{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31376328", "kind": "science-record", "revision": 6, "content_hash": "sha256:3ddbcd6a35174263e449d20a01367e0238c1d4f8ac80e56d81e837dd6462dd84", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T22:00:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Regulatory Network Analysis to Reveal Important miRNAs and Genes in Non-Small Cell Lung Cancer.", "doi": "10.22074/cellj.2020.6281", "pmid": "31376328", "authors": ["Xingni Zhou", "Zhenghua Zhang", "Xiaohua Liang"], "journal": "Cell journal", "year": 2020, "abstract": "OBJECTIVE: Lung cancer has high incidence and mortality rate, and non-small cell lung cancer (NSCLC) takes up approximately 85% of lung cancer cases. This study is aimed to reveal miRNAs and genes involved in the mechanisms of NSCLC.\nMATERIALS AND METHODS: In this retrospective study, GSE21933 (21 NSCLC samples and 21 normal samples), GSE27262 (25 NSCLC samples and 25 normal samples), GSE43458 (40 NSCLC samples and 30 normal samples) and GSE74706 (18 NSCLC samples and 18 normal samples) were searched from gene expression omnibus (GEO) database. The differentially expressed genes (DEGs) were screened from the four microarray datasets using MetaDE package, and then conducted with functional annotation using DAVID tool. Afterwards, protein-protein interaction (PPI) network and module analyses were carried out using Cytoscape software. Based on miR2Disease and Mirwalk2 databases, microRNAs (miRNAs)-DEG pairs were selected. Finally, Cytoscape software was applied to construct miRNA-DEG regulatory network.\nRESULTS: Totally, 727 DEGs (382 up-regulated and 345 down-regulated) had the same expression trends in all of the four microarray datasets. In the PPI network, TP53 and FOS could interact with each other and they were among the top 10 nodes. Besides, five network modules were found. After construction of the miRNA-gene network, top 10 miRNAs (such as hsa-miR-16-5p, hsa-let-7b-5p, hsa-miR-15a-5p, hsa-miR-15b-5p, hsa-let-7a-5p and hsa-miR-34a- 5p) and genes (such as HMGA1, BTG2, SOD2 and TP53) were selected.\nCONCLUSION: These miRNAs and genes might contribute to the pathogenesis of NSCLC.", "claims": [{"id": "claim-method", "statement": "Using the MetaDE package in R software (https:// cran.r-project.org/web/packages/MetaDE/) (15), DEGs were screened from the four microarray datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31376328", "locator": "sections[5] \"Meta-analysis\" paragraph 2", "quote": "Using the MetaDE package in R software (https:// cran.r-project.org/web/packages/MetaDE/) (15), DEGs were screened from the four microarray datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31376328", "locator": "sections[3] \"Expression profile data\" paragraph 2", "quote": "Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted."