SwissRegulon

SwissRegulon annotates regulatory elements genome-wide to identify regulatory motifs, promoters, and transcription factor binding sites using Bayesian probabilistic inference and explicit evolutionary models.

Key Features:

• Organism coverage: Annotations for 17 prokaryotic organisms and three eukaryotic organisms.
• Regulatory element types: Genome-wide annotations of regulatory motifs, promoters, and transcription factor binding sites (TFBSs) within promoter regions.
• Bayesian inference: Predictions derived using Bayesian probabilistic methods that leverage orthologous genomic regions from related species.
• Evolutionary modeling: Incorporates explicit evolutionary models to evaluate evidence of purifying selection on each site.
• Mammalian motif collection: A curated set of 190 mammalian regulatory motifs linked with approximately 340 transcription factors (TFs).
• Human and mouse promoters: TFBS annotations across a curated set of around 35,000 promoters for both human and mouse genomes.
• Saccharomyces cerevisiae coverage: Predictions covering 158 out of roughly 180 yeast transcription factors (TFs).

Scientific Applications:

• Gene regulation studies: Identification of regulatory motifs and TFBSs to support analyses of gene regulation and regulatory network reconstruction.
• Comparative genomics: Use of orthologous-region-based annotations for cross-species comparisons of regulatory element conservation.
• Evolutionary analysis: Evaluation of purifying selection on candidate regulatory sites to infer functional constraint.
• Mammalian transcriptional studies: Mapping motifs to ~340 TFs and promoter annotations for human and mouse to study mammalian regulatory programs.
• Yeast functional genomics: Exploitation of predictions covering 158 S. cerevisiae TFs for yeast regulatory and functional analyses.

Methodology:

Predictions are produced using Bayesian probabilistic methods that leverage orthologous genomic regions from related species and employ explicit evolutionary models to assess evidence of purifying selection at each site.