Recent studies have revealed that alternative splicing plays an important role in the observed protein and interaction diversity. Special microarrays allow for measuring gene expression at the exon level and thus for studying alternative transcripts and their corresponding protein domain architecture. We have developed the Cytoscape plugin DomainGraph that enables the visualization and detailed study of domain-domain interactions forming protein interaction networks. In addition, the integration of exon expression data supports the analysis of alternative splicing events and the characterization of their effects on the protein and domain interaction network. Different expression patterns between human tissues or cells can be identified by comparing the generated domain graphs.