FIGURE 4.

Comparative pattern analysis to uncover genes responding to opposing RA manipulations. (A) Genes were grouped into discretized expression patterns based on up-regulation (yellow), down-regulation (blue), or no change (gray) compared to the control sample at the same time point. The numbers below the patterns indicate the number of genes that show the corresponding expression pattern in RA vs. control or DEAB vs. control. Only 32 out of 81 theoretically possible (four time points, 3*3*3*3 = 81) dynamic patterns were exhibited by at least one gene and are included in the figure. (B) COMPACT matrix comparing gene expression changes due to RA and DEAB relative to control. The subset of 32 × 32 patterns with non-zero number of genes in either perturbation group are shown. The gene counts were grouped within related patterns based on the time of initial up- or down-regulation. Supplementary Data 1 contains a version of the COMPACT matrix shown with the gene identifiers corresponding to the counts. The different quadrants are labeled a to d. (C) Dynamic expression patterns of genes showing opposite changes in response to RA and DEAB treatments (quadrant b).