Examples of communities found. a) A representation of a community in the A network at resolution parameter value log(λ) = 0, with nodes (proteins) coloured according to the partition of this community at log(λ) = 0.5. The colours are the same as for Figure 1 a), where this group of proteins has labels roughly in the range 0 - 500. Almost all of the nodes have some relationship to the ribosome. The proteins in the yellow community are mostly ribosomal subunits, those in the red community are mostly pre-cursors to and processors of the small ribosomal subunit, and those in the blue community have similar roles to those in the red community but for the large subunit. The shading of the links has no significance; its purpose is to ease visualisation. Black nodes are not located in one of the three largest communities discussed in the text. b) A representation of a community at log(λ) = 0.5, with nodes (proteins) coloured according to the partition of this community at log(λ) = 0.75. The proteins identified at the lower resolution almost all play some role in transcription initiation. At the higher resolution, more structure is revealed: the pink community consists mostly of proteins from the RNA polymerase II mediator complex and the green community mostly consists of proteins from the TFIID and SAGA complexes. c) The partition at a higher resolution (log(λ) = 1.6). The green community from b) has split into the SAGA complex (green) and the TFIID complex (orange). The names and descriptions of the proteins in these example communities are given in Additional File 2. The node positions for visualisation were computed in the same way as for Figure 1.