Genome-Wide Pathway Analysis of Microarray Data Identifies Risk Pathways Related to Salt Stress in Arabidopsis Thaliana

Salt stress is a common abiotic stress in agricultural production, which is affected by multiple genes and environmental factors. Although transcriptome analyses have detected some salt-related genes in Arabidopsis thaliana, these genes are often major genes and can not adequately explain the molecular mechanism of salt tolerance. Some genes related to salt stress, but does not reach significant threshold in gene expression analysis (called modest effect genes), are often ignored. Therefore, we took full account of the role of modest effect genes and performed a pathway-based analysis of three gene microarray datasets to identify the pathways related to salt stress. We also compared these results with the pathways identified by major genes. Finally, three pathways were identified as salt-related pathways, some of which were previously reported to be related to salt stress in plants, while others are novel. These findings will help us to study the molecular mechanism of salt stress, but also provide a new perspective for the study of salt tolerance in Arabidopsis thaliana.