title: Construction and comparison of gene co-expression networks shows complex plant immune responses.
abstract: Gene co-expression networks (GCNs) are graphic representations that depict the coordinated transcription of genes in response to certain stimuli. GCNs provide functional annotations of genes whose function is unknown and are further used in studies of translational functional genomics among species. In this work, a methodology for the reconstruction and comparison of GCNs is presented. This approach was applied using gene expression data that were obtained from immunity experiments in Arabidopsis thaliana, rice, soybean, tomato and cassava. After the evaluation of diverse similarity metrics for the GCN reconstruction, we recommended the mutual information coefficient measurement and a clustering coefficient-based method for similarity threshold selection. To compare GCNs, we proposed a multivariate approach based on the Principal Component Analysis (PCA). Branches of plant immunity that were exemplified by each experiment were analyzed in conjunction with the PCA results, suggesting both the robustness and the dynamic nature of the cellular responses. The dynamic of molecular plant responses produced networks with different characteristics that are differentiable using our methodology. The comparison of GCNs from plant pathosystems, showed that in response to similar pathogens plants could activate conserved signaling pathways. The results confirmed that the closeness of GCNs projected on the principal component space is an indicative of similarity among GCNs. This also can be used to understand global patterns of events triggered during plant immune responses.
authors.affiliation: Department of Statistics, Universidad Nacional de Colombia , Bogotá , Colombia.
authors.forename: Luis Guillermo
authors.initials: LG
authors.lastname: Leal
authors.affiliation: Department of Biology, Universidad Nacional de Colombia , Bogotá , Colombia.
authors.forename: Camilo
authors.initials: C
authors.lastname: López
authors.affiliation: Department of Statistics, Universidad Nacional de Colombia , Bogotá , Colombia.
authors.forename: Liliana
authors.initials: L
authors.lastname: López-Kleine
keywords: Gene co-expression networks; Networks comparison; Plant immunity; Principal Component Analysis; Similarity measures; Similarity threshold