A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes
A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes
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DOI：
10.1145/369133.369253
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发表时间：
2001-04
期刊：
影响因子：
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通讯作者：
G. Thijs;K. Marchal;M. Lescot;S. Rombauts;B. Moor;P. Rouzé;Y. Moreau
中科院分区：
文献类型：
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作者：
G. Thijs;K. Marchal;M. Lescot;S. Rombauts;B. Moor;P. Rouzé;Y. Moreau
Microarray experiments can reveal useful information on the transcriptional regulation. We try to find regulatory elements in the region upstream of translation start of coexpressed genes. Here we present a modification to the original Gibbs Sampling algorithm [12]. We introduce a probability distribution to estimate the number of copies of the motif in a sequence. The second modification is the incorporation of a higher-order background model. We have successfully tested our algorithm on several data sets. First we show results on two selected data set: sequences from plants containing the G-box motif and the upstream sequences from bacterial genes regulated by O2-responsive protein FNR. In both cases the motif sampler is able to find the expected motifs. Finally, the sampler is tested on 4 clusters of coexpressed genes from a wounding experiment in Arabidopsis thaliana. We find several putative motifs that are related to the pathways involved in the plant defense mechanism.
