Supplement Text S1 Discovering Biological Progression underlying Microarray Samples

1. Sample Progression Discovery (SPD) results on cell cycle time series In cell cycle time series data, the correct order of the samples during the progression of cell cycle was known but not used in SPD. Our goal was to test whether SPD could recover the progression among the samples, and identify genes that reflect the progression. We applied SPD to only samples in one cell cycle, because we did not want SPD to make inference based on the cyclic behavior of cell cycle regulated genes.