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PMID: 11071941 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Predicting regulons and their cis-regulatory motifs by comparative genomics.

Nucleic acids research ·Vol. 28 ·No. 22 ·2000-11-15 ·Pages 4523-30

Manson McGuire A, Church GM

Abstract

We have combined and compared three techniques for predicting functional interactions based on comparative genomics (methods based on conserved operons, protein fusions and correlated evolution) and optimized these methods to predict coregulated sets of genes in 24 complete genomes, including Saccharomyces cerevisiae, Caenorhabditis elegans and 22 prokaryotes. The method based on conserved operons was the most useful for this purpose. Upstream regions of the genes comprising these predicted regulons were then used to search for regulatory motifs in 22 prokaryotic genomes using the motif-discovery program AlignACE. Many significant upstream motifs, including five known Escherichia coli regulatory motifs, were identified in this manner. The presence of a significant regulatory motif was used to refine the members of the predicted regulons to generate a final set of predicted regulons that share significant regulatory elements.

MeSH Terms
Animals Base Sequence Caenorhabditis elegans/genetics,metabolism Computational Biology Databases, Factual Escherichia coli/genetics,metabolism Genes/genetics Genome Phylogeny Prokaryotic Cells/metabolism Regulatory Sequences, Nucleic Acid/genetics Regulon/genetics Saccharomyces cerevisiae/genetics,metabolism Sequence Alignment
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Manson McGuire A
Department of Genetics, Warren Alpert Building, Room 513, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
Church G M
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/28.22.4523
Published
2000-11-15
Pages
4523-30
Language
English
Region
England
NLM ID
0411011
PMCID
PMC113887
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/28.22.4523 PMC Full Text View journal details
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