Identifying differentially regulated subnetworks from phosphoproteomic data

Background: Various high throughput methods are available for detecting regulations at the level of transcription, translation or posttranslation (e.g. phosphorylation). Integrating these data with protein networks should make it possible to identify subnetworks that are significantly regulated. Furthermore, such integration can support identification of regulated entities from often noisy high throughput data. In particular, processing mass spectrometry-based phosphoproteomic data in this manner may expose signal transduction pathways and, in the case of experiments with drug-treated cells, reveal the drug's mode of action. Results: Here, we introduce SubExtractor, an algorithm that combines phosphoproteomic data with protein network information from STRING to identify differentially regulated subnetworks and individual proteins. The method is based on a Bayesian probabilistic model combined with a genetic algorithm and rigorous significance testing. The Bayesian model accounts ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Martin Klammer, Klaus Godl, Andreas Tebbe, Christoph Schaab
• Keywords: BMCBI 2010, Phosphoproteomic Data, Protein Networks, Proteins