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Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions

Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions

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POPIK, Olga Vasilevna, Olga Vladimirovna SAIK, Evgeny Dmitrievich PETROVSKIY, Björn SOMMER, Ralf HOFESTÄDT, Inna Nikolaevna LAVRIK, Vladimir Aleksandrovich IVANISENKO, 2014. Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions. In: BMC Genomics. 15(Suppl 12), S7. eISSN 1471-2164. Available under: doi: 10.1186/1471-2164-15-S12-S7

@article{Popik2014Analy-34509, title={Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions}, year={2014}, doi={10.1186/1471-2164-15-S12-S7}, number={Suppl 12}, volume={15}, journal={BMC Genomics}, author={Popik, Olga Vasilevna and Saik, Olga Vladimirovna and Petrovskiy, Evgeny Dmitrievich and Sommer, Björn and Hofestädt, Ralf and Lavrik, Inna Nikolaevna and Ivanisenko, Vladimir Aleksandrovich}, note={Article Number: S7} }

Sommer, Björn Background<br />Biological processes are usually distributed over various intracellular compartments. Proteins from diverse cellular compartments are often involved in similar signaling networks. However, the difference in the reaction rates between similar proteins among different compartments is usually quite high. We suggest that the estimation of frequency of intracompartmental as well as intercompartmental protein-protein interactions is an appropriate approach to predict the efficiency of a pathway.<br /><br />Results<br />Using data from the databases STRING, ANDSystem, IntAct and UniProt, a PPI frequency matrix of intra/inter-compartmental interactions efficiencies was constructed. This matrix included 15 human-specific cellular compartments. An approach for estimating pathway efficiency using the matrix of intra/inter-compartmental PPI frequency, based on analysis of reactions efficiencies distribution was suggested. An investigation of KEGG pathway efficiencies was conducted using the developed method. The clusterization and the ranking of KEGG pathways based on their efficiency were performed. "Amino acid metabolism" and "Genetic information processing" revealed the highest efficiencies among other functional classes of KEGG pathways. "Nervous system" and "Signaling molecules interaction" contained the most inefficient pathways. Statistically significant differences were found between efficiencies of KEGG and randomly-generated pathways. Based on these observations, the validity of this approach was discussed.<br /><br />Conclusion<br />The estimation of efficiency of signaling networks is a complicated task because of the need for the data on the kinetic reactions. However, the proposed method does not require such data and can be used for preliminary analysis of different protein networks. Ivanisenko, Vladimir Aleksandrovich Hofestädt, Ralf Sommer, Björn Lavrik, Inna Nikolaevna 2014 Hofestädt, Ralf Popik, Olga Vasilevna eng Saik, Olga Vladimirovna Popik, Olga Vasilevna Petrovskiy, Evgeny Dmitrievich Ivanisenko, Vladimir Aleksandrovich Petrovskiy, Evgeny Dmitrievich Saik, Olga Vladimirovna Lavrik, Inna Nikolaevna Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions 2016-06-23T12:10:34Z 2016-06-23T12:10:34Z

Dateiabrufe seit 23.06.2016 (Informationen über die Zugriffsstatistik)

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