WGCNA was performed by following the tutorial written by Langfelder and Horvath (Langfelder and Horvath, 2008). Co-expression networks were built using the R program. Clusters of genes that behaved similarly were grouped into different color modules. Modules were annotated by Database for Annotation, Visualization and Integrated Discovery (DAVID) Functional Annotation Bioinformatics Microarray Tools (Huang da et al., 2009). Pathway analysis was done by Kyoto Encyclopedia of Genes and Genomes (KEGG). HIVE 0.0.11 was downloaded and ran on Mac OS X 10.7.4. Edges and nodes were normalized to uploaded data. STAMP motif analysis was performed according to the tutorial provided by authors (Mahony et al., 2007; Mahony and Benos, 2007). Top five sequence matches were output in TRANSFAC Transcription Factor Binding Sites database (v.1.1.3).
