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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 and five other organisms based on user feedback.

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 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; in situ functional enrichment analysis based on pathways or gene ontology; network editing - node deletion, module extraction, and image exporting.

Network analysis: topology analysis - hubs and shortest paths analysis, as well as community or module detection (currently supporting three algorithms - Walktrap, InfoMap and Label Propagation).

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

News & Updates

  • Both Network and Heatmap now support Retina display (11/20/2016);
  • Enhanced clustering analysis for heatmap visualization (11/18/2016);
  • Added support for miRNA-target network (11/15/2016);
  • Added support for t-SNE clustering 3D visualization. (11/10/2016);
  • Now showing DE gene table from single gene expression analysis. (11/05/2016);
  • Enhanced interface for differential expression analysis. (11/05/2016);
  • NetworkAnalyst now supports limma, edgeR or DEseq2 for RNAseq data analysis. (10/28/2016);
  • Added support for two module detection algorithms (Infomap & Label Propagation) (09/28/2016);
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