Evaluating Functional Annotations of Enzymes Using the Gene Ontology.
The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of interest to predicting where misannotation has occurred to knowing how confident you can be in the annotations assigned to those proteins is critical. In this chapter we explore what makes an enzyme unique and how we can use GO to infer aspects of protein function based on sequence similarity. These can range from identification of misannotation or other errors in a predicted function to accurate function prediction for an enzyme of entirely unknown function. Although GO annotation applies to any gene products, we focus here a describing our approach for hierarchical classification of enzymes in the Structure-Function Linkage Database (SFLD) (Akiva et al., Nucleic Acids Res 42(Database issue):D521-530, 2014) as a guide for informed utilisation of annotation transfer based on GO terms.
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA. gemma.l.holliday@gmail.com.
Gemma L
GL
Holliday
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA.
Rebecca
R
Davidson
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA.
Eyal
E
Akiva
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA.
Patricia C
PC
Babbitt
D000818:Animals; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D004798:Enzymes / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D063990:Gene Ontology; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*
D004798:Enzymes
Catalytic function; Enzyme; Evidence of function; Misannotation