NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis

TLDR

Gene expression profiling increasingly requires user‑friendly bioinformatics tools for systems‑level data understanding. NetworkAnalyst 3.0 offers continuous updates, supports 17 species, and enables creation of diverse PPI, regulatory, co‑expression, toxicogenomics, and pharmacogenomics networks that can be explored in 2D, 3D, or VR, while allowing interactive meta‑analysis of multiple gene lists via heatmaps, enrichment networks, Venn and chord diagrams. NetworkAnalyst was first released in 2014 to interpret gene expression data within PPI networks, later updated for meta‑analysis, and the latest 3.0 release adds extensive new features and is freely available at https://www.networkanalyst.ca.

Abstract

The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first released in 2014 to address the key need for interpreting gene expression data within the context of protein-protein interaction (PPI) networks. It was soon updated for gene expression meta-analysis with improved workflow and performance. Over the years, NetworkAnalyst has been continuously updated based on community feedback and technology progresses. Users can now perform gene expression profiling for 17 different species. In addition to generic PPI networks, users can now create cell-type or tissue specific PPI networks, gene regulatory networks, gene co-expression networks as well as networks for toxicogenomics and pharmacogenomics studies. The resulting networks can be customized and explored in 2D, 3D as well as Virtual Reality (VR) space. For meta-analysis, users can now visually compare multiple gene lists through interactive heatmaps, enrichment networks, Venn diagrams or chord diagrams. In addition, users have the option to create their own data analysis projects, which can be saved and resumed at a later time. These new features are released together as NetworkAnalyst 3.0, freely available at https://www.networkanalyst.ca.