CONSTRUCTION AND ANALYSIS OF GENETIC REGULATORY NETWORKS WITH RNA-SEQ DATA FROM ARABIDOPSIS THALIANA

Abstract

Reconstruction of gene regulatory networks (GRNs) is a fundamental aspect of genetic engineering and provides a deeper understanding of the biological processes of an organism. Two methods were implemented to reconstruct the gene regulatory networks of Arabidopsis thaliana under two treatments: methyl jasmonate (MeJa) and salicylic acid (SA). The Joint Reconstruction of multiple Gene Regulatory Networks (JRmGRN) method was utilized to construct a joint network for identifying hub genes common to both conditions in addition to networks specific to each condition. The Differential Network Analysis with False Discover Rate Control method constructed a network of connections unique to only one of the two conditions. Both methods produced biologically significant results and complemented each other. The two methods were tested and found to have efficacy to identify notable hub genes involved in MeJa/SA signaling pathways and downstream response.