Fig. 2: Knockdown of aco-2 upregulates various pathogen response genes.
a Experimental variables used for our RNA-seq analyses [control RNAi (Ctrli) and aco-2 RNAi (aco-2i), black: E. coli, red: PA14]. b A principal component (PC) analysis showing the separation of samples based on indicated biological conditions. c A scatter plot showing transcriptomic changes conferred by PA14 infection (x axis) and aco-2 RNAi (y axis). PA14 infection respectively increased and decreased the expression of 798 genes (Group i) and 297 genes (Group ii) that were upregulated by aco-2 RNAi, whereas it respectively increased and decreased the expression of 4 genes (Group iii) and 60 genes (Group iv) that were downregulated by aco-2 RNAi. Absolute fold change > 2, two-sided test, Benjamini and Hochberg (BH)-adjusted p < 0.05. d A Gaussian kernel density plot showing transcriptomic changes elicited by PA14 infection or aco-2 RNAi, categorized to Groups i, ii, iii, and iv. e Overlaps between genes that were differentially regulated by PA14 infection and genes that were upregulated by aco-2 RNAi (Groups i and ii) (top) and genes that were downregulated by aco-2 RNAi (Groups iii and iv) (bottom). RF: representation factor. p values were calculated by using two-sided hypergeometric test. f, g Overrepresented WormCat terms at high levels (f), including “stress response” (g) of genes included in Group i and Group ii. p values were calculated by using two-sided hypergeometric test. h Comparison of expression changes caused by aco-2 RNAi and those by other mitochondrial dysfunctions in genes associated with GO term “Defense response to other organism (GO:0098542)”. Black dots represent average values. Average fold change is shown on top of each condition. Conditions were sorted based on average fold changes in a descending order. i Overrepresented WormCat terms at intermediate levels (category 2) of genes upregulated by aco-2 RNAi and by other mitochondrial dysfunctions19, 21,22,23,24. p values were calculated by using two-sided hypergeometric test. Ten representative terms were selected based on minimum p values among different conditions. j Representation factors of overlaps between Group i genes and immune signaling gene sets§33, 55, 83,84,85,86 (See Supplementary Data 3 for details). §data (GSE82238) in GEO.
