ArticleBioinformatics (Oxford, England)2009
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Article
- Statistical significance of combinatorial regulations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome.BMC genomics · 2012Article
- Discriminative prediction of mammalian enhancers from DNA sequence.Genome research · 2011Article
- Article
- Exploiting physico-chemical properties in string kernels.BMC bioinformatics · 2010Article
- Article
- Article
- Identifying transcriptional cis-regulatory modules in animal genomes.Wiley interdisciplinary reviews. Developmental biologyReview
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5 authors.
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Abstract
motivationUnderstanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor (TF) binding sites in promoter regions of potential TF target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cis-regulatory modules.
resultsWe propose a new algorithm that combines the benefits of existing motif finding with the ones of support vector machines (SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules. In experiments on microarray data from Arabidopsis thaliana, we were able to show that the newly developed strategy significantly improves the recognition of TF targets. AVAILABILITY: The python source code (open source-licensed under GPL), the data for the experiments and a Galaxy-based web service are available at http://www.fml.mpg.de/raetsch/suppl/kirmes/.
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