ArticleGenome biology2007
Combined analysis reveals a core set of cycling genes.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 2 of them syntheses that pooled it.
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Who cites it
26 citing papers in PubMed, 2 syntheses or guidelines pooled it, 44 citations in OpenAlex.
- Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics.Ecotoxicology (London, England) · 2011Pooled it
- Phase Coupled Meta-analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast.BMC genomics · 2009Pooled it
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- CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis.bioRxiv : the preprint server for biology · 2023Article
- The Human Cell Atlas.eLife · 2017Article
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- Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity.Current genetics · 2016Review
- Regulation of a transcription factor network by Cdk1 coordinates late cell cycle gene expression.The EMBO journal · 2014Article
- Identifying novel cell cycle proteins in Apicomplexa parasites through co-expression decision analysis.PloS one · 2014Article
- Review
- Bck2 acts through the MADS box protein Mcm1 to activate cell-cycle-regulated genes in budding yeast.PLoS genetics · 2013Article
- A novel method for cross-species gene expression analysis.BMC bioinformatics · 2013Article
- Mitotic exit and separation of mother and daughter cells.Genetics · 2012Review
- Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes.Nucleic acids research · 2012Article
- Studying and modelling dynamic biological processes using time-series gene expression data.Nature reviews. Genetics · 2012Review
- Coordination of cell growth and division by the ubiquitin-proteasome system.Seminars in cell & developmental biology · 2012Review
- Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein.Genes & development · 2011Article
- Cross species expression analysis of innate immune response.Journal of computational biology : a journal of computational molecular cell biology · 2010Article
- Large scale comparison of global gene expression patterns in human and mouse.Genome biology · 2010Article
- Circadian control of global gene expression patterns.Annual review of genetics · 2010Review
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGlobal transcript levels throughout the cell cycle have been characterized using microarrays in several species. Early analysis of these experiments focused on individual species. More recently, a number of studies have concluded that a surprisingly small number of genes conserved in two or more species are periodically transcribed in these species. Combining and comparing data from multiple species is challenging because of noise in expression data, the different synchronization and scoring methods used, and the need to determine an accurate set of homologs.
resultsTo solve these problems, we developed and applied a new algorithm to analyze expression data from multiple species simultaneously. Unlike previous studies, we find that more than 20% of cycling genes in budding yeast have cycling homologs in fission yeast and 5% to 7% of cycling genes in each of four species have cycling homologs in all other species. These conserved cycling genes display much stronger cell cycle characteristics in several complementary high throughput datasets. Essentiality analysis for yeast and human genes confirms these findings. Motif analysis indicates conservation in the corresponding regulatory mechanisms. Gene Ontology analysis and analysis of the genes in the conserved sets sheds light on the evolution of specific subfunctions within the cell cycle.
conclusionOur results indicate that the conservation in cyclic expression patterns is much greater than was previously thought. These genes are highly enriched for most cell cycle categories, and a large percentage of them are essential, supporting our claim that cross-species analysis can identify the core set of cycling genes.
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