Coherence Scores. Given the expression profile for four genes A, B, C, and D in two studies 1 and 2 shown in panel (a), we can calculate the correlation of the expression profiles for every pair of genes in each of the two studies. In panel (b) those pairwise correlations are plotted for study 1 against study 2. For example, pair AB is positively correlated in both studies and pair BD is negatively correlated in study 1 and positively in study 2. Correlations for pairs AB, AC, AD lie approximately on a line of positive slope, so gene A is called "coherent". The coherence score of A is the correlation coefficient of those points, which is positive. Gene D has a negative correlation coefficient and so is incoherent. Study 3 in panel (c) is study 2 where condition and control have been swapped; all genes are perfectly coherent for studies 2 and 3, yet each gene which is up-regulated in study 2 is down-regulated in study 3.