Gene Ontology: Pitfalls, Biases, and Remedies.
The Gene Ontology (GO) is a formidable resource, but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its structure or how it is developed, which is both a strength and a weakness. In this chapter, we discuss some common misinterpretations of the ontology and the annotations. A better understanding of the pitfalls and the biases in the GO should help users make the most of this very rich resource. We also review some of the misconceptions and misleading assumptions commonly made about GO, including the effect of data incompleteness, the importance of annotation qualifiers, and the transitivity or lack thereof associated with different ontology relations. We also discuss several biases that can confound aggregate analyses such as gene enrichment analyses. For each of these pitfalls and biases, we suggest remedies and best practices.
CALIPHO group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel-Servet, 1211, Geneva 4, Switzerland. pascale.gaudet@sib.swiss.|Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland. pascale.gaudet@sib.swiss.
Pascale
P
Gaudet
Department of Genetics, Evolution & Environment, University College London, Gower St, London, WC1E 6BT, UK.|Swiss Institute of Bioinformatics, Biophore Building, 1015, Lausanne, Switzerland.|Department of Ecology and Evolution, University of Lausanne, Street Biophore, 1015, Lausanne, Switzerland.|Center of Integrative Genomics, University of Lausanne, Biophore, 1015, Lausanne, Switzerland.|Department of Computer Science, University College London, Gower St, WC1E 6BT, London, UK.
Christophe
C
Dessimoz
D000818:Animals; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D063990:Gene Ontology; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D011506:Proteins / Q000235:genetics; D013045:Species Specificity
D011506:Proteins
Bias; Confounding; Data mining; Gene ontology; Gene/protein annotation; Simpson’s paradox