Figure 1. Overview of basic types of functional analysis.

(A) Individual Entity Analysis (IEA) uses firstly a statistical test to define a set of up- and/or down-regulated entities (differentially expressed entities, DEEs). In the second step a hyper geometric or Fisher Exact test is used to test for over or under representation of entities for each functional set. (B) Entity Set Analysis (ESA) for each functional set a sub expression data matrix for only the entities in the set is created. Next a statistical test applied to the sub-matrix enquires if the functional set is significantly regulated across sample groups. (C) Complete Entity Analysis (CEA) extracts entities identified (positive expression detected) across samples. For each sample type a Hypergeometric test or Fischer Exact test is used to test for over or under representation of entities for each functional set. (D) Complete functional regulation analysis performs the analysis in B and C to generate a visual display that illustrates and summarize information from both types of methods.