EPSILON

EPSILON is a framework for prioritizing the most likely causal gene in expression quantitative trait loci (eQTL) datasets. It constructs a local network to mitigate the effect of highly connected genes and unreliable interactions before applying a network-based similarity measure. EPSILON outperformed two reference prioritization methods in predicting knockout interactions from yeast knockout compendium. Using a local network significantly increased prioritization performance compared to using the same network similarity measures on the global network.

Topic

Molecular interactions, pathways and networks

Detail

  • Operation: Gene expression QTL analysis

  • Software interface: Graphical user interface

  • Language: MATLAB;C++

  • License: GNU General Public License, version 3

  • Cost: Free

  • Version name: -

  • Credit: Ghent University Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’, Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO), Katholieke Universiteit Leuven funding (NATAR).

  • Input: -

  • Output: -

  • Contact: kathleen.marchal@intec.ugent.be, lieven.verbeke@intec.ugent.be, jan.fostier@intec.ugent.be

  • Collection: -

  • Maturity: -

Publications

  • EPSILON: an eQTL prioritization framework using similarity measures derived from local networks.
  • Verbeke LP, et al. EPSILON: an eQTL prioritization framework using similarity measures derived from local networks. EPSILON: an eQTL prioritization framework using similarity measures derived from local networks. 2013; 29:1308-16. doi: 10.1093/bioinformatics/btt142
  • https://doi.org/10.1093/bioinformatics/btt142
  • PMID: 23595663
  • PMC: -

Download and documentation

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