10.1371/journal.pone.0098165.g004 Nicholas S. Kirkby Nicholas S. Kirkby Martina H. Lundberg Martina H. Lundberg William R. Wright William R. Wright Timothy D. Warner Timothy D. Warner Mark J. Paul-Clark Mark J. Paul-Clark Jane A. Mitchell Jane A. Mitchell Deletion of COX-2 is associated with up-regulation of lymphocyte-related gene expression patterns, and down-regulation of rgl1 in tissue from fat-fed apoE<sup>−/−</sup> mice. Public Library of Science 2014 Computational biology immunology cardiology Cardiovascular pharmacology Clinical medicine cox-2 up-regulation lymphocyte-related down-regulation rgl1 fat-fed 2014-06-02 04:41:35 Figure https://plos.figshare.com/articles/figure/_Deletion_of_COX_2_is_associated_with_up_regulation_of_lymphocyte_related_gene_expression_patterns_and_down_regulation_of_rgl1_in_tissue_from_fat_fed_apoE_8722_8722_mice_/1042660 <p>Microarray analysis indicated 82, 87 and 90 differentially expressed genes (DEGs), respectively, in thymus (a), liver (b) and lung (c) from fat-fed apoE<sup>−/−</sup>/COX-2<sup>+/+</sup> and apoE<sup>−/−</sup>/COX-2<sup>−/−</sup> mice. Volcano plot summaries of these data sets illustrate the distribution of effect size and statistical significance. Gene expression differing between genotypes >1.2-fold with p<0.05 highlighted in red, were considered for pathway analysis. Differential gene expression patterns demonstrated only weak overlap between tissues, but one gene, rgl1, was altered (down-regulated) in all tissues studied (d). Rgl1 down-regulation was confirmed in each tissue of apoE<sup>−/−</sup>/COX-2<sup>−/−</sup> mice by qPCR (e). Ingenuity pathway analysis of this data showed that in the thymus (f), liver (g) and lung (h), biological pathways/processes related to T- and/or B-lymphocyte function were amongst the most consistently altered pathways in each tissue. Tables show the top 15 altered biological pathways/processes and implicated genes (green: increased expression; red: decreased expression). Statistical testing of microarray data was performed using a linear model for microarray data modified t-test. n = 4.</p>