The Nemesis
Semper Tyrannus
They changed that story so many times...in the comics, starting with issue #5, it was something called "The Creation Matrix" which was held by Optimus Prime, and the reason Shockwave kept Optimus' head alive separate from his body. I think the cartoon had a couple different story arcs related to different things that gave "life" to Transformers, and the Michael Bay movies of course had the stupid magic box in the first movie and the fairy dust in the second.
Yeah. A lot of ideas got criss-crossed between different stories and parts of the franchise.
The Matrix started in the cartoon/movie as the symbol of Autobot leadership and a receptacle of all the knowledge of Primes past. It was quite separate from Vector Sigma and the means of giving life to transformers.
When Simon Furman got to the comics, he started cannibalizing elements of the movie/series including the Matrix, which he turned into the Creation Matrix and made it responsible for TF reproduction/creation, as it was a conduit for the power of the Transformers' creator/god, Primus.
The Matrix was also sometimes considered equivalent to an afterlife for Transformers, as it's mentioned in both G1 and Beast Wars that dying Transformers will join/be one with The Matrix.
Later on, Beast Machines (in perhaps the only good thing that series ever contributed) merged all those things together by creating the AllSpark (alternatively called the Well of All Sparks), a combo afterlife and "beforelife" repository for the sparks (souls) of all Transformers who aren't alive. The Matrix is a conduit to it, allowing communication with the deceased to share knowledge (like the tv/movie matrix) and to channel new sparks created by Primus (though not always explicitly stated as being created in that fashion) into bodies to bring new Transformers to life (like the comic matrix)
The Bay Movies and the TF: Animated series confused things by introducing the "Allspark" (note the uncapitalized "s") which basically was the Creation Matrix portrayed in cubey/boxy form. The Matrix, when it appeared, was some sort of vaguely subservient/offshot piece of tech that was related to the Allspark, but not the same thing (and thus not the same as the Creation Matrix)
This is what happens when you have 25+ years of a franchise where there are basic continuity elements but no expectation to rigidly adhere to the same exact lore every time.
http://tfwiki.net/wiki/Creation_Matrix