Protein complex prediction using an integrative bioinformatics approach.
Since protein complexes play a crucial role in biological cells, one of the major goals in bioinformatics is the elucidation of protein complexes. A general approach is to build a prediction rule based on multiple data sources, e.g. gene expression data and protein interaction data, to assess the likelihood of two proteins having complex association. We critically revisit the step of predictor construction, i.e. the determination of a proper training set, an optimal classifier, and, most importantly, an optimal feature set. We use an exhaustive set of features, which includes the 2hop-feature as introduced by Wong et al. for predicting synthetic sick or lethal interactions. Post-processing of the likelihoods of protein interaction is then required to extract protein complexes. We propose a new protocol for combining these likelihood estimates. The protocol interprets the probabilities of complex association as output by the prediction rule as distances and employs hierarchical clustering to find groups of interacting proteins. In contrast to the computationally expensive search-and-score approach of Sharan et al., this protocol is very fast and can be applied to fully connected graphs. The protocol identifies trusted protein complexes with high confidence. We show that the 2hop-feature is relevant for predicting protein complexes. Furthermore, several interesting hypotheses about new protein complexes have been generated. For example, our approach linked the protein FYV4 to the mitochondrial ribosomal subunit. Interestingly, it is known that this protein is located in the mitochondrion, but its biological role is unknown. Vid22 and YGR071C were also linked, which corresponds to the new TAP data of Krogan et al.
van Berlo
Rogier J P
RJ
Information and Communication Theory Group, Delft University of Technology, Mekelweg 4, Delft, Zuid-Holland, 2628 CD, The Netherlands. r.j.p.vanBerlo@tudelft.nl
Wessels
Lodewyk F A
LF
De Ridder
Dick
D
Reinders
Marcel J T
MJ
D000465:Algorithms; D001665:Binding Sites / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D003663:Decision Trees; D011336:Probability; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D040901:Proteomics; D017386:Sequence Homology, Amino Acid; D018511:Systems Integration