Circular reasoning rather than cyclic expression.
Bottom Line: A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph.Genome Biol 2007, 8:R146.
A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146.
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Mentions: Despite claims to the contrary from Jensen et al., previous analyses of cell-cycle expression data resulted in opposing views regarding the conservation of expression between different species. While some investigators have concluded that this conservation is surprisingly low [4,14], others have determined that it is rather large. For example, Oliva et al.  found that more than 30% of top cycling genes in budding and fission yeast are cycling and conserved in both species, and Ota et al.  identified more than 15% of cycling human genes as cycling and conserved in plants and yeast. The major reason for this discrepancy seems to be the use of strict thresholding for determining whether a gene is cycling or not. Such an analysis on a species-by-species basis may lead to inconsistencies in cell-cycle assignments. Figure 2 of this Correspondence exemplifies this difficulty. While only expression of the human Mcm6 gene was determined to be cycling by Jensen et al. , as Figure 2 shows, its curated homologs in budding and fission yeast (which were annotated as non-cycling by Jensen et al.) actually display strong cyclic expression patterns. This is a general problem with cell-cycle analysis. As Figure 3 shows, while some orthologs of cycling budding-yeast genes may fall just below the fission-yeast threshold, they are still (at least weakly) cycling, significantly more than expected by chance, indicating that expression is conserved at a stronger rate than the rate determined by thresholding. To address these issues, we have developed a new method for combining expression data from multiple species . Using our method we concluded that cell-cycle expression is conserved at much higher rates than those claimed by Jensen et al. .