Protein interaction maps are valuable tools in the understanding of the actions of genes and proteins in a real-life context. However, many proteins and genes interact functionally - without physical contact - via transcriptional coregulation of the genes, which is partially manifested in functional promoter structures called promoter modules. Here, the example of interleukin 9 (IL-9) induction by IL-1 and tumour necrosis factor (TNF) is used to demonstrate how comparative promoter analysis can identify a shared promoter module and thus indicate the crucial partners. This strategy can be used for genes from a small initial set of coregulated genes, such as can be derived from expression array data. The combination of expression and promoter analysis with proteomics should be considered as an important link in functional genomics.