It's coming from the side.
--> ok
It's coming from the room side by.
--> No, better: It's coming from the room next door, It's coming from the room next to us
It's coming from the upside.
--> No, "upside" has a different meaning, not about location, more like "benefit". (e.g. "The upside of the rainy weather is that I tested my new umbrella")
It's coming from the underside.
--> No. "underside" really describes the bottom of something (e.g. "I drove over a rock and scratched the underside of my car")
It's coming from the room under.
--> Better: It's coming from the room below.
"Under" implies more direct/closer location, e.g. "I keep my money under the bed", "He's hiding under the table"
It's coming from the room above. --> ok!