Gene Expression Profiling of Valvular Interstitial Cells in Rapacz Familial Hypercholesterolemic Swine.

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However, while these animals have been used extensively for the study of atherosclerosis, the heart valves from RFH swine have not previously been examined. We report the analysis of valvular interstitial cell gene expression in adult (two year old) and juvenile (three months old) RFH and WT swine by microarray analysis via the Affymetrix Porcine Genome Array (GEO #: GSE53997). Principal component and hierarchical clustering analysis revealed grouping and almost no variability between the RFH juvenile and WT juvenile groups. Additionally, only 21 genes were found differentially expressed between these two experimental groups whereas over 900 genes were differentially expressed when comparing either RFH or WT juvenile swine to RFH adults.", "claims": [{"id": "claim-method", "statement": "The Empirical Bayes t-test statistic from the limma package within BioConductor was used to determine the differential gene expression between experimental groups and generate significant gene lists [4] (Table 2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25229013", "locator": "sections[11] \"Differential gene expression\" paragraph 2", "quote": "The Empirical Bayes t-test statistic from the limma package within BioConductor was used to determine the differential gene expression between experimental groups and generate significant gene lists [4] (Table 2)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:25229013"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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Cut off: 2-fold, p < 0.05.", "structure": {"pmcid": "PMC4163136", "section_index": 11, "section_title": "Differential gene expression", "row_count": 4, "column_count": 2}, "table": {"label": "Table 2", "caption": "Summary of differential expression analysis. Cut off: 2-fold, p < 0.05.", "rows": [["Comparison", "Number of differentially expressed transcripts"], ["RFH Juv vs. WT Juv", "21"], ["RFH Juv vs. RFH Adult", "916"], ["WT Juv vs. RFH Adult", "1459"]], "row_count": 4, "column_count": 2, "numeric_cells": 3, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t0010"}}, {"id": "asset:table:pmid:25229013:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:aa50704a56bb7df30911058573d0bc463de00f9dba1a2cf92deaad231b52b63e", "bytes": 1563, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#t0015", "version": null, "note": "Differentially expressed genes in RFH juvenile versus WT juvenile valvular interstitial cells.", "structure": {"pmcid": "PMC4163136", "section_index": 11, "section_title": "Differential gene expression", "row_count": 22, "column_count": 4}, "table": {"label": "Table 3", "caption": "Differentially expressed genes in RFH juvenile versus WT juvenile valvular interstitial cells.", "rows": [["Gene symbol", "Gene name", "Fold change", "P value"], ["C8orf37", "", "6.06", "0.0082"], ["CR2", "Complement receptor type 2 precursor", "5.66", "0.049"], ["TXNL4B", "Thioredoxin-like protein 4B (Dim1-like protein)", "4.29", "0.022"], ["BTBD1", "BTB/POZ domain containing protein 1", "3.25", "0.011"], ["C7orf58", "", "2.46", "0.027"], ["DDX19A", "DDX19-like protein; RNA helicase", "2.30", "0.0025"], ["AKAP11", "A-kinase anchor protein 11", "2.30", "0.022"], ["DIDO1", "Death associated transcription factor 1", "2.14", "0.014"], ["PTPRK", "Receptor-type protein-tyrosine phosphatase kappa precursor", "0.47", "0.0025"], ["PGA5", "Pepsin A precursor", "0.47", "0.011"], ["SDK1", "Sidekick homolog 1", "0.44", "0.014"], ["C6orf98", "Nesprin 1 (nuclear envelope spectrin repeat protein 1)", "0.41", "0.049"], ["PCDHB16", "Protocadherin beta 16 precursor", "0.38", "0.037"], ["SELL", "L-selectin precursor (lymph node homing receptor)", "0.33", "0.017"], ["PEA15", "Astrocytic phosphoprotein PEA-15", "0.29", "0.028"], ["OAS1", "2-5-Oligoadenylate synthetase 1", "0.16", "0.0082"], ["TIMD4", "T-cell immunoglobulin and mucin domain containing 4", "0.25", "0.049"], ["CLEC3B", "Tetranectin precursor", "0.25", "0.049"], ["PCNP", "PEST-containing nuclear protein", "0.25", "0.049"], ["LOX", "Protein-lysine 6-oxidase precursor", "0.23", "0.049"], ["PLAGL1", "Zinc finger protein PLAGL1", "0.05", "0.017"]], "row_count": 22, "column_count": 4, "numeric_cells": 62, "header_rows": 1, "locator": "section[11]/table-wrap[2]#t0015"}}], "gaps": []}, "analysis": {"state": "partial", "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": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-2", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "hierarchical clustering"}}, {"id": "method-3", "family": null, "specific": null, "label": "Empirical Bayes t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Empirical Bayes t-test statistic from the limma package within BioConductor was used to determine the differential gene expression between experimental groups and generate significant gene lists [4] (Table 2)."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "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. 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