ABSTRACT: In order to test the idea that the cell is an attractor and to examine in detail the connectivity relationships among genes, it was essential to have a very reproducible and precise biological system. Oscillations in respiratory activity in budding yeast and other organisms have been known for many years. This benchmark oscillation is now shown to be a global manifestation of a genome wide oscillation in transcription. Using Affymetrix S98 chips, the patterns of gene expression were followed by sampling at 4-minute intervals through three cycles of the DO oscillation. Phase assignments were made based on the dissolved oxygen cycle. Two different cultures were sampled and a total of 68 RNA samples were prepared. Choices of samples for microarray analysis were based on RNA quality, consistent with having a complete set of 32 samples chosen to represent three cycles of the DO oscillation. Ten were chosen from the first experiment and 22 from the second experiment. Analysis using singular value decomposition recognizes a small difference in cycle time between the two experiments. Strictly speaking, there are no replicates. The time of maximum gene expression in the cycle was determined by phase grouping and averaging gene expression in the three replicates, assigning the phase of maximum expression to each transcript then examining how well this assignment is reproduced through the three cycles. We found that 5329 expressed genes were present in at least one sample and used them in our analysis. The correct order is GSM48136, GSM48137, GSM48138, GSM48139, GSM48140, GSM48131, GSM48132, GSM48133, GSM48134, GSM48135, GSM48149, GSM48150, GSM48141, GSM48151, GSM48142, GSM48143, GSM48144, GSM48145, GSM48146, GSM48147, GSM48148, GSM48160, GSM48161, GSM48162, GSM48157, GSM48158, GSM48152, GSM48159, GSM48153, GSM48154, GSM48155, GSM48156 Keywords: time-course
