Abstract
BackgroundA growing number of gene expression-profiling datasets provides a reliable source of information about gene co-expression. In silico analyses of the properties shared among the promoters of co-expressed genes facilitates the identification of transcription factors (TFs) involved in the co-regulation of those genes. Our previous experience with microarray data led to the development of a database suitable for the examination of regulatory motifs in the promoters of co-expressed genes.MethodologyWe introduce the cREMaG (cis-Regulatory Elements in the Mammalian Genome) system designed for in silico studies of the promoter properties of co-regulated mammalian genes. The cREMaG system offers an analysis of data obtained from human, mouse, rat, bovine and canine gene expression-profiling studies. More than eight analysis parameters can be utilized in user-defined combinations. The selection of alternative transcription start sites and information about CpG islands are also available.ConclusionsUsing the cREMaG system, we successfully identified TFs mediating transcriptional responses in reference gene sets. The cREMaG system facilitates in silico studies of mammalian transcriptional gene regulation. The resource is freely available at http://www.cremag.org.
Highlights
It is estimated that more than 5% of the mammalian genome encodes functional information, including regions involved in the regulation of gene expression, whereas only 1.5% of the mammalian genome contains protein-coding information [1]
The cREMaG system facilitates in silico studies of mammalian transcriptional gene regulation
If the co-regulated genes share regulation pathways, their promoter regions are likely to share common properties [3]. The analysis of these common properties could allow for the identification of factors responsible for the regulation of the expression of particular sets of genes [4]. Such analyses include the identification of overrepresented transcription factor binding sites (TFBSs), regulatory modules or CpG islands
Summary
It is estimated that more than 5% of the mammalian genome encodes functional information, including regions involved in the regulation of gene expression, whereas only 1.5% of the mammalian genome contains protein-coding information [1]. The analysis of these common properties could allow for the identification of factors responsible for the regulation of the expression of particular sets of genes [4]. Such analyses include the identification of overrepresented transcription factor binding sites (TFBSs), regulatory modules or CpG islands. This approach provides novel insights into the molecular mechanisms controlling the process of gene transcription. To develop a core promoter background dataset, sequences containing the region 200 bp upstream of the gene start position for every gene in a genome were retrieved and concatenated. The frequencies at all thresholds were stored in a set of TFBS frequency tables
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