An important research field in bioinformatics is the study of functionally related gene groups. Analytical tools are developed for studying such known genes sets as well as for identifying new ones. These tools could also be used in functional annotation for new or uncharacterized genes. Functionally related gene groups could be regulated by common cellular signals, or co-expressed. At the same time, genes which do not co-express could still share a common characteristic under different cellular or phenotypic states. Using the pattern of similarity measure, we can discover genes that function together, playing multiple roles, and we can also identify gene groups which function differently across phenotypic states.