Integration of relational and hierarchical network information for protein function prediction |
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Authors: | Xiaoyu Jiang Naoki Nariai Martin Steffen Simon Kasif Eric D Kolaczyk |
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Affiliation: | (1) Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA;(2) Bioinformatics Program, Boston University, Boston, MA 02215, USA;(3) Department of Genetics and Genomics, Boston University, Boston, MA 02118, USA;(4) Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA |
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Abstract: | Background In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions. |
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