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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 (eight model organisms & five common species).

Expression analysis & meta-analysis: support limma, edgeR and DESeq2. The interface allows paired comparisons, time series, common reference, as well as two-factor nested comparisons; for meta-analysis - p values, fold changes, effect sizes, vote counts, and direct merge.

Network creation & customization: support protein-protein interactions, TF-gene interactions, miRNA-gene interactions, protein-drug interactions and protein-chemical interactions; multiple functions for network refinement;

Network visual analytics: interactive visual exploration - zooming, searching, highlighting, point-and-click, drag-and-drop; network customization - six layout algorithms, background color, edge size/shape, node size/color/visibility; in situ functional enrichment analysis (GO, pathways, etc.); network editing - node deletion, module extraction, and image exporting; topology analysis - hubs, shortest paths analysis, as well as three module detection algorithms.

Other visual analytics: interactive heatmaps, clustering (PCA & t-SNE), Venn diagram and chord diagrams for pattern discovery & complex comparisons.

News & Updates

  • Added support for P. aeruginosa (02/13/2018);
  • Minor bug fix for subnetwork rendering (02/07/2018);
  • Added support for M. tuberculosis (12/05/2017);
  • Added support for gene expression analysis for Japanese quail (11/09/2017);
  • Added support to correct node overlaps in network layout (09/15/2017);
  • Improved method for computing minimum network (07/10/2017);
  • Enhanced heatmap resolutions and network node highlighting (06/01/2017);
  • Fixed name mapping issue with A. thaliana (02/27/2017);
  • Fixed node name display issue for fruitfly and C. elegans (02/06/2017);
  • Fixed ID mapping issue with STRING database (01/23/2017);
  • Fixed the issue with SIF file generation (01/16/2017);
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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. (PPI data analysis and visualization)
  • Xia, J., Lyle, N.H., Mayer, M., Pena, O.M. and Hancock, R.E.W. (2013) “INVEX - a web-based tool for integrative visualization of expression data”. Bioinformatics 29 (24), 3232-3234 (gene expression data analysis)
  • Xia, J., Fjell, C.D., Mayer, M., Pena, O.M., Wishart, D.S. and Hancock, R.E.W. (2013) “INMEX - a web-based tool for integrative meta-analysis of expression data”. Nucleic Acids Research 41, W63-W70. (meta-analysis)
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