We describe here an exploratory tool, called FunNet, which implements an original systems biology approach, aiming to improve the biological relevance of the modular interaction patterns identified in transcriptional co-expression networks. A suitable analytical model, involving two abstraction layers, has been devised to relate expression profiles to the knowledge on transcripts biological roles, extracted from genomic databases, into a comprehensive exploratory framework. This approach has been implemented into a user-friendly web tool to promote its open use by the community.