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Updated: Dec 18, 2025
08:09
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
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Codon usage pattern and predicted gene expression in Arabidopsis thaliana.
Satyabrata Sahoo1, Shib Sankar Das2, Ria Rakshit3
1Department of Physics, Dhruba Chand Halder College, Dakshin Barasat, South 24 Parganas, W.B., India.
Gene: X
|June 19, 2020
Summary
Predicting highly expressed genes in Arabidopsis thaliana using modified relative codon bias (MRCBS) reveals codon composition
Area of Science:
- Plant Genomics
- Molecular Biology
- Bioinformatics
Background:
- Predicting highly expressed genes in plant genomes is crucial for understanding molecular plant biology.
- Codon usage patterns in Arabidopsis thaliana have been a long-standing research topic.
Purpose of the Study:
- To elucidate gene expression patterns in Arabidopsis thaliana using a novel gene expression profiling methodology.
- To analyze predicted highly expressed (PHE) genes using the modified relative codon bias score (MRCBS).
Main Methods:
- Utilized the modified relative codon bias score (MRCBS) for gene expression profiling.
- MRCBS relies on sequence features to identify highly expressed genes.
- Performed a critical analysis of predicted highly expressed genes in Arabidopsis thaliana.
Main Results:
- Codon composition significantly influences gene expression regulation in Arabidopsis thaliana.
- A strong correlation was observed between MRCBS and codon adaptation index (CAI) or other expression measures.
- MRCBS demonstrated good correlation with experimental gene expression data.
Conclusions:
- Gene expression is closely linked to compositional signatures and codon usage bias in Arabidopsis thaliana.
- This study provides a foundation for further research into the evolution of protein-coding genes in plant genomes.
Keywords:
Arabidopsis thalianaCAICAI, Codon adaptation indexCP, Chloroplast Pltd CPCodon usage biasGC contentGEO, Gene Expression OmnibusGene expressionMADS, Minichromosome maintenance1, Agamous, Deficiens and Serum response factorMBP, Megabase pairMRCBS, Score of Modified relative codon biasMT, MitochondrionPHE genesPHE, Predicted Highly ExpressedRCA, Relative Codon AdaptationRCB, Relative codon biasRCBS, Relative Codon Bias StrengthRMA, Relative Molecular AbundanceRP, Ribosomal proteinSAGE, Serial Analysis of Gene ExpressionTAIR, The Arabidopsis Information Resourses
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