Calculated protein abundance vs experimental studies.

<p>Correlations between protein abundances calculated in our model (as times ) and those obtained in experimental studies <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073943#pone.0073943-Newman1" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073943#pone.0073943-Lu1" target="_blank">[11]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073943#pone.0073943-Nagaraj1" target="_blank">[13]</a>; n – sample size, – Spearman correlation coefficient and its 95% confidence interval.</p

The summary of translational parameters calculated in the model.

<p>Column description: () transcript length; () number of gene transcripts; () number of proteins produced from one transcript; () ribosome density in number of ribosomes per 100 codons; () number of ribosomes on a transcript; () initiation time in s; () elongation time in s; () mean elongation time of one transcript codon in ms; and () mean transcript lifetime in min (bacteria, yeast), or in h (humans). For all parameters, except and , the rows 1–15 were calculated for 1738, 4470, and 7494 genes for bacteria, yeast, and humans, respectively. For parameter and , the rows were calculated for 1574, 3425, and 6205 genes, respectively.</p

Summary of data sets and variables used as an input of the model.

<p>Details on data parsing and calculations may be found in the main text. Cell lines and growth conditions (temperature and medium) denote those used in the ribosome profiling experiments. The numbers marked by an asterix were taken from the RNA Tools and Calculators section at the Invitrogen Website (<a href="http://www.invitrogen.com" target="_blank">www.invitrogen.com</a>, accessed April 2013). The coding sequences were downloaded from the following databases: NCBI (<a href="http://www.ncbi.nlm.nih.gov.ftp" target="_blank">www.ncbi.nlm.nih.gov.ftp</a>, accessed May 2012), SGD (<a href="http://www.yeastgenome.org" target="_blank">www.yeastgenome.org</a>, accessed June 2009), and UCSC (<a href="http://genome.ucsc.edu" target="_blank">http://genome.ucsc.edu</a>, accessed July 2012).</p

Translation speed plot generated by Transimulation.

<p>An example plot of translation speed (in aa/sec) in relation to the coding sequence of one of the <i>E.coli</i> genes. To facilitate analysis, the plot was smoothed by calculating translation speed over a 10-codon sliding window. Similar plots for window sizes of 1, 2, 5, 10, 20, 30, and 50 codons are generated for all analyzed genes and sequences uploaded by the user.</p