ArticleBMC bioinformatics2002
Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.
Article in BMC bioinformatics, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- In silico analysis of promoter regions and regulatory elements (motifs and CpG islands) of the genes encoding for alcohol production in Saccharomyces cerevisiaea S288C and Schizosaccharomyces pombe 972h.Journal, genetic engineering & biotechnology · 2021Article
- Identification of Structural Elements of the Lysine Specific Demethylase 2B CxxC Domain Associated with Replicative Senescence Bypass in Primary Mouse Cells.The protein journal · 2020Article
- Motif discovery and transcription factor binding sites before and after the next-generation sequencing era.Briefings in bioinformatics · 2013Article
- COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.Nucleic acids research · 2013Article
- VIP1 response elements mediate mitogen-activated protein kinase 3-induced stress gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum.BMC genomics · 2009Article
- An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis.BMC systems biology · 2008Article
- Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.BMC structural biology · 2007Article
- Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors.BMC genomics · 2007Article
- Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions.BMC bioinformatics · 2007Article
- The identification of functional motifs in temporal gene expression analysis.Evolutionary bioinformatics online · 2007Article
- A survey of motif discovery methods in an integrated framework.Biology direct · 2006Article
- Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species.Annals of botany · 2005Article
- A multistep bioinformatic approach detects putative regulatory elements in gene promoters.BMC bioinformatics · 2005Article
- Ab initio identification of putative human transcription factor binding sites by comparative genomics.BMC bioinformatics · 2005Article
- Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs.BMC bioinformatics · 2004Article
- A nonlinear discrete dynamical model for transcriptional regulation: construction and properties.Biophysical journal · 2004Article
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3 authors.
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Abstract
backgroundGene 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.
resultsThe method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined.
conclusionsWe have described and successfully tested a simple computational method to identify upstream motifs relevant to gene regulation in eukaryotes by studying the statistical correlation between overepresented upstream motifs and gene expression levels.
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