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

Titel in Übersetzung: 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

Publikation: Beitrag in FachzeitschriftArtikel

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.

Titel in ÜbersetzungD-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements
OriginalspracheEnglisch
Aufsatznummer140
Seiten (von - bis)1-8
FachzeitschriftBMC Bioinformatics
Jahrgang14
DOIs
PublikationsstatusVeröffentlicht - 24 Apr 2013

Systematik der Wissenschaftszweige 2012

  • 106 Biologie
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