}], "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:31376328"], "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:GSE21933"], "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:GSE21933"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31376328", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.22074/cellj.2020.6281", "sha256": "sha256:2dd7a2615c97e3a29eaad80dbb42853076d3e3507f67b010b6027cf20cee4930", "bytes": 17524, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.22074/cellj.2020.6281", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6722447", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21933", "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=GSE21933", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21933", "version": null, "note": "Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM545615", "GSM545616", "GSM545617", "GSM545618", "GSM545619", "GSM545620", "GSM545621", "GSM545622", "GSM545623", "GSM545624", "GSM545625", "GSM545626", "GSM545627", "GSM545628", "GSM545629", "GSM545630", "GSM545631", "GSM545632", "GSM545633", "GSM545634", "GSM545635", "GSM545636", "GSM545637", "GSM545638", "GSM545639", "GSM545640", "GSM545641", "GSM545642", "GSM545643", "GSM545644", "GSM545645", "GSM545646", "GSM545647", "GSM545648", "GSM545649", "GSM545650", "GSM545651", "GSM545652", "GSM545653", "GSM545654", "GSM545655", "GSM545656"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "6254", "taxon": "Homo sapiens", "title": "Gene expression profiles of tumor and paired normal lung tissues from primary non-small cell lung cancer (NSCLC) patients in Taiwan.", "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:GSE27262", "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=GSE27262", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27262", "version": null, "note": "Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM673870", "GSM673871", "GSM673872", "GSM673873", "GSM673874", "GSM673875", "GSM673876", "GSM673877", "GSM673878", "GSM673879", "GSM673880", "GSM673881", "GSM673882", "GSM673883", "GSM673884", "GSM673885", "GSM673886", "GSM673887", "GSM673888", "GSM673889", "GSM673890", "GSM673891", "GSM673892", "GSM673893", "GSM673894", "GSM673895", "GSM673896", "GSM673897", "GSM673898", "GSM673899", "GSM673900", "GSM673901", "GSM673902", "GSM673903", "GSM673904", "GSM673905", "GSM673906", "GSM673907", "GSM673908", "GSM673909", "GSM673910", "GSM673911", "GSM673912", "GSM673913", "GSM673914", "GSM673915", "GSM673916", "GSM673917", "GSM673918", "GSM673919"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling of Non-small cell lung cancer in Taiwan", "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:GSE43458", "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=GSE43458", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43458", "version": null, "note": "Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1062765", "GSM1062766", "GSM1062767", "GSM1062768", "GSM1062769", "GSM1062770", "GSM1062771", "GSM1062772", "GSM1062773", "GSM1062774", "GSM1062775", "GSM1062776", "GSM1062777", "GSM1062778", "GSM1062779", "GSM1062780", "GSM1062781", "GSM1062782", "GSM1062783", "GSM1062784", "GSM1062785", "GSM1062786", "GSM1062787", "GSM1062788", "GSM1062789", "GSM1062790", "GSM1062791", "GSM1062792", "GSM1062793", "GSM1062794", "GSM1062795", "GSM1062796", "GSM1062797", "GSM1062798", "GSM1062799", "GSM1062800", "GSM1062801", "GSM1062802", "GSM1062803", "GSM1062804", "GSM1062805", "GSM1062806", "GSM1062807", "GSM1062808", "GSM1062809", "GSM1062810", "GSM1062811", "GSM1062812", "GSM1062813", "GSM1062814", "GSM1062815", "GSM1062816", "GSM1062817", "GSM1062818", "GSM1062819", "GSM1062820", "GSM1062821", "GSM1062822", "GSM1062823", "GSM1062824", "GSM1062825", "GSM1062826", "GSM1062827