1 Search Results for "Pesch, Robert"

Document
DOI: 10.4230/OASIcs.GCB.2012.69
ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes

Authors: Robert Pesch, Matthias Böck, and Ralf Zimmer

Published in: OASIcs, Volume 26, German Conference on Bioinformatics 2012

Abstract
Transcription factors (TFs) play a fundamental role in cellular regulation by binding to promoter regions of target genes (TGs) in order to control their gene expression. TF-TG networks are widely used as representations of regulatory mechanisms, e.g. for modeling the cellular response to input signals and perturbations. As the experimental identification of regulatory interactions is time consuming and expensive, one tries to use knowledge from related species when studying an organism of interest. Here, we present ConReg, an interactive web application to store regulatory relations for various species and to investigate their level of conservation in related species. Currently, ConReg contains data for eight model organisms. The regulatory relations stored in publicly available databases cover only a small fraction both of the actual interactions and also of the regulatory relations described in the scientific literature. Therefore, we included regulatory relations extracted from PubMed and PubMedCentral using sophisticated text-mining approaches and from binding site predictions into ConReg. We applied ConReg for the investigation of conserved regulatory motifs in D. melanogaster. From the 471 regulatory relations in REDfly our system was able to identify 66 confirmed conserved regulations in at least one vertebrate model organism (H. sapiens, M. musculus, R. norvegicus, D. rerio). The conserved network consists among others of the well studied motifs for eye-development and the pan-bilaterian kernel for heart specification, which are well-known examples for conserved regulatory relations between different organisms. ConReg is available at http://services.bio.ifi.lmu.de/ConReg/ and can be used to analyze and visualize regulatory networks and their conservation among eight model organisms. It also provides direct links to annotations including literature references to potentially conserved regulatory relations.
Cite as

Robert Pesch, Matthias Böck, and Ralf Zimmer. ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes. In German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, pp. 69-81, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

Copy BibTex To Clipboard

@InProceedings{pesch_et_al:OASIcs.GCB.2012.69,
  author =	{Pesch, Robert and B\"{o}ck, Matthias and Zimmer, Ralf},
  title =	{{ConReg: Analysis and Visualization of Conserved Regulatory Networks in Eukaryotes}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{69--81},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{B\"{o}cker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2012.69},
  URN =		{urn:nbn:de:0030-drops-37194},
  doi =		{10.4230/OASIcs.GCB.2012.69},
  annote =	{Keywords: web application, evolutionary biology, regulatory networks, text-mining}
}
  • Refine by Author
  • 1 Böck, Matthias
  • 1 Pesch, Robert
  • 1 Zimmer, Ralf

  • Refine by Classification

  • Refine by Keyword
  • 1 evolutionary biology
  • 1 regulatory networks
  • 1 text-mining
  • 1 web application

  • Refine by Type
  • 1 document

  • Refine by Publication Year
  • 1 2012

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2024 Schloss Dagstuhl – LZI GmbH Imprint Privacy Contact