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Combined analysis reveals a core set of cycling genes.

ABSTRACT: BACKGROUND: Global 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. RESULTS: To 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. CONCLUSION: Our 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.

SUBMITTER: Lu Y

PROVIDER: S-EPMC2323241 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

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Combined analysis reveals a core set of cycling genes.

Lu Yong Y Mahony Shaun S Benos Panayiotis V PV Rosenfeld Roni R Simon Itamar I Breeden Linda L LL Bar-Joseph Ziv Z

Genome biology 20070101 7

<h4>Background</h4>Global 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 synchronizat ...[more]

PMID: 17650318

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Project description:Environmental risk assessment relies heavily on the use of bioassays to assess the environmental impact of chemicals. Gene expression is gaining acceptance as a valuable mechanistic endpoint in bioassays and effect-based screening. Data analysis and its results however, are often complex and not directly applicable in risk assessment. Classifier analysis is a promising method to turn complex gene expression analysis results into answers suitable for risk assessment. We have assembled a large gene expression dataset assembled from multiple studies and experiments in the springtail Folsomia candida, with the aim of selecting a set of genes that can be trained to classify general toxic stress. By performing differential expression analysis prior to classification we were able to select a set of 135 genes which was enriched in stress related processes. This set was then used to classify two test sets comprised of chemical spiked soils, polluted soils and clean soils and compared to another, more traditional feature selection for classification. The gene set presented here outperformed the more traditionally selected gene set. This gene set has the potential to be used as a biomarker to test for adverse effects caused by chemicals in springtails to provide endpoints in environmental risk assessment. The data presented in our manuscript is part of a larger experiment which was performed in single, large loop design. Only the samples used in the study presented here are named while the other samples will remain unnamed. All the data can still be used for normalization after which the analysis presented in the manuscript can be replicated. A single channel, interwoven loop design was used to test animals exposed to a control and to 5 concentrations of cadmium and phenanthrene (cadmium concentrations are: cad_1 till cad_5: 5.8, 14.5, 28.9, 57.9 and 115.8 mg/Kg respectively and phenanthrene concentrations are: phe_1 till Phe_5: 0, 4.6, 11.4, 22.9, 45.8 and 91.6 mg/Kg soil respectively). Exposures lasted for 2 days and used 4 biological replicates per condition each containing 30 grams soil and 30 individuals.

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Combined analysis reveals a core set of cycling genes.

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Combined analysis reveals a core set of cycling genes.

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