Construction of reliable protein-protein interaction networks with a new interaction generality measure.
BACKGROUND
Recent screening techniques have made large amounts of protein-protein interaction data available, from which biologically important information such as the function of uncharacterized proteins, the existence of novel protein complexes, and novel signal-transduction pathways can be discovered. However, experimental data on protein interactions contain many false positives, making these discoveries difficult. Therefore computational methods of assessing the reliability of each candidate protein-protein interaction are urgently needed.


RESULTS
We developed a new 'interaction generality' measure (IG2) to assess the reliability of protein-protein interactions using only the topological properties of their interaction-network structure. Using yeast protein-protein interaction data, we showed that reliable protein-protein interactions had significantly lower IG2 values than less-reliable interactions, suggesting that IG2 values can be used to evaluate and filter interaction data to enable the construction of reliable protein-protein interaction networks.
Saito
Rintaro
R
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Tsurumi-ku, Yokohama 230-0045, Japan. rgscerg@gsc.riken.go.jp
Suzuki
Harukazu
H
Hayashizaki
Yoshihide
Y
D001665:Binding Sites; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D046911:Macromolecular Substances; D008660:Metabolism / Q000502:physiology*; D008954:Models, Biological; D008956:Models, Chemical; D015233:Models, Statistical; D025341:Principal Component Analysis; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D015003:Yeasts / Q000737:chemistry / Q000378:metabolism
D005656:Fungal Proteins; D046911:Macromolecular Substances; D011506:Proteins