GenMAPP local pathway comparison. This plot shows for each local pathway in GenMAPP the percentage of total genes in the pathway that we were able to visualize using our approach (y-axis) versus the RefSeq-based annotation (x-axis). Each dot in the plot represents a single pathway, colored by its main category (blue: Metabolic Pathways; red: Cellular Pathways; yellow: Molecular Pathways; black: Physiological Pathways). The sizes of the dots represent the size of the map, varying between 4 and 551 gene product identifiers. For the Incyte array (left) we were able to improve the visualization for 96 out of 101 pathways. Three pathways remained identical. Our methods were able to add two more pathways to the list. For the Agilent array (right) 92 pathways showed an improvement in visualization power, whereas 3 pathways remained unchanged and 4 small pathway decreased in visualization power. Note that 10 small pathways (pathways with less than 20 genes present) are now fully visualized due to our efforts.