The three phrases are used in different contexts. I might miss a few possible meanings, but I'll do my best. It's gone - This typically means either something already left, like "my mother is already gone, so I'll need to call her cell phone to speak to her", or that something is missing when you look for it, like "My wallet is gone!". Sometimes it's used as part of an expression to say an opportunity is no longer available, like "that job offer is long gone". It's over - On its own, this implies something with a particular duration in time is finished. Examples could be a romantic relationship, a television show, or the term of a politician. Usually, when said on its own, and emphatically, it's to mean either a relationship or project will no longer continue. For example, an angry spouse might yell "it's over" before starting divorce proceedings. I ran out of something - This implies that you normally, or used to have something, and used it or gave it away until there was none left. For example, "The baker ran out of flour because he baked it all into bread." "The car ran out of gas on a long trip." "I ran out of reasons to love you!" "I ran out of money after being unemployed for so long." There could be some overlap with the situation in which you say "it's gone". However, if something was stolen, or misplaced, you would probably not use "I ran out of it", but you could use "it's gone".