Systematic reverse engineering of network topologies: A case study of resettable bistable cellular responses

Debasish Mondal, Edward Dougherty, Abhishek Mukhopadhyay, Adria Carbo, Guang Yao, Jianhua Xing

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

A focused theme in systems biology is to uncover design principles of biological networks, that is, how specific network structures yield specific systems properties. For this purpose, we have previously developed a reverse engineering procedure to identify network topologies with high likelihood in generating desired systems properties. Our method searches the continuous parameter space of an assembly of network topologies, without enumerating individual network topologies separately as traditionally done in other reverse engineering procedures. Here we tested this CPSS (continuous parameter space search) method on a previously studied problem: the resettable bistability of an Rb-E2F gene network in regulating the quiescence-to-proliferation transition of mammalian cells. From a simplified Rb-E2F gene network, we identified network topologies responsible for generating resettable bistability. The CPSS-identified topologies are consistent with those reported in the previous study based on individual topology search (ITS), demonstrating the effectiveness of the CPSS approach. Since the CPSS and ITS searches are based on different mathematical formulations and different algorithms, the consistency of the results also helps cross-validate both approaches. A unique advantage of the CPSS approach lies in its applicability to biological networks with large numbers of nodes. To aid the application of the CPSS approach to the study of other biological systems, we have developed a computer package that is available in Information S1.

Original languageEnglish (US)
Article numbere105833
JournalPLoS One
Volume9
Issue number8
DOIs
StatePublished - Aug 29 2014

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Reverse engineering
topology
engineering
Topology
case studies
Retinoblastoma Genes
Gene Regulatory Networks
Systems Biology
Genes
Biological systems
Cells
Biological Sciences
methodology

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Systematic reverse engineering of network topologies : A case study of resettable bistable cellular responses. / Mondal, Debasish; Dougherty, Edward; Mukhopadhyay, Abhishek; Carbo, Adria; Yao, Guang; Xing, Jianhua.

In: PLoS One, Vol. 9, No. 8, e105833, 29.08.2014.

Research output: Contribution to journalArticle

Mondal, Debasish ; Dougherty, Edward ; Mukhopadhyay, Abhishek ; Carbo, Adria ; Yao, Guang ; Xing, Jianhua. / Systematic reverse engineering of network topologies : A case study of resettable bistable cellular responses. In: PLoS One. 2014 ; Vol. 9, No. 8.
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