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

Research output: Contribution to journal › Journal article › Research › peer-review

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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

Harvard

Legeay, M, Doncheva, NT, Morris, JH & Jensen, LJ 2020, 'Visualize omics data on networks with Omics Visualizer, a Cytoscape App', F1000Research, vol. 9. https://doi.org/10.12688/f1000research.22280.2

APA

Legeay, M., Doncheva, N. T., Morris, J. H., & Jensen, L. J. (2020). Visualize omics data on networks with Omics Visualizer, a Cytoscape App. F1000Research, 9. https://doi.org/10.12688/f1000research.22280.2

Vancouver

Legeay M, Doncheva NT, Morris JH, Jensen LJ. Visualize omics data on networks with Omics Visualizer, a Cytoscape App. F1000Research. 2020;9. https://doi.org/10.12688/f1000research.22280.2

Author

Legeay, Marc ; Doncheva, Nadezhda T. ; Morris, John H. ; Jensen, Lars Juhl. / Visualize omics data on networks with Omics Visualizer, a Cytoscape App. In: F1000Research. 2020 ; Vol. 9.

Bibtex

@article{42bcb570fbd44680966325e19cdaea77,
title = "Visualize omics data on networks with Omics Visualizer, a Cytoscape App",
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 = "app, Cytoscape, network biology, network visualization, omics data",
author = "Marc Legeay and Doncheva, {Nadezhda T.} and Morris, {John H.} and Jensen, {Lars Juhl}",
year = "2020",
doi = "10.12688/f1000research.22280.2",
language = "English",
volume = "9",
journal = "F1000Research",
issn = "2046-1402",
publisher = "F1000Research",

}

RIS

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