ArticleNucleic acids research2013
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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101 citing papers in PubMed, 169 citations in OpenAlex.
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- Systematic functional characterization of non-coding regulatory SNPs associated with central obesity.American journal of human genetics · 2025Article
- Recent advances in designing synthetic plant regulatory modules.Frontiers in plant science · 2025Review
- Identification of an ArgR-controlled promoter within the outermost region of the ISJournal of bacteriology · 2024Article
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- Neuronal transcription of autism gene PTCHD1 is regulated by a conserved downstream enhancer sequence.Scientific reports · 2023Article
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- Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2023Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of genomic regulatory elements is essential for understanding the dynamics of cellular processes. This task has been substantially facilitated by the availability of genome sequences for many species and high-throughput data of transcripts and transcription factor (TF) binding. However, rigorous computational methods are necessary to derive accurate genome-wide annotations of regulatory sites from such data. SwissRegulon (http://swissregulon.unibas.ch) is a database containing genome-wide annotations of regulatory motifs, promoters and TF binding sites (TFBSs) in promoter regions across model organisms. Its binding site predictions were obtained with rigorous Bayesian probabilistic methods that operate on orthologous regions from related genomes, and use explicit evolutionary models to assess the evidence of purifying selection on each site. New in the current version of SwissRegulon is a curated collection of 190 mammalian regulatory motifs associated with ∼340 TFs, and TFBS annotations across a curated set of ∼35 000 promoters in both human and mouse. Predictions of TFBSs for Saccharomyces cerevisiae have also been significantly extended and now cover 158 of yeast's ∼180 TFs. All data are accessible through both an easily navigable genome browser with search functions, and as flat files that can be downloaded for further analysis.
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