Accuracy of different prediction methods of insertional RNA editing sites in <i>Didymium</i>.

<p>Each graph shows the percentage of editing sites which are correctly predicted, predicted by one, two, or at least three positions away from the experimentally known correct editing site. (a) shows results for all 15 genes studied, (b) for the more conserved genes, and (c) for the less conserved genes.</p

Number of C insertional editing sites shared by <i>Physarum</i> and <i>Didymium</i>.

<p>Number of C insertional editing sites shared by <i>Physarum</i> and <i>Didymium</i>.</p

Background frequencies for conservation between <i>Physarum</i> and <i>Didymium</i>.

<p>Background frequencies for conservation between <i>Physarum</i> and <i>Didymium</i>.</p

Comparison of observed and expected conservation.

<p>The observed conservation and background conservation for all 16 genes are compared for editing site at the (a) first and (b) third codon position.</p

Graphical representation of the positions of predicted editing sites.

<p>These predicted editing sites are in the seven newly identified <i>Didymium</i> mitochondrial genes as well as in nad3 for which it is experimentally known that it is unedited in <i>Didymium </i><a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002400#pcbi.1002400-Hendrickson2" target="_blank">[24]</a>. The predictions for the nad2 gene are incomplete due to a lack of genomic sequence, indicated by the dashed lines for that gene.</p

-values for the differences between the observed and the background conservation.

<p>These -values are calculated for shared editing sites in all 16 genes at the (a) first and (b) third codon position. The threshold for statistical significance ( as the -value cut off) is not indicated in the figure as it is far above the top of the graphs.</p

Comparison of (a) overall conservation and (b) codon bias for real and predicted mRNA sequences.

<p>The data is close to the diagonal in both cases indicating that predicted sequences can be used to estimate these quanitities in cases where the true sequences are not known.</p

Relationship between codon bias () and the conservation at the second codon position.

<p> and are the number of second and third codon position editing sites. Based on the conservation at the second codon position, the genes are separated into (a) four groups and (b) two groups. For the case of 16 known genes, we counted all unambiguous C insertional editing sites in <i>Physarum</i> and <i>Didymium</i>). For the case of 16 known genes + 8 genes in <i>Physarum</i>, we counted all unambiguous C insertional editing sites in <i>Physarum</i> and <i>Didymium</i> for the 16 known genes and unambiguous C insertional editing sites only in <i>Physarum</i> for the additional 8 genes. For 16 known genes + 8 genes in <i>Physarum</i> and <i>Didymium</i>, we counted all unambiguous C insertional editing sites in <i>Physarum</i> and <i>Didymium</i> for all 24 genes.</p

Additional file 8: of Impact of FHIT loss on the translation of cancer-associated mRNAs

Scatterplots of average ribosome density of duplicate Fhit- negative (E1) and Fhit-expressing (D1) H1299 cells. (PDF 770 kb

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