Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution

Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Kel, Valentina Giansanti, Ivan Merelli

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)
61 Downloads (Pure)


Expression quantitative trait loci (eQTL) analysis is an emerging method for establishing the impact of genetic variations (such as single nucleotide polymorphisms) on the expression levels of genes. Although different methods for evaluating the impact of these variations are proposed in the literature, the results obtained are mostly in disagreement, entailing a considerable number of false-positive predictions. For this reason, we propose an approach based on Logistic Model Trees that integrates the predictions of different eQTL mapping tools to produce more reliable results. More precisely, we employ a machine learning-based method using logistic functions to perform a linear regression able to classify the predictions of three eQTL analysis tools (namely, R/qtl, MatrixEQTL, and mRMR). Given the lack of a reference dataset and that computational predictions are not so easy to test experimentally, the performance of our approach is assessed using data from the DREAM5 challenge. The results show the quality of the aggregated prediction is better than that obtained by each single tool in terms of both precision and recall. We also performed a test on real data, employing genotypes and microRNA expression profiles from Caenorhabditis elegans, which proved that we were able to correctly classify all the experimentally validated eQTLs. These good results come both from the integration of the different predictions, and from the ability of this machine learning algorithm to find the best cutoff thresholds for each tool. This combination makes our integration approach suitable for improving eQTL predictions for testing in a laboratory, reducing the number of false-positive results.

Original languageEnglish
Pages (from-to)1091-1105
Number of pages15
JournalJournal of Computational Biology
Issue number10
Publication statusPublished - 1 Oct 2018


  • data integration
  • eQTL analysis
  • evolutionary algorithm
  • genetic programming
  • machine learning


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