期刊
JOURNAL OF PROTEOME RESEARCH
卷 14, 期 10, 页码 4332-4341出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.5b00529
关键词
posttranslational modifications; biological network analysis; phosphosite-centric dynamics; Cytoscape; signaling; phosphoproteomics; computational proteomics
资金
- Netherlands Organization for Scientific Research (NWO) [723.012.102]
- NWO VICI
- Dutch Cancer Society (KWF Kankerbestrijding)
- Netherlands Organisation for Scientific Research (NWO) as part of the National Roadmap Large-scale Research Facilities of The Netherlands [184.032.201]
Protein phosphorylation is an essential post-translational modification (PTM) regulating many biological processes at the cellular and multicellular level. Continuous improvements in phosphoproteomics technology allow the analysis of this PTM in an expanding biological content, yet up until now proteome data visualization tools are still very gene centric, hampering the ability to comprehensively map and study PTM dynamics. Here we present PhosphoPath, a Cytoscape app designed for the visualization and analysis of quantitative proteome and phosphoproteome data sets. PhosphoPath brings knowledge into the biological network by importing publically available data and enables PTM site-specific visualization of information from quantitative time series. To showcase PhosphoPath performance we use a quantitative proteomics data set comparing patient-derived melanoma cell lines grown in either conventional cell culture or xenografts.
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