MSUM strains show the gene-expression signatures of <i>GCN4</i> activation.

<p>(<b>A</b>) Comparison of RNA-seq and Ribo-seq RPKM changes in <i>uba4Δ</i>. <i>GCN4</i> targets and statistically significant Ribo-seq changes are indicated. Values are the means of 2 biological replicates. (<b>B</b>) Venn diagram of overlap between <i>GCN4</i> functional targets (blue) and significant Ribo-seq RPKM changes in <i>uba4Δ</i> (pink) and <i>ncs6Δ</i> (green). The significance of the overlap was computed using the hypergeometric distribution. (<b>C</b>) Cumulative distribution plots of fold Ribo-seq changes for <i>GCN4</i> targets (solid lines) compared to all other genes (dashed lines) in <i>uba4Δ</i> (top) and <i>ncs6Δ.</i> P values are from a KS test of <i>GCN4</i> targets against the rest of the genome. (<b>D</b>) Mean±SEM of predicted Gcn4p occupancy for groups of genes from panel B and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003675#pgen.1003675.s005" target="_blank">figure S5</a>, as determined by high-throughput <i>in vitro</i> binding assays <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003675#pgen.1003675-Nutiu1" target="_blank">[40]</a>. Bars are colored to match groups in panel B. P values are from t-tests comparing the indicated gene set against all genes in the genome.