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Stat Appl Genet Mol Biol. 2015 Apr;14(2):221-4. doi: 10.1515/sagmb-2014-0045.

GenePEN: analysis of network activity alterations in complex diseases via the pairwise elastic net.


Complex diseases are often characterized by coordinated expression alterations of genes and proteins which are grouped together in a molecular network. Identifying such interconnected and jointly altered gene/protein groups from functional omics data and a given molecular interaction network is a key challenge in bioinformatics. We describe GenePEN, a penalized logistic regression approach for sample classification via convex optimization, using a newly designed Pairwise Elastic Net penalty that favors the selection of discriminative genes/proteins according to their connectedness in a molecular interaction graph. An efficient implementation of the method finds provably optimal solutions on high-dimensional omics data in a few seconds and is freely available at

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