Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods. Export

@article{citeulike:682603, abstract = {Microarray analysis of gene expression during the yeast division cycle has led to the proposal that a significant number of genes in Saccharomyces cerevisiae are expressed in a cell-cycle-specific manner. Four different methods of synchronization were used for cell-cycle analysis. Randomized data exhibit periodic patterns of lesser strength than the experimental data. Thus the cyclicities in the expression measurements in the four experiments presented do not arise from chance fluctuations or noise in the data. However, when the degree of cyclicity for genes in different experiments are compared, a large degree of non-reproducibility is found. Re-examining the phase timing of peak expression, we find that three of the experiments (those using alpha-factor, CDC28 and CDC15 synchronization) show consistent patterns of phasing, but the elutriation synchrony results demonstrate a different pattern from the other arrest-release synchronization methods. Specific genes can show a wide range of cyclical behavior between different experiments; a gene with high cyclicity in one experiment can show essentially no cyclicity in another experiment. The elutriation experiment, possibly being the least perturbing of the four synchronization methods, may give the most accurate characterization of the state of gene expression during the normal, unperturbed cell cycle. Under this alternative explanation, the observed cyclicities in the other three experiments are a stress response to synchronization, and may not reproduce in unperturbed cells.}, address = {Department of Statistics, University of Michigan, Ann Arbor, MI 48109-1285, USA. kshedden@umich.edu}, author = {Shedden, K. and Cooper, S.}, citeulike-article-id = {682603}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkf414}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/30/13/2920}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/12087178}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=12087178}, day = {1}, doi = {10.1093/nar/gkf414}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {dmbi-gem-time-series}, month = {July}, number = {13}, pages = {2920--2929}, posted-at = {2008-02-25 19:48:37}, priority = {2}, title = {Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods.}, url = {http://dx.doi.org/10.1093/nar/gkf414}, volume = {30}, year = {2002} }

TY - JOUR ID - citeulike:682603 L3 - citeulike-article-id:682603 N2 - Microarray analysis of gene expression during the yeast division cycle has led to the proposal that a significant number of genes in Saccharomyces cerevisiae are expressed in a cell-cycle-specific manner. Four different methods of synchronization were used for cell-cycle analysis. Randomized data exhibit periodic patterns of lesser strength than the experimental data. Thus the cyclicities in the expression measurements in the four experiments presented do not arise from chance fluctuations or noise in the data. However, when the degree of cyclicity for genes in different experiments are compared, a large degree of non-reproducibility is found. Re-examining the phase timing of peak expression, we find that three of the experiments (those using alpha-factor, CDC28 and CDC15 synchronization) show consistent patterns of phasing, but the elutriation synchrony results demonstrate a different pattern from the other arrest-release synchronization methods. Specific genes can show a wide range of cyclical behavior between different experiments; a gene with high cyclicity in one experiment can show essentially no cyclicity in another experiment. The elutriation experiment, possibly being the least perturbing of the four synchronization methods, may give the most accurate characterization of the state of gene expression during the normal, unperturbed cell cycle. Under this alternative explanation, the observed cyclicities in the other three experiments are a stress response to synchronization, and may not reproduce in unperturbed cells. IS - 13 JF - Nucleic Acids Res SN - 1362-4962 AD - Department of Statistics, University of Michigan, Ann Arbor, MI 48109-1285, USA. kshedden@umich.edu EP - 2929 TI - Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods. VL - 30 SP - 2920 KW - dmbi-gem-time-series AU - Shedden, K AU - Cooper, S PY - 2002/07/01/ UR - http://dx.doi.org/10.1093/nar/gkf414 ER -