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SELPHI / Systematic Extraction of Linked Phospho-Interactions
A computational workflow that aims to help non-bioinformaticians perform biological meaningful analyses of global phospho-proteomics datasets easily and to guide the design of downstream experiments to uncover the mechanistic details of signal transduction in their system. SELPHI uses correlation analysis of phospho-sites to extract kinase/phosphatase and phospho-peptide associations, and highlights the potential flow of signaling in the system under study.
PTMapper / Post Translational Modification mapper
A bioinformatical platform to characterize the structures of phosphorylation site-oriented PPI networks. From the quantitative phosphoproteome data on EGF-stimulated glioblastoma stem cells, our PTMapper-based network analysis unveiled p70S6K-related signaling as one of the most significantly regulated sub-networks, which was not observed in the conventional PPI network. As some previous studies demonstrated that p70S6K was correlated with survival and stemness maintenance of glioblastoma stem cells, the strategy based on phosphorylation site-oriented network analysis proved to be effective to unbiasedly extract crucial signaling pathways from the complex signaling networks.
PhosD
Predicts kinase-substrate relationships based on protein domains with the assumption that kinase-substrate interactions are accomplished with kinase-domain interactions. PhosD identifies the kinases that phosphorylate corresponding proteins by further considering protein-protein interactions. Some predictions were validated by signaling pathways in which they were involved, indicating the predictive power of PhosD. In addition, it was found that the number of known substrates will affect the prediction accuracy when predicting new substrates for a kinase and the domains in proteins targeted by multiple kinases are more conserved.
PhosphoSiteAnalyzer
Retrieves kinase-substrate predictions from NetworKIN algorithm and contains various statistical modules for further analysis. PhosphoSiteAnalyzer is a bioinformatical tool for analyzing (quantitative) phosphoproteome datasets. It has a modular design where each module represents a statistical analysis method for extracting various biological features from the phosphoproteomic data set. It also is a computational tool created with the aim of facilitating complex kinase−substrate network analysis in a user-friendly and user-tailored way.
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