The measures for studying over-representation of classes. Over-representation of classes is measured by using A) the whole sample gene list as a sample and the reference gene list as a remainder population, O.log(p); B) a single cluster as a sample and the rest of the sample gene list and the reference gene list as a remainder population, C.log(p); and C) a single cluster as a sample and the rest of the sample gene list as a remainder population excluding the reference gene list, S.log(p). In each situation, Fisher's exact test f(x, M, n, k)  is used to determine the over-representation. O.log(p) presents the original over-representation of sample gene list without clustering. C.log(p) highlights the classes that are over-represented in the original sample gene list and in individual cluster. S.log(p) reports the contribution to the formation of cluster structure.