GAGE captured canonical pathways which are significantly perturbed towards both directions following 8 h BMP6 treatment in human MSC. (a) Gene expression level changes in the top 3 different significant canonical pathways inferred by GAGE and PAGE. (b) Gene expression level changes in the canonical TGF beta signaling pathway and (c) plotted in pseudo-color on the pathway topology derived from KEGG database. The solid horizontal line and dashed lines in (a-b) mark the mean fold changes of all genes and the positive/negative two times standard deviation from the mean respectively. Note that in (c), one KEGG node may correspond to multiple closely related genes with the same function, and the maximum fold changes among these genes are plotted as the color of the node.