Development of a novel in silico prediction program, MAMA, associated with microarray analysis, for the survey of functional cis-elements, and its application to iron deficiency-inducible genes in rice

Abstract

To predict putative cis-elements in promoters, we developed a novel in silico method with Microarray Associated Motif Analysis program (MAMA), and applied it to the microarray analysis of iron deficient and iron sufficient rice. As a result, sequences including binding core sequence (CATGC) of IDEF1, ABI3/VP1 transcription factor involved in response to iron deficiency in rice, were predicted as 2nd, 4th and 5th probable candidates of cis-elements. Sequence including binding core sequence (CA[AC]G[TC][TCA][TCA]) of IDEF2, NAC transcription factor involved in iron distribution in rice, was predicted as 12th probable cis-element candidate. Sequence similar to binding core sequence (CACGTGG) of OsIRO2, iron deficiency inducible bHLH transcription factor, was predicted as 10th probable candidate. Most of these predicted cis-elements were predicted as one of numerous candidates by existing methods. This result demonstrated that MAMA is useful for finding new functional cis-elements.