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Correlating overrepresented upstream motifs to gene expression a computational approach to regulatory element discovery in eukaryotes.doc

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Correlating overrepresented upstream motifs to gene expression a computational approach to regulatory element discovery in eukaryotes

BMC Bioinformatics BioMedCentral BMC M 20 e 02 t Bioinformatics, hodology article 3 Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes Michele Caselle1, Ferdinando Di Cunto2 and Paolo Provero*3,1 Address: 1Dipartimento di Fisica Teorica, Università di Torino, and INFN, Sezione di Torino, Torino, Italy, 2Dipartimento di Genetica, Biologia e Biochimica, Università di Torino, Torino, Italy and 3Dipartimento di Scienze e Tecnologie Avanzate, Università del Piemonte Orientale, Alessandria, Italy E-mail: Michele Caselle - caselle@to.infn.it; Ferdinando Di Cunto - ferdinando.dicunto@unito.it; Paolo Provero* - provero@to.infn.it *Corresponding author Published: 14 February 2002 Received: 13 December 2001 Accepted: 14 February 2002 BMC Bioinformatics 2002, 3:7 This article is available from: /1471-2105/3/7 ? 2002 Caselle et al; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any purpose, provided this notice is preserved along with the articles original URL. Abstract Background: Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. Results: The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA m