Cytoscape stringApp: Network analysis and visualization of proteomics data

Research output: Contribution to journalJournal articlepeer-review

Standard

Cytoscape stringApp : Network analysis and visualization of proteomics data. / Doncheva, Nadezhda T; Morris, John; Gorodkin, Jan; Jensen, Lars J.

In: Journal of Proteome Research, Vol. 18, No. 2, 2019, p. 623-632.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Doncheva, NT, Morris, J, Gorodkin, J & Jensen, LJ 2019, 'Cytoscape stringApp: Network analysis and visualization of proteomics data', Journal of Proteome Research, vol. 18, no. 2, pp. 623-632. https://doi.org/10.1021/acs.jproteome.8b00702

APA

Doncheva, N. T., Morris, J., Gorodkin, J., & Jensen, L. J. (2019). Cytoscape stringApp: Network analysis and visualization of proteomics data. Journal of Proteome Research, 18(2), 623-632. https://doi.org/10.1021/acs.jproteome.8b00702

Vancouver

Doncheva NT, Morris J, Gorodkin J, Jensen LJ. Cytoscape stringApp: Network analysis and visualization of proteomics data. Journal of Proteome Research. 2019;18(2):623-632. https://doi.org/10.1021/acs.jproteome.8b00702

Author

Doncheva, Nadezhda T ; Morris, John ; Gorodkin, Jan ; Jensen, Lars J. / Cytoscape stringApp : Network analysis and visualization of proteomics data. In: Journal of Proteome Research. 2019 ; Vol. 18, No. 2. pp. 623-632.

Bibtex

@article{2fd6bf5d1e1a4a03ac9441931a5da020,
title = "Cytoscape stringApp: Network analysis and visualization of proteomics data",
abstract = "Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics dataset, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.",
keywords = "Cytoscape, functional enrichment, network analysis, network visualization, protein networks, proteomics data, STRING database",
author = "Doncheva, {Nadezhda T} and John Morris and Jan Gorodkin and Jensen, {Lars J.}",
note = "This article is part of the Software Tools and Resources 2019 special issue",
year = "2019",
doi = "10.1021/acs.jproteome.8b00702",
language = "English",
volume = "18",
pages = "623--632",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "2",

}

RIS

TY - JOUR

T1 - Cytoscape stringApp

T2 - Network analysis and visualization of proteomics data

AU - Doncheva, Nadezhda T

AU - Morris, John

AU - Gorodkin, Jan

AU - Jensen, Lars J.

N1 - This article is part of the Software Tools and Resources 2019 special issue

PY - 2019

Y1 - 2019

N2 - Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics dataset, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.

AB - Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics dataset, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.

KW - Cytoscape

KW - functional enrichment

KW - network analysis

KW - network visualization

KW - protein networks

KW - proteomics data

KW - STRING database

U2 - 10.1021/acs.jproteome.8b00702

DO - 10.1021/acs.jproteome.8b00702

M3 - Journal article

C2 - 30450911

VL - 18

SP - 623

EP - 632

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 2

ER -

ID: 210016604