Fig. 2

Transcription factor rewiring for Module 51, Ribosomal Protein (RP) genes. Here we describe the meaning of this and several following graphs. The species tree is partitioned into two groups: M is the set of species in one branch (labeled “10” in Fig. 1) and M ^⋆ consists of the rest of the 23 species. In this and related figures, a dashed vertical line (or two) separates M from M ^⋆. For each of the 23 species on the horizontal axis, we plot two dots, each of which is an average of binding probabilities that a transcription factor binds to a gene. Here for example each red dot is the average of 57 (=3 transcription factors in the red team times 19 genes) binding probabilities for the species in question, i.e., averaging over the genes in G and the transcription factors in team T (red dots) or in team T ^⋆ (blue dots). The two dots for each species are connected with a solid line using the color of the upper dot. The first row in Table 1 reports on this case. Note that the box in the lower right specifies first the blue team T ^⋆ (which here consists of a single transcription factor, TBF1), then the red team T (which here consists of three transcription factors, namely RAP1 SFP1 and SFL1), and finally the number of genes in the block. When there are too many transcription factors to fit in the box, only a few are given, but full data is given in the Additional file 5: Supplementary material for this graph (and all related graphs) including the names of the 19 genes that are discussed here