Thu, 21 Aug 2008 01:16:11 BST CiteULike: heliopais's Mendes http://www.citeulike.org/user/heliopais/author/Mendes CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/heliopais/article/1973094 <i>Nucleic Acids Res (21 November 2007)</i><br /><br />The Yeast search for transcriptional regulators and consensus tracking (YEASTRACT) information system (www.yeastract.com) was developed to support the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in September 2007, this database contains over 30 990 regulatory associations between Transcription Factors (TFs) and target genes and includes 284 specific DNA binding sites for 108 characterized TFs. Computational tools are also provided to facilitate the exploitation of the gathered data when solving a number of biological questions, in particular the ones that involve the analysis of global gene expression results. In this new release, YEASTRACT includes DISCOVERER, a set of computational tools that can be used to identify complex motifs over-represented in the promoter regions of co-regulated genes. The motifs identified are then clustered in families, represented by a position weight matrix and are automatically compared with the known transcription factor binding sites described in YEASTRACT. Additionally, in this new release, it is possible to generate graphic depictions of transcriptional regulatory networks for documented or potential regulatory associations between TFs and target genes. The visual display of these networks of interactions is instrumental in functional studies. Tutorials are available on the system to exemplify the use of all the available tools. YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Pedro T Monteiro Nuno D Mendes Miguel C Teixeira Sofia d'Orey Sandra Tenreiro Nuno P Mira Hélio Pais Alexandre P Francisco Alexandra M Carvalho Artur B Lourenço Isabel Sá-Correia Arlindo L Oliveira Ana T Freitas doi:10.1093/nar/gkm976 Nucleic Acids Res (21 November 2007) 2007-11-24T16:19:17-00:00 2007 Nucleic Acids Res 1362-4962 database genetic_regulatory_network http://www.citeulike.org/user/heliopais/article/1634691 <i>Trends Genet, Vol. 18, No. 8. (August 2002), pp. 395-398.</i><br /><br />Modern microarray technology is capable of providing data about the expression of thousands of genes, and even of whole genomes. An important question is how this technology can be used most effectively to unravel the workings of cellular machinery. Here, we propose a method to infer genetic networks on the basis of data from appropriately designed microarray experiments. In addition to identifying the genes that affect a specific other gene directly, this method also estimates the strength of such effects. We will discuss both the experimental setup and the theoretical background. Linking the genes: inferring quantitative gene networks from microarray data. A de la Fuente P Brazhnik P Mendes Trends Genet, Vol. 18, No. 8. (August 2002), pp. 395-398. 2007-09-08T18:05:42-00:00 2002 Trends Genet 0168-9525 18 8 395 398 grn