title: Mean of the typical decoding rates: a new translation efficiency index based on the analysis of ribosome profiling data.
abstract: Gene translation modeling and prediction is a fundamental problem that has numerous biomedical implementations. In this work we present a novel, user-friendly tool/index for calculating the mean of the typical decoding rates that enables predicting translation elongation efficiency of protein coding genes for different tissue types, developmental stages, and experimental conditions. The suggested translation efficiency index is based on the analysis of the organism's ribosome profiling data. This index could be used for example to predict changes in translation elongation efficiency of lowly expressed genes that usually have relatively low and/or biased ribosomal densities and protein levels measurements, or can be used for example for predicting translation efficiency of new genetically engineered genes. We demonstrate the usability of this index via the analysis of six organisms in different tissues and developmental stages. Distributable cross platform application and guideline are available for download at: http://www.cs.tau.ac.il/~tamirtul/MTDR/MTDR_Install.html.
authors.affiliation: Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Dana
authors.affiliation: Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel Segol School, Tel Aviv University, Ramat Aviv 69978, Israel tamirtul@post.tau.ac.il.
authors.forename: Tamir
authors.initials: T
authors.lastname: Tuller
mesh_terms: D000818:Animals; D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism; D003062:Codon; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D006801:Humans; D051379:Mice; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D029742:Caenorhabditis elegans Proteins; D003062:Codon; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins
keywords: codon decoding rate; codon usage bias; gene translation; ribosome profiling; transcript evolution