SwissRegulon: web-based analysis tools for genome-wide regulatory sites
Project funded by own resources
Project title SwissRegulon: web-based analysis tools for genome-wide regulatory sites
Principal Investigator(s) van Nimwegen, Erik
Project Members Pachkov, Mikhail
Organisation / Research unit Departement Biozentrum / Bioinformatics (van Nimwegen)
Project Website http://swissregulon.unibas.ch/fcgi/sr
Project start 01.01.2008
Probable end 31.12.2021
Status Active
Abstract

Our group provides a number of online services and database associated with the gene regulatory networks through our SwissRegulon website. First of all, our group has developed a number of algorithms for the discovery of regulatory motifs and the genome-wide annotation of regulatory sites based on high-throughput data. For example, our PhyloGibbs algorithm integrates the search for over-represented sequence motifs with comparative genomic analysis of sequence conservation patterns within a rigorous Bayesian probabilistic frame work. In addition to distributing the PhyloGibbs source code, PhyloGibbs is also provided on a Web server that allows users to discover regulatory motifs in their own sequences. Similarly, MotEvo is a state-of-the-art algorithm for genome-wide transcription factor binding site prediction that is made available through SwissRegulon. In addition, we provide genome-wide annotation of regulatory sites for a large number of transcription factors across a range of model organisms including human, mouse, yeast, and E. coli both through a genome-browser and in downloadable form. Through a collaboration with the Omics Science Center at Riken, Yokohama, we also provide comprehensive genome-wide annotations of promoter regions in human and mouse. Finally, beyond annotation regulatory sites and regions on the genomes of model organisms, SwissRegulon now also provides automated tools for analyzing gene expression and ChIP-seq data-sets in terms of the predicted regulatory sites. In particular, MARA (Motif Activity Response Analysis) is a fully-automated web-service that takes gene expression or ChIP-seq data-sets as input and predicts the key transcription factors involved in the regulation, their sample dependent activities, and their genome-wide target genes. MARA allows users to reconstruct transcription regulatory networks for any model system of interest ab initio.

Websites for Further Information
SwissRegulon: http://www.swissregulon.unibas.ch/
MARA: http://www.mara.unibas.ch/
PhyloGibbs: http://www.phylogibbs.unibas.ch/

Financed by Other funds

Published results ()

  ID Autor(en) Titel ISSN / ISBN Erschienen in Art der Publikation
156672  Pachkov, M.; Erb, I.; Molina, N.; van Nimwegen, E.  SwissRegulon : a database of genome-wide annotations of regulatory sites  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
1166189  Arnold, Phil; Erb, Ionas; Pachkov, Mikhail; Molina, Nacho; van Nimwegen, Erik  MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences  1367-4803  Bioinformatics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
1471083  Pachkov, Mikhail; Balwierz, Piotr J.; Arnold, Phil; Ozonov, Evgeniy; van Nimwegen, Erik  SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
1445147  Arnold, Phil; Schöler, Anne; Pachkov, Mikhail; Balwierz, Piotr J; Jørgensen, Helle; Stadler, Michael B; van Nimwegen, Erik; Schübeler, Dirk  Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting  1088-9051  Genome research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2420414  Balwierz, Piotr J; Pachkov, Mikhail; Arnold, Phil; Gruber, Andreas J; Zavolan, Mihaela; van Nimwegen, Erik  ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs  1088-9051  Genome research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
   

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