Removing ubuntu-desktop though Software Center

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http://askubuntu.com – So, i try to delete some applications that i really don't need (Or that i've read reviews and there are better alternatives). But then i got on some application that tells me "If you unistall "X Application", future updates will not include new items in The Ubuntu desktop systme set" What does that mean? It's still safe to delete it? I'm running Ubuntu 12.10 64 bit. (HowTos)