Figure 3

K-Means clustering analysis of Tat-induced genes. The temporal differential gene expression in Tat cells was compared to respective control samples and analyzed using the k-means clustering algorithm. The coordinated expression profiles are representative of the 32 chips analyzed (16 eTat and 16 pCep4). The y-axis represents the log scale of the normalized intensity of the genes shown (data was normalized against the corresponding control samples). The x-axis corresponds to the various cell cycle phases: 1) M phase, 2) early G₁, 3) middle G₁, 4) late G₁, 5) G₁/S, 6) early S, 7) late S, and 8) G₂. Fifteen clusters were found based on the parameters used [see Additional File 7] and three are shown in 3A-C. Figure 3A shows altered genes at the G1/S for cathepsins, and various cellular receptors, while Figure 3B shows a close-up of apoptotic regulated genes, signal transduction and transcription factors. Figure 3C shows genes that dramatically oscillate at every stages of cell cycle in Tat expressing cells, including ribosome and actin/cytoskeleton genes.