GO‐Compass: Visual Navigation of Multiple Lists of GO terms

Abstract

AbstractAnalysis pipelines in genomics, transcriptomics, and proteomics commonly produce lists of genes, e.g., differentially expressed genes. Often these lists overlap only partly or not at all and contain too many genes for manual comparison. However, using background knowledge, such as the functional annotations of the genes, the lists can be abstracted to functional terms. One approach is to run Gene Ontology (GO) enrichment analyses to determine over‐ and/or underrepresented functions for every list of genes. Due to the hierarchical structure of the Gene Ontology, lists of enriched GO terms can contain many closely related terms, rendering the lists still long, redundant, and difficult to interpret for researchers.In this paper, we present GO‐Compass (Gene Ontology list comparison using Semantic Similarity), a visual analytics tool for the dispensability reduction and visual comparison of lists of GO terms. For dispensability reduction, we adapted the RE‐VIGO algorithm, a summarization method based on the semantic similarity of GO terms, to perform hierarchical dispensability clustering on multiple lists. In an interactive dashboard, GO‐Compass offers several visualizations for the comparison and improved interpretability of GO terms lists. The hierarchical dispensability clustering is visualized as a tree, where users can interactively filter out dispensable GO terms and create flat clusters by cutting the tree at a chosen dispensability. The flat clusters are visualized in animated treemaps and are compared using a correlation heatmap, UpSet plots, and bar charts. With two use cases on published datasets from different omics domains, we demonstrate the general applicability and effectiveness of our approach. In the first use case, we show how the tool can be used to compare lists of differentially expressed genes from a transcriptomics pipeline and incorporate gene information into the analysis. In the second use case using genomics data, we show how GO‐Compass facilitates the analysis of many hundreds of GO terms. For qualitative evaluation of the tool, we conducted feedback sessions with five domain experts and received positive comments. GO‐Compass is part of the Tue‐Vis Visualization Server as a web application available at https://go‐compass‐tuevis.cs.uni‐tuebingen.de/