Comparative evaluation of set-level techniques in predictive classification of gene expression
Typ dokumentu
článek z elektronického periodikaAutor
Holec, Matěj
Kléma, Jiří
Železný, Filip
Tolar, Jakub
Práva
open accessMetadata
Zobrazit celý záznamAbstrakt
Background: Analysis of gene expression data in terms of a priori-defined gene sets has recently received
significant attention as this approach typically yields more compact and interpretable results than those produced
by traditional methods that rely on individual genes. The set-level strategy can also be adopted with similar
benefits in predictive classification tasks accomplished with machine learning algorithms. Initial studies into the
predictive performance of set-level classifiers have yielded rather controversial results. The goal of this study is to
provide a more conclusive evaluation by testing various components of the set-level framework within a large
collection of machine learning experiments.
Results: Genuine curated gene sets constitute better features for classification than sets assembled without
biological relevance. For identifying the best gene sets for classification, the Global test outperforms the gene-set
methods GSEA and SAM-GS as well as two generic feature selection methods. To aggregate expressions of genes
into a feature value, the singular value decomposition (SVD) method as well as the SetSig technique improve on
simple arithmetic averaging. Set-level classifiers learned with 10 features constituted by the Global test slightly
outperform baseline gene-level classifiers learned with all original data features although they are slightly less
accurate than gene-level classifiers learned with a prior feature-selection step.
Conclusion: Set-level classifiers do not boost predictive accuracy, however, they do achieve competitive accuracy if
learned with the right combination of ingredients.
Availability: Open-source, publicly available software was used for classifier learning and testing. The gene
expression datasets and the gene set database used are also publicly available. The full tabulation of experimental
results is available at http://ida.felk.cvut.cz/CESLT.
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