D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements

Josef Laimer, Clemens J Zuzan, Tobias Ehrenberger, Monika Freudenberger, Simone Gschwandtner, Carina Lebherz, Peter Lackner

Research output: Contribution to journalArticle

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.

Translated title of the contributionD-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements
Original languageEnglish
Article number140
Pages (from-to)1-8
JournalBMC Bioinformatics
Volume14
DOIs
Publication statusPublished - 24 Apr 2013

Fields of Science and Technology Classification 2012

  • 106 Biology
  • 102 Computer Sciences

Keywords

  • Binding Sites
  • Computer Graphics
  • Genome
  • Promoter Regions, Genetic
  • Software
  • Transcription Factors/metabolism

Cite this