When applying model-based techniques to the engineering of embedded application software, a typical challenge is the complexity of dependencies between application elements. In many situations, e.g., during rollout of products or in the evolution of product lines, the understanding of these dependencies is a key capability. In this paper, we discuss how model-based techniques, in particular, model transformations can help to reduce the complexity of such analysis tasks. To this end, we realised a representation of Simulink models based on the Eclipse Modeling Framework (EMF). The resulting integration allows us to apply various modelbased frameworks from the Eclipse ecosystem. On this basis we developed a view that increases the visibility of functional dependencies, which otherwise would have been hidden due to a lack of abstraction in the native Simulink representation. The provided analysis framework comes in handy, when such a model has to be modified. Consequently, the developer is supported in reusing existing models and avoiding errors. The concepts and techniques are illustrated with a running example, which is derived from a real industry model from Automotive Software Engineering.