"Time is up" and "We are over time" are both correct. "We are out time" should be "we are out of time" — you'd say the same thing about food in your house if you needed to buy more, for instance "We are out of salt". These three all mean that we have no more time, and you'd probably use them in the context of a specific task, like saying "Time's up" at the end of an exam. "Time is over" is a bit harder. I can't think of a situation where anyone would naturally say it, except perhaps at the end of the universe to mean that time itself has stopped. It's not grammatically wrong, but I would avoid it if I were you. You could use it with a qualifier, for instance "My time is over" — here, "my time" might be the period of time where I was in power as a politician, or at the centre of social life, or many other things depending on context. "My time is over" would then mean that that period had come to an end - I have been deposed from power, perhaps, or I am old and my life has become uneventful.

They all mean the same thing, but are all different ways of expressing the sentence. It would be contextual based on how each sentence is used. The end meaning is the same.