ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

BMC Genomics

Research Article

David Sundell¹  Nathaniel R Street¹  Sergiu Netotea¹  Torgeir R Hvidsten² 

[1] Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden;Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden;Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden;Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden;Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås NO-1432, Norway;

关键词: Gene Ontology;    Gene Regulation Network;    Betweenness Centrality;    Network Property;    Network Motif;   

DOI  :  10.1186/1471-2164-15-106

 received in 2013-11-04, accepted in 2014-01-29,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundDivergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes.ResultsWe inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds. In addition to quantifying gene-gene link and network neighbourhood conservation, we also applied recent advancements in network analysis to do cross-species comparisons of network properties such as scale free characteristics and gene centrality as well as network motifs. We found that in all species the networks emerged as scale free only above a certain co-expression threshold, and that the high-centrality genes upholding this organization tended to be conserved. Network motifs, in particular the feed-forward loop, were found to be significantly enriched in specific functional subnetworks but where much less conserved across species than gene centrality. Although individual gene-gene co-expression had massively diverged, up to ~80% of the genes still had a significantly conserved network neighbourhood. For genes with multiple predicted orthologs, about half had one ortholog with conserved regulation and another ortholog with diverged or non-conserved regulation. Furthermore, the most sequence similar ortholog was not the one with the most conserved gene regulation in over half of the cases.ConclusionsWe have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Com parative analysis of Pl ant co-Ex pression networks (ComPlEx, http://complex.plantgenie.org/). The tool can be particularly useful for identifying the ortholog with the most conserved regulation among several sequence-similar alternatives and can thus be of practical importance in e.g. finding candidate genes for perturbation experiments.

【 授权许可】

Unknown   
© Netotea et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.