Figure 3

Functional similarity networks. A, E. coli; B, S. cerevisiae; C, P. falciparum. From left to right, BP-score, CC-score, MF-score, and funSim matrices. Nodes represent individual proteins and edges represent a category GOscore or funSim of ≥ 0.95. Individual clusters in the functional similarity networks are highlighted in color to show functional category of proteins. For the BP-score networks (left panels), green nodes represent proteins involved in transcription (GO:0006350 and its children nodes), blue nodes represent proteins involved in transport (GO:0006810), purple nodes represent proteins involved in pathogenesis (GO:0009405) (for P. falciparum, Fig. 3C) or signaling (GO:0007165) (for E. coli and yeast, Fig 3A,B), and red nodes represent proteins involved in protein modification (GO:0043687). For the CC-score networks (the second panels from the left in Fig. 3), yellow nodes represent proteins localized in the membrane (GO:0016020), orange nodes represent proteins localized in the ribosome (GO:0005840), and blue nodes represent proteins localized in the cell wall (GO:0005618) (for E. coli) or in the nucleus (GO:0005634) (for malaria and yeast). For the MF-score networks (the second panels from the right), light green nodes represent proteins which bind ATP (GO:0005524), pink nodes represent proteins which bind rRNA (GO:0019843), light purple nodes represent proteins which bind ions (GO:0043167), and olive nodes represent proteins exhibiting transporter activity (GO:0005215). For the FunSim networks (the panels on the right), burgundy nodes represent proteins which bind ATP (GO:0005524), blue nodes represent proteins localized in the ribosome (GO:0005840), and light green nodes represent proteins exhibiting transmembrane receptor activity (GO:0004888).