Comparative Analysis of Gene Regulatory Networks in Plants

We are intrigued by the regulatory complexity of plants in general and trees in particular. We use systems biology methods to study how perturbations propagate through, potentially complex, network interactions and how such responses are conserved across species. More specifically, we have used co-expression networks to study the evolution of gene regulation across A. thaliana, O. sativa and Populus spp., but we are working on integrating Picea abies in addition to other species. The approach highlights conservation and divergence of various network properties, rather than that of protein sequence, and offers some novel perspectives related to orthologs and paralogs in plants. For example, we observe that for genes with multiple ortholog predictions the ortholog with the most conserved sequence is in more than half the cases not the ortholog with the most conserved gene regulation.  In P. trichocarpa, we have studied the phenotypic effects of perturbing a number of genes including transcription factors in the context of a wood development network, and have made a number of interesting observations relating to the predictive capabilities of the network.

We have developed tools for network analysis of tree transcriptomes including ComPlEx (Comparative Analysis of Plant Expression Networks) and new capabilities within the PopGenIE/ConGenIE platforms (The Populus and Conifer Genome Integrative Explorer). All tools are available from the PlantGenIE web resource (http://plantgenie.org).