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Theory on the dynamics of feedforward loops in the transcription factor networks
Published in
2012
PMID: 22911735
Volume: 7
   
Issue: 7
Abstract
Feedforward loops (FFLs) consist of three genes which code for three different transcription factors A, B and C where B regulates C and A regulates both B and C. We develop a detailed model to describe the dynamical behavior of various types of coherent and incoherent FFLs in the transcription factor networks. We consider the deterministic and stochastic dynamics of both promoter-states and synthesis and degradation of mRNAs of various genes associated with FFL motifs. Detailed analysis shows that the response times of FFLs strongly dependent on the ratios (wh = γpc/γph where h = a, b, c corresponding to genes A, B and C) between the lifetimes of mRNAs (1/γmh) of genes A, B and C and the protein of C (1/γpc). Under strong binding conditions we can categorize all the possible types of FFLs into groups I, II and III based on the dependence of the response times of FFLs on wh. Group I that includes C1 and I1 type FFLs seem to be less sensitive to the changes in wh. The coherent C1 type seems to be more robust against changes in other system parameters. We argue that this could be one of the reasons for the abundant nature of C1 type coherent FFLs. © 2012 Rajamanickam Murugan.
About the journal
JournalPLoS ONE
ISSN19326203
Open AccessNo
Concepts (26)
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    Messenger rna
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    Transcription factor
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    Article
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    Binding affinity
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    Binding site
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    Controlled study
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    GENE IDENTIFICATION
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    Gene regulatory network
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    Genetic association
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    Genetic variability
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    Mathematical computing
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    Mathematical model
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    Molecular dynamics
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    Molecular interaction
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    Positive feedback
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    Probability
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    Promoter region
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    RNA BINDING
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    RNA DEGRADATION
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    Rna synthesis
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    Algorithms
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    Gene expression regulation
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    Models, theoretical
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    Promoter regions, genetic
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    Rna, messenger
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    Transcription factors