title: Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction.
abstract: BACKGROUND
  While the number of newly sequenced genomes and genes is constantly increasing, elucidation of their function still is a laborious and time-consuming task. This has led to the development of a wide range of methods for predicting protein functions in silico. We report on a new method that predicts function based on a combination of information about protein interactions, orthology, and the conservation of protein networks in different species.
  
  
  RESULTS
  We show that aggregation of these independent sources of evidence leads to a drastic increase in number and quality of predictions when compared to baselines and other methods reported in the literature. For instance, our method generates more than 12,000 novel protein functions for human with an estimated precision of ~76%, among which are 7,500 new functional annotations for 1,973 human proteins that previously had zero or only one function annotated. We also verified our predictions on a set of genes that play an important role in colorectal cancer (MLH1, PMS2, EPHB4 ) and could confirm more than 73% of them based on evidence in the literature.
  
  
  CONCLUSIONS
  The combination of different methods into a single, comprehensive prediction method infers thousands of protein functions for every species included in the analysis at varying, yet always high levels of precision and very good coverage.
authors.affiliation: Knowledge Management in Bioinformatics, Humboldt-Universitat zu Berlin Unter den Linden 6, 10099 Berlin, Germany. sjaeger@informatik.hu-berlin.de
authors.forename: Samira
authors.initials: S
authors.lastname: Jaeger
authors.forename: Christine T
authors.initials: CT
authors.lastname: Sers
authors.forename: Ulf
authors.initials: U
authors.lastname: Leser
mesh_terms: D000818:Animals; D020137:Base Pair Mismatch / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics*; D004260:DNA Repair / Q000235:genetics; D019143:Evolution, Molecular; D006801:Humans; D011485:Protein Binding / Q000235:genetics; D025941:Protein Interaction Mapping; D011506:Proteins / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
chemical_list: D011506:Proteins