Causal network inference using biochemical kinetics

Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee

Research output: Contribution to journalArticle

29 Scopus citations

Abstract

Motivation: Networks are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of biochemical systems are generally non-linear, suggesting that suitable non-linear formulations may offer gains with respect to causal network inference and aid in associated prediction problems. Results: We present a general framework for network inference and dynamical prediction using time course data that is rooted in nonlinear biochemical kinetics. This is achieved by considering a dynamical system based on a chemical reaction graph with associated kinetic parameters. Both the graph and kinetic parameters are treated as unknown; inference is carried out within a Bayesian framework. This allows prediction of dynamical behavior even when the underlying reaction graph itself is unknown or uncertain. Results, based on (i) data simulated from a mechanistic model of mitogen-activated protein kinase signaling and (ii) phosphoproteomic data from cancer cell lines, demonstrate that non-linear formulations can yield gains in causal network inference and permit dynamical prediction and uncertainty quantification in the challenging setting where the reaction graph is unknown.

Original languageEnglish (US)
Pages (from-to)i468-i474
JournalBioinformatics
Volume30
Issue number17
DOIs
StatePublished - Sep 1 2014

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ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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