Integration of metabolic networks with -omics data has been a subject of recent research in order to better understand the behaviour of such networks with respect to differences between biological and clinical phenotypes. Under the conditions of steady state of the reaction network and the non-negativity of fluxes, metabolic networks can be algebraically decomposed into a set of sub-pathways often referred to as extreme currents (ECs). Our objective is to find the statistical association of such sub-pathways with given clinical outcomes, resulting in a particular instance of a self-contained gene set analysis method. In this direction, we propose a method based on sparse group lasso (SGL) to identify phenotype associated ECs based on gene expression data. SGL selects a sparse set of feature groups and also introduces sparsity within each group. Features in our model are clusters of ECs, and feature groups are defined based on correlations among these features.