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-r...

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Published inInternational journal of bioinformatics research and applications Vol. 5; no. 5; p. 525
Main Authors Kumar, Ashutosh, Smita, Shuchi, Sahu, Neeti, Sharma, Vivekanand, Shankaracharya, Vidyarthi, Ambarish, Pandey, Dev Mani
Format Journal Article
LanguageEnglish
Published Switzerland 2009
Subjects
Base Sequence
Computational Biology - methods
DNA, Plant - chemistry
Gene Expression Regulation, Plant
Genes, Plant
Genome, Plant
Oryza - genetics
Plant Proteins - genetics
Promoter Regions, Genetic
Transcriptional Activation
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Summary: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.
ISSN:1744-5485
DOI:10.1504/IJBRA.2009.028681