Visualize omics data on networks with Omics Visualizer, a Cytoscape App
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Visualize omics data on networks with Omics Visualizer, a Cytoscape App. / Legeay, Marc; Doncheva, Nadezhda T.; Morris, John H.; Jensen, Lars Juhl.
In: F1000Research, Vol. 9, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Visualize omics data on networks with Omics Visualizer, a Cytoscape App
AU - Legeay, Marc
AU - Doncheva, Nadezhda T.
AU - Morris, John H.
AU - Jensen, Lars Juhl
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
KW - app
KW - Cytoscape
KW - network biology
KW - network visualization
KW - omics data
U2 - 10.12688/f1000research.22280.2
DO - 10.12688/f1000research.22280.2
M3 - Journal article
C2 - 32399202
AN - SCOPUS:85084626722
VL - 9
JO - F1000Research
JF - F1000Research
SN - 2046-1402
ER -
ID: 242782327