Protein annotation from protein interaction networks and Gene Ontology

Authors:
Cao D. Nguyen;Katheleen J. Gardiner;Krzysztof J. Cios
Affiliations:
Centre for Diabetes Research, The Western Australian Institute for Medical Research, Australia and Centre for Medical Research, University of Western Australia, WA, Australia and Virginia Commonwe ...;Department of Pediatrics, Intellectual and Developmental Disabilities Research Center, Programs in Computational Biology, Neuroscience and Human Medical Genetics, University of Colorado Denver, CO ...;Virginia Commonwealth University, VA, United States and Institute of Theoretical and Applied Informatics, Polish Academy of Sciences, Poland
Venue:
Journal of Biomedical Informatics
Year:
2011

Citing 11
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Abstract

We introduce a novel method for annotating protein function that combines Naive Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precision and 60% recall versus 45% and 26% for Majority and 24% and 61% for @g^2-statistics, respectively.