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Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

  • Vân Anh Huynh-Thu ,

    vahuynh@ulg.ac.be

    Affiliations Department of Electrical Engineering and Computer Science, Systems and Modeling, University of Liège, Liège, Belgium, GIGA-Research, Bioinformatics and Modeling, University of Liège, Liège, Belgium

  • Alexandre Irrthum,

    Affiliations Department of Electrical Engineering and Computer Science, Systems and Modeling, University of Liège, Liège, Belgium, GIGA-Research, Bioinformatics and Modeling, University of Liège, Liège, Belgium

  • Louis Wehenkel,

    Affiliations Department of Electrical Engineering and Computer Science, Systems and Modeling, University of Liège, Liège, Belgium, GIGA-Research, Bioinformatics and Modeling, University of Liège, Liège, Belgium

  • Pierre Geurts

    Affiliations Department of Electrical Engineering and Computer Science, Systems and Modeling, University of Liège, Liège, Belgium, GIGA-Research, Bioinformatics and Modeling, University of Liège, Liège, Belgium

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

  • Vân Anh Huynh-Thu, 
  • Alexandre Irrthum, 
  • Louis Wehenkel, 
  • Pierre Geurts
PLOS
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Abstract

One of the pressing open problems of computational systems biology is the elucidation of the topology of genetic regulatory networks (GRNs) using high throughput genomic data, in particular microarray gene expression data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) challenge aims to evaluate the success of GRN inference algorithms on benchmarks of simulated data. In this article, we present GENIE3, a new algorithm for the inference of GRNs that was best performer in the DREAM4 In Silico Multifactorial challenge. GENIE3 decomposes the prediction of a regulatory network between p genes into p different regression problems. In each of the regression problems, the expression pattern of one of the genes (target gene) is predicted from the expression patterns of all the other genes (input genes), using tree-based ensemble methods Random Forests or Extra-Trees. The importance of an input gene in the prediction of the target gene expression pattern is taken as an indication of a putative regulatory link. Putative regulatory links are then aggregated over all genes to provide a ranking of interactions from which the whole network is reconstructed. In addition to performing well on the DREAM4 In Silico Multifactorial challenge simulated data, we show that GENIE3 compares favorably with existing algorithms to decipher the genetic regulatory network of Escherichia coli. It doesn't make any assumption about the nature of gene regulation, can deal with combinatorial and non-linear interactions, produces directed GRNs, and is fast and scalable. In conclusion, we propose a new algorithm for GRN inference that performs well on both synthetic and real gene expression data. The algorithm, based on feature selection with tree-based ensemble methods, is simple and generic, making it adaptable to other types of genomic data and interactions.

Introduction

Genetic regulatory networks (GRNs) [1] are central to all biological organisms, and their deciphering is crucial to understand the development, functioning and pathology of these organisms. Once a remote theoretical possibility, this deciphering is now made possible by advances in genomics, most notably high-throughput profiling of gene expression patterns with DNA microarrays. These advances have prompted the development of a plethora of models of GRNs and algorithms to reverse-engineer them from expression data [2][5].

The simplest models of genetic regulatory networks are based on Boolean logic. Because of their simplicity, these Boolean network models have provided high-level insights into the design principles and emerging properties of GRNs [6]. At the other end of the complexity spectrum are physical models mimicking the biological mechanisms at play, including promoter recognition, mRNA transcription and protein translation. These models, typically based on systems of ordinary or stochastic differential equations, can generate realistic behavior [7]. One of their main drawbacks is that they have high-dimensional parameter spaces, and thus a large number of experimental data are needed for their identification. Nevertheless, hybrid methods involving ordinary differential equations have shown good performances on real-life genome-wide GRN inference [8].

Models based on the statistical analysis of dependencies between expression patterns have an intermediate complexity, and have already been successfully applied to the inference of large GRNs. Early models used correlation coefficients between expression patterns of all pairs of genes to infer “coexpression networks” [9]. However, correlation coefficients fail to capture more complex statistical dependencies (e.g. non-linear ones) between expression patterns, and thus more general measures of dependency based on mutual information (MI), have been proposed. The simplest model based on this measure, the “relevance network”, computes MI between all pairs of genes and infers the presence of a regulatory interaction when MI is larger than a given threshold [10]. Various refinements have been proposed to try to discriminate between direct and indirect interactions in relevance networks. The CLR algorithm [11] modifies the MI score based on the empirical distribution of all MI scores. The ARACNE algorithm [12] filters out indirect interactions from triplets of genes with the Data Processing Inequality [13]. Finally, MRNET [14] uses an iterative feature selection method based on a maximum relevance/minimum redundancy criterion.

Probabilistic graphical models have been widely used to model GRNs [15]. With respect to correlation or mutual information based approaches, these methods are potentially able to model higher-order dependencies between the expression patterns of genes. Among these methods, Bayesian networks have been used since the advent of microarray technologies for GRN modeling and inference [16]. A Bayesian network represents conditional dependencies between random variables with a directed acyclic graph. Learning the structure of a Bayesian network is a non trivial problem, both from a theoretical and computational point of view, and several sophisticated heuristics have been proposed in the context of GRN inference [17], [18]. One limitation of Bayesian networks for GRN inference is that these models do not allow the presence of cycles (feedback loops). While this limitation is partially circumvented by dynamic Bayesian networks [17], [19], these models can only be learned from time-series expression data. Another family of probabilistic models that gained interest recently for GRN inference are Gaussian graphical models. These methods assume that gene expression values are jointly Gaussian distributed and represent conditional dependencies between genes by an undirected graph. The estimation of this graph for high-dimensional data is difficult but several robust solutions have been proposed in the literature [20][23]. Although often very effective, the main limitations of these methods is of course the Gaussianity assumption, which also implies linear dependencies between variables, and the undirected nature of the inferred regulatory links (although some heuristics have been proposed to direct them [24]).

Within this context, this article presents GENIE3 (for “GEne Network Inference with Ensemble of trees”), a new GRN inference method based on variable selection with ensembles of regression trees. This method was best performer in the DREAM4 In Silico Multifactorial challenge [25]. Its main features with respect to existing techniques is that it makes very few assumptions about the nature of the relationships between the variables (which can thus be non-linear) and can potentially capture high-order conditional dependencies between expression patterns. It also produces a directed graph of regulatory interactions and naturally allows for the presence of feedback loops in the network. At the same time, it remains intuitive, computationally tractable, and easy to implement. In addition to its good performance on the synthetic data of the DREAM4 challenge, we show that GENIE3 compares favorably with existing algorithms to decipher the genetic regulatory network of Escherichia coli.

Methods

Problem Definition

We address the problem of recovering regulatory networks from gene expression data. The targeted networks are directed graphs with p nodes, where each node represents a gene, and an edge directed from one gene i to another gene j indicates that gene i (directly) regulates the expression of gene j. We only consider unsigned edges; when gene i is connected to gene j, the former can be either an activator or a repressor of the latter.

The goal of (unsupervised) gene regulatory network inference is to recover the network solely from measurements of the expression of the genes in various conditions. Given the dynamic and combinatorial nature of genetic regulation, measurements of different kinds can be obtained, including steady-state expression profiles resulting from the systematic knockout or knockdown of genes or time series measurements resulting from random perturbations. In this paper, we focus on multifactorial perturbation data as generated for the DREAM4 In Silico Size 100 Multifactorial subchallenge. Multifactorial expression data are static steady-state measurements obtained by (slightly) perturbing all genes simultaneously. Multifactorial data might correspond for example to expression profiles obtained from different patients or biological replicates. Such data are easier and less expensive to obtain than knockout/knockdown or time series data and are thus more common in practice. They are however also less informative for the prediction of edge directionality [3], [26], [27] and therefore make the regulatory network inference task more challenging.

In what follows, we define a (multifactorial) learning sample from which to infer the network as a sample of N measurements:where is a vector of expression values of all p genes in the kth experiment:

From this learning sample, the goal of network inference algorithms is to make a prediction of the underlying regulatory links between genes. Most network inference algorithms work first by providing a ranking of the potential regulatory links from the most to the less significant. A practical network prediction is then obtained by setting a threshold on this ranking. In this paper, we focus only on the first task, which is also targeted by the evaluation procedure of the DREAM4 challenge. The question of the choice of an optimal confidence threshold, although important, will be left open.

A network inference algorithm is thus defined in this paper as a procedure that exploits a LS to assign weights to putative regulatory links from any gene i to any gene j, with the aim of yielding large values for weights which correspond to actual regulatory interactions.

Network Inference with Tree-based Methods

The basic idea of our procedure is to decompose the problem of recovering a network involving p genes into p different subproblems, where each of these subproblems consists in identifying the regulators of one of the genes of the network. Exploiting expression data, the identification of the regulatory genes for a given target gene is defined as determining the subset of genes whose expression directly influences or is predictive of the expression of the target gene. Within the framework of supervised learning, this problem is equivalent to a feature selection problem. In this context, our solution will exploit the embedded feature ranking mechanism of tree-based ensemble methods.

We first describe our procedure to solve the network inference problem using feature selection techniques and then specialize it to the case of tree-based ensemble methods.

Network Inference