title: PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN.
abstract: Phosphoproteomic experiments are routinely conducted in laboratories worldwide, and because of the fast development of mass spectrometric techniques and efficient phosphopeptide enrichment methods, researchers frequently end up having lists with tens of thousands of phosphorylation sites for further interrogation. To answer biologically relevant questions from these complex data sets, it becomes essential to apply computational, statistical, and predictive analytical methods. Here we provide an advanced bioinformatic platform termed "PhosphoSiteAnalyzer" to explore large phosphoproteomic data sets that have been subjected to kinase prediction using the previously published NetworKIN algorithm. NetworKIN applies sophisticated linear motif analysis and contextual network modeling to obtain kinase-substrate associations with high accuracy and sensitivity. PhosphoSiteAnalyzer provides an algorithm to retrieve kinase predictions from the public NetworKIN webpage in a semiautomated way and applies hereafter advanced statistics to facilitate a user-tailored in-depth analysis of the phosphoproteomic data sets. The interface of the software provides a high degree of analytical flexibility and is designed to be intuitive for most users. PhosphoSiteAnalyzer is a freeware program available at http://phosphosite.sourceforge.net .
authors.affiliation: Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark , Odense, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Martin V
authors.initials: MV
authors.lastname: Bennetzen
authors.forename: Jürgen
authors.initials: J
authors.lastname: Cox
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.forename: Jens S
authors.initials: JS
authors.lastname: Andersen
mesh_terms: D020816:Amino Acid Motifs; D019295:Computational Biology; D003198:Computer Simulation; D008954:Models, Biological; D010750:Phosphoproteins / Q000737:chemistry*; D010766:Phosphorylation; D011494:Protein Kinases / Q000737:chemistry*; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D010750:Phosphoproteins; D020543:Proteome; D011494:Protein Kinases