In-depth investigation on abiotic stress-responsive differentially expressed genes in Arabidopsis roots through GEO database

Abstract

Abiotic stresses limit the plant growth and productivity. Plants have developed various responsive mechanisms to survive these adverse environmental conditions. To better understand plants how to adapt environmental stress, we retrieved the Arabidopsis root responsive genes related to eight abiotic stresses (salt, cold, drought, osmotic, UV, wounding, heat, and heavy metal stresses) from the Gene Expression Omnibus (GEO) database. After quantile normalization of microarray data, a robust rank aggregation (RRA) algorithm was applied to determine the differentially expressed genes (DEGs). The resultant 213 DEGs, including 139 up-regulated and 74 down-regulated genes out of more than 20,000 genes, were further analyzed by the integrated bioinformatics approaches of PUBMED, PANTHER, DAVID, and STRING. The results indicated that the up-regulated DEGs were more positively involved in response to oxidative stress, regulation of transcription, and structure organization than the down-regulated DEGs. The former also had more complicated PPI interactions than the latter. Furthermore, qRT-PCR and enzyme activity have been done to validate the outcome of integrated bioinformatics analysis. Our work will facilitate to demonstrate the common molecular mechanisms responsive to differential abiotic stresses and these DEGs might be potential biomarkers for future abiotic stress-resistance studies.

Keywords

• arabidopsis root
• abiotic stress
• integrated bioinformatics analysis
• experimental validation
• antioxidant activity