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Title: A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
Authors: Thijs, Gert ×
Marchal, Kathleen
Lescot, M.
Rombauts, S.
De Moor, Bart
Rouze, P.
Moreau, Yves #
Issue Date: 2002
Publisher: Mary Ann Liebert
Series Title: Journal of computational biology vol:9 issue:3 pages:447-464
Abstract: AB - Microarray experiments can reveal important information about transcriptional regulation. In our case, we look for potential promoter regulatory elements in the upstream region of coexpressed genes. Here we present two modifications of the original Gibbs sampling algorithm for motif finding (Lawrence et al., 1993). First, we introduce the use of a probability distribution to estimate the number of copies of the motif in a sequence. Second, we describe the technical aspects of the incorporation of a higher-order background model whose application we discussed in Thijs et al. (2001). Our implementation is referred to as the Motif Sampler. We successfully validate our algorithm on several data sets. First, we show results for three sets of upstream sequences containing known motifs: 1) the G-box light-response element in plants, 2) elements involved in methionine response in Saccharomyces cerevisiae, and 3) the FNR O(2)-responsive element in bacteria. We use these data sets to explain the influence of the parameters on the performance of our algorithm. Second, we show results for upstream sequences from four clusters of coexpressed genes identified in a microarray experiment on wounding in Arabidopsis thaliana. Several motifs could be matched to regulatory elements from plant defence pathways in our database of plant cis-acting regulatory elements (PlantCARE). Some other strong motifs do not have corresponding motifs in PlantCARE but are promising candidates for further analysis
ISSN: 1066-5277
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Electrical Engineering - miscellaneous
ESAT - STADIUS, Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics
Centre of Microbial and Plant Genetics
× corresponding author
# (joint) last author

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