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Title: Boolean dynamics of genetic regulatory networks inferred from microarray time series data

Journal Article · · Bioinformatics
 [1];  [2];  [3];  [4]
  1. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Computational Biology Dept.
  2. Sandia National Lab. (SNL-CA), Livermore, CA (United States). Biosystems Research
  3. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Biomolecular Analysis and Imaging
  4. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Computational Biosciences Dept.
+ Show Author Affiliations

Methods available for the inference of genetic regulatory networks strive to produce a single network, usually by optimizing some quantity to fit the experimental observations. In this paper we investigate the possibility that multiple networks can be inferred, all resulting in similar dynamics. This idea is motivated by theoretical work which suggests that biological networks are robust and adaptable to change, and that the overall behavior of a genetic regulatory network might be captured in terms of dynamical basins of attraction. We have developed and implemented a method for inferring genetic regulatory networks for time series microarray data. Our method first clusters and discretizes the gene expression data using k-means and support vector regression. We then enumerate Boolean activation–inhibition networks to match the discretized data. In conclusion, the dynamics of the Boolean networks are examined. We have tested our method on two immunology microarray datasets: an IL-2-stimulated T cell response dataset and a LPS-stimulated macrophage response dataset. In both cases, we discovered that many networks matched the data, and that most of these networks had similar dynamics.

Research Organization:
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA); SNL Laboratory Directed Research and Development (LDRD) Program
Grant/Contract Number:
AC04-94AL85000
OSTI ID:
1427005
Report Number(s):
SAND2007-0437J; 524009
Journal Information:
Bioinformatics, Vol. 23, Issue 7; ISSN 1367-4803
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 105 works
Citation information provided by
Web of Science

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Inferring Gene Regulatory Networks Using Hybrid Parallel Computing book July 2018
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Boolean modeling in systems biology: an overview of methodology and applications journal September 2012
Big Data Analytics in Healthcare journal January 2015
A novel parametric approach to mine gene regulatory relationship from microarray datasets journal December 2010
Adapted Boolean network models for extracellular matrix formation journal July 2009
Deriving a Boolean dynamics to reveal macrophage activation with in vitro temporal cytokine expression profiles journal December 2019
Reconstruction of a gene regulatory network of the induced systemic resistance defense response in Arabidopsis using boolean networks journal April 2020
Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size journal June 2017
Repairing Boolean logical models from time-series data using Answer Set Programming journal March 2019
Big Data Analytics in Healthcare book January 2021
Big Data Analytics in Healthcare book October 2020
Inferring cluster-based networks from differently stimulated multiple time-course gene expression data journal March 2010
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking journal September 2010
Polynomial-Time Algorithm for Controllability Test of a Class of Boolean Biological Networks journal January 2010
Neutral space analysis for a Boolean network model of the fission yeast cell cycle network journal January 2014
Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference journal October 2009
Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference journal August 2008
Subcellular proteomic characterization of the high-temperature stress response of the cyanobacterium Spirulina platensis journal January 2009
Comparative analysis of the Spirulina platensis subcellular proteome in response to low- and high-temperature stresses: uncovering cross-talk of signaling components journal July 2011
The correlation between architecture and mRNA abundance in the genetic regulatory network of Escherichia coli journal July 2007
Dynamical pathway analysis journal January 2008
Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks journal January 2012
Gene perturbation and intervention in context-sensitive stochastic Boolean networks journal May 2014
Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions journal August 2007
Differential Dynamic Properties of Scleroderma Fibroblasts in Response to Perturbation of Environmental Stimuli journal February 2008
Analysis and Practical Guideline of Constraint-Based Boolean Method in Genetic Network Inference journal January 2012
A Relative Variation-Based Method to Unraveling Gene Regulatory Networks journal February 2012
Gene Regulatory Network Inference from Multifactorial Perturbation Data Using both Regression and Correlation Analyses journal September 2012
An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data journal June 2013
A Kalman-Filter Based Approach to Identification of Time-Varying Gene Regulatory Networks journal October 2013
Refining Ensembles of Predicted Gene Regulatory Networks Based on Characteristic Interaction Sets journal February 2014
Data- and knowledge-based modeling of gene regulatory networks: an update text January 2015
Inference of Gene Regulatory Networks Using Time-Series Data: A Survey journal September 2009
Validation of gene regulatory network inference based on controllability journal January 2013
A new mathematical approach for qualitative modeling of the insulin-TOR-MAPK network journal January 2013

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