KB005485: Meaning of colors in the heat map -GeneSpring GX 

The Heat Map would display the normalized signal values of the conditions in the active interpretation and for the active entity list. The color given to the entities in Heat map based on their normalized intensity expression values. The Color and Saturation Threshold of the Heat Map can be changed from the Properties Dialog. To access properties, right click on the Heat map and select the properties option from the drop down menu.