How were the gene coexpression analyses performed?
The rice gene coexpression analyses were performed by analyzing 15 public rice expression data sets. Analyzed data had been generated using the Affymetrix Rice Genome Array platform. All Affymetrix probes had been remapped to the MSU release 6.1 gene models. Expression data were processed using Weighted Gene Coexpression Network Analysis. With release 7 of the MSU Rice Genome Annotation Project, the coexpression analyses were not rerun because the coexpression analyses are rather complex and time consuming and because the gene models were mostly unchanged from release 6.1. A manuscript describing the rice gene coexpression work has been published Childs KL, Davidson RM, Buell CR (2011) Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes.