", "GSM1062828", "GSM1062829", "GSM1062830", "GSM1062831", "GSM1062832", "GSM1062833", "GSM1062834", "GSM1062835", "GSM1062836", "GSM1062837", "GSM1062838", "GSM1062839", "GSM1062840", "GSM1062841", "GSM1062842", "GSM1062843", "GSM1062844", "GSM1062845", "GSM1062846", "GSM1062847", "GSM1062848", "GSM1062849", "GSM1062850", "GSM1062851", "GSM1062852", "GSM1062853", "GSM1062854", "GSM1062855", "GSM1062856", "GSM1062857", "GSM1062858", "GSM1062859", "GSM1062860", "GSM1062861", "GSM1062862", "GSM1062863", "GSM1062864", "GSM1062865", "GSM1062866", "GSM1062867", "GSM1062868", "GSM1062869", "GSM1062870", "GSM1062871", "GSM1062872", "GSM1062873", "GSM1062874"], "sample_count": 110, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profiling of lung adenocarcinomas 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"version": null, "note": "Pathways enriched for the nodes in module a, b, c, d and e", "structure": {"pmcid": "PMC6722447", "section_index": 8, "section_title": "Construction of miRNA-DEG regulatory network", "row_count": 39, "column_count": 6}, "table": {"label": "Table 1", "caption": "Pathways enriched for the nodes in module a, b, c, d and e", "rows": [[""], ["Module", "Pathway ID", "Pathway name", "Count", "P value", "Genes"], [""], ["a", "hsa03040", "Spliceosome", "5", "1.53E-05", "PRPF8, SNRNP200, SNRPA, SNRPD2, SF3B2"], ["hsa03020", "RNA polymerase", "3", "7.33E-04", "POLR2G, POLR2I, POLR2B"], ["hsa00240", "Pyrimidine metabolism", "3", "7.54E-03", "POLR2G, POLR2I, POLR2B"], ["hsa00230", "Purine metabolism", "3", "2.06E-02", "POLR2G, POLR2I, POLR2B"], ["hsa05169", "Epstein-Barr virus infection", "3", "2.38E-02", "POLR2G, POLR2I, POLR2B"], ["hsa05016", "Huntington’s disease", "3", "2.43E-02", "POLR2G, POLR2I, POLR2B"], ["a", "hsa05166", "HTLV-I infection", "7", "4.62E-04", "EGR1, FOS, ETS1, TP53, NFKBIA, TCF3, NFATC1"], ["hsa04660", "T cell receptor signaling pathway", "5", "7.24E-04", "PTPRC, FOS, MAPK3, NFKBIA, NFATC1"], ["hsa05161", "Hepatitis B", "5", "2.57E-03", "FOS, MAPK3, TP53, NFKBIA, NFATC1"], ["hsa04662", "B cell receptor signaling pathway", "4", "2.61E-03", "FOS, MAPK3, NFKBIA, NFATC1"], ["hsa04010", "MAPK signaling pathway", "6", "3.22E-03", "FOS, MAPK3, TP53, DDIT3, NFATC1, DUSP6"], ["hsa05133", "Pertussis", "4", "3.31E-03", "FOS, IRF8, MAPK3, PYCARD"], ["hsa05215", "Prostate cancer", "4", "5.19E-03", "MAPK3, TP53, NFKBIA, MTOR"], ["hsa04668", "TNF signaling pathway", "4", "8.70E-03", "FOS, MAPK3, EDN1, NFKBIA"], ["hsa04151", "PI3K-Akt signaling pathway", "6", "1.15E-02", "MAPK3, COL3A1, COL6A3, TP53, ITGB4, MTOR"], ["hsa04380", "Osteoclast differentiation", "4", "1.54E-02", "FOS, MAPK3, NFKBIA, NFATC1"], ["hsa04621", "NOD-like receptor signaling pathway", "3", "2.06E-02", "MAPK3, PYCARD, NFKBIA"], ["hsa04921", "Oxytocin signaling pathway", "4", "2.53E-02", "FOS, PRKAG1, MAPK3, NFATC1"], ["hsa05210", "Colorectal cancer", "3", "2.58E-02", "FOS, MAPK3, TP53"], ["hsa05230", "Central carbon metabolism in cancer", "3", "2.73E-02", "MAPK3, TP53, MTOR"], ["hsa05214", "Glioma", "3", "2.81E-02", "MAPK3, TP53, MTOR"], ["hsa04920", "Adipocytokine signaling pathway", "3", "3.23E-02", "PRKAG1, NFKBIA, MTOR"], ["hsa05140", "Leishmaniasis", "3", "3.31E-02", "FOS, MAPK3, NFKBIA"], ["hsa05220", "Chronic myeloid leukemia", "3", "3.40E-02", "MAPK3, TP53, NFKBIA"], ["hsa05132", "Salmonella