YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae

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.

[1]  C. Ball,et al.  Saccharomyces Genome Database. , 2002, Methods in enzymology.

[2]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[3]  Arlindo L. Oliveira,et al.  Bioinformatics Original Paper Musa: a Parameter Free Algorithm for the Identification of Biologically Significant Motifs , 2022 .

[4]  Liisa Holm,et al.  POXO: a web-enabled tool series to discover transcription factor binding sites , 2006, Nucleic Acids Res..

[5]  Wen-Hsiung Li,et al.  MYBS: a comprehensive web server for mining transcription factor binding sites in yeast , 2007, Nucleic Acids Res..

[6]  Nicola J. Rinaldi,et al.  Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.

[7]  Panayiotis V. Benos,et al.  DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies , 2007, PLoS Comput. Biol..

[8]  Jacques van Helden,et al.  Regulatory Sequence Analysis Tools , 2003, Nucleic Acids Res..

[9]  Pooja Jain,et al.  The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae , 2005, Nucleic Acids Res..

[10]  S. Shen-Orr,et al.  Networks Network Motifs : Simple Building Blocks of Complex , 2002 .

[11]  M. Gerstein,et al.  Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. , 2002, Genes & development.

[12]  Marie-France Sagot,et al.  An efficient algorithm for the identification of structured motifs in DNA promoter sequences , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[13]  R. Milo,et al.  Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[14]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[15]  Xin Chen,et al.  The TRANSFAC system on gene expression regulation , 2001, Nucleic Acids Res..

[16]  Mark Gerstein,et al.  Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms , 2007, Functional & Integrative Genomics.

[17]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[18]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[19]  Miguel C. Teixeira,et al.  Early transcriptional response of Saccharomyces cerevisiae to stress imposed by the herbicide 2,4-dichlorophenoxyacetic acid. , 2006, FEMS yeast research.

[20]  Charles Boone,et al.  Identifying transcription factor functions and targets by phenotypic activation , 2006, Proceedings of the National Academy of Sciences.

[21]  T. Ideker,et al.  Supporting Online Material for A Systems Approach to Mapping DNA Damage Response Pathways , 2006 .