Bréhélin et al. BMC Genomics 2010, 11:35 http://www.biomedcentral.com/1471-2164/11/35 Page 5 of 14 Figure 2(a) summarizes the accuracy achieved on the BP and MF ontologies, when varying the ξ threshold to decide on the annotation transfer. In addition, the accu- racy of the RBH method alone was also computed. For this method, a BLAST e-value cutoff was introduced to control the accuracy and number of functional transfers —i.e. all RBH pairs above the cutoff are not considered. Accuracies achieved on the BP and MF ontologies strongly differ. For the MF ontology, sequence informa- tion alone (RBH) is accurate (around 80%) and no improvement is observed using coexpression context. However, for the BP ontology, the RBH accuracy is below 60%, and using coexpression context clearly improves the results. As expected, the number of gene pairs authorizing a functional transfer (x-axis) increases with the ξ threshold, while the accuracy of the method decreases. Surprisingly, the e-value cutoff introduced in the RBH approach fails to control the accuracy, which tends to prove that the RBH strategy already captures most of the sequence information relevant for the anno- tation transfer. We next investigated the potential of the approach to assess functional conservation between gene pairs with less stringent sequence similarity. To this end, all gene pairs with BLAST sequence similarity below a loose e- value threshold (0.1) were considered. This list contains all pairs selected by the RBH strategy, but also many others. Figure 2(b) summarizes the accuracy achieved for the MF and BP ontologies. For the purpose of com- parison, we also estimated the accuracy of the approach Figure 2 Estimate of the method accuracy with GO: D. melanogaster vs. S. cerevisiae. Accuracy achieved on the MF (left) and BP (right) ontologies when using sequence information alone (orange curves, for different e-value cutoffs) and when exploiting the expression context (blue curves, for different ξ thresholds). The x-axis shows the number of gene pairs authorizing annotation transfers. (a) Results achieved on RBH gene pairs. (b) Results achieved on gene pairs with potentially low sequence similarity.