A new method was developed for revealing of composite clusters of cis-elements in promoters of eukaryotic genes that are functionally related or coexpressed. A software system "ClusterScan" have been created that enables: (i) to train system on representative samples of promoters to reveal cis-elements that tend to cluster, (ii) to train system on a number of samples of functionally related promoters to identify functionally coupled transcription factors; (iii) to provide tools for searching of this clusters in genomic sequences to identify and functionally characterize regulatory regions in genome. A number of training samples of different functional and structural groups of promoters were analysed. Search for composite clusters in human chromosomes 21 and 22 reveals a number of interesting examples. Finally, a decision tree system was constructed to classify promoters of several functionally related gene groups. The decision tree system enables to identify new promoters and computationally predict their possible function.