title: Comment on and reply to "Analysis of variation of amplitudes in cell cycle gene expression" by Liu, Gaido and Wolfinger: on the analysis of gene expression during the normal, eukaryotic, cell cycle.
abstract: BACKGROUND
  The paper of Liu, Gaido and Wolfinger on gene expression during the division cycle of HeLa cells using the data of Whitfield et al. are discussed in order to see whether their analysis is related to gene expression during the division cycle.
  
  
  RESULTS
  The results of Liu, Gaido and Wolfinger demonstrate that different inhibition methods proposed to "synchronize" cells lead to different levels of gene expression. This result, in and of itself, should be taken as evidence that the original work of Whitfield et al. is flawed and should not be used to support the notion that the cells studied were synchronized or that the microarray analyses identify cell-cycle-regulated genes. Furthermore, the DNA content evidence presented by Whitfield et al. supports the proposal that the cells described as 'synchronized' are not synchronized. A comparison of the gene expression amplitudes from two different experiments indicates that the results are not reproducible.
  
  
  CONCLUSIONS
  It is concluded that the analysis of Liu, Gaido, and Wolfinger is problematic because their work assumes that the cells they analyze are or were synchronized. The very fact that different inhibition methods lead to different degrees of gene expression should be taken as additional evidence that the experiments should be viewed skeptically rather than accepted as an approach to understanding gene expression during the cell cycle.
authors.affiliation: Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-0620, USA. cooper@umich.edu
authors.forename: Stephen
authors.initials: S
authors.lastname: Cooper
mesh_terms: D002453:Cell Cycle / Q000187:drug effects / Q000235:genetics*; D018797:Cell Cycle Proteins / Q000235:genetics; D003627:Data Interpretation, Statistical; D005786:Gene Expression Regulation / Q000187:drug effects; D006367:HeLa Cells; D006801:Humans; D008954:Models, Biological; D015739:Nocodazole / Q000494:pharmacology; D009687:Nuclear Proteins / Q000235:genetics; D018809:Proliferating Cell Nuclear Antigen / Q000235:genetics; D015203:Reproducibility of Results; D013936:Thymidine
chemical_list: D018797:Cell Cycle Proteins; D009687:Nuclear Proteins; D018809:Proliferating Cell Nuclear Antigen; D015739:Nocodazole; D013936:Thymidine