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Title: An unbiased evaluation of gene prioritization tools
Authors: Böringen, D ×
Tranchevent, Léon-Charles
Bonachela Capdevila, Francisco
Devriendt, Koenraad
De Moor, Bart
De Causmaecker, Patrick
Moreau, Yves #
Issue Date: Dec-2012
Publisher: Oxford University Press
Series Title: Bioinformatics vol:28 issue:23 pages:3081-3088
Abstract: MOTIVATION: Gene prioritization aims at identifying the most promising candidate genes among a large pool of candidates-so as to maximize the yield and biological relevance of further downstream validation experiments and functional studies. During the past few years, several gene prioritization tools have been defined and some of them have been implemented and made available through freely available web tools. In this study, we aim at comparing the predictive performance of eight publicly available prioritization tools on novel data. We have performed an analysis in which 42 recently reported disease gene associations from literature are used to benchmark these tools before the underlying databases are updated. RESULTS: Cross-validation on retrospective data provides performance estimate likely to be overoptimistic because some of the data sources are contaminated with knowledge from the disease-gene association. Our approach mimics a novel discovery more closely and thus provides more realistic performance estimates. There are however marked differences, and tools that rely on more advanced data integration schemes appear more powerful. CONTACT: yves.moreau@esat.kuleuven.be.
URI: 
ISSN: 1367-4803
Publication status: published
KU Leuven publication type: IT
Appears in Collections:ESAT - STADIUS, Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics
Computer Science @ Kulak
Department of Human Genetics - miscellaneous
× corresponding author
# (joint) last author

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