title: D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements.
abstract: BACKGROUND
  The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistical models for predicting potential transcription factor binding sites (TFBS). The rapidly increasing number of genome sequence data requires sophisticated computational approaches to manage and query experimental and predicted TFBS data in the context of other epigenetic factors and across different organisms.
  
  
  RESULTS
  We have developed D-Light, a novel client-server software package to store and query large amounts of TFBS data for any number of genomes. Users can add small-scale data to the server database and query them in a large scale, genome-wide promoter context. The client is implemented in Java and provides simple graphical user interfaces and data visualization. Here we also performed a statistical analysis showing what a user can expect for certain parameter settings and we illustrate the usage of D-Light with the help of a microarray data set.
  
  
  CONCLUSIONS
  D-Light is an easy to use software tool to integrate, store and query annotation data for promoters. A public D-Light server, the client and server software for local installation and the source code under GNU GPL license are available at http://biwww.che.sbg.ac.at/dlight.
authors.affiliation: Department of Molecular Biology, University of Salzburg, Hellbrunnerstr, 34, 5020 Salzburg, Austria.
authors.forename: Josef
authors.initials: J
authors.lastname: Laimer
authors.forename: Clemens J
authors.initials: CJ
authors.lastname: Zuzan
authors.forename: Tobias
authors.initials: T
authors.lastname: Ehrenberger
authors.forename: Monika
authors.initials: M
authors.lastname: Freudenberger
authors.forename: Simone
authors.initials: S
authors.lastname: Gschwandtner
authors.forename: Carina
authors.initials: C
authors.lastname: Lebherz
authors.forename: Peter
authors.initials: P
authors.lastname: Lackner
mesh_terms: D001665:Binding Sites; D003196:Computer Graphics; D016678:Genome; D011401:Promoter Regions, Genetic; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors