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: https://swissregulon.unibas.ch
ISMARA: https://ismara.unibas.ch
REALPHY: https://realphy.unibas.ch
RECOPHY: https://recophy.unibas.ch
CREMA: https://crema.unibas.ch
CRUNCH: https://crunch.unibas.ch
PhyloGibbs: https://phylogibbs.unibas.ch