We consider dynamical gene-environment networks under ellipsoidal uncertainty and discuss the corresponding set-theoretic regression models. Clustering techniques are applied for an identification of functionally related groups of genes and environmental factors. Clusters can partially overlap as single genes possibly regulate multiple groups of data items. The uncertain states of cluster elements are represented in terms of ellipsoids referring to stochastic dependencies between the multivariate data variables. The time-dependent behaviour of the system variables and clusters is determined by a regulatory system with (affine-) linear coupling rules. Explicit representations of the uncertain multivariate future states of the system are calculated by ellipsoidal calculus. Various set-theoretic regression models are introduced in order to estimate the unknown system parameters. Hereby, we extend our Ellipsoidal Operations Research previously introduced for gene-environment networks of strictly disjoint clusters to possibly overlapping clusters. We analyze the corresponding optimization problems, in particular in view of their solvability by interior point methods and semidefinite programming and we conclude with a discussion of structural frontiers and future research challenges.