Analysis of signaling networks distributed over intracellular compartments based on proteinprotein interactions

Olga Vasil'evna Popik, Olga Vladimirovna Saik, Evgeny Dmitrievich Petrovskiy, Bjorn Sommer, Ralf Hofestadt, Inna Nikolaevna Lavrik, Vladimir Aleksandrovich Ivanisenko

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4 Citations (Scopus)


Background 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. Results 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. Conclusion 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.
Original languageEnglish
Article numberS7
Number of pages6
JournalBMC Genomics
Issue numberSupplement 12
Publication statusPublished - Jun 2014
Externally publishedYes


  • Functional Classis
  • Intracellular Compartment
  • Reaction Efficiency
  • Correlation Distance
  • Boolean Model

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