Bréhélin et al. BMC Genomics 2010, 11:35 http://www.biomedcentral.com/1471-2164/11/35 R E S E A R C H A R T I C L E Open Access Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum Laurent Bréhélin1*, Isabelle Florent2, Olivier Gascuel1, Éric Maréchal3 Abstract Background: Plasmodium falciparum is the main causative agent of malaria. Of the 5 484 predicted genes of P. falciparum, about 57% do not have sufficient sequence similarity to characterized genes in other species to warrant functional assignments. Non-homology methods are thus needed to obtain functional clues for these uncharacterized genes. Gene expression data have been widely used in the recent years to help functional annotation in an intra-species way via the so-called Guilt By Association (GBA) principle. Results: We propose a new method that uses gene expression data to assess inter-species annotation transfers. Our approach starts from a set of likely orthologs between a reference species (here S. cerevisiae and D. melanogaster) and a query species (P. falciparum). It aims at identifying clusters of coexpressed genes in the query species whose coexpression has been conserved in the reference species. These conserved clusters of coexpressed genes are then used to assess annotation transfers between genes with low sequence similarity, enabling reliable transfers of annotations from the reference to the query species. The approach was used with transcriptomic data sets of P. falciparum, S. cerevisiae and D. melanogaster, and enabled us to propose with high confidence new/ refined annotations for several dozens hypothetical/putative P. falciparum genes. Notably, we revised the annotation of genes involved in ribosomal proteins and ribosome biogenesis and assembly, thus highlighting several potential drug targets. Conclusions: Our approach uses both sequence similarity and gene expression data to help inter-species gene annotation transfers. Experiments show that this strategy improves the accuracy achieved when using solely sequence similarity and outperforms the accuracy of the GBA approach. In addition, our experiments with P. falciparum show that it can infer a function for numerous hypothetical genes. Background Malaria is one of the deadliest infectious diseases, threa- tening half a billion humans worldwide with a yearly death toll of 1 to 2 million people, mainly in developing countries (World Malaria Report 2005, Geneva, World health Organization, WHO/UNICEF; 2005). Malaria is due to infections by protozoan parasites of the Plasmo- dium genus, transmitted by bites of female Anopheles mosquitoes. Of the four species that infect humans, P. falciparum causes the greatest incidence of illness and death [1]. Despite sustained efforts to combat the dis- ease, safe and affordable new drugs, and new drug * Correspondence: brehelin@lirmm.fr 1Méthodes et algorithmes pour la Bioinformatique, LIRMM, Univ. Montpellier 2, CNRS; 161 rue Ada, 34392 MONTPELLIER, France targets, are still required to circumvent drug resistance outbreaks triggered by the use of existing drugs, as anti- malarial vaccines are not yet available [2,3]. The P. falci- parum genome was published in 2002, initially revealing 5 268 protein coding genes, of which about 60% did not have sufficient similarity to characterized genes in other species to justify provision of functional assignments [4]. At the date of writing, the PlasmoDB 5.4 database includes 5 484 coding genes, 3 155 of which (57%) are still annotated as hypothetical. Thus, more than half of P. falciparum genes lack a functional annotation, which is a high proportion compared to that usually observed in other eukaryotic genomes [4]. Although this situation may be explained by the existence of genes that are unique to the P. falciparum species, the Plasmodium © 2010 Bréhélin et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.