title: Network2Canvas: network visualization on a canvas with enrichment analysis.
abstract: BACKGROUND
  Networks are vital to computational systems biology research, but visualizing them is a challenge. For networks larger than ∼100 nodes and ∼200 links, ball-and-stick diagrams fail to convey much information. To address this, we developed Network2Canvas (N2C), a web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas. The network nodes are clustered on the canvas using simulated annealing to maximize local connections where a node's brightness is made proportional to its local fitness. The interactive canvas is implemented in HyperText Markup Language (HTML)5 with the JavaScript library Data-Driven Documents (D3). We applied N2C to visualize 30 canvases made from human and mouse gene-set libraries and 6 canvases made from the Food and Drug Administration (FDA)-approved drug-set libraries. Given lists of genes or drugs, enriched terms are highlighted on the canvases, and their degree of clustering is computed. Because N2C produces visual patterns of enriched terms on canvases, a trained eye can detect signatures instantly. In summary, N2C provides a new flexible method to visualize large networks and can be used to perform and visualize gene-set and drug-set enrichment analyses.
  
  
  BACKGROUND
  N2C is freely available at http://www.maayanlab.net/N2C and is open source.
  
  
  BACKGROUND
  avi.maayan@mssm.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Tan
authors.forename: Edward Y
authors.initials: EY
authors.lastname: Chen
authors.forename: Ruth
authors.initials: R
authors.lastname: Dannenfelser
authors.forename: Neil R
authors.initials: NR
authors.lastname: Clark
authors.forename: Avi
authors.initials: A
authors.lastname: Ma'ayan
mesh_terms: D000818:Animals; D003196:Computer Graphics; D064420:Drug-Related Side Effects and Adverse Reactions; D053595:Embryonic Stem Cells / Q000378:metabolism; D015723:Gene Library; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D051379:Mice; D004364:Pharmaceutical Preparations / Q000737:chemistry; D012984:Software; D049490:Systems Biology
chemical_list: D004364:Pharmaceutical Preparations