Visualizing Gene Ontology annotations

TL;DR

This paper reviews various visualization methods for gene ontology annotations, emphasizing their importance in interpreting complex biological data and aiding biological discovery.

Contribution

It provides a comprehensive survey of existing GO visualization tools, comparing their features and illustrating their use in biological research.

Findings

Catalogues availability of GO visualization tools

Highlights importance of visualization in biological discovery

Provides examples of tool applications

Abstract

Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO terms that describe gene function and that can be used to summarize the results of the genome-scale experiments. However, making sense of such GO enrichment analyses may be challenging. For instance, overrepresented GO functions in a set of differentially expressed genes are typically output as a flat list, a format not adequate to capture the complexities of the hierarchical structure of the GO annotation labels. In this chapter, we survey the various methods to visualize large, difficult-to-interpret lists of GO terms. We catalogue their availability (web-based or standalone), the main principles they employ in summarizing large lists of GO terms, and the visualization styles they support. These brief commentaries on each software are intended as a helpful inventory, rather than comprehensive descriptions of the underlying algorithms. Instead, we show examples of their use and suggest that the choice of an appropriate visualization tool may be crucial to the utility of GO in biological discovery.