PMID: 10705431Mar 8, 2000Paper

Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes

Bioinformatics
A Wagner

Abstract

The question addressed here is how cooperative interactions among transcription factors (TFs), a very frequent phenomenon in eukaryotic transcriptional regulation, can be used to identify genes that are regulated by one or more TFs with known DNA binding specificities. Cooperativity may be homotypic, involving binding of only one transcription factor to multiple sites in a gene's regulatory region. It may also be heterotypic, involving binding of more than one TF. Both types of cooperativity have in common that the binding sites for the respective TFs form tightly linked 'clusters', groups of binding sites often more closely associated than expected by chance alone. A statistical technique suitable for the identification of statistically significant homotypic or heterotypic TF binding site clusters in whole eukaryotic genomes is presented. It can be used to identify genes likely to be regulated by the TFs. Application of the technique is illustrated with two transcription factors involved in the cell cycle and mating control of the yeast Saccharomyces cerevisiae, indicating that the results obtained are biologically meaningful. This rapid and inexpensive computational method of generating hypotheses about gene regulation thus g...Continue Reading

Citations

Jun 5, 2004·Ageing Research Reviews·João Pedro de Magalhães, Olivier Toussaint
Apr 6, 2004·Molecular Phylogenetics and Evolution·Sonja J ProhaskaPeter F Stadler
Sep 2, 2003·Journal of Molecular Biology·Lawrence S Hon, Ajay N Jain
Nov 13, 2001·European Neuropsychopharmacology : the Journal of the European College of Neuropsychopharmacology·J Vilo, K Kivinen
Nov 7, 2000·Current Opinion in Cell Biology·B Futcher
Jun 12, 2002·Current Opinion in Microbiology·Nila Banerjee, Michael Q Zhang
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Saurabh Sinha
Jun 6, 2009·Briefings in Functional Genomics & Proteomics·Leelavati Narlikar, Ivan Ovcharenko
Sep 18, 2004·Bioinformatics·Steve W ColeJerome A Zack
Jul 18, 2006·Bioinformatics·Yu-Hsiang ChangBor-Sen Chen
Apr 2, 2009·Bioinformatics·Rasa JurgelenaiteTom Heskes
Oct 5, 2002·Nucleic Acids Research·Sridhar Hannenhalli, Samuel Levy
Jun 26, 2003·Nucleic Acids Research·Martin C FrithZhiping Weng
Jun 26, 2003·Nucleic Acids Research·Michal Lapidot, Yitzhak Pilpel
Nov 25, 2003·Nucleic Acids Research·Nilanjana Banerjee, Michael Q Zhang
Feb 28, 2004·Nucleic Acids Research·Martin C FrithZhiping Weng
Dec 31, 2005·Nucleic Acids Research·Xin ChenEdgar Wingender
Jul 21, 2006·Nucleic Acids Research·Debraj GuhaThakurta
Feb 8, 2007·Genome Research·Guoyan ZhaoGary D Stormo
Apr 3, 2003·Genome Research·Alexander P LifanovDmitri A Papatsenko
Aug 24, 2005·BMC Bioinformatics·Deendayal DinakarpandianPeter K Rogan
Jan 24, 2007·BMC Bioinformatics·Dustin E SchonesMichael Q Zhang
Dec 10, 2008·BMC Bioinformatics·Geir Kjetil SandveFinn Drabløs
Mar 7, 2008·BMC Immunology·Martin KorbHamid Bolouri

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