Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli. Export

@article{citeulike:300313, abstract = {Although codon usage is often represented by a 61-dimensional vector, the ability of determining the codon bias in a gene relies on a uni-dimensional vector which measures the total bias in usage of synonymous codons. Codon usage is receiving more and more focus because codon biases might be valuable tools to predict and optimize gene/protein expression. How good any of these measures is for correlating codon usage with gene and protein expression has yet to be investigated. In this study, we correlated gene transcript levels in Escherichia coli with codon usage, using a number of different codon bias measures. We found that there is a significant correlation between transcript levels and codon bias measures, suggesting that these measures can be used to assess or predict gene expression. The codon bias measure performing best in this context was the codon adaptation index.}, address = {Structural Biology Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, USA.}, author = {Goetz, R. M. and Fuglsang, A.}, citeulike-article-id = {300313}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.bbrc.2004.11.134}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15629421}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15629421}, doi = {10.1016/j.bbrc.2004.11.134}, issn = {0006-291X}, journal = {Biochem Biophys Res Commun}, keywords = {ecoli, expression, refs\_jme05}, month = {February}, number = {1}, pages = {4--7}, posted-at = {2005-08-22 14:46:22}, priority = {3}, title = {Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli.}, url = {http://dx.doi.org/10.1016/j.bbrc.2004.11.134}, volume = {327}, year = {2005} }

TY - JOUR ID - citeulike:300313 L3 - citeulike-article-id:300313 N2 - Although codon usage is often represented by a 61-dimensional vector, the ability of determining the codon bias in a gene relies on a uni-dimensional vector which measures the total bias in usage of synonymous codons. Codon usage is receiving more and more focus because codon biases might be valuable tools to predict and optimize gene/protein expression. How good any of these measures is for correlating codon usage with gene and protein expression has yet to be investigated. In this study, we correlated gene transcript levels in Escherichia coli with codon usage, using a number of different codon bias measures. We found that there is a significant correlation between transcript levels and codon bias measures, suggesting that these measures can be used to assess or predict gene expression. The codon bias measure performing best in this context was the codon adaptation index. IS - 1 JF - Biochem Biophys Res Commun SN - 0006-291X AD - Structural Biology Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, USA. EP - 7 TI - Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli. VL - 327 SP - 4 KW - ecoli KW - expression KW - refs_jme05 AU - Goetz, RM AU - Fuglsang, A PY - 2005/02/04/ UR - http://dx.doi.org/10.1016/j.bbrc.2004.11.134 ER -