Title: In silico analysis of motifs in promoters of Differentially Expressed Genes in rice (Oryza sativa L.) under anoxia

Authors: Ashutosh Kumar, Shuchi Smita, Neeti Sahu, Vivekanand Sharma, Shankaracharya, Ambarish S. Vidyarthi, Dev Mani Pandey

Addresses: Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835 215, Jharkhand, India. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835 215, Jharkhand, India. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835 215, Jharkhand, India. ' Department of Plant Biology, Marsh Life Sciences Building, University of Vermont, Burlington 05405 Vermont, USA. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835 215 Jharkhand, India. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835 215 Jharkhand, India. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835 215 Jharkhand, India

Abstract: The aim of this study was to characterise the molecular mechanisms of transcriptional regulation of Differentially Expressed Genes (DEGs) in rice coleoptiles under anoxia by identifying motifs that are common in the promoter region of co-regulated genes. Un-changed DEGs (<2 fold and >−2), up-regulated DEGs (≥2 fold) and down-regulated DEGs (≤2 fold) were separated in three different data sets. Their gene promoters were extracted from eukaryotic promoter database. Statistically significant consensus promoter motifs were detected by in silico method. A significant variation in the number of promoter motifs, consensus promoter motif and their sequences between UR-DEGs and DR-DEGs were detected that might be responsible for their related expression.

Keywords: anoxia; AREs; anaerobic response elements; DEGs; differentially expressed genes; in silico motifs; motif detection; microarrays; Oryza sativa; consensus promoter motif; rice; bioinformatics; molecular mechanisms; transcriptional regulation; gene promoters; eukaryotic promoters; promoter motifs; in-silico motifs.

DOI: 10.1504/IJBRA.2009.028681

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.5, pp.525 - 547

Received: 09 Dec 2008
Accepted: 04 Feb 2009
Published online: 22 Sep 2009 *

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