Motif-enrichment validations. Gene clusters with significant motif enrichment were compared to published datasets. For example, cluster 30 was enriched for EcR/USP binding sites, so genes within cluster 30 were compared to independently identified EcR/USP target genes (A). This analysis was repeated for clusters 29 and 13, which were both enriched for the starvation-associated motif (B), the Myc motif (C), and the Drosophila E2F motif (D). In every case but one, significant enrichment for independently validated target genes was observed. Confirmed Myc target genes within Cluster 13 are generally induced by Myc expression, whereas cluster 29 genes are generally repressed by Myc expression (see heat map (C)). Similarly, verified E2F targets within clusters 13 and 29 are generally upregulated and downregulated by E2F expression, respectively (see heat map and expression plot (D)).