Up-Regulated Gene Sets of Arabidopsis Thaliana in Response to Nanoparticles: An In Silico Approach Based on the Microarray Data

Abstract

A meta-analysis on two microarray-based data was performed to identify the statistically enriched gene sets in Arabidopsis thaliana treated with nanoparticle (NPs) using Gene Set Enrichment Analysis (GSEA) based on Kyoto Encyclopedia of Genes and Genomes (KEGG). Log fold change (FC) of the gene expression under NPs treatment, compared to the control, was manually calculated in excel after data merging, to find gens with the highest expression under the treatment. GSEA analysis revealed that under NPs treatment, different pathways related to organ morphogenesis, cell adhesion molecule binding, epithelial development, immune response regulating signaling pathway, regulatory region nucleic acid binding, supramolecular complex, taxis (directed movement in response to stimulus), tube development, and vacuole were differentially expressed. Top 10 up-regulated genes under NPs treatment based on the Enrichment Score (ES) were AT1G69510, AT5G29000, AT3G17880, AT5G14590, AT5G57655, AT2G30530, AT1G55530, AT1G01770, AT2G17220, and AT2G25460. Many of these genes are involved in the response to stress and in the plant defense signaling.