ArticleBMC bioinformatics2005
A multistep bioinformatic approach detects putative regulatory elements in gene promoters.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- IQGAP3 May Serve as a Promising Biomarker in Clear Cell Renal Cell Carcinoma.International journal of general medicine · 2021Article
- Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets.Genome research · 2012Article
- Transcriptional control of the human glucocorticoid receptor: identification and analysis of alternative promoter regions.Human genetics · 2011Article
- Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays.BMC bioinformatics · 2009Article
- New scoring schema for finding motifs in DNA Sequences.BMC bioinformatics · 2009Article
- Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.Nucleic acids research · 2009Article
- Computational methods to dissect cis-regulatory transcriptional networks.Journal of biosciences · 2007Review
- Improved benchmarks for computational motif discovery.BMC bioinformatics · 2007Article
- Comparative analysis of regulatory motif discovery tools for transcription factor binding sites.Genomics, proteomics & bioinformatics · 2007Article
- Mapping of transcription start sites of human retina expressed genes.BMC genomics · 2007Article
- Detecting seeded motifs in DNA sequences.Nucleic acids research · 2005Article
- Immunoregulatory Enzymes.Acta naturaeArticle
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSearching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge for definition of a sheltered search space and of appropriate search parameters, in order to develop a method for identification of a tractable number of sequence motifs.
resultsNovel software (COOP) was developed for extraction of sequence motifs, based on clustering of exact or approximate patterns according to the frequency of their overlapping occurrences. Genomic sequences of 1 Kb upstream of 91 genes differentially expressed and/or encoding proteins with relevant function in adult human retina were analyzed. Methodology and results were tested by analysing 1,000 groups of putatively unrelated sequences, randomly selected among 17,156 human gene promoters. When applied to a sample of human promoters, the method identified 279 putative motifs frequently occurring in retina promoters sequences. Most of them are localized in the proximal portion of promoters, less variable in central region than in lateral regions and similar to known regulatory sequences. COOP software and reference manual are freely available upon request to the Authors.
conclusionThe approach described in this paper seems effective for identifying a tractable number of sequence motifs with putative regulatory role.
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