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

Research output: Contribution to journalArticleResearchpeer-review

3 Citations (Scopus)

Abstract

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
Volume15
Issue numberSupplement 12
DOIs
Publication statusPublished - Jun 2014
Externally publishedYes

Keywords

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

Cite this

Popik, O. V., Saik, O. V., Petrovskiy, E. D., Sommer, B., Hofestadt, R., Lavrik, I. N., & Ivanisenko, V. A. (2014). Analysis of signaling networks distributed over intracellular compartments based on proteinprotein interactions. BMC Genomics, 15(Supplement 12), [S7]. https://doi.org/10.1186/1471-2164-15-S12-S7
Popik, Olga Vasil'evna ; Saik, Olga Vladimirovna ; Petrovskiy, Evgeny Dmitrievich ; Sommer, Bjorn ; Hofestadt, Ralf ; Lavrik, Inna Nikolaevna ; Ivanisenko, Vladimir Aleksandrovich. / Analysis of signaling networks distributed over intracellular compartments based on proteinprotein interactions. In: BMC Genomics. 2014 ; Vol. 15, No. Supplement 12.
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abstract = "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.",
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Popik, OV, Saik, OV, Petrovskiy, ED, Sommer, B, Hofestadt, R, Lavrik, IN & Ivanisenko, VA 2014, 'Analysis of signaling networks distributed over intracellular compartments based on proteinprotein interactions', BMC Genomics, vol. 15, no. Supplement 12, S7. https://doi.org/10.1186/1471-2164-15-S12-S7

Analysis of signaling networks distributed over intracellular compartments based on proteinprotein interactions. / Popik, Olga Vasil'evna; Saik, Olga Vladimirovna; Petrovskiy, Evgeny Dmitrievich; Sommer, Bjorn; Hofestadt, Ralf; Lavrik, Inna Nikolaevna; Ivanisenko, Vladimir Aleksandrovich.

In: BMC Genomics, Vol. 15, No. Supplement 12, S7, 06.2014.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Analysis of signaling networks distributed over intracellular compartments based on proteinprotein interactions

AU - Popik, Olga Vasil'evna

AU - Saik, Olga Vladimirovna

AU - Petrovskiy, Evgeny Dmitrievich

AU - Sommer, Bjorn

AU - Hofestadt, Ralf

AU - Lavrik, Inna Nikolaevna

AU - Ivanisenko, Vladimir Aleksandrovich

PY - 2014/6

Y1 - 2014/6

N2 - 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.

AB - 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.

KW - Functional Classis

KW - Intracellular Compartment

KW - Reaction Efficiency

KW - Correlation Distance

KW - Boolean Model

UR - http://www.biomedcentral.com/content/pdf/1471-2164-15-S12-S7.pdf

U2 - 10.1186/1471-2164-15-S12-S7

DO - 10.1186/1471-2164-15-S12-S7

M3 - Article

VL - 15

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - Supplement 12

M1 - S7

ER -