Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

Here we present a computational study focused on identification of the novel PCW genes in Arabidopsis based on the co-expression analyses of transcriptomic data collected under 351 conditions, using a bi-clustering technique. Our analysis identified 217 highly co-expressed gene clusters (modules) under some experimental conditions, each containing at least one gene annotated as PCW related according to the Purdue Cell Wall Gene Families database. These co-expression modules cover 349 known/annotated PCW genes and 2,438 new candidates. For each candidate gene, we annotated the specific PCW synthesis stages in which it is involved and predicted the detailed function. In addition, for the co-expressed genes in each module, we predicted and analyzed their cis regulatory motifs in the promoters using our motif discovery pipeline, providing strong evidence that the genes in each co-expression module are transcriptionally co-regulated. From the all co-expression modules, we infer that 108 modules are related to four major PCW synthesis components, using three complementary methods.We believe our approach and data presented here will be useful for further identification and characterization of PCW genes. All the predicted PCW genes, co-expression modules, motifs and their annotations are available at a web-based database: http://csbl.bmb.uga.edu/publications/materials/shanwang/CWRPdb/index.html webcite.Plant cell walls (PCWs) are mainly composed of polysaccharides and lignins, forming the major component of plant biomass. Knowing which genes are involved in the formation and remodeling of PCWs is of great importance as they play many critical roles during plant growth, including regulation of cell differentiation, intercellular adhesion and communication, control of water movement, and defense against invasions by pests and pathogens [1-4], not to mention that it is the focal point of cellulosic biofuel studies. It is estimated that genes involved in the PCW synthesis, remo