title: Identification of cis-regulatory elements in the mammalian genome: the cREMaG database.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Molecular Neuropharmacology, Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland. marpiech@if-pan.krakow.pl
authors.forename: Marcin
authors.initials: M
authors.lastname: Piechota
authors.forename: Michal
authors.initials: M
authors.lastname: Korostynski
authors.forename: Ryszard
authors.initials: R
authors.lastname: Przewlocki
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D016678:Genome / Q000235:genetics*; D006801:Humans; D020407:Internet; D011401:Promoter Regions, Genetic / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors
references.citation: BMC Bioinformatics. 2009 Jan 07;10:7
references.pmid: 19128472
references.citation: Genome Biol. 2007;8(6):R128
references.pmid: 17598886
references.citation: Genome Biol. 2005;6(8):R72
references.pmid: 16086854
references.citation: Biol Reprod. 2004 Aug;71(2):560-9
references.pmid: 15115731
references.citation: FASEB J. 2008 Aug;22(8):2872-9
references.pmid: 18424767
references.citation: BMC Bioinformatics. 2006 Aug 31;7:396
references.pmid: 16945132
references.citation: Mol Pharmacol. 2007 Apr;71(4):1148-58
references.pmid: 17234898
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W247-52
references.pmid: 19487240
references.citation: Bioinformatics. 2008 Jun 1;24(11):1325-31
references.pmid: 18426806
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D707-14
references.pmid: 18000006
references.citation: BMC Genomics. 2008 Apr 02;9:152
references.pmid: 18384671
references.citation: Bioinformatics. 2005 Aug 15;21(16):3439-40
references.pmid: 16082012
references.citation: BMC Bioinformatics. 2008 Nov 26;9:495
references.pmid: 19036135
references.citation: Cell. 1993 Dec 3;75(5):875-86
references.pmid: 8252624
references.citation: Science. 1986 Oct 3;234(4772):80-3
references.pmid: 3749894
references.citation: Nucleic Acids Res. 1982 May 11;10(9):2997-3011
references.pmid: 7048259
references.citation: Genome Biol. 2009;10(4):R40
references.pmid: 19374775
references.citation: BMC Genomics. 2006 Jun 13;7:146
references.pmid: 16772024
references.citation: Genome Biol. 2004;5(7):R48
references.pmid: 15239833
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W245-52
references.pmid: 17576675
references.citation: Genes Dev. 2008 Nov 1;22(21):2941-52
references.pmid: 18981473
references.citation: Psychopharmacol Bull. 2003 Summer;37(3):51-83
references.pmid: 14608240
references.citation: Oncogene. 2003 Apr 3;22(13):1955-64
references.pmid: 12673201
references.citation: Nat Rev Genet. 2004 Apr;5(4):276-87
references.pmid: 15131651
references.citation: Bioinformatics. 2005 Jul 1;21(13):2933-42
references.pmid: 15860560
references.citation: PLoS Genet. 2006 Apr;2(4):e54
references.pmid: 16683032
references.citation: Bioinformatics. 2006 Feb 15;22(4):430-7
references.pmid: 16332706
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D773-9
references.pmid: 18086701
references.citation: Bioinformatics. 2002 Aug;18(8):1135-6
references.pmid: 12176838
references.citation: Biochim Biophys Acta. 2008 Jun-Jul;1779(6-7):383-9
references.pmid: 18498781
references.citation: FASEB J. 2010 Jul;24(7):2427-35
references.pmid: 20223941
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6
references.pmid: 18006571
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D82-5
references.pmid: 16381980
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W393-6
references.pmid: 15980497
references.citation: Genome Res. 2007 Sep;17(9):1245-53
references.pmid: 17690206
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):374-8
references.pmid: 12520026
references.citation: Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5745-9
references.pmid: 18408151
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W238-44
references.pmid: 17517777
references.citation: Genome Biol. 2010;11(5):R48
references.pmid: 20459597
references.citation: J Mol Biol. 1987 Jul 20;196(2):261-82
references.pmid: 3656447
references.citation: Nat Neurosci. 2005 Jun;8(6):759-67
references.pmid: 15880109
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3576-9
references.pmid: 12824369
references.citation: DNA Res. 2006 Jun 30;13(3):123-34
references.pmid: 16980320
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W447-50
references.pmid: 15980509