title: EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression.
abstract: BACKGROUND
  Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome biology is to map protein-DNA interaction networks of all regulatory regions in a genome of interest. Both transcription factor -and gene-centered methods can be used to systematically identify such interactions. We use high-throughput yeast one-hybrid assays as a gene-centered method to identify protein-DNA interactions between regulatory sequences (e.g. gene promoters) and transcription factors in the nematode Caenorhabditis elegans. We have already mapped several hundred protein-DNA interactions and analyzed the transcriptional consequences of some by examining differential gene expression of targets in the presence or absence of an upstream regulator. The rapidly increasing amount of protein-DNA interaction data at a genome scale requires a database that facilitates efficient data storage, retrieval and integration.
  
  
  METHODS
  Here, we report the implementation of a C. elegans differential gene expression database (EDGEdb). This database enables the storage and retrieval of protein-DNA interactions and other data that relate to differential gene expression. Specifically, EDGEdb contains: i) sequence information of regulatory elements, including gene promoters, ii) sequence information of all 934 predicted transcription factors, their DNA binding domains, and, where available, their dimerization partners and consensus DNA binding sites, iii) protein-DNA interactions between regulatory elements and transcription factors, and iv) expression patterns conferred by regulatory elements, and how such patterns are affected by interacting transcription factors.
  
  
  CONCLUSIONS
  EDGEdb provides a protein-DNA -and protein-protein interaction resource for C. elegans transcription factors and a framework for similar databases for other organisms. The database is available at http://edgedb.umassmed.edu.
authors.affiliation: Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA. inmaculada.barrasa@umassmed.edu <inmaculada.barrasa@umassmed.edu>
authors.forename: M Inmaculada
authors.initials: MI
authors.lastname: Barrasa
authors.forename: Philippe
authors.initials: P
authors.lastname: Vaglio
authors.forename: Fabien
authors.initials: F
authors.lastname: Cavasino
authors.forename: Laurent
authors.initials: L
authors.lastname: Jacotot
authors.forename: Albertha J M
authors.initials: AJ
authors.lastname: Walhout
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012045:Regulatory Sequences, Nucleic Acid; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors