Current analyses of co-expressed genes are often based on global approaches such as clustering or bi-clustering. An alternative way is to employ local methods and search for patterns–sets of genes displaying specific expression properties in a set of situations. The main bottleneck of this type of analysis is twofold–computational costs and an overwhelming number of candidate patterns which can hardly be further exploited. A timely application of background knowledge available in literature databases, biological ontologies and other sources can help to focus on the most plausible patterns only. The paper proposes, implements and tests a flexible constraint-based framework that enables the effective mining and representation of meaningful over-expression patterns representing intrinsic associations among genes and biological situations. The framework can be simultaneously applied to a wide spectrum of genomic data and we demonstrate that it allows to generate new biological hypotheses with clinical implications.