Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization

Microarray analysis of gene expression patterns for thousands of human genes has led to the proposal that a large number of genes are expressed in a cell-cycle-specific manner. The identification of cyclically expressed genes was based on Affymetrix microarray analysis of gene expression after double-thymidine block synchronization. A statistical reanalysis of the original data leads to three principal findings. (i) Randomized data exhibit periodic patterns of similar or greater strength than the experimental data. This finding suggests that all apparent cyclicities in the expression measurements may arise from chance fluctuations. (ii) The presence of cyclicity and the timing of peak cyclicity in a given gene are not reproduced in two replicate experiments. This fact suggests there is an uncontrolled source of experimental variation that is stronger than the innate variation of gene expression in cells over time. (iii) The amplitude of peak expression in the second cycle is not consistently smaller than the corresponding amplitude in the first cycle. This finding places doubt on the assumption that the cells are actually synchronized. We propose that the microarray results do not support the proposal that there are numerous cell-cycle-specifically expressed genes in human cells.