ABSTRACT
We constructed a genome-wide Arabidopsis gene co-expression network (AGCN) by using 1,094 microarrays. We then analyzed the topological properties of AGCN and partitioned the network into modules by using an effi cient graph clustering algorithm. In the AGCN, 382 hub genes formed a clique, and they were densely connected only to a small subset of the network. At the module level, the network clustering results provide a systems-level understanding of the gene modules that coordinate multiple biological processes to carry out specifi c biological functions. For instance, the photosynthesis module in AGCN involves a very large number (>1,000) of genes which participate in various biological processes including photosynthesis, electron transport, pigment metabolism, chloroplast organization and biogenesis, cofactor metabolism, protein biosynthesis, and vitamin metabolism. The cell cycle module orchestrated the coordinated expression of hundreds of genes involved in cell cycle, DNA metabolism, and cytoskeleton organization and biogenesis. We also compared the AGCN constructed in this study with a graphical Gaussian model (GGM) based Arabidopsis gene network. The photosynthesis, protein biosynthesis, and cell cycle modules identifi ed from the GGM network had much smaller module sizes compared with the modules found in the AGCN, respectively.
