Proteins clustered by their interaction profiles. BD fused proteins (y-axis) and AD fused proteins (x-axis) were independently clustered according to the similarities of their interaction profiles using a hierarchical clustering algorithm (see Materials and methods). An interaction between a BD and AD protein is indicated by a small colored square. The squares are colored according to the level of two-hybrid reporter activity, which is the sum of LEU2 (0-3) and lacZ (0-5) scores, where higher scores indicate more reporter activity (1, yellow; 5+, red). The cluster circled in blue (center) corresponds to interactions involving SkpA, SkpB and SkpC BD fusions, which are mapped in Figure 4. Maps of other clusters (circled in green) are shown in Additional data file 7. The large cluster at upper left is due primarily to AD proteins that interact with many different BD proteins. A larger version of the figure with the gene names indicated in the axes is in Additional data file 8.