Visualize omics data on networks with Omics Visualizer, a Cytoscape App

F1000Res. 2020 Feb 28;9:157. doi: 10.12688/f1000research.22280.2. eCollection 2020.

Abstract

Cytoscape is an open-source software used to analyze and visualize biological networks. In addition to being able to import networks from a variety of sources, Cytoscape allows users to import tabular node data and visualize it onto networks. Unfortunately, such data tables can only contain one row of data per node, whereas omics data often have multiple rows for the same gene or protein, representing different post-translational modification sites, peptides, splice isoforms, or conditions. Here, we present a new app, Omics Visualizer, that allows users to import data tables with several rows referring to the same node, connect them to one or more networks, and visualize the connected data onto networks. Omics Visualizer uses the Cytoscape enhancedGraphics app to show the data either in the nodes (pie visualization) or around the nodes (donut visualization), where the colors of the slices represent the imported values. If the user does not provide a network, the app can retrieve one from the STRING database using the Cytoscape stringApp. The Omics Visualizer app is freely available at https://apps.cytoscape.org/apps/omicsvisualizer.

Keywords: Cytoscape; app; network biology; network visualization; omics data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Data Visualization*
  • Proteomics
  • Software*

Grant support

This work was funded by the Novo Nordisk Foundation(NNF14CC0001). NTD was also funded by InnovationFund Denmark “Brainstem” (4108-00008B).