The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data
Open accessAbstract
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 data set, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp .
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Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
UniProt: the Universal Protein knowledgebase
Apweiler, R. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,498
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw937 · Cited by 6,980
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Stelzer, G., Rosen, N., Plaschkes, I., Zimmerman, S., Twik, M., Fishilevich, S., Stein, T. I., Nudel, R., Lieder, I., Mazor, Y., et al. (2016) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.5 · Cited by 5,550
Architectural styles and the design of network-based software architectures
Fielding, R. T., & Taylor, R. N. (2000) · Cited by 5,094
UniProt: the universal protein knowledgebase
The UniProt Consortium (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1099 · Cited by 4,436
An efficient algorithm for large-scale detection of protein families
Enright, A. J. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1575 · Cited by 3,588
Integration of biological networks and gene expression data using Cytoscape
Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., et al. (2007) · Nature Protocols · doi:10.1038/nprot.2007.324 · Cited by 2,507
Self-citationSTITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data
Szklarczyk, D., Santos, A., von Mering, C., Jensen, L. J., Bork, P., & Kuhn, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1277 · Cited by 1,687
Self-citationColorBrewer.org: An Online Tool for Selecting Colour Schemes for Maps
Harrower, M., & Brewer, C. A. (2003) · The Cartographic Journal · doi:10.1179/000870403235002042 · Cited by 1,099
Cited by
Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1000 · Cited by 9,726
Self-citationSzklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1074 · Cited by 8,056
Self-citationThe STRING database in 2025: protein networks with directionality of regulation
Szklarczyk, D., Nastou, K., Koutrouli, M., Kirsch, R., Mehryary, F., Hachilif, R., Hu, D., Peluso, M. E., Huang, Q., Fang, T., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1113 · Cited by 668
Self-citationYin, K., Peluso, M. J., Luo, X., Thomas, R., Shin, M.-G., Neidleman, J., Andrew, A., Young, K. C., Ma, T., Hoh, R., et al. (2024) · Nature Immunology · doi:10.1038/s41590-023-01724-6 · Cited by 394
Grissa, D., Junge, A., Oprea, T. I., & Jensen, L. J. (2022) · Database · doi:10.1093/database/baac019 · Cited by 144
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Metadata
- Authors
- Doncheva, N. T., Morris, J. H., Gorodkin, J., & Jensen, L. J.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-11-19
- Volume
- 18
- Issue
- 2
- Pages
- 623-632
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2950764390
- Cited by
- 2,306
- References
- 25
- FWCI
- 38.53
- Type
- journal article
- Language
- en
- Open access
- green
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- Doncheva, N. T., Morris, J. H., Gorodkin, J., & Jensen, L. J. (2019). Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.8b00702
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