title: Differential evolutionary conservation of motif modes in the yeast protein interaction network.
abstract: BACKGROUND
  The importance of a network motif (a recurring interconnected pattern of special topology which is over-represented in a biological network) lies in its position in the hierarchy between the protein molecule and the module in a protein-protein interaction network. Until now, however, the methods available have greatly restricted the scope of research. While they have focused on the analysis in the resolution of a motif topology, they have not been able to distinguish particular motifs of the same topology in a protein-protein interaction network.
  
  
  RESULTS
  We have been able to assign the molecular function annotations of Gene Ontology to each protein in the protein-protein interactions of Saccharomyces cerevisiae. For various motif topologies, we have developed an algorithm, enabling us to unveil one million "motif modes", each of which features a unique topological combination of molecular functions. To our surprise, the conservation ratio, i.e., the extent of the evolutionary constraints upon the motif modes of the same motif topology, varies significantly, clearly indicative of distinct differences in the evolutionary constraints upon motifs of the same motif topology. Equally important, for all motif modes, we have found a power-law distribution of the motif counts on each motif mode. We postulate that motif modes may very well represent the evolutionary-conserved topological units of a protein interaction network.
  
  
  CONCLUSIONS
  For the first time, the motifs of a protein interaction network have been investigated beyond the scope of motif topology. The motif modes determined in this study have not only enabled us to differentiate among different evolutionary constraints on motifs of the same topology but have also opened up new avenues through which protein interaction networks can be analyzed.
authors.affiliation: Department of Information Management, National University of Kaohsiung, Taiwan. wplee@nuk.edu.tw
authors.forename: Wei-Po
authors.initials: WP
authors.lastname: Lee
authors.forename: Bing-Chiang
authors.initials: BC
authors.lastname: Jeng
authors.forename: Tun-Wen
authors.initials: TW
authors.lastname: Pai
authors.forename: Chin-Pei
authors.initials: CP
authors.lastname: Tsai
authors.forename: Chang-Yung
authors.initials: CY
authors.lastname: Yu
authors.forename: Wen-Shyong
authors.initials: WS
authors.lastname: Tzou
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D019143:Evolution, Molecular; D025941:Protein Interaction Mapping / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins