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PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks.
- Source :
-
Journal of proteome research [J Proteome Res] 2015 Oct 02; Vol. 14 (10), pp. 4332-41. Date of Electronic Publication: 2015 Sep 08. - Publication Year :
- 2015
-
Abstract
- 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.
- Subjects :
- Cell Line, Tumor
Computer Graphics
Gene Regulatory Networks
Humans
Melanoma genetics
Melanoma pathology
Phosphoproteins genetics
Phosphoproteins isolation & purification
Phosphorylation
Proteome genetics
Proteome isolation & purification
Proteomics
Skin Neoplasms genetics
Skin Neoplasms pathology
Tandem Mass Spectrometry
Melanoma metabolism
Mobile Applications
Phosphoproteins metabolism
Protein Processing, Post-Translational
Proteome metabolism
Skin Neoplasms metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1535-3907
- Volume :
- 14
- Issue :
- 10
- Database :
- MEDLINE
- Journal :
- Journal of proteome research
- Publication Type :
- Academic Journal
- Accession number :
- 26317507
- Full Text :
- https://doi.org/10.1021/acs.jproteome.5b00529