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Shown is an example of the output of the EDGI tool (http://luna.bioc.columbia.edu/alona/EDGI/). Motifs shared among a set of related Drosophila species are shown by the vertical lines. Clusters of conserved motifs are indicated by the graph in the lower panel. See Sosinsky et. al., (2007) for details. Back to Projects page | ||
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Computational approaches for identifying transcription factor target genes (in collaboration with B. Honig, A. Califano, and A. Sosinsky, Columbia University) With the increasing number of eukaryotic genomes available, high-throughput automated tools for identification of regulatory DNA sequences are becoming increasingly feasible. Several computational approaches for the prediction of regulatory elements were recently developed. Here we combine the prediction of clusters of binding sites for transcription factors with context information taken from genome annotations. Target Explorer automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors. It was specifically designed for the well-annotated D. melanogaster genome, but most options can be used for sequences from other genomes as well. Target Explorer is available at http://trantor.bioc.columbia.edu/Target_Explorer/ The lab continues to refine these methods and to combine them with other approaches that combine experimental and computational methods for the prediction of transcription factor target genes. Recently, we have developed a novel tool, called EDGI (Enhancer Detection with only Genomic Information) (Sosinsky, et. al., 2007). This tool identifies clusters of conserved sequence 'motifs' that are shared between related genomes, without the need for extensive alignments,. allowing the identification of enhancers as they typically evolve. Try this new tool out at: http://luna.bioc.columbia.edu/alona/EDGI/ Relevant papers: Sosinsky A, Bonin CP, Mann RS, Honig B. (2003) Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res. 31:3589-92. Sosinsky, A, Honig, B., Mann, RS, and Califano, A. (2007) Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6305-10 Back to Projects page | ||
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