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. 2006 Jul 1;34(Web Server issue):W566-70.
doi: 10.1093/nar/gkl285.

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes

Giulio Pavesi  1 , Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, Graziano Pesole
Affiliations

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes

Giulio Pavesi et al. Nucleic Acids Res. .

Abstract

Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif Discovery) Tools web server comprises a set of tools for the discovery of novel conserved sequence and structure motifs in nucleotide sequences, motifs that in turn are good candidates for regulatory activity. The server includes the following programs: Weeder, for the discovery of conserved transcription factor binding sites (TFBSs) in nucleotide sequences from co-regulated genes; WeederH, for the discovery of conserved TFBSs and distal regulatory modules in sequences from homologous genes; RNAProfile, for the discovery of conserved secondary structure motifs in unaligned RNA sequences whose secondary structure is not known. In this way, a given gene can be compared with other co-regulated genes or with its homologs, or its mRNA can be analyzed for conserved motifs regulating its post-transcriptional fate. The web server thus provides researchers with different strategies and methods to investigate the regulation of gene expression, at both the transcriptional and post-transcriptional levels. Available at http://www.pesolelab.it/modtools/ and http://www.beacon.unimi.it/modtools/.

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Figures

Figure 1
Figure 1
The output of WeederH, shown within the UCSC genome browser. (a) For the 500 bp upstream and first non-coding exon of the p53 gene of human, mouse and rat. Known TFBSs annotated for the human gene in the TRANSFAC database (14) are also shown. Motifs that do not match the TRANSFAC annotations correspond to the human homologs of sites annotated in the mouse promoter. (b) Obtained from the analysis of the intergenic region upstream of the interleukin-5 gene of human, mouse and rat. The second track from the top shows the 500 bp regions selected by WeederH as containing motifs with significantly high score. The regions selected cover the promoter of the gene and an experimentally validated enhancer at −6500 bp from the gene (15).
Figure 2
Figure 2
Output of RNAprofile, showing instances of a motif corresponding to the IRE (13), obtained from the analysis of five ferritin mRNA 5′-UTRs. Notice that the last region, with a very low fitness score, is very unlikely to be a true instance of the motif.
See this image and copyright information in PMC

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