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Quantifying protein function specificity in the gene ontology.

ABSTRACT: Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable 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 (IC). We discuss the relationship between the metrics and the strengths and weaknesses of each.

SUBMITTER: Louie B

PROVIDER: S-EPMC3035283 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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Quantifying protein function specificity in the gene ontology.

Louie Brenton B Bergen Silas S Higdon Roger R Kolker Eugene E

Standards in genomic sciences 20100330 2

Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable 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 (IC). We discuss the relationship between the metrics and the strengths and weaknesses of each. ...[more]

PMID: 21304708

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