Transcriptome-interactome correlation maps. a-f, We calculated the protein interaction density (PID) for each square in the matrix as the ratio of interaction pairs assigned to the square (IP)over the total number of protein pairs possibly formed by combinations of the genes in the square (PP). PIDs are represented in the map by a color system, as indicated in the scale on the left side of a,c,e. Control maps can be generated by the same approach from randomized protein pairs (a,c,e, right side). The average PIDs from all intracluster squares (in the diagonal) and inter-cluster squares (outside the diagonal) can be calculated from the correlation maps (b,d,f). The unit of PID in each panel is 'interactionpairs/100,000 ORF pairs'. We constructed transcriptome-interactome correlation maps using cell-cycle expression-profiling clusters and protein interaction data from the literature (a,b), from genome-wide yeast two hybrid screens (c,d) or from the combination of both (e,f).

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