infection", "3", "4.40E-02", "FOS, MAPK3, PYCARD"], ["hsa04024", "cAMP signaling pathway", "4", "4.49E-02", "FOS, MAPK3, NFKBIA, NFATC1"], ["hsa04512", "ECM-receptor interaction", "3", "4.79E-02", "COL3A1, COL6A3, ITGB4"], ["hsa04510", "Focal adhesion", "4", "4.95E-02", "MAPK3, COL3A1, COL6A3, ITGB4"], ["c", "hsa03022", "Basal transcription factors", "3", "1.24E-04", "CCNH, ERCC3, GTF2B"], ["hsa03420", "Nucleotide excision repair", "2", "2.03E-02", "CCNH, 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"Top 10 miRNAs and genes in the miRNA-gene regulatory network", "structure": {"pmcid": "PMC6722447", "section_index": 8, "section_title": "Construction of miRNA-DEG regulatory network", "row_count": 14, "column_count": 4}, "table": {"label": "Table 2", "caption": "Top 10 miRNAs and genes in the miRNA-gene regulatory network", "rows": [[""], ["miRNA", "Degree", "Gene", "Degree"], [""], ["hsa-miR-16-5p", "89", "HMGA1", "11"], ["hsa-let-7b-5p", "84", "BAZ2A", "9"], ["hsa-miR-15a-5p", "44", "CALU", "9"], ["hsa-miR-15b-5p", "41", "BTG2", "8"], ["hsa-let-7a-5p", "40", "SOD2", "8"], ["hsa-miR-34a-5p", "37", "TP53", "7"], ["hsa-miR-21-5p", "33", "UBN2", "7"], ["hsa-miR-222-3p", "24", "CBX5", "6"], ["hsa-miR-221-3p", "23", "ITGA2", "6"], ["hsa-miR-372-3p", "23", "SLC10A7", "6"], [""]], "row_count": 14, "column_count": 4, "numeric_cells": 32, "header_rows": 0, "locator": "section[12]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:31376328:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:042cd37244a1dedd9077168c7b2ac7885c9232ce02a1e938f205dc5f0f0c9253", "bytes": 3128, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "Pathways enriched for the nodes in module a, b, c, d and e", "structure": {"pmcid": "PMC6722447", "section_index": 12, "section_title": "Construction of miRNA-DEG regulatory network", "row_count": 39, "column_count": 6}, "table": {"label": "Table 1", "caption": "Pathways enriched for the nodes in module a, b, c, d and e", "rows": [[""], ["Module", "Pathway ID", "Pathway name", "Count", "P value", "Genes"], [""], ["a", "hsa03040", "Spliceosome", "5", "1.53E-05", "PRPF8, SNRNP200, SNRPA, SNRPD2, SF3B2"], ["hsa03020", "RNA polymerase", "3", "7.33E-04", "POLR2G, POLR2I, POLR2B"], ["hsa00240", "Pyrimidine metabolism", "3", "7.54E-03", "POLR2G, POLR2I, POLR2B"], ["hsa00230", "Purine metabolism", "3", "2.06E-02", "POLR2G, POLR2I, POLR2B"], ["hsa05169", "Epstein-Barr virus infection", "3", "2.38E-02", "POLR2G, POLR2I, POLR2B"], ["hsa05016", "Huntington’s disease", "3", "2.43E-02", "POLR2G, POLR2I, POLR2B"], ["a", "hsa05166", "HTLV-I infection", "7", "4.62E-04", "EGR1, FOS, ETS1, TP53, NFKBIA, TCF3, NFATC1"], ["hsa04660", "T cell receptor signaling pathway", "5", "7.24E-04", "PTPRC, FOS, MAPK3, NFKBIA, NFATC1"], ["hsa05161", "Hepatitis B", "5", "2.57E-03", "FOS, MAPK3, TP53, NFKBIA, NFATC1"], ["hsa04662", "B cell receptor signaling pathway", "4", "2.61E-03", "FOS, MAPK3, NFKBIA, NFATC1"], ["hsa04010", "MAPK signaling pathway", "6", "3.22E-03", "FOS, MAPK3, TP53, DDIT3, NFATC1, DUSP6"], ["hsa05133", "Pertussis", "4", "3.31E-03", "FOS, IRF8, MAPK3, PYCARD"], ["hsa05215", "Prostate cancer", "4", "5.19E-03", "MAPK3, TP53, NFKBIA, MTOR"], ["hsa04668", "TNF signaling pathway", "4", "8.70E-03", "FOS, MAPK3, EDN1, NFKBIA"], ["hsa04151", "PI3K-Akt