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The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughput Map-O-Matic tool matches co-expression(More)
Plant cell walls are complex composites largely consisting of carbohydrate-based polymers, and are generally divided into primary and secondary walls based on content and characteristics. Cellulose microfibrils constitute a major component of both primary and secondary cell walls and are synthesized at the plasma membrane by cellulose synthase (CESA)(More)
A vital quest in biology is comprehensible visualization and interpretation of correlation relationships on a genome scale. Such relationships may be represented in the form of networks, which usually require disassembly into smaller manageable units, or clusters, to facilitate interpretation. Several graph-clustering algorithms that may be used to(More)
The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed) genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species,(More)
Transcriptional coordination, or co-expression, of genes may signify functional relatedness of the corresponding proteins. For example, several genes involved in secondary cell wall cellulose biosynthesis are co-expressed with genes engaged in the synthesis of xylan, which is a major component of the secondary cell wall. To extend these types of analyses,(More)
Plant primary metabolism is a highly coordinated, central, and complex network of biochemical processes regulated at both the genetic and post-translational levels. The genetic basis of this network can be explored by analyzing the metabolic composition of genetically diverse genotypes in a given plant species. Here, we report an integrative strategy(More)
Introduction Recent advances in high-throughput techniques allow for simultaneously measuring huge amounts of biological data. Handling the tremendous mass of data produced by these methods currently poses major challenges in the field of theoretical biology. One way of illustrating the data is to represent it as a correlation network, such as metabolic(More)
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