Threshold-free functional analysis. A list of genes is ranked by their differential expression between two experimental conditions (A and B) using, for example, a t-test which is applied individually to each gene. Columns 1, 2 and 3 represent the position of the genes belonging to three different functional classes (e.g. GO terms, etc.) across the arrangement. The first functional class is completely uncorrelated with the arrangement, while functional classes 2 and 3 are clearly associated to high expression in the experimental conditions B and A, respectively. Dotted lines represent a threshold based on the individual t-tests with some adjustment for multiple testing. The arrow makes reference to the multi-functional character of the genes: a gene can belong to more than one functional class. In this case the gene pointed out by the arrow is in this position not because of its membership to functional class 1 but because is fulfilling the role corresponding to functional class 3, which is related to high expression in experimental condition A.
Al-Shahrour et al. BMC Bioinformatics 2007 8:114 doi:10.1186/1471-2105-8-114