SwissRegulon


23180783	SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. [PMID: 23180783] Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E. 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. Nucleic Acids Res. 2013:41(Database issue) \| 93 Citations (from Europe PMC, 2025-03-15)
17130146	SwissRegulon: a database of genome-wide annotations of regulatory sites. [PMID: 17130146] Pachkov M, Erb I, Molina N, van Nimwegen E. Abstract SwissRegulon (http://www.swissregulon.unibas.ch) is a database containing genome-wide annotations of regulatory sites in the intergenic regions of genomes. The regulatory site annotations are produced using a number of recently developed algorithms that operate on multiple alignments of orthologous intergenic regions from related genomes in combination with, whenever available, known sites from the literature, and ChIP-on-chip binding data. Currently SwissRegulon contains annotations for yeast and 17 prokaryotic genomes. The database provides information about the sequence, location, orientation, posterior probability and, whenever available, binding factor of each annotated site. To enable easy viewing of the regulatory site annotations in the context of other features annotated on the genomes, the sites are displayed using the GBrowse genome browser interface and can be queried based on any annotated genomic feature. The database can also be queried for regulons, i.e. sites bound by a common factor. Nucleic Acids Res. 2007:35(Database issue) \| 101 Citations (from Europe PMC, 2025-03-15)

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. [PMID: 23180783]

Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E.

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.

Nucleic Acids Res. 2013:41(Database issue) | 93 Citations (from Europe PMC, 2025-03-15)

SwissRegulon: a database of genome-wide annotations of regulatory sites. [PMID: 17130146]

Pachkov M, Erb I, Molina N, van Nimwegen E.

Abstract

SwissRegulon (http://www.swissregulon.unibas.ch) is a database containing genome-wide annotations of regulatory sites in the intergenic regions of genomes. The regulatory site annotations are produced using a number of recently developed algorithms that operate on multiple alignments of orthologous intergenic regions from related genomes in combination with, whenever available, known sites from the literature, and ChIP-on-chip binding data. Currently SwissRegulon contains annotations for yeast and 17 prokaryotic genomes. The database provides information about the sequence, location, orientation, posterior probability and, whenever available, binding factor of each annotated site. To enable easy viewing of the regulatory site annotations in the context of other features annotated on the genomes, the sites are displayed using the GBrowse genome browser interface and can be queried based on any annotated genomic feature. The database can also be queried for regulons, i.e. sites bound by a common factor.

Nucleic Acids Res. 2007:35(Database issue) | 101 Citations (from Europe PMC, 2025-03-15)

URL:	http://swissregulon.unibas.ch/fcgi/sr
Full name:	A Database of Genome-wide Annotations of Regulatory Sites
Description:	Swissregulon Database contains genome-wide annotations of regulatory sites, we currently have annotations for 17 prokaryotes and 3 eukaroytes in our collection
Year founded:	2007
Last update:	2006-12-06
Version:	v1.0
Accessibility:	Accessible
Country/Region:	Switzerland

Data type:	DNA Protein
Data object:	Animal Bacteria Fungi
Database category:	Gene genome and annotation
Major species:	Agrobacterium tumefaciens Bacillus subtilis Brucella suis Corynebacterium glutamicum Ehrlichia canis Homo sapiens Mus musculus Saccharomyces cerevisiae
Keywords:	regulatory sites

University/Institution:	University of Basel
Address:	Klingelbergstrasse 50/70,CH-4056 Basel,Switzerland
City:	Basel
Province/State:
Country/Region:	Switzerland
Contact name (PI/Team):	Erik van Nimwegen
Contact email (PI/Helpdesk):	erik.vannimwegen@unibas.ch

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