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- W20341849 abstract "Several pattern discovery programs have been developed for detecting cis-acting regulatory elements from upstream regions of co-regulated genes. These programs were generally developed, evaluated and optimized on the basis of microbial sequences (principally Escherichia coli and Saccharomyces cerevisiae). The specificity of transcriptional regulation in the model organism (motif size, degeneracy, position-specificity, stranddependency of the motifs...) plays an important role in the algorithmic choices, and the rate of success of each program may depend on the organism considered. The extension of existing approaches to higher organisms is thus not trivial, because regulatory elements are dispersed far away from the transcription start, and can be found upstream, downstream, and within introns. We used different programs to detect cis-acting regulatory elements in several families of co-regulated genes (regulons). A regulon is defined as a set of genes regulated by a same transcription factor. We collected information on experimentally proven regulons from the database PlantCARE [4]. Eleven regulons were built based on promoter sequences from Arabidopsis thaliana and other plant species, and ten from Drosophila melanogaster promoters. Nine of the plant regulons were deduced from PlantCARE. Two regulons were built based on literature studies. The ten Drosophila datasets were extracted from literature. For each gene, we extracted the upstream sequences of 1 to 1.6 kb from the transcription start (or, in the case of lack of data about the transcription start, the translation start)." @default.
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- W20341849 date "2002-01-01" @default.
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- W20341849 title "Deciphering cis-acting regulatory elements in plant and drosophila promoter sequences" @default.
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