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

Guangyan Zhou, Othman Soufan, Jessica Ewald, Robert E.W. Hancock, Niladri Basu, Jianguo Xia

Research output: Contribution to journalArticlepeer-review

355 Citations (Scopus)


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

Original languageEnglish
Pages (from-to)W234-W241
JournalNucleic Acids Research
Issue numberW1
Publication statusPublished or Issued - 1 Jul 2019

ASJC Scopus subject areas

  • Genetics

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