Stabilizing and destabilizing effects of embedding 3-node subgraphs on the state space of boolean networks

Chikoo Oosawa, Michael A. Savageau, Abdul S. Jarrah, Reinhard C. Laubenbacher, Eduardo D. Sontag

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

We demonstrate the effects of embedding subgraphs in a Boolean network, which is one of the discrete dynamic models for transcriptional regulatory networks. After comparing the dynamic properties of networks embedded with seven different subgraphs including feedback and feedforward subgraphs, we found that complexity of the state space increases with longer lengths of attractors, and the number of attractors is reduced for networks with more feedforward subgraphs. In addition, feedforward subgraphs can provide higher mutual information with lower entropy in a temporal program of gene expression. Networks with the other six subgraphs show opposite effects on network dynamics. This is roughly consistent with Thomas's conjecture. These results suggest that feedforward subgraph is favorable local structure in complex biological networks.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages100-107
Number of pages8
Volume5191 LNCS
DOIs
StatePublished - 2008
Event8th International Conference on Cellular Automata for Research and Industry, ACRI 2008 - Yokohama, Japan
Duration: Sep 23 2008Sep 26 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5191 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other8th International Conference on Cellular Automata for Research and Industry, ACRI 2008
CountryJapan
CityYokohama
Period9/23/089/26/08

Keywords

  • Boolean networks
  • Entropy
  • Feedback
  • Feedforward
  • Mutual information
  • Subgraph
  • Thomas's conjecture
  • Transcriptional regulatory networks

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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    Oosawa, C., Savageau, M. A., Jarrah, A. S., Laubenbacher, R. C., & Sontag, E. D. (2008). Stabilizing and destabilizing effects of embedding 3-node subgraphs on the state space of boolean networks. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 5191 LNCS, pp. 100-107). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5191 LNCS). https://doi.org/10.1007/978-3-540-79992-4_13