Figure 3

Uncoupling between transcriptome and translatome is conserved in the enriched biological themes. (A) Summary of semantic specificity estimates (based on the optimized quantification of semantic specificity described in SI Materials and Methods). Red dotted lines represent semantic specificity estimates relative to the transcriptome and translatome comparisons within all datasets. Box and whisker plots show the reference distributions of semantic specificities (whiskers indicating minimal and maximal distribution values), characteristic of each dataset and reflecting semantic specificity estimates between the transcriptomes of unrelated dataset pairs. A semantic specificity falling within or below the reference distribution is indicative of very poor semantic similarity between the transcriptome and the translatome in a dataset pair. The color associated to the box of each dataset pair corresponds to the normalized difference between the number of GO terms over-represented only at the translatome level and the number of GO terms over-represented only at the transcriptome level, a quantity ranging from −1 (all the terms are enriched only at the transcriptome level, in blue) to 1 (all the terms are enriched only at the translatome level, in yellow). This measure is positive for the first three datasets on the left and negative for all the others (divided by a vertical dashed line in the figure). Having no overrepresented ontological terms, the dataset + mTOR.diff is not displayed. (B) For each GO term the transcriptome and translatome specificity degrees are calculated as the ratio between the number of datasets in which the term is transcriptome or translatome specific and the number of datasets in which the term is overrepresented. Terms are grouped into the broader GOslim categories and the median specificity values are calculated. The number of GO terms grouped in each GOslim category is specified in round brackets. Within each of the three GO domains (from left to right: Biological Process, Cellular Component and Molecular Function), categories are sorted from the most translatome-specific (in yellow) to the most transcriptome-specific (in blue).