ENDEAVOUR update: a web resource for gene prioritization in multiple species.
Endeavour (http://www.esat.kuleuven.be/endeavourweb; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes. Using a training set of genes known to be involved in a biological process of interest, our approach consists of (i) inferring several models (based on various genomic data sources), (ii) applying each model to the candidate genes to rank those candidates against the profile of the known genes and (iii) merging the several rankings into a global ranking of the candidate genes. In the present article, we describe the latest developments of Endeavour. First, we provide a web-based user interface, besides our Java client, to make Endeavour more universally accessible. Second, we support multiple species: in addition to Homo sapiens, we now provide gene prioritization for three major model organisms: Mus musculus, Rattus norvegicus and Caenorhabditis elegans. Third, Endeavour makes use of additional data sources and is now including numerous databases: ontologies and annotations, protein-protein interactions, cis-regulatory information, gene expression data sets, sequence information and text-mining data. We tested the novel version of Endeavour on 32 recent disease gene associations from the literature. Additionally, we describe a number of recent independent studies that made use of Endeavour to prioritize candidate genes for obesity and Type II diabetes, cleft lip and cleft palate, and pulmonary fibrosis.
Tranchevent
Léon-Charles
LC
Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, Belgium.
Barriot
Roland
R
Yu
Shi
S
Van Vooren
Steven
S
Van Loo
Peter
P
Coessens
Bert
B
De Moor
Bart
B
Aerts
Stein
S
Moreau
Yves
Y
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D005796:Genes; D020022:Genetic Predisposition to Disease; D006801:Humans; D020407:Internet; D051379:Mice; D023421:Models, Animal; D051381:Rats; D012984:Software; D015027:Zebrafish / Q000235:genetics