title: Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map).
abstract: BACKGROUND
  Many genomes have been completely sequenced. However, detecting and analyzing their protein-protein interactions by experimental methods such as co-immunoprecipitation, tandem affinity purification and Y2H is not as fast as genome sequencing. Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein-protein interaction rules within and among complete genomes.
  
  
  RESULTS
  We confirmed that all the predicted protein family interactomes (the full set of protein family interactions within a proteome) of 146 species are scale-free networks, and they share a small core network comprising 36 protein families related to indispensable cellular functions. We found two fundamental differences among prokaryotic and eukaryotic interactomes: (1) eukarya had significantly more hub families than archaea and bacteria and (2) certain special hub families determined the topology of the eukaryotic interactomes. Our comparative analysis suggests that a very small number of expansive protein families led to the evolution of interactomes and seemed to have played a key role in species diversification.
  
  
  BACKGROUND
  http://interactomics.org.
authors.affiliation: Object Interaction Technologies Inc., CMS Building 705, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea.
authors.forename: Daeui
authors.initials: D
authors.lastname: Park
authors.forename: Semin
authors.initials: S
authors.lastname: Lee
authors.forename: Dan
authors.initials: D
authors.lastname: Bolser
authors.forename: Michael
authors.initials: M
authors.lastname: Schroeder
authors.forename: Michael
authors.initials: M
authors.lastname: Lappe
authors.forename: Donghoon
authors.initials: D
authors.lastname: Oh
authors.forename: Jong
authors.initials: J
authors.lastname: Bhak
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000235:genetics* / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D020543:Proteome