Document Detail


An unbiased evaluation of gene prioritization tools.
MedLine Citation:
PMID:  23047555     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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.
Authors:
Daniela Börnigen; Léon-Charles Tranchevent; Francisco Bonachela-Capdevila; Koenraad Devriendt; Bart de Moor; Patrick De Causmaecker; Yves Moreau
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-10-9
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  -     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-10     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Department of Electrical Engineering, ESAT-SCD, IBBT-KULeuven Future Health Department, Katholieke Universiteit Leuven, Leuven, Belgium.
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