OmicsTIDE: interactive exploration of trends in multi-omics data

Abstract Motivation The increasing amount of data produced by omics technologies has enabled researchers to study phenomena across multiple omics layers. Besides data-driven analysis strategies, interactive visualization tools have been developed for a more transparent analysis. However, most state-of-the-art tools do not reconstruct the impact of a single omics layer on the integration result. Results We developed a data classification scheme focusing on different aspects of multi-omics datasets for a systemic understanding. Based on this classification, we developed the Omics Trend-comparing Interactive Data Explorer (OmicsTIDE), an interactive visualization tool for the comparison of gene-based quantitative omics data. The tool consists of a computational part that clusters omics datasets to determine trends and an interactive visualization. The trends are visualized as profile plots and are connected by a Sankey diagram that allows for an interactive pairwise trend comparison to discover concordant and discordant trends. Moreover, large-scale omics datasets are broken down into small subsets that can be analyzed functionally using Gene Ontology enrichment within few analysis steps. We demonstrate the interactive analysis using OmicsTIDE with two case studies focusing on different experimental designs. Availability and implementation OmicsTIDE is a web tool available via http://omicstide-tuevis.cs.uni-tuebingen.de/. Supplementary information Supplementary data are available at Bioinformatics Advances online.