A regulon could be identified by using microarray assays. By obtaining baseline transcription levels of the genome of the organism of interest, individual transcription factors can then be added. Upregulation of transcription would be visible in the microarray results, allowing genes within the regulons for each transcription factor to be identified.
Larger groups of functionally linked genes could be identified by exposing cells to an extracellular signalling ligand. This could be studied to observe whether signalling pathways are activated within the cell, and how these influence transcriptional activities.