{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32938406", "kind": "science-record", "revision": 8, "content_hash": "sha256:64334fb225f162bc28488324fc8160902da7382f9eb494e81efce324f523e19b", "created_at": "2026-11-01T15:41:10Z", "updated_at": "2026-11-01T22:45:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis.", "doi": "10.1186/s12872-020-01701-z", "pmid": "32938406", "authors": ["Dinghui Wang", "Bin Liu", "Tianhua Xiong", "Wenlong Yu", "Qiang She"], "journal": "BMC cardiovascular disorders", "year": 2020, "abstract": "BACKGROUND: Familial hypercholesterolemia (FH) is one of the commonest inherited metabolic disorders. Abnormally high level of low-density lipoprotein cholesterol (LDL-C) in blood leads to premature atherosclerosis onset and a high risk of cardiovascular disease (CVD). However, the specific mechanisms of the progression process are still unclear. Our study aimed to investigate the potential differently expressed genes (DEGs) and mechanism of FH using various bioinformatic tools.\nMETHODS: GSE13985 and GSE6054 were downloaded from the Gene Expression Omnibus (GEO) database for bioinformatic analysis in this study. First, limma package of R was used to identify DEGs between blood samples of patients with FH and those from healthy individuals. Then, the functional annotation of DEGs was carried out by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Gene Ontology (GO) analysis. Based on Search Tool for the Retrieval of Interacting Genes (STRING) tool, we constructed the Protein-Protein Interactions (PPIs) network among DEGs and mined the core genes as well.\nRESULTS: A total of 102 communal DEGs (49 up-regulated and 53 down-regulated) are identified in FH samples compared with control samples. The functional changes of DEGs are mainly associated with the focal adhere and glucagon signaling pathway. Ten genes (ITGAL, TLN1, POLR2A, CD69, GZMA, VASP, HNRNPUL1, SF1, SRRM2, ITGAV) were identified as core genes. Bioinformatic analysis showed that the core genes are mainly enriched in numerous processes related to cell adhesion, integrin-mediated signaling pathway and cell-matrix adhesion. In the transcription factor (TF) target regulating network, 219 nodes were detected, including 214 DEGs and 5 TFs (SP1, EGR3, CREB, SEF1, HOX13). In conclusion, the DEGs and hub genes identified in this study may help us understand the potential etiology of the occurrence and development of AS.\nCONCLUSION: Up-regulated ITGAL, TLN1, POLR2A, VASP, HNRNPUL1, SF1, SRRM2, and down-regulated CD69, GZMA and ITGAV performed important promotional effects for the formation of atherosclerotic plaques those suffering from FH. Moreover, SP1, EGR3, CREB, SEF1 and HOX13 were the potential transcription factors for DEGs and could serve as underlying targets for AS rupture prevention. These findings provide a theoretical basis for us to understand the potential etiology of the occurrence and development of AS in FH patients and we may be able to find potential diagnostic and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "DEGs between FH patients and those of matched controls of the two expression profile data sets were screened out respectively using the Linear Models for Microarray (LIMMA; Version: 3.30.3) affy in R package12 [19].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32938406", "locator": "sections[5] \"Screening genes of differential expression\" paragraph 2", "quote": "DEGs between FH patients and those of matched controls of the two expression profile data sets were screened out respectively using the Linear Models for Microarray (LIMMA; Version: 3.30.3) affy in R package12 [19]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32938406", "locator": "sections[21] \"notes\" paragraph 1", "quote": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054)."