Genes that change significantly in all pairwise comparisons define the four regulatory patterns. Genes whose expression changed significantly in all pairwise comparisons (Additional File 4 Table S3) are organized in a graph according to their level of coexpression (grey lines connecting nodes; edge width is representative of the extent of coexpression) and similar cellular localization of the respective proteins (grey dashed lines). Note that for this particular set of genes, there are no known PPIs. The changes in the color-coded expression values of these genes (see color gradient on the right) across the four pairwise comparisons define the patterns A to D. The terms Hsp90act, Hsp90rep, p23act and p23rep refer to the hypothesized gene regulatory activities of Hsp90 and p23 as direct or indirect activators or repressors. Some of the cellular functions (GO terms) for the same set of genes are indicated at the bottom.