ArticleNucleic acids research2004
Conservation of adjacency as evidence of paralogous operons.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- The gene regulatory network ofFrontiers in microbiology · 2022Article
- OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data.PLoS computational biology · 2022Article
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- An analysis of the validity and utility of the proximon proposition.Functional & integrative genomics · 2016Article
- A functional and phylogenetic comparison of quorum sensing related genes in Brucella melitensis 16M.Journal of microbiology (Seoul, Korea) · 2014Article
- Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss?PloS one · 2014Article
- Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M.PloS one · 2014Article
- Global analysis of transcriptional regulators in Staphylococcus aureus.BMC genomics · 2013Article
- The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective.Nucleic acids research · 2012Article
- Constructing de novo biosynthetic pathways for chemical synthesis inside living cells.Biochemistry · 2011Review
- High accuracy operon prediction method based on STRING database scores.Nucleic acids research · 2010Article
- Relationship between operon preference and functional properties of persistent genes in bacterial genomes.BMC genomics · 2010Article
- Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.PLoS biology · 2009Article
- GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways.Nucleic acids research · 2008Article
- Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.Genome biology · 2008Article
- Operon prediction in Pyrococcus furiosus.Nucleic acids research · 2007Article
- Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes.PLoS genetics · 2006Article
- Bacterial regulatory networks are extremely flexible in evolution.Nucleic acids research · 2006Article
- The distinctive signatures of promoter regions and operon junctions across prokaryotes.Nucleic acids research · 2006Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Most of the analyses on the conservation of gene order are limited to orthologous genes. However, the organization of genes into operons might also result in the conservation of gene order of paralogous genes. Thus, we sought computational evidence that conservation of gene order of paralogous genes represents another level of conservation of genes in operons. We found that pairs of genes within experimentally characterized operons of Escherichia coli K12 and Bacillus subtilis tend to have more adjacently conserved paralogs than pairs of genes at transcription unit boundaries. The fraction of same strand gene pairs corresponding to conserved paralogs averages 0.07 with a maximum of 0.22 in Borrelia burgdorferi. The use of evidence from the conservation of adjacency of paralogous genes can improve the prediction of operons in E.coli K12 by approximately 0.27 over predictions using conservation of adjacency of orthologous genes alone.
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