Dynamic network topology changes as result of cellular stress

Peddinti Gopalacharuyly, Vidya Velagapudi, Erno Lindfors, Matej Oresic

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

Abstract

The topology of metabolic or protein-protein interaction networks has been an extensively studied subject. Our primary interest on the topic is how the context, such as changing physiological state of the system, affects the network topology and connectivity within- and between the cellular functional modules and through this obtain better understating about the control mechanisms of biological systems. In this study we investigated the changes in network structure as results of oxidative stress. We collected S. cerevisiae data on protein-protein interactions (DIP), metabolic pathways (KEGG), gene regulatory relationships (TRANSFAC) into our bioinformatics system [1]. We collected available experimental gene expression data from S. cerevisiae during oxidative stress response at different time points [2]. The data was integrated into the network context by defining criteria for evaluating presence or absence of proteins in the integrated network. Swissprot index of S. cerevisiae proteins [3] was used to translate ORF identifiers into the expression dataset to Swissprot protein accession numbers. We thus reduced the networks and reconstructed condition specific networks corresponding to each expression data by removing all the proteins that are absent and their incident links. Structural organization of these networks was compared by studying topological characteristics. We found that the degree distribution of most of the networks obtained was different from the power law. Additionally, we found changes in clustering coefficient, i.e. local connectivity properties, at two specific time points during the oxidative stress response. Our results suggest the connectivity of the system is being modulated as a response to stress or other external stimuli.
Original languageEnglish
Title of host publicationInternational Specialised Symposium on Yeasts ISSY25
Subtitle of host publicationSystems Biology of Yeasts - from Models to Applications
Place of PublicationEspoo
PublisherVTT Technical Research Centre of Finland
Pages67
ISBN (Electronic)951-38-6308-5
ISBN (Print)951-38-6307-7
Publication statusPublished - 2006
EventInternational Specialised Symposium on Yeasts, ISSY 25 - Espoo, Finland
Duration: 18 Jun 200621 Jun 2006

Publication series

NameVTT Symposium
PublisherVTT
Number242
ISSN (Print)0357-9387
ISSN (Electronic)1455-0873

Conference

ConferenceInternational Specialised Symposium on Yeasts, ISSY 25
Abbreviated titleISSY 25
CountryFinland
CityEspoo
Period18/06/0621/06/06

Fingerprint

Protein Databases
Proteins
Oxidative Stress
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins
Protein Interaction Maps
Regulator Genes
Metabolic Networks and Pathways
Computational Biology
Open Reading Frames
Cluster Analysis
Gene Expression
Datasets

Cite this

Gopalacharuyly, P., Velagapudi, V., Lindfors, E., & Oresic, M. (2006). Dynamic network topology changes as result of cellular stress. In International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications (pp. 67). [P15] Espoo: VTT Technical Research Centre of Finland. VTT Symposium, No. 242
Gopalacharuyly, Peddinti ; Velagapudi, Vidya ; Lindfors, Erno ; Oresic, Matej. / Dynamic network topology changes as result of cellular stress. International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo : VTT Technical Research Centre of Finland, 2006. pp. 67 (VTT Symposium; No. 242).
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Gopalacharuyly, P, Velagapudi, V, Lindfors, E & Oresic, M 2006, Dynamic network topology changes as result of cellular stress. in International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications., P15, VTT Technical Research Centre of Finland, Espoo, VTT Symposium, no. 242, pp. 67, International Specialised Symposium on Yeasts, ISSY 25 , Espoo, Finland, 18/06/06.

Dynamic network topology changes as result of cellular stress. / Gopalacharuyly, Peddinti; Velagapudi, Vidya; Lindfors, Erno; Oresic, Matej.

International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo : VTT Technical Research Centre of Finland, 2006. p. 67 P15 (VTT Symposium; No. 242).

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsScientific

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T1 - Dynamic network topology changes as result of cellular stress

AU - Gopalacharuyly, Peddinti

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PY - 2006

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N2 - The topology of metabolic or protein-protein interaction networks has been an extensively studied subject. Our primary interest on the topic is how the context, such as changing physiological state of the system, affects the network topology and connectivity within- and between the cellular functional modules and through this obtain better understating about the control mechanisms of biological systems. In this study we investigated the changes in network structure as results of oxidative stress. We collected S. cerevisiae data on protein-protein interactions (DIP), metabolic pathways (KEGG), gene regulatory relationships (TRANSFAC) into our bioinformatics system [1]. We collected available experimental gene expression data from S. cerevisiae during oxidative stress response at different time points [2]. The data was integrated into the network context by defining criteria for evaluating presence or absence of proteins in the integrated network. Swissprot index of S. cerevisiae proteins [3] was used to translate ORF identifiers into the expression dataset to Swissprot protein accession numbers. We thus reduced the networks and reconstructed condition specific networks corresponding to each expression data by removing all the proteins that are absent and their incident links. Structural organization of these networks was compared by studying topological characteristics. We found that the degree distribution of most of the networks obtained was different from the power law. Additionally, we found changes in clustering coefficient, i.e. local connectivity properties, at two specific time points during the oxidative stress response. Our results suggest the connectivity of the system is being modulated as a response to stress or other external stimuli.

AB - The topology of metabolic or protein-protein interaction networks has been an extensively studied subject. Our primary interest on the topic is how the context, such as changing physiological state of the system, affects the network topology and connectivity within- and between the cellular functional modules and through this obtain better understating about the control mechanisms of biological systems. In this study we investigated the changes in network structure as results of oxidative stress. We collected S. cerevisiae data on protein-protein interactions (DIP), metabolic pathways (KEGG), gene regulatory relationships (TRANSFAC) into our bioinformatics system [1]. We collected available experimental gene expression data from S. cerevisiae during oxidative stress response at different time points [2]. The data was integrated into the network context by defining criteria for evaluating presence or absence of proteins in the integrated network. Swissprot index of S. cerevisiae proteins [3] was used to translate ORF identifiers into the expression dataset to Swissprot protein accession numbers. We thus reduced the networks and reconstructed condition specific networks corresponding to each expression data by removing all the proteins that are absent and their incident links. Structural organization of these networks was compared by studying topological characteristics. We found that the degree distribution of most of the networks obtained was different from the power law. Additionally, we found changes in clustering coefficient, i.e. local connectivity properties, at two specific time points during the oxidative stress response. Our results suggest the connectivity of the system is being modulated as a response to stress or other external stimuli.

M3 - Conference abstract in proceedings

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T3 - VTT Symposium

SP - 67

BT - International Specialised Symposium on Yeasts ISSY25

PB - VTT Technical Research Centre of Finland

CY - Espoo

ER -

Gopalacharuyly P, Velagapudi V, Lindfors E, Oresic M. Dynamic network topology changes as result of cellular stress. In International Specialised Symposium on Yeasts ISSY25: Systems Biology of Yeasts - from Models to Applications. Espoo: VTT Technical Research Centre of Finland. 2006. p. 67. P15. (VTT Symposium; No. 242).