Abstract: A method for analyzing and identifying functional linkages between biological processes which are regulated in a coordinate manner. An especially preferred example of a biological process to which the method of the present invention may be applied is the analysis of groups of coordinately regulated genes. More preferably, the present invention analyzes large set of genome-wide expression data or transcriptional data in order to discover coordinately regulated genes, which can be termed “transcriptional modules”. Optionally and most preferably, the groups of genes are identified with their corresponding cis-regulatory elements. Thus, if the cis-regulatory elements for the transcriptional module are not known, they can optionally be identified with the method of the present invention, for example if functional linkages between genes are known and the associated cis-regulatory element is also available, this information can be used to identify the corresponding transcriptional module.