Quantifying Protein Function Specificity in the Gene Ontology

Brenton Louie, Silas Bergen, Roger Higdon, Eugene Kolker

Abstract


Quantitative or numerical metrics of protein function specificity, made possible by the Gene Ontology, are useful in that they enable the development of distance or similarity measures between protein functions.  Here we describe how to calculate four measures of function specificity for GO terms:  1) number of ancestor terms, 2) number of offspring terms, 3) proportion of terms, and 4) Information Content.  We discuss the relationship between the metrics as well as discuss the strengths and weaknesses of each.

doi:10.4056/sigs.561626


Keywords


protein annotation, protein function, function specificity

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Acknowledgements

We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.

Funding for SIGS is provided by a grant from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707.

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