A distance difference matrix approach to identifying transcription factors that regulate differential gene expression

We introduce a method that considers target genes of a transcription factor, and searches for transcription factor binding sites (TFBSs) of secondary factors responsible for differential responses among these targets. Based on the distance difference matrix concept, the method simultaneously integra...

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Detalles Bibliográficos
Autores principales: De Bleser, Pieter, Hooghe, Bart, Vlieghe, Dominique, van Roy, Frans
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929144/
https://www.ncbi.nlm.nih.gov/pubmed/17504544
http://dx.doi.org/10.1186/gb-2007-8-5-r83
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author De Bleser, Pieter
Hooghe, Bart
Vlieghe, Dominique
van Roy, Frans
author_facet De Bleser, Pieter
Hooghe, Bart
Vlieghe, Dominique
van Roy, Frans
author_sort De Bleser, Pieter
collection PubMed
description We introduce a method that considers target genes of a transcription factor, and searches for transcription factor binding sites (TFBSs) of secondary factors responsible for differential responses among these targets. Based on the distance difference matrix concept, the method simultaneously integrates statistical overrepresentation and co-occurrence of TFBSs. Our approach is validated on datasets of differentially regulated human genes and is shown to be highly effective in detecting TFBSs responsible for the observed differential gene expression.
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spelling pubmed-19291442007-07-21 A distance difference matrix approach to identifying transcription factors that regulate differential gene expression De Bleser, Pieter Hooghe, Bart Vlieghe, Dominique van Roy, Frans Genome Biol Method We introduce a method that considers target genes of a transcription factor, and searches for transcription factor binding sites (TFBSs) of secondary factors responsible for differential responses among these targets. Based on the distance difference matrix concept, the method simultaneously integrates statistical overrepresentation and co-occurrence of TFBSs. Our approach is validated on datasets of differentially regulated human genes and is shown to be highly effective in detecting TFBSs responsible for the observed differential gene expression. BioMed Central 2007 2007-05-16 /pmc/articles/PMC1929144/ /pubmed/17504544 http://dx.doi.org/10.1186/gb-2007-8-5-r83 Text en Copyright © 2007 De Bleser et al.; licensee BioMed Central Ltd. http://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) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
De Bleser, Pieter
Hooghe, Bart
Vlieghe, Dominique
van Roy, Frans
A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
title A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
title_full A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
title_fullStr A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
title_full_unstemmed A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
title_short A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
title_sort distance difference matrix approach to identifying transcription factors that regulate differential gene expression
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929144/
https://www.ncbi.nlm.nih.gov/pubmed/17504544
http://dx.doi.org/10.1186/gb-2007-8-5-r83
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