They are used to attenuate the emissive color, ambient color and diffuse color. Have nothing to do with alpha.
In FBX:
Emissive color = Emissive*EmissiveFactor;
Ambient color = Ambient *AmbientFactor;
Diffuse color = Diffuse *DiffuseFactor;

TransparentColor and TransparencyFactor are the ones that can be used to calculate alpha.

From Maya Online Help: http://download.autodesk.com/glo...ert.html#attrtransparency
Transparency controls how transparent or opaque the material is. Black means completely opaque (the default), and white means completely transparent. You can set it to any level in between. You can also control transparency on a per-channel basis; for example, if you set this to red, then only the red channel will be transparent.

From Wikipedia:
http://en.wikipedia.org/wiki/Transparency_(graphic)
Transparency can be supported through either a transparent color or an alpha channel or a combination of the two.

Maybe you should make a quick google before throw an question next time :).

If you only want alpha value, TransparencyFactor is the one, and do not need to use TransparencyColor.