signaling pathway", "6", "1.15E-02", "MAPK3, COL3A1, COL6A3, TP53, ITGB4, MTOR"], ["hsa04380", "Osteoclast differentiation", "4", "1.54E-02", "FOS, MAPK3, NFKBIA, NFATC1"], ["hsa04621", "NOD-like receptor signaling pathway", "3", "2.06E-02", "MAPK3, PYCARD, NFKBIA"], ["hsa04921", "Oxytocin signaling pathway", "4", "2.53E-02", "FOS, PRKAG1, MAPK3, NFATC1"], ["hsa05210", "Colorectal cancer", "3", "2.58E-02", "FOS, MAPK3, TP53"], ["hsa05230", "Central carbon metabolism in cancer", "3", "2.73E-02", "MAPK3, TP53, MTOR"], ["hsa05214", "Glioma", "3", "2.81E-02", "MAPK3, TP53, MTOR"], ["hsa04920", "Adipocytokine signaling pathway", "3", "3.23E-02", "PRKAG1, NFKBIA, MTOR"], ["hsa05140", "Leishmaniasis", "3", "3.31E-02", "FOS, MAPK3, NFKBIA"], ["hsa05220", "Chronic myeloid leukemia", "3", "3.40E-02", "MAPK3, TP53, NFKBIA"], ["hsa05132", "Salmonella infection", "3", "4.40E-02", "FOS, MAPK3, PYCARD"], ["hsa04024", "cAMP signaling pathway", "4", "4.49E-02", "FOS, MAPK3, NFKBIA, NFATC1"], ["hsa04512", "ECM-receptor interaction", "3", "4.79E-02", "COL3A1, COL6A3, ITGB4"], ["hsa04510", "Focal adhesion", "4", "4.95E-02", "MAPK3, COL3A1, COL6A3, ITGB4"], ["c", "hsa03022", "Basal transcription factors", "3", "1.24E-04", "CCNH, ERCC3, GTF2B"], ["hsa03420", "Nucleotide excision repair", "2", "2.03E-02", "CCNH, ERCC3"], ["d", "hsa03010", "Ribosome", "5", "1.44E-07", "MRPL24, MRPL1, MRPL13, RPL15, RPL27"], ["e", "hsa05169", "Epstein-Barr virus infection", "5", "9.95E-04", "POLR3K, SPI1, CD40, ENTPD1, POLR3E"], ["hsa00240", "Pyrimidine metabolism", "4", "1.93E-03", "POLR3K, DPYD, ENTPD1, POLR3E"], ["hsa00230", "Purine metabolism", "4", "8.49E-03", "POLR3K, AK3, ENTPD1, POLR3E"], ["hsa04620", "Toll-like receptor signaling pathway", "3", "2.73E-02", "IRAK4, TLR1, CD40"], [""]], "row_count": 39, "column_count": 6, "numeric_cells": 118, "header_rows": 0, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:31376328:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bac230a5b550fd7423c4904195df31d92f37abc5ae9145375533d8d0df35710e", "bytes": 612, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#T2", "version": null, "note": "Top 10 miRNAs and genes in the miRNA-gene regulatory network", "structure": {"pmcid": "PMC6722447", "section_index": 12, "section_title": "Construction of miRNA-DEG regulatory network", "row_count": 14, "column_count": 4}, "table": {"label": "Table 2", "caption": "Top 10 miRNAs and genes in the miRNA-gene regulatory network", "rows": [[""], ["miRNA", "Degree", "Gene", "Degree"], [""], ["hsa-miR-16-5p", "89", "HMGA1", "11"], ["hsa-let-7b-5p", "84", "BAZ2A", "9"], ["hsa-miR-15a-5p", "44", "CALU", "9"], ["hsa-miR-15b-5p", "41", "BTG2", "8"], ["hsa-let-7a-5p", "40", "SOD2", "8"], ["hsa-miR-34a-5p", "37", "TP53", "7"], ["hsa-miR-21-5p", "33", "UBN2", "7"], ["hsa-miR-222-3p", "24", "CBX5", "6"], ["hsa-miR-221-3p", "23", "ITGA2", "6"], ["hsa-miR-372-3p", "23", "SLC10A7", "6"], [""]], "row_count": 14, "column_count": 4, "numeric_cells": 32, "header_rows": 0, "locator": "section[12]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:GSE21933 not downloaded", "asset:data:geo:GSE21933 licence not read", "asset:data:geo:GSE27262 not downloaded", "asset:data:geo:GSE27262 licence not read", "asset:data:geo:GSE43458 not downloaded", "asset:data:geo:GSE43458 licence not read", "asset:data:geo:GSE74706 not downloaded", "asset:data:geo:GSE74706 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "Meta-analysis using the MetaDE package in R software", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using the MetaDE package in R software (https:// cran.r-project.org/web/packages/MetaDE/) (15), DEGs were screened from the four microarray datasets."