I was not familiar with Emma Donoghue's Room. I had to look it up to see if I could remember any novels with a similar theme or action.
One novel which came immediately to mind was Cherie Priest's Boneshaker. This is a Steampunk novel which tells of a mother and son relationship (like Room). The novel follows the son (Zeke) on his quest to clear his father's name (he has been "charged" with the destruction of the city). Wanting to change the concept of his family, the son goes out on his own (beyond what he has known--kind of like Jack when he leaves his own walls). The mother (Briar) must track down her son to insure his survival. It really sounds like both novels contain the same themes.