Meta Analysis of Microarray Studies Identifies Distinct Molecular Profiles of Abiotic and Biotic Stress Responses in Plants

Plant stress response is a complex trait involving multiple genes that are regulated in several layers involving epigenomic, transcriptomic, proteomic and metabolomic factors. Further, more often than not plants are simultaneously exposed to multiple stresses resulting in enormous changes in the molecular landscape within the cell. Currently multiple transcriptomic studies identifying these changes exist for the same or related stress conditions. So far only a few meta-analyses based on plant stress microarray studies are reported. Here, we performed meta-analysis of drought and salinity (abiotic), bacterial and fungal (biotic) stress microarray studies in rice and Arabidopsis to identify the differentially expressed genes (DEGs) in each of the stresses. We analyzed a total of 386 and 482 microarray samples belonging to 20 and 25 microarray studies in rice and Arabidopsis, respectively. The microarray CEL files of each stress were normalized together using Robust Multichip Average (RMA), quality checked with arrayQualityMetrics package in R and differentially expressed genes (DEGs) were identified using RankProduct method. The identified DEGs were exhaustively characterized for enrichment of a number of molecular features, compared to DEGs reported by other studies and orthologous genes between rice and Arabidopsis were also identified.  An all vs all comparison of DEG lists were performed to identify the common and unique genes and molecular features of each stress type.  Weighted Gene Co-expression Network Analysis (WGCNA) was performed to break-down the lists into small modules with genes showing similar expression patterns and high co-expression and identified stress specific hub genes showing high connectivity.