}], "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:32938406"], "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:GSE13985"], "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:GSE13985"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32938406", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12872-020-01701-z", "sha256": "sha256:43aeaad6cd69668dc8cd22e00656ed6104d927589a96bf43dcd4a33e34ca0340", "bytes": 38252, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12872-020-01701-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7493348", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13985", "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=GSE13985", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13985", "version": null, "note": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM351336", "GSM351337", "GSM351338", "GSM351339", "GSM351340", "GSM351341", "GSM351342", "GSM351343", "GSM351344", "GSM351345"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Atherosclerotic markers in human blood - a study in patients with familial hypercholesterolemia ", "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:GSE6054", "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=GSE6054", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6054", "version": null, "note": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM140232", "GSM140233", "GSM140234", "GSM140235", "GSM140236", "GSM140237", "GSM140239", "GSM140240", "GSM140241", "GSM140244", "GSM140245", "GSM140246", "GSM140247", "GSM140248", "GSM140249", "GSM140250", "GSM140251", "GSM140252", "GSM140253", "GSM140254", "GSM140255", "GSM140256", "GSM140257"], "sample_count": 23, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Monocytes of patients with familial hypercholesterolemia show alterations in cholesterol metabolism", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32938406:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1a3b516f4325b3b1e7bda069b53b6546a7767c57042f72201e0962c810275302", "bytes": 3829, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab1", "version": null, "note": "The functional enrichment analyses of DEGs ranked by P-value", "structure": {"pmcid": "PMC7493348", "section_index": 11, "section_title": "Functional annotation of DEGs through GO and KEGG analysis", "row_count": 31, "column_count": 4}, "table": {"label": "Table 1", "caption": "The functional enrichment analyses of DEGs ranked by P-value", "rows": [["Term", "Count", "Genes", "P-Value"], ["GO-BPs"], ["GO:0001843 ~ neural tube closure", "4", "TMED2, SKI, PRKACB, VASP", "0.006332314"], ["GO:0010942 ~ positive regulation of cell death", "3", "AKR1C3, UCP2, TRIM13", "0.008780361"], ["GO:0007596 ~ blood coagulation", "5", "P2RX5, F5, ENPP4, PRKACB, WAS", "0.012574205"], ["GO:0007229 ~ integrin-mediated signaling pathway", "4", "ITGAL, ITGAV, PRAM1, ZYX", "0.012578224"], ["GO:0038027 ~ apolipoprotein A-I-mediated signaling pathway", "2", "ABCA7, ITGAV", "0.024181939"], ["GO:0051289 ~ protein homotetramerization", "3", "CRTC2, VASP, GOLGA2", "0.034735707"], ["GO:0048208 ~ COPII vesicle coating", "3", "F5, TMED2, GOLGA2", "0.035801513"], ["GO:0035019 ~ somatic stem cell population maintenance", "3", "BCL9L, SKI, POLR2A", "0.040189117"], ["GO:0006888 ~ ER to Golgi vesicle-mediated transport", "4", "F5, TMED2, GOLGA2, SPTAN1", "0.043542377"], ["GO:0098609 ~ cell-cell adhesion", "5", "PKM, BAG3, VASP, GOLGA2, SPTAN1", "0.043641603"], ["GO-CCs"], ["GO:0005913 ~ cell-cell adherens junction", "7", "PKM, TLN1, BAG3, ZYX, VASP, GOLGA2, SPTAN1", "0.004005355"], ["GO:0032587 ~ ruffle membrane", "4", "ABCA7, TLN1, ITGAV, IFIT5", "0.00665283"], ["GO:0005886 ~ plasma membrane", "30", "ABCA7, ITGAL, TLN1, LRRC8B, ENPP4, MMP25, PKM, DYSF, ITGAV, BAG3, ANKRD11, CD4, PRKACB, KLRF1, ZYX, FLVCR1, FMNL1, KLRB1, RHBDF2, CD160, EDA2R, VASP, P2RX5, LSP1, PRKD2, NEDD1, F5, IFIT5, P2RY14, CYBRD1", "0.010121246"], ["GO:0016020 ~ membrane", "19", "FMNL1, ITGAL, MOB4, ENPP4, MAP 4 K1, RPS9, PRRC2A, CAD, MMP25, TAPBP, LSP1, PIGK, F5, PEX2, ITGAV, CD4, KLRF1, NCOR2, SPTAN1", "0.011799738"], ["GO:0070062 ~ extracellular exosome", "22", "FMNL1, ITGAL, CRTC2, TLN1, ENPP4, RPS9, MINK1, PRRC2A, CAD, WAS, VASP, AKR1C3, PKM, LSP1, DYSF, CLIC3, UBA1, ITGAV, BEX5, CYBRD1, PRKACB, SPTAN1", "0.017083511"], ["GO:1903561 ~ extracellular vesicle", "3", "PKM, F5, SPTAN1", "0.022786951"], ["GO:0017053 ~ transcriptional repressor complex", "3", "MIER1, SKI, NCOR2", "0.027213685"], ["GO:0005654 ~ nucleoplasm", "21", "CRTC2, SF1, RPS9, CAD, SKI, BOD1L1, POLR2A, FEM1C, PRKD2, NEDD1, HNRNPUL1, MIER1, SRRM2, FYTTD1, ANKRD11, SP4, BCL9L, KPNA5, PRKACB, NCOR2, CHD3", "0.02939589"], ["GO:0033116 ~ endoplasmic reticulum-Golgi intermediate compartment membrane", "3", "F5, TMED2, GOLGA2", "0.035966686"], ["GO:0005737 ~ cytoplasm", "33", "CRTC2, TLN1, MOB4, LRRC8B, MAP 4 K1, TRIM13, PRRC2A, AKR1C3, DNAJC17, PKM, MIER1, BAG3, ANKRD11, HECTD3, ZYX, MTMR6, CHD3, C15ORF39, RPS9, MINK1, SKI, VASP, P2RX5, FEM1C, PRKD2, CLIC3, UBA1, RFK, SP4, BEX5, CMIP, KPNA5, FPGT", "0.045491399"], ["GO:0032580 ~ Golgi cisterna membrane", "3", "MOB4, TMED2, GOLGA2", "0.049065899"], ["GO-MFs"], ["GO:0005515 ~ protein binding", "62", "RARRES3, TLN1, LRRC8B, HMGN4, TAPBP, PKM, PIGK, DYSF, PEX2, MIER1, BAG3, ZYX, PRKACB, MATK, FLVCR1, GOLGA2, FMNL1, GZMA, SF1, CD160, MINK1, LENG8, WAS, VASP, PRKD2, F5, CLIC3, PRAM1, CYBRD1, KPNA5, CMIP, ITGAL, CRTC2, MOB4, TRIM13, MAP 4 K1, PRRC2A, CIC, POLR2A, TMED2, CD69, ITGAV, HECTD3, LIMD2, CD4, MTMR6, TRAM1, CHD3, EDA2R, RPS9, ZNF26, SKI, FEM1C, MRFAP1L1, HNRNPUL1, UCP2, UBA1, FYTTD1, SP4, BEX5, NCOR2, SPTAN1", "0.0000906709830702394"], ["GO:0098641 ~ cadherin binding involved in cell-cell adhesion", "6", "PKM, TLN1, BAG3, VASP, GOLGA2, SPTAN1", "0.014824041"], ["GO:0004888 ~ transmembrane signaling receptor activity", "5", "KLRB1, P2RX5, CD69, CD4, KLRF1", "0.02204474"], ["GO:0044822 ~ poly(A) RNA binding", "12", "PKM, HNRNPUL1, UBA1, FYTTD1, SRRM2, IFIT5, SF1, RPS9, PRRC2A, ZYX, CHD3, POLR2A", "0.023879125"], ["GO:0032393 ~ MHC class I receptor activity", "2", "CD160, KLRF1", "0.02949141"], ["GO:0005522 ~ profilin binding", "2", "FMNL1, VASP", "0.043913166"]], "row_count": 31, "column_count": 4, "numeric_cells": 89, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32938406:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43d086adb5d2fc1b60902a88230a1090bb094436b7bff7ae5ec2b0f620745f42", "bytes": 3752, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab2", "version": null, "note": "Summary of the function of 10 hub genes", "structure": {"pmcid": "PMC7493348", "section_index": 12, "section_title": "PPI network and hub genes analysis", "row_count": 11, "column_count": 3}, "table": {"label": "Table 2", "caption": "Summary of the function of 10 hub genes", "rows": [["Symbol", "Full name", "Function"], ["ITGAL", "Integrin Subunit Alpha L", "Involved in a variety of immune phenomena including leukocyte-endothelial cell interaction, cytotoxic T-cell mediated killing, and antibody dependent killing by granulocytes and monocytes. Contributes to natural killer cell cytotoxicity. Involved in leukocyte adhesion and transmigration of leukocytes including T-cells and neutrophils.contributes to apoptotic neutrophil phagocytosis by macrophages."], ["TLN1", "Talin 1", "Probably involved in connections of major cytoskeletal structures to the plasma membrane. High molecular weight cytoskeletal protein concentrated at regions of cell-substratum contact and, in lymphocytes, at cell-cell contacts"], ["POLR2A", "RNA Polymerase II Subunit A", "DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery."], ["CD69", "CD69 Molecule", "Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. By antigens, mitogens or activators of PKC on the surface of T and B-lymphocytes. By interaction of IL-2 with the p75 IL-2R on the surface of NK cells."], ["GZMA", "Granzyme A", "activates caspase-independent cell death with morphological features of apoptosis when delivered into the target cell through the immunological synapse. It cleaves after Lys or Arg. Cleaves APEX1 after ‘Lys-31’ and destroys its oxidative repair activity. Cleaves the nucleosome assembly protein SET after ‘Lys-189’, which disrupts its nucleosome assembly activity and allows the SET complex to translocate into the nucleus to nick and degrade the DNA."], ["VASP", "Vasodilator Stimulated Phosphoprotein", "Ena/VASP proteins are actin-associated proteins involved in a range of processes dependent on cytoskeleton remodeling and cell polarity such as axon guidance, lamellipodial and filopodial dynamics, platelet activation and cell migration. VASP promotes actin filament elongation. Plays a role in actin-based mobility of Listeria