ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

We present ModuleMiner, a novel algorithm for computationally detecting cis-regulatory modules (CRMs) in a set of co-expressed genes. ModuleMiner outperforms other methods for CRM detection on benchmark data, and successfully detects CRMs in tissue-specific microarray clusters and in embryonic devel...

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Detalles Bibliográficos
Autores principales: Van Loo, Peter, Aerts, Stein, Thienpont, Bernard, De Moor, Bart, Moreau, Yves, Marynen, Peter
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643937/
https://www.ncbi.nlm.nih.gov/pubmed/18394174
http://dx.doi.org/10.1186/gb-2008-9-4-r66
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author Van Loo, Peter
Aerts, Stein
Thienpont, Bernard
De Moor, Bart
Moreau, Yves
Marynen, Peter
author_facet Van Loo, Peter
Aerts, Stein
Thienpont, Bernard
De Moor, Bart
Moreau, Yves
Marynen, Peter
author_sort Van Loo, Peter
collection PubMed
description We present ModuleMiner, a novel algorithm for computationally detecting cis-regulatory modules (CRMs) in a set of co-expressed genes. ModuleMiner outperforms other methods for CRM detection on benchmark data, and successfully detects CRMs in tissue-specific microarray clusters and in embryonic development gene sets. Interestingly, CRM predictions for differentiated tissues exhibit strong enrichment close to the transcription start site, whereas CRM predictions for embryonic development gene sets are depleted in this region.
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spelling pubmed-26439372009-02-17 ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Van Loo, Peter Aerts, Stein Thienpont, Bernard De Moor, Bart Moreau, Yves Marynen, Peter Genome Biol Method We present ModuleMiner, a novel algorithm for computationally detecting cis-regulatory modules (CRMs) in a set of co-expressed genes. ModuleMiner outperforms other methods for CRM detection on benchmark data, and successfully detects CRMs in tissue-specific microarray clusters and in embryonic development gene sets. Interestingly, CRM predictions for differentiated tissues exhibit strong enrichment close to the transcription start site, whereas CRM predictions for embryonic development gene sets are depleted in this region. BioMed Central 2008-04-07 /pmc/articles/PMC2643937/ /pubmed/18394174 http://dx.doi.org/10.1186/gb-2008-9-4-r66 Text en Copyright © 2008 Van Loo et al.; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Van Loo, Peter
Aerts, Stein
Thienpont, Bernard
De Moor, Bart
Moreau, Yves
Marynen, Peter
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
title ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
title_full ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
title_fullStr ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
title_full_unstemmed ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
title_short ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
title_sort moduleminer - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643937/
https://www.ncbi.nlm.nih.gov/pubmed/18394174
http://dx.doi.org/10.1186/gb-2008-9-4-r66
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