1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Identification of oxidative stress responsive hub genes and their related miRNAs in Arabidopsis thaliana based on integrated bioinformatics meta-analysis
Paper ID : 1253-ICB10
Authors:
Samaneh Hosseinpour, Homa Hosseinpour, Mohammad rezaei, Mansoureh Azadeh *
Zist Fanavari Novin biotechnology institute
Abstract:
Oxidative stress is an integral component of various stress conditions in plants, and determines the substantial overlap in physiological and molecular responses to biotic and abiotic environmental challenges [1]. To better understand plants how to adapt environmental stress, we retrieved the oxidative-responsive genes of Arabidopsis thaliana, the main model plant for the experimental analysis [2]. The purpose of our study was the identification of oxidative-responsive genes and their related miRNAs and associated pathways in A. thaliana under stress conditions using a high-throughput in silico meta-analysis. In this study we integrate three microarray datasets (GSE20009, GSE40574 and GSE57286) in the Gene Expression Omnibus (GEO) [3] database. Normalization and processing of raw data performed by (SVA) [4] and (limma) [5] packages of R (version 1.4.1). The DEGs were identified by the thresholds of p-value < 0.05, and |log2fold change (FC)| > 1. The analysis of gene ontology enrichment (GO), protein-protein interaction (PPI), pathway analysis, and potential miRNAs for hub genes, were performed using bioinformatics online tools DAVID [6], STRING [7], KEGG [8], psRNATarget [9] and RNAhybrid [10]. The result 90 DEGs, including 46 up-regulated and 44 down-regulated genes, were analyzed by integrated bioinformatics approaches enriched in glutathione metabolism, flavonoid biosynthesis, oxidation-reduction process, and response to stress. DFR, GSTU5, PGDH, GSTF6, GSTF12, PYD4, APL3, CYP81D1 and F3H was hub genes in oxidative stress. All hub genes except GSTF6, APL3 and F3H were target genes of 11 miRNAs. This research indicated that two hub genes DFR and GSTU5 and their related miRNAs: ath-miR418 and ath-miR391 have effect on flavonoid biosynthesis and glutathione metabolism pathways respectively in oxidative response adaptation. They also can be considered in breeding programs and genetic engineering for the production of tolerant plants.
Keywords:
Oxidative stress; Arabidopsis thaliana; miRNA; integrated bioinformatics meta-analysis
Status : Paper Accepted (Poster Presentation)