Transtube

The Transtube was an underground train on Gallifrey. Its central station was under the Time Lord Capitol.

Before the outbreak of the War in Heaven, when the Edifice began to turn Romana III's Gallifrey into a crumbling and superstitious shadow of its former self, the system had fallen somewhat into disuse. The tunnels were accessible from MidTown. (PROSE: The Ancestor Cell)

Behind the scenes
According to Steve Lyons and Chris Howarth's Guide to Gallifrey in DWM, The Ancestor Cell 's Transtube is the same transport system as the rail system briefly mentioned in The Infinity Doctors.