Fig. 3

Genomic analyses of GAF target genes and Gaf mutation on gene expression. a GAF binding motif. The sequences of GAF peaks were analyzed by MEME. The most significant motif is shown with the statistical value (p value = 1.6 × 10⁻⁷⁸⁸). The statistical comparison with previously identified Trl motif is also shown (E value = 2.92 × 10⁻⁴). b Summary of GAF distribution. GAF binding sites identified by ChIP-sequencing and evaluated by statistical analyses are summarized in a pie chart. GAF peaks with more than twofold enrichment over the input are grouped into four categories: promoter only (from −500 to TSS), both promoter and intragenic region (UTR, intron and exon), intragenic region only, and intergenic region (beyond −500 or 3’ end). A small percentage of GAF peaks with less than twofold enrichment in the promoter region are also indicated. c Biological functions enriched in GAF targets. Putative GAF-target genes were subjected to DAVID for functional annotation clustering analysis. The GO term and the enrichment score of clusters above 10 (FDR < 0.0001) are shown. d The global effect of Gaf mutation on gene expression. Triplicate RNA samples from WT and Gaf mutants were subjected to microarray analysis. A scatter plot summarizes statistically significant changes in gene expression (p < 0.05 and >1.5-fold change). Each gene is assigned an ID number according to the ascending order of its expression level as shown in the log₂ scale in the y-axis. The central curve represents the WT expression level of genes that show significant changes in mutants. Approximately 80 or 20 % of genes show reduced (green) or increased expression (red) in mutants, respectively. e GO analysis of GAF targets with affected expression in mutants. GAF targets with significant changes in expression were subjected to analysis for functional clustering. The GO term and the enrichment score of clusters above 2 (FDR < 0.05) are shown