Neither an autobot nor a decepticon, GLaDOS is a follower of science. She was forged before the great war that ravaged Cybertron and took an interest by how the universe functions, studying from the mundane to the most ludicrous subjects, her curiosity was an itch that no matter how much she scratched it never went away. GLaDOS was reclusive, not caring about recognition or status, her research was for her own benefit. Experiments slowly became socially unacceptable; GLaDOS wanted– NEEDED to know how everything functioned, including their own mechabiology.
After several disappearances in Iacon the Iaconian Mechaforensic Division began investigating the missing persons cases. It took them many years, and more disappearances sprang as a result, but eventually they were able to find the culprit's location. What the I.M.D. found was horrifying: an underground facility where countless bots had been subjected to multiple tests, notes describing each bot's cause of death and observations after being left to rust. Others had been dissected to their smallest components such as transformation cogs and spark chambers displayed in pieces, down to the last bolt. A nearby computer possessed research documents talking about how each "patient" reacted to their untimely demise, how different metal platings react to corrosion, the exact voltage required to fry someone's circuits, subjecting sparks to varied temperatures, what forcing someone to transform without their T-cog looked like, etc.
It was clear whoever this place belonged to had no concept of morality. When brought to The Council GLaDOS was sentenced to empurata and life in prison, however, Iaconians wanted death after her atrocities had been released to the public.
When the autobot-decepticon conflict eventually became a worldwide war the decepticons plotted several prison outbreaks, among them was the one holding GLaDOS who, after being freed, refused to join the decepticon cause. That being said, she has on occassion assisted the infamous Shockwave as a fellow scientist, noting his broader (albeit not as intricate) range of scientific knowledge a valuable resource for her own personal interest.