Global Analysis of Gene Expression and Identification of Modules in Echinacea purpurea Using Systems Biology Approach

Co-expression analysis is a useful tool to analysis data and detection of genes that act in the same pathway or biological process. Echinacea purpurea is one of the most important medicinal plant of the Asteraceae family that is known as antioxidative and antiviral agent. Despite medicinal importance of E. purpurea, very few reports are available for metabolic mechanisms in this plant. With the aim to elucidate the gene expression profiling and identification of modules in E. purpurea, we performed a systems biology analysis on publicly available transcriptome data. Gene ontology and KEGG pathway enrichment analysis revealed that the unigenes were highly related to the cellular process, primary metabolic process, carbon metabolism and biosynthesis of antibiotics. The co-expression networks divided genes into multiple modules. Of these, module M2 associated with secondary metabolic process. Moreover, a total of 47 transcription factor families such as bHLH, bZIP, C2H2, MYB and WRKY in modules were identified. These findings can provide an overall picture for better understanding the gene expression patterns and common transcriptional mechanisms in E. purpurea.