Monitoring changes in the Gene Ontology and their impact on genomic data analysis

Abstract

The Gene Ontology (GO) is one of the most widely used resources in molecular and cellular biology, largely through the use of \"enrichment analysis\". To facilitate informed use of GO, we present GOTrack (https://gotrack.msl.ubc.ca), which provides access to historical records and trends in the Gene Ontology and GO annotations (GOA). GOTrack gives users access to gene- and term-level information on annotations for nine model organisms as well as an interactive tool that measures the stability of enrichment results over time for user-provided \"hit lists\" of genes. To document the effects of GO evolution on enrichment, we analyzed over 2500 published hit lists of human genes (most over 9 years old). 53% of hit lists were considered to yield significantly stable enrichment results. Because stability is far from assured for any individual hit list, GOTrack can lead to more informed and cautious application of GO to genomics research.