One way to do it is to use a ramp or something similar for the transparency. Just delete all but one colour on it so it is a flat colour.
Then on the colour node for the ramp just set a key. This will create an expression and you can now animate it in the curve editor.![](http://c3.ac-images.myspacecdn.com/images02/22/l_d8581038268540be80cf01ab11a4088e.jpg)