Combining tree-based and dynamical systems for the inference of gene regulatory networks

Bioinformatics. 2015 May 15;31(10):1614-22. doi: 10.1093/bioinformatics/btu863. Epub 2015 Jan 7.

Abstract

Motivation: Reconstructing the topology of gene regulatory networks (GRNs) from time series of gene expression data remains an important open problem in computational systems biology. Existing GRN inference algorithms face one of two limitations: model-free methods are scalable but suffer from a lack of interpretability and cannot in general be used for out of sample predictions. On the other hand, model-based methods focus on identifying a dynamical model of the system. These are clearly interpretable and can be used for predictions; however, they rely on strong assumptions and are typically very demanding computationally.

Results: Here, we propose a new hybrid approach for GRN inference, called Jump3, exploiting time series of expression data. Jump3 is based on a formal on/off model of gene expression but uses a non-parametric procedure based on decision trees (called 'jump trees') to reconstruct the GRN topology, allowing the inference of networks of hundreds of genes. We show the good performance of Jump3 on in silico and synthetic networks and applied the approach to identify regulatory interactions activated in the presence of interferon gamma.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Computational Biology / methods*
  • Databases, Factual
  • Decision Trees*
  • Gene Expression Regulation*
  • Gene Regulatory Networks*
  • Macrophages / metabolism
  • Mice
  • Oligonucleotide Array Sequence Analysis
  • Saccharomyces cerevisiae / genetics
  • Systems Biology / methods*
  • Transcription Factors / metabolism

Substances

  • Transcription Factors