Figure 3

Conserved network elements. (a) Hub proteins can be categorized into single-interface and multi-interface hubs based on the number of physical interaction surfaces available on the hub protein [56]. (b) Network motifs are interaction patterns found in interaction networks that occur significantly more or less frequently that in a randomized network. Examples are shown of an overrepresented network motif in the protein-protein interaction network involving members of the regulatory particle non-ATPase complex [53], and an underrepresented network motif in the transcription factor-target network involving the minichromosome maintenance 1 (Mcm1), switching deficient 5 (Swi5) and asymmetric synthesis of HO 1 (Ash1) genes [5] for Saccharomyces cerevisiae. (c) A protein interaction network alignment of three species: S. cerevisiae (yeast), Caenorhabditis elegans (worm) and Drosophila melanogaster (fly), whose proteins are involved in transcriptional regulation (adapted from Sharan et al. [66]). Nodes, continuous edges and dashed edges represent proteins, protein-protein interactions and ortholog relationships, respectively. Nodes of the same color indicate orthologous proteins. Proteins in the illustrated subnetwork (1) for yeast are chromatin organization modifier helicase and DNA-binding domains 1 (Chd1p), human sap homolog 49 (Hsh49p) and target of Sbf (Tos8p); (2) for worm are C27B7.4, excretory canal abnormal 7 (Exc-7), T28F12.2 and F31E3.2; and (3) for fly are CG33070, homothorax (Hth) and extradenticle (Exd) [66].