Schematic overview of mammary stem cell-like cells to differentiation transcriptome transition. Gene categories (as defined by the Gene Ontology Consortium) over-represented among differentially expressed genes during the transition from stem-like mammary epithelial cells via pre-differentiated cells to fully differentiated cells. Over-representation analysis was performed using Expression Analysis Systematic Explorer (EASE) software, with an EASE score (a conservative adjustment of Fisher's exact probability to weigh significance in favor of gene ontology categories supported by many genes) cut-off below 0.02. Boxes A and B denote overall changes between the first and second transitions (stem cell-like stage compared with pre-differentiated stage). Boxes C to J denote subgroups where a changed or unchanged value is acquired in the microarray analysis for both transitions (stem cell-like stage compared with pre-differentiated stage, as well as pre-differentiated stage compared with fully differentiated stage). Number of genes within each group and process are shown within parentheses.