Flowchart of Prosecutor. Flowchart of the functional prediction process in Prosecutor. First, the expression profiles from DNA microarrays (1A) are used to create a correlation matrix (1B). For every gene, the correlations with the remaining genes are retrieved from the correlation matrix and sorted (1B2). The sorted gene list is used to perform an iterative Group Analysis for every functional category (1B3). The resulting p-value is indicative for the prediction of a gene as a member of a functional category (1C). At this step, the regular iGBA process ends. However, to also assess the reliability of each prediction, the following steps are added. The complete list of p-values for every functional category is sorted (1C4), after which the positions of the members of the functional category are determined (1C5). These positions are used to create ROC curves (1D; see Results section for more information concerning ROC curves). The corresponding Area Under the ROC Curve (AUC) is then used as a measure of expression coherence value of a functional category.