Abstract
Prediction of cis-elements is essential to accelerate the study of gene transcription mechanisms. In eukaryotes, especially in higher organisms, transcription mechanisms are extremely complex. Moreover, sequences homologous to cis-elements exist abundantly, rendering the in silico search for novel cis-elements unsuccessful in many cases by existing methods. To predict putative cis-elements in promoters, we developed a highly sensitive in silico method, Microarray Associated Motif Analysis program (MAMA). MAMA extracts sequences which are highly conserved in promoters of highly regulated genes by various stresses, and which exist more frequently near the transcription start site. In this study, MAMA method was applied to some microarray analysis data from Oryza sativa, Arabidopsis thaliana, and Homo sapiens. As a result, known functional cis-elements were included with the highest score among the predicted elements. This result demonstrated that MAMA is more sensitive for finding functional cis-elements than existing methods.
