Defining functional distances over Gene Ontology |
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Authors: | Angela del Pozo Florencio Pazos Alfonso Valencia |
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Affiliation: | (1) Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain;(2) Computational Systems Biology Group, National Biotechnology Centre (CNB-CSIC), Darwin 3, 28049 Madrid, Spain |
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Abstract: | Background A fundamental problem when trying to define the functional relationships between proteins is the difficulty in quantifying functional similarities, even when well-structured ontologies exist regarding the activity of proteins (i.e. 'gene ontology' -GO-). However, functional metrics can overcome the problems in the comparing and evaluating functional assignments and predictions. As a reference of proximity, previous approaches to compare GO terms considered linkage in terms of ontology weighted by a probability distribution that balances the non-uniform 'richness' of different parts of the Direct Acyclic Graph. Here, we have followed a different approach to quantify functional similarities between GO terms. |
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