Comparative co-expression analysis in plant biology

Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
Plant Cell and Environment (Impact Factor: 6.96). 04/2012; 35(10):1787-98. DOI: 10.1111/j.1365-3040.2012.02517.x
Source: PubMed


The analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has shown that transcriptionally coordinated genes are often functionally related. Based on large-scale expression compendia grouping multiple experiments, this guilt-by-association principle has been applied to study modular gene programmes, identify cis-regulatory elements or predict functions for unknown genes in different model plants. Recently, several studies have demonstrated how, through the integration of gene homology and expression information, correlated gene expression patterns can be compared between species. The incorporation of detailed functional annotations as well as experimental data describing protein-protein interactions, phenotypes or tissue specific expression, provides an invaluable source of information to identify conserved gene modules and translate biological knowledge from model organisms to crops. In this review, we describe the different steps required to systematically compare expression data across species. Apart from the technical challenges to compute and display expression networks from multiple species, some future applications of plant comparative transcriptomics are highlighted.

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    • "A strong correlation among transcripts for MRC components has been found by this type of coexpression analysis in plants. In the case of plant MRC genes, it has been shown that genes belonging to MRCs are clustered into the same coexpression group [10]. Similarly, several mtDNA-encoded mitochondrial genes form a small cluster with a nuclear-encoded mitochondrial gene module and the glycolysis module [12]. "
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    ABSTRACT: As energy producers, mitochondria play a pivotal role in multiple cellular processes. Although several lines of evidence suggest that differential expression of mitochondrial respiratory complexes (MRCs) has a significant impact on mitochondrial function, the role of integrated MRCs in the whole coexpression network has yet to be revealed. In this study, we construct coexpression networks based on microarray datasets from different tissues and chemical treatments to explore the role of integrated MRCs in the coexpression network and the effects of different chemicals on the mitochondrial network. By grouping MRCs as one seed target, the hypergeometric distribution allowed us to identify genes that are significantly coexpress with whole MRCs. Coexpression among 46 MRC genes (approximately 78% of MRC genes tested) was significant in the normal tissue transcriptome dataset. These MRC genes are coexpressed with genes involved in the categories "muscle system process," "metabolic process," and "neurodegenerative disease pathways," whereas, in the chemically treated tissues, coexpression of these genes mostly disappeared. These results indicate that chemical stimuli alter the normal coexpression network of MRC genes. Taken together, the datasets obtained from the different coexpression networks are informative about mitochondrial biogenesis and should contribute to understanding the side effects of drugs on mitochondrial function.
    International Journal of Plant Genomics 06/2014; 2014:452891. DOI:10.1155/2014/452891
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    • "Patterns of gene expression have now been characterized in a large number of species (reviewed in Snell-Rood et al., 2010), but relatively few have compared species to identify which genes have conserved or divergent patterns of expression. While genes with conserved patterns can be identified by comparing co-expression networks characterized in different experiments (reviewed in Movahedi et al., 2012), such meta-analyses have less power to assess divergent expression in response to environment, because experimental conditions differ among studies. Here, we describe the results of a study on gene expression in lodgepole pine (Pinus contorta) and interior spruce (natural hybrid Picea engelmannii 9 Picea glauca) seedlings in response to a range of climatic and photoperiodic treatments. "
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    ABSTRACT: Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change.By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii).We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11 658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression.We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.
    New Phytologist 04/2014; 203(2). DOI:10.1111/nph.12819 · 7.67 Impact Factor
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    • "In plants, three particularly interesting network-based studies of co-expression conservation have been published (for a review see Movahedi et al. [24]). Mutwil et al.[25] computed the similarity of co-expression network vicinities based on Pfam [26] across seven plant species. "
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    ABSTRACT: Divergence 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. We 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. We have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Comparative analysis of Plant co-Expression networks (ComPlEx, 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.
    BMC Genomics 02/2014; 15(1):106. DOI:10.1186/1471-2164-15-106 · 3.99 Impact Factor
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