Promoter motif analysis

For the analysis of promoter motifs, ensemble IDs of genes were used as input in the eukaryotic promoter database (EPD) selection tool (https://epd.expasy.org/epd/EPDnew_select.php), where promoters with TATA, GC, or CCAAT motifs were selected, for each gene, only the most representative promoter was selected. We ran the selection for 3 gene groups: all genes with burst kinetic parameters (All), genes that had larger burst frequency in FS interneurons (Alpha larger in FS), and genes that had larger burst size in Pyr cells (Beta larger in Pyr). Burst frequency and burst size values of genes with different promoter motifs were compared by Kruskal-Wallis test followed by pairwise comparisons using Wilcoxon rank sum test with continuity correction test in R with functions ‘kruskal.test’ and ‘pairwise.wilcox.test’ of ‘stats’ package. Next, we generated signal occurrence profiles of promoter motifs using the Oprof tool of EPD. Relevant promoter regions were set as the following: TATA: from -80 position relative to transcription start site (TSS) to 20; CCAAT: from -200 to 20; GC: from -140 to 50. Occurrence profiles of promoter motifs of all genes with burst kinetic parameters were compared to frequency distributions of genes with alpha parameter larger in FS and genes with beta parameter larger in Pyr with two-sided Kolmogorov-Smirnoff test in R with ‘ks.test’ function of the ‘stats’ package. We integrated the relevant regions of the frequency plots - generated by Oprof - for each promoter motifs in OriginPro 9.0.0 to visualize promoter frequency differences between gene groups.