Yeah the differences are substantial. Between Shimano and S-A the part of the cable that ends in the trigger/indexer is different. Also the mechanism to change gears is difference (S-A uses an indicator chain, Shimano uses a bell-crank that pushes a rod). S-A also has two different types of ways to interface the indexer chain from the cable. The "cheap way" for pre-sized cables has an end cap crimped onto the end and a lug that rests against it that's threaded to screw onto the indicator chain. The other way has a lug that has a screw peice that lets you adjust the cable length.
Anyway. I suspect you have a Shimano system because you'd have a very hard time fitting a derailleur cable into a S-A trigger. Unfortunatly I'm not too good with them because I avoid them because I think they're crap.