DREAM4: Combining genetic and dynamic information to identify biological networks and Dynamical Models

Alex Greenfield, Aviv Madar, Harry Ostrer, Richard Bonneau

Research output: Contribution to journalArticle

114 Citations (Scopus)

Abstract

Background: Current technologies have lead to the availability of multiple genomic data types in sufficient quantity and quality to serve as a basis for automatic global network inference. Accordingly, there are currently a large variety of network inference methods that learn regulatory networks to varying degrees of detail. These methods have different strengths and weaknesses and thus can be complementary. However, combining different methods in a mutually reinforcing manner remains a challenge. Methodology: We investigate how three scalable methods can be combined into a useful network inference pipeline. The first is a novel t-test-based method that relies on a comprehensive steady-state knock-out dataset to rank regulatory interactions. The remaining two are previously published mutual information and ordinary differential equation based methods (tlCLR and Inferelator 1.0, respectively) that use both time-series and steady-state data to rank regulatory interactions; the latter has the added advantage of also inferring dynamic models of gene regulation which can be used to predict the system's response to new perturbations. Conclusion/Significance: Our t-test based method proved powerful at ranking regulatory interactions, tying for first out of 19 methods in the DREAM4 100-gene in-silico network inference challenge. We demonstrate complementarity between this method and the two methods that take advantage of time-series data by combining the three into a pipeline whose ability to rank regulatory interactions is markedly improved compared to either method alone. Moreover, the pipeline is able to accurately predict the response of the system to new conditions (in this case new double knock-out genetic perturbations). Our evaluation of the performance of multiple methods for network inference suggests avenues for future methods development and provides simple considerations for genomic experimental design. Our code is publicly available at http://err.bio.nyu.edu/inferelator/.

Original languageEnglish (US)
Article numbere13397
JournalPLoS One
Volume5
Issue number10
DOIs
StatePublished - 2010
Externally publishedYes

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Pipelines
Time series
Gene expression
Ordinary differential equations
Design of experiments
Dynamic models
Genes
methodology
Availability
time series analysis
genomics
Computer Simulation
dynamic models
Research Design
experimental design
Technology

ASJC Scopus subject areas

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

Cite this

DREAM4 : Combining genetic and dynamic information to identify biological networks and Dynamical Models. / Greenfield, Alex; Madar, Aviv; Ostrer, Harry; Bonneau, Richard.

In: PLoS One, Vol. 5, No. 10, e13397, 2010.

Research output: Contribution to journalArticle

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