NetworkAnalyst is designed to support integrative analysis of gene expression data through statistical, visual and network-based approaches:

Data inputs: one or more gene/protein lists with optional fold changes; one or more gene expression tables from microarray or RNAseq experiments. Network currently supports 13 species including eight model organisms (human, mouse, fruit fly, zebrafish, C. elegans, yeast, E. coli & Arabidopdid) and other five common organims (cow, chicken, B. subtilis, T. brucei & P. falciparum)

Statistical analysis: for single data - paired comparisons, time series, common reference, and nested comparisons; for integrating multiple data sets - p values, fold changes, effect sizes, vote counts, and direct merge.

Network construction: zero-order, first-order, higher-order interaction network or minimum interaction networks;

Network analysis & visualization: interactive visual exploration - zooming, searching, highlighting, point-and-click; network customization - layout (supporting five automatic layout algorithms, as well as manual drag-and-drop), background color, edge size/shape, node size/color/visibility; topology analysis - hubs, modules, shortest paths; in situ functional enrichment analysis based on pathways or gene ontology; network editing - node deletion, module extraction, and image exporting.

Visual analytics: interactive heatmaps, 3D PCA and chord diagrams for data exploration.