monocytogenes in host cells. Regulates actin dynamics in platelets and plays an important role in regulating platelet aggregation."], ["HNRNPUL1", "Heterogeneous Nuclear Ribonucleoprotein U Like 1", "Acts as a basic transcriptional regulator. Represses basic transcription driven by several virus and cellular promoters. When associated with BRD7, activates transcription of glucocorticoid-responsive promoter in the absence of ligand-stimulation. Plays also a role in mRNA processing and transport. Binds avidly to poly(G) and poly(C) RNA homopolymers in vitro."], ["SF1", "Splicing Factor 1", "Necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5′-UACUAAC-3′ of the pre-mRNA. May act as transcription repressor."], ["SRRM2", "Serine/Arginine Repetitive Matrix 2", "Required for pre-mRNA splicing as component of the spliceosome."], ["ITGAV", "Integrin Subunit Alpha V", "The alpha-V (ITGAV) integrins are receptors for vitronectin, cytotactin, fibronectin, fibrinogen, laminin, matrix metalloproteinase-2, osteopontin, osteomodulin, prothrombin, thrombospondin and vWF. They recognize the sequence R-G-D in a wide array of ligands."]], "row_count": 11, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:GSE13985 not downloaded", "asset:data:geo:GSE13985 licence not read", "asset:data:geo:GSE6054 not downloaded", "asset:data:geo:GSE6054 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "DEGs between FH patients and those of matched controls of the two expression profile data sets were screened out respectively using the Linear Models for Microarray (LIMMA; Version: 3.30.3) affy in R package12 [19]."}}, {"id": "method-2", "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-3", "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": 0.8, "band": "high", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE13985", "GSE6054"], "resolved_accessions": ["GSE13985", "GSE6054"], "statements": ["Availability of data and materialsThe gene expression profiles of GSE13985 and GSE6054 were downloaded from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13985 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6054)."], "basis": "The paper names GSE13985, GSE6054 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32938406", "data:geo:GSE13985", "asset:table:pmid:32938406:1", "asset:table:pmid:32938406:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13985"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28873, "completion_tokens": 1515, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32938406", "type": "paper", "label": "pmid:32938406"}, {"id": "source:pmid:32938406", "type": "manuscript", "label": "PMID 32938406 full text"}, {"id": "data:geo:GSE13985", "type": "dataset", "label": "GEO GSE13985"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32938406", "type": "paper", "label": "pmid:32938406"}, {"id": "source:pmid:32938406", "type": "manuscript", "label": "PMID 32938406 full text"}, {"id": "data:geo:GSE13985", "type": "dataset", "label": "GEO GSE13985"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32938406", "type": "extraction", "used": ["source:pmid:32938406"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13985", "type": "accession_resolution", "used": ["data:geo:GSE13985"], "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:32938406", "parent_hash": "sha256:ed901de94bf1589bc495154d44b231cab70ead18f6d54da36e4ec5de783282ca", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE13985 licence not read", "asset:data:geo:GSE13985 not downloaded", "asset:data:geo:GSE6054 licence not read", "asset:data:geo:GSE6054 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["ed to identify DEGs between blood samples of patients with FH and those from healthy individuals. Then,"], "order_basis": "paper_text_order:770", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["DEGs between FH patients and those of matched controls of the two expression profile data sets were screened out respectively using the Linear Models for Microarray (LIMMA; Version: 3.30.3) affy in R package12 [19]."], "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":"2026-11-04T01:46:38+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}}}