A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes

By Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, B. De Moor, Pierre Rouzé, Yves Moreau. Annual International Conference on Research in Computational Molecular Biology, 2001

428 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/508bd8683dc11ddeada504a72b84867b41741706

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Citations in the corpus

The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. (2005, methodology): “The alignment method is exempliﬁed by MotifSampler, which uses a Gibbs sampling method (Thijs et al. , 2002).”
Computational analysis of core promoters in the Drosophila genome (2002, methodology): “We sorted the resulting 986 motifs by their log-likelihood score (see [28]), which ranged from negative infinity (the logarithm of zero) to 1,353.”
Quantifying similarity between motifs (2007, neutral): “Kullback-Leibler divergence The KLD has been used by several research groups to quantify similarity between motifs [11-13].”
A survey of DNA motif finding algorithms (2007, methodology): “[46] developed the motif finding algorithm MotifSampler using a modification of the original Gibbs sampling algorithm.”
Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development (2008, background): “2 [92,93]) and an exhaustive in silico testing of 6-mer and 8-mer nucleotide sequences.”
Interdependency of Brassinosteroid and Auxin Signaling in Arabidopsis (2004, methodology): “Improvements on these methods use so-called higher-order models based on Markov chain statistics (Thijs et al. 2001, 2002; Marchal et al. 2003), building the background model by estimating the probability at each nucleotide position based on the previous bases in the sequence.”
ABA Is an Essential Signal for Plant Resistance to Pathogens Affecting JA Biosynthesis and the Activation of Defenses in Arabidopsis[W] (2007, methodology): “Using motif analysis (The Arabidopsis Information Resource [TAIR]), Promomer (http:// bbc.botany.utoronto.ca), and motif sampler (Thijs et al., 2002), several statistically significant candidate cis-regulatory elements were found for each cluster (only known boxes are shown; Figure 5).”
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences (2002, methodology): “These are a new quality-based clustering method (5) and a motif search algorithm called Motif Sampler ( 6 ), and a probabilistic approach based on Gibbs Sampling (7,8) which looks for over-represented motifs in upstream regions.”
The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. (2007, methodology): “The alignment methods are exemplified by programs that use a Gibbs sampling method (Thijs et al. 2002).”
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling (2001, methodology): “An elaborate description of our algorithm is given elsewhere (Thijs et al., 2001).”