Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.

<h4>Background</h4>A 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...

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Autores principales:	Marcin Piechota, Michal Korostynski, Ryszard Przewlocki
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b35238f2ecb94c339654317bdf5e32fb
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spelling	oai:doaj.org-article:b35238f2ecb94c339654317bdf5e32fb2021-11-18T06:35:34ZIdentification of cis-regulatory elements in the mammalian genome: the cREMaG database.1932-620310.1371/journal.pone.0012465https://doaj.org/article/b35238f2ecb94c339654317bdf5e32fb2010-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20824209/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>A 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.<h4>Methodology</h4>We 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.<h4>Conclusions</h4>Using 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.Marcin PiechotaMichal KorostynskiRyszard PrzewlockiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 8, p e12465 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Marcin Piechota Michal Korostynski Ryszard Przewlocki Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.
description	<h4>Background</h4>A 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.<h4>Methodology</h4>We 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.<h4>Conclusions</h4>Using 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.
format	article
author	Marcin Piechota Michal Korostynski Ryszard Przewlocki
author_facet	Marcin Piechota Michal Korostynski Ryszard Przewlocki
author_sort	Marcin Piechota
title	Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.
title_short	Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.
title_full	Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.
title_fullStr	Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.
title_full_unstemmed	Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.
title_sort	identification of cis-regulatory elements in the mammalian genome: the cremag database.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/b35238f2ecb94c339654317bdf5e32fb
work_keys_str_mv	AT marcinpiechota identificationofcisregulatoryelementsinthemammaliangenomethecremagdatabase AT michalkorostynski identificationofcisregulatoryelementsinthemammaliangenomethecremagdatabase AT ryszardprzewlocki identificationofcisregulatoryelementsinthemammaliangenomethecremagdatabase
_version_	1718424438018408448

Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.

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