Figure 3

Specificity and sensitivity of PCM ranks. Each gene is plotted as a 2-dimensional point where the x-coordinate is its PCM rank and the y-coordinate is its Marguerat et al. rank. Genes with higher phase consistency are marked with darker points. Clearly there are many more darker points above the diagonal (y = x) line, suggesting that genes with consistent phases across experiments get higher ranks (i.e. ranked closer to the top) by PCM than Marguerat et al. The sparse upper left quadrant of the plot shows that if genes did not receive a high rank by Marguerat et al., due to their poor Periodicity and Expression scores, then they did not get high a PCM rank either. However, many genes in the lower right quadrant received a high score from Marguerat et al. on the basis of good Periodicity and expression scores, but a low PCM score on the basis of poor phase consistency.