General hypergeometric distribution (GHGD) describes the following distribution: from a finite space containing N elements, select T subsets with each subset contains M[i] (T-1 >= i >= 0) elements, what is the probability that exactly x elements are overlapped exactly t times or at least t times (XLO=t or XLO>=t, T >= t >= 0, here LO is level of overlap)? The classical hypergeometric distribution (HGD) describes the situation of two subsets, while the general situation has not been resolved, despite the overlapped elements has been visualized with the Venn diagram method for about 140 years. GHGD described not only the distribution of XLO=t or XLO>=t that are overlapped in all of the subsets (XLO=T), but also the XLO=t or XLO>=t that are overlapped in a portion of the subsets (LO = t or LO >= t, T >= t >= 0). Here, we developed algorithms to calculate the GHGD and discovered graceful formulas of the essential statistics for the GHGD, including mathematical expectation, variance, and high order moments. In addition, statistical theory to infer a statistically reliable gene set from multiple datasets based on these formulas was established by applying Chebyshev's inequalities.