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A multistep bioinformatic approach detects putative regulatory elements in gene promoters

BACKGROUND: Searching 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 identif...

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Detalles Bibliográficos
Autores principales: Bortoluzzi, Stefania, Coppe, Alessandro, Bisognin, Andrea, Pizzi, Cinzia, Danieli, Gian Antonio
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1173081/
https://www.ncbi.nlm.nih.gov/pubmed/15904489
http://dx.doi.org/10.1186/1471-2105-6-121
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author Bortoluzzi, Stefania
Coppe, Alessandro
Bisognin, Andrea
Pizzi, Cinzia
Danieli, Gian Antonio
author_facet Bortoluzzi, Stefania
Coppe, Alessandro
Bisognin, Andrea
Pizzi, Cinzia
Danieli, Gian Antonio
author_sort Bortoluzzi, Stefania
collection PubMed
description BACKGROUND: Searching 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. RESULTS: Novel 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. CONCLUSION: The approach described in this paper seems effective for identifying a tractable number of sequence motifs with putative regulatory role.
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spelling pubmed-11730812005-07-07 A multistep bioinformatic approach detects putative regulatory elements in gene promoters Bortoluzzi, Stefania Coppe, Alessandro Bisognin, Andrea Pizzi, Cinzia Danieli, Gian Antonio BMC Bioinformatics Research Article BACKGROUND: Searching 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. RESULTS: Novel 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. CONCLUSION: The approach described in this paper seems effective for identifying a tractable number of sequence motifs with putative regulatory role. BioMed Central 2005-05-18 /pmc/articles/PMC1173081/ /pubmed/15904489 http://dx.doi.org/10.1186/1471-2105-6-121 Text en Copyright © 2005 Bortoluzzi et al; licensee BioMed Central Ltd.
spellingShingle Research Article
Bortoluzzi, Stefania
Coppe, Alessandro
Bisognin, Andrea
Pizzi, Cinzia
Danieli, Gian Antonio
A multistep bioinformatic approach detects putative regulatory elements in gene promoters
title A multistep bioinformatic approach detects putative regulatory elements in gene promoters
title_full A multistep bioinformatic approach detects putative regulatory elements in gene promoters
title_fullStr A multistep bioinformatic approach detects putative regulatory elements in gene promoters
title_full_unstemmed A multistep bioinformatic approach detects putative regulatory elements in gene promoters
title_short A multistep bioinformatic approach detects putative regulatory elements in gene promoters
title_sort multistep bioinformatic approach detects putative regulatory elements in gene promoters
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1173081/
https://www.ncbi.nlm.nih.gov/pubmed/15904489
http://dx.doi.org/10.1186/1471-2105-6-121
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