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE21933", "GSE27262", "GSE43458", "GSE74706"], "resolved_accessions": ["GSE21933", "GSE27262", "GSE43458", "GSE74706"], "statements": ["Finally, the raw data and platform annotation files under GSE21933 (21 NSCLC and 21 normal samples; platform: GPL6254 Phalanx Human OneArray), GSE27262 (25 NSCLC and 25 normal samples; platform: GPL570 [HG-U133_ Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array), GSE43458 (40 NSCLC and 30 normal samples; platform: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array) and GSE74706 (18 NSCLC and 18 normal samples; platform: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2) were extracted."], "basis": "The paper names GSE21933, GSE27262, GSE43458, GSE74706 in gene expression omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:31376328", "data:geo:GSE21933", "asset:table:pmid:31376328:1", "asset:table:pmid:31376328:2", "asset:table:pmid:31376328:3", "asset:table:pmid:31376328:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21933"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:44Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 14754, "completion_tokens": 2094, "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:31376328", "type": "paper", "label": "pmid:31376328"}, {"id": "source:pmid:31376328", "type": "manuscript", "label": "PMID 31376328 full text"}, {"id": "data:geo:GSE21933", "type": "dataset", "label": "GEO GSE21933"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31376328", "type": "paper", "label": "pmid:31376328"}, {"id": "source:pmid:31376328", "type": "manuscript", "label": "PMID 31376328 full text"}, {"id": "data:geo:GSE21933", "type": "dataset", "label": "GEO GSE21933"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31376328", "type": "extraction", "used": ["source:pmid:31376328"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21933", "type": "accession_resolution", "used": ["data:geo:GSE21933"], "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:31376328", "parent_hash": "sha256:f0efea7961a4cabfd74502bc7a0f78886b11703d5379aa9d73edeffa12d7459c", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE21933 licence not read", "asset:data:geo:GSE21933 not downloaded", "asset:data:geo:GSE27262 licence not read", "asset:data:geo:GSE27262 not downloaded", "asset:data:geo:GSE43458 licence not read", "asset:data:geo:GSE43458 not downloaded", "asset:data:geo:GSE74706 licence not read", "asset:data:geo:GSE74706 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["sed genes (DEGs) were screened from the four microarray datasets using MetaDE package, and then cond", "he same expression trends in all of the four microarray datasets. In the PPI network, TP53 and FOS c"], "order_basis": "paper_text_order:672", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T01:20:29+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}}}