Genes that show downregulated expression when <i>ash-2</i> was knocked down are more likely to acquire H3K4me3 markings during the adult stage.

<p>(A) For genes exhibiting significantly downregulated expression when <i>ash-2</i> was knocked down, GSEA revealed a significant enrichment for genes associated with higher D2 H3K4me3 markings compared to L3 (top). For genes exhibiting significantly upregulated expression when <i>ash-2</i> was knocked down, GSEA revealed no bias (bottom). Genes with detectable expression from the published <i>ash-2</i> RNAi microarray experiment (GSM756690-GSM756695) were ranked according to the difference in H3K4me3 levels between D2 and L3 (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007466#pgen.1007466.s012" target="_blank">S5 Table</a>). The enrichment scores were computed using the GSEAPreranked tool. The genes that showed significant expression change (FDR <0.05) between <i>ash-2</i> and control RNAi were identified using Limma in the R package (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007466#pgen.1007466.s016" target="_blank">S9 Table</a>). (B) Average plots show that the genes that exhibited significantly downregulated expression upon <i>ash-2</i> RNAi (top) were marked with higher levels of H3K4me3 at D2 compared to L3. For the genes that exhibited significant upregulated expression upon <i>ash-2</i> RNAi (bottom), their average H3K4me3 levels did not change at the different developmental time points. (C) Clusters k, l, w and y were enriched for genes with a downregulated expression upon <i>ash-2</i> RNAi, and clusters h, i, and j were enriched for genes with an upregulated expression upon <i>ash-2</i> RNAi. Genes in all of the 25 clusters were ranked according to their expression fold change as detected in the <i>ash-2</i> microarray experiment. GSEA was used to determine the enrichment of downregulated or upregulated genes in each cluster. (**) FDR<0.01, (*) FDR<0.05.