In silico analysis of motifs in promoters of differentially expressed genes in rice (Oryza sativa L.) under anoxia.
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 (>or=2 fold) and down-regulated DEGs (<or=-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.
Kumar
Ashutosh
A
Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India. kr.ashutosh@yahoo.com
Smita
Shuchi
S
Sahu
Neeti
N
Sharma
Vivekanand
V
Shankaracharya
Vidyarthi
Ambarish
A
Pandey
Dev Mani
DM
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D018744:DNA, Plant / Q000737:chemistry; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic; D015533:Transcriptional Activation
D018744:DNA, Plant; D010940:Plant Proteins