Gems are a girl's version of cybertronians. Let's look at the show's format.
The main cast is a small group of plucky rebels trying fight off the main force of "evil" homeworlders from draining earth of it's resources to further their "war". They happen to have a plucky human sidekick who, after a while, gets the ability to transform just like them and can fight along side the rebels.
They have the ability to combine and form a larger, more powerful being, but unless they're united in their desires, they'll fall apart(menasor, predaking, abominus) or at least be mostly uncontrollable force of destruction (sugalite, menasor).
They are both nongendered, however transformers tend to be male shaped, and use a masculine pronouns to refer