Bréhélin et al. BMC Genomics 2010, 11:35 http://www.biomedcentral.com/1471-2164/11/35 measurements from both P. falciparum and P. yoelii. The OPI approach provides us with an interesting refer- ence to compare annotation transfers allowed by co- coexpression and GBA. To this end, we first estimated the global accuracy of the OPI method using GO. OPI provides for each GO term an estimate of the False Dis- covery Rate (FDR) associated with the term. For exam- ple, a GO term with a FDR of 20% means that all predictions in this term have an error probability of 20%. We used this FDR as a cutoff to control the accu- racy and the number of OPI annotation predictions. Namely, all GO terms with FDR below the cutoff are considered, and the already annotated genes predicted in these terms by OPI are used to estimate the global accuracy of the method in a way similar to that used to assess the accuracy of our approach (see Methods). Fig- ure 4 shows the OPI results achieved when varying the FDR threshold, as well as the accuracy of the already described LR-GA and BO-SP experiments. As we can see on this figure, the results obtained with expression data alone are not as accurate as those obtained when also using sequence information. Note that in reference [15], the authors also further corroborated some of their predictions by applying the OPI method to known orthologous genes of P. falci- parum in S. cerevisiae and Homo sapiens (using yeast and Homo sapiens microarray gene expression data sets), and checking that these genes are predicted in the same GO terms as their P. falciparum orthologs. This approach to combine sequence and gene expression data for purpose of annotation transfer is different from ours. Zhou et al. rely on the GBA principle to transfer the annotations in an intra-species way; they use another organism to validate some of their predictions by running a second independent GBA procedure. On the other hand, we use conserved co-expression to Page 10 of 14 assess inter-species annotation transfers suggested by borderline sequence similarity. Finally, we investigated whether the results, collected here by co-coexpression analysis between P. falciparum, S. cerevisiae and D. melanogaster overlapped the results obtained by Zhou et al. (2008) [15], but also the results of previous GBA studies on P. falciparum [14,47]. Our work allowed a systematic revision of the annotation of ribosomal proteins, and of proteins involved in ribosome biogenesis. From the “hypothetical” genes of this series, OPI proposes consistent annotations for one of the genes coding for ribosomal proteins (PF07_121) and 3 genes involved in ribosome biogenesis and assembly (PF14_0055, PF11_090 and PF11_0471). These annota- tions were further corroborated by applying OPI on the same yeast genes as those presented here. In the case of PF07_121, this gene was reported in one of the expres- sion clusters in the study of Le Roch et al (2003), although it was not annotated at that time. Of the other 43 hypothetical genes that have been functionally anno- tated here, none was attributed any function in previous studies by Le Roch et al. (2003) [14], Young et al (2005) [47] and Zhou et al (2008) [15], either because they were not part of expression clusters in their analyses or because the homology searches were not conclusive. Conclusions We propose a method that uses coexpression to anno- tate genes in an inter-species way. Classical GBA approaches work in an intra-species way, by transferring annotations between coexpressed genes. Our approach searches for conserved coexpression between a query species and a reference species, and uses this informa- tion to increase confidence of annotation transfers between genes with borderline sequence similarity. Our analyses show that this strategy improves the accuracy Figure 4 Comparison with a GBA approach. Accuracy achieved by the OPI approach (brown curves) on the MF (left) and BP (right) ontologies when using different FDR thresholds. The orange and blue curves show the accuracy achieved on the Le Roch-Gasch and Bozdech- Spellman experiments, respectively.