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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

  • Added support for two module detection algorithms (Infomap & Label Propagation) (09/28/2016);
  • Added support for eight new species including three animals (zebrafish, cow & chicken), two bacteria (E. coli & B. subtilis), two parasites (T. brucei & P. falciparum) and one plant (A. thaliana) (09/22/2016);
  • Added support for PPI data from STRING (09/12/2016);
  • Added support for node edge coloring (08/16/2016);
  • Updated major data I/O functions for better performance (08/05/2016);
  • Updated SVG Export to fully capture the network view (07/12/2016);
Read more .....

Please Cite

  • Xia J, Gill E, and Hancock REW (2015) "NetworkAnalyst for Statistical, Visual and Network-based Approaches for Meta-analysis of Expression Data" Nature Protocols 10, 823–844
  • Xia J, Benner MJ, and Hancock REW (2014) "NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration" Nucl. Acids Res. 42 (W1): W167-W174.
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