Nucleic Acids Research Advance Access originally published online on May 28, 2008
Nucleic Acids Research 2008 36(Web Server issue):W377-W384; doi:10.1093/nar/gkn325
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W377-W384
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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ENDEAVOUR update: a web resource for gene prioritization in multiple species
1Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, 2Human Genome Laboratory, Department of Molecular and Developmental Genetics, VIB, Leuven, 3Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine and 4Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven (Belgium)
*To whom correspondence should be addressed. Tel: +32 16 32 17 09; Fax: +32 16 32 19 70; Email: yves.moreau{at}esat.kuleuven.be
Received February 7, 2008. Revised April 30, 2008. Accepted May 7, 2008.
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.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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