|The motif sampler is a method to find cis-acting
regulatory elements from a set of co-regulated DNA sequences (e.g. promoters).
The basic assumption is that a cluster of co-regulated genes is regulated
by the same transcription factors and the genes of a given cluster share
common regulatory motifs.
For instance, large-scale transcriptome expression analysis such as microarrays produce large sets of co-regulated genes.
There are several methods available to search for over-represented motif in the upstream region of a set of co-regulated genes. Our approach is based on probabilistic sequence models (e.g. Gibbs Sampling).
Before using the Motif sampler, make sure you follow all the recommandations.
* A gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.
THIJS G, MARCHAL K, LESCOT M, ROMBAUTS S, DE MOOR B, ROUZE P, MOREAU Y.
J Comput Biol. 2002;9(2):447-64. PMID: 12015892
* INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling.
THIJS G, MOREAU Y, DE SMET F, MATHYS J, LESCOT M, ROMBAUTS S, ROUZE P, DE MOOR B, MARCHAL K.
Bioinformatics. 2002 Feb;18(2):331-2. PMID: 11847086
* A higher order background model improves the detection by Gibbs sampling of potential promoter regulatory elements in DNA sequences.
THIJS, G., LESCOT, M., MARCHAL, K., ROMBAUTS, S., DE MOOR, B.,MOREAU,Y. and ROUZÉ, P.
Bioinformatics. 2001 Dec;17(12):1113-22.
* Detection of cis-acting regulatory elements in plants: a Gibbs sampling approach.
Thijs,G., Rombauts,S., Lescot,M., Marchal,K., De Moor,B., Moreau,Y. and Rouzé,P. Proceedings of the second International conference on bioinformatics of genome regulation and structure, Novosibirsk, Russia, August 7-11, 2000, ICG, Novosibirsk, V. 1, p:118-126.
* Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
Lawrence et. al. Science (1993). Vol:262, p:208-14. PMID: 8211139.