Physical network models

Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach

The number of complete, publicly available genome sequences is now greater than 200, and this number is expected to rapidly grow in the near future as metagenomic and environmental sequencing efforts escalate and the cost of sequencing drops. In order to make use of this data for understanding particular organisms and for discerning general principles about how organisms function, it will be necessary to reconstruct their various biochemical reaction networks. Principal among these will be transcriptional regulatory networks. Given the physical and logical complexity of these networks, the various sources of (often noisy) data that can be utilized for their elucidation, the monetary costs involved, and the huge number of potential experiments (~10¹²) that can be performed, experiment design algorithms will be necessary for synthesizing the various computational and experimental data to maximize the efficiency of regulatory network reconstruction. This paper presents an algorithm for experimental design to systematically and efficiently reconstruct transcriptional regulatory networks. It is meant to be applied iteratively in conjunction with an experimental laboratory component. The algorithm is presented here in the context of reconstructing transcriptional regulation for metabolism in Escherichia coli, and, through a retrospective analysis with previously performed experiments, we show that the produced experiment designs conform to how a human would design experiments. The algorithm is able to utilize probability estimates based on a wide range of computational and experimental sources to suggest experiments with the highest potential of discovering the greatest amount of new regulatory knowledge.

In recent years, the exploration of life has been bolstered through the advent of whole genome sequencing. This new data source significantly enables the reconstruction of genome-scale metabolic networks. After a metabolic reconstruction, it will be necessary to discover the genetic control mechanisms that operate within an organism. Transcriptional regulatory network (TRN) reconstruction is costly both in terms of time and money, so it is critical that the reconstruction efforts be made as efficient as possible. Experiments must be designed so that the most new regulatory knowledge is discovered in each experiment. The huge number of possible experiments (~10¹²) and the vast amount of heterogeneous data available for designing experiments overwhelms the human ability to assimilate. The authors have developed an algorithm that utilizes a mathematical model of a reconstructed metabolic network integrated with a partially reconstructed TRN to identify the experiment designs with the highest potential of yielding the most new regulatory knowledge. The authors show that the produced experiment designs are similar to those a human expert would produce, and that the algorithm has a facility to incorporate any relevant data source to design such experiments.

Non-transcriptional pathway features reconstructed from secondary effects of RNA interference

MOTIVATION

Cellular signaling pathways, which are not modulated on a transcriptional level, cannot be directly deduced from expression profiling experiments. The situation changes, when external interventions such as RNA interference or gene knock-outs come into play. Even if the expression of the signaling genes is not changed, secondary effects in downstream genes shed light on the pathway, and allow partial reconstruction of its topology.

RESULTS

We introduce an algorithm to infer non-transcriptional pathway features based on differential gene expression in silencing assays. We demonstrate the power of our algorithm in the controlled setting of simulation studies, and explain its practical use in the context of an RNA interference dataset investigating the response to microbial challenge in Drosophila melanogaster.

Validation and refinement of gene-regulatory pathways on a network of physical interactions

As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. Towards this goal, we describe an automated procedure for prioritizing genetic perturbations in order to discriminate optimally between alternative models of a gene-regulatory network. Using this procedure, we evaluate 38 candidate regulatory networks in yeast and perform four high-priority gene knockout experiments. The refined networks support previously unknown regulatory mechanisms downstream of SOK2 and SWI4.