Regulatory Circuits of MicroRNAs and Transcription Factors in Plant

We selected differentially expressed genes induced by cold, drought and salinity in the root and shoot of Arabidopsis seedlings, and up-regulated genes at different developmental stages with a method called Rank Products [2] (Figure 1). The microarray data were from AtGenExpress [4]. Using our genome-wide WordSpy motif algorithm [7, 8], we discovered many significant motifs. The expression relevance of a motif was measured by a p-value from a cumulative hypergeometric test [1], and by the average pairwise cosine similarity (gscore) of genes containing the motif. Figure 1E shows the distribution of the motifs from the coldinduced genes in shoot, and 258 motifs obtained with the p-value cutoff of 0.01 and gscore cutoff of 0.1. Similarly, significant motifs were obtained for the drought and salt stresses, and different development stages.