemistry staining Patients with advanced CRC (n = 102", "they were blocked with bovine serum albumin, immunostained with primary antibodies against SATB-2 (2130"], "order_basis": "paper_text_order:2017", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["and incubated with goat anti-rabbit or anti-mouse secondary antibody (1:200) for about 30 min"], "order_basis": "paper_text_order:3874", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e 1: Table S1. Sequences of primers used for real-time quantitative PCR. Additional file 2: Figure S1. ROC curves fo"], "order_basis": "paper_text_order:6550", "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": ["Kaplan - Meier survival curve and Log - rank test analysis was applied to investigated the predictive valued of identified DEGs for patients with CRC and receiving cetuximab contained therapy."], "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":"2026-11-04T02:16:59+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}}}