Enrichment of core promoter types and regulatory motifs within gene expression clusters. (A) Clusters were grouped based on temporal patterns of expression, which are represented by the heat map (y-axis is time). Average expression values for genes within a cluster are shown. For each cluster, the most significantly enriched gene ontology (GO) term is listed (only when p < 10-5). (B) All 30 clusters were examined for statistically significant (z-score > |3|) enrichment (red) or depletion (green) of ten core Drosophila promoter motifs (see Materials and Methods). The search space was defined as the 100 bp spanning the transcriptional start site (−60 to +40 bp). Certain core promoter motifs were frequently enriched in the same clusters. For example, DRE, CP-1, CP-7, and CP-6 motifs were typically enriched within a similar subset of clusters. In addition, these clusters tended to decrease expression over time. In contrast, INR, DPE, and MTE motifs were often found together in clusters that increased expression over time. TATA motifs were rarely enriched or depleted. (C) All 30 clusters were examined for significant enrichment or depletion of 87 known Drosophila transcription factor binding motifs. The search space was defined as the 1 kb immediately upstream of the transcriptional start site. A group of motifs known to regulate cell growth, protein synthesis, and the cell cycle (e.g., E2F, Myc, Dref, Mad/Med/Brinker) were enriched and frequently found together in clusters that decreased expression over time and upon cell-cycle exit. Clusters that decrease expression over time were also depleted for a group of motifs associated with tissue differentiation (e.g., Cad, Croc, En, Ubx). These differentiation-associated motifs were instead enriched in clusters that increased expression during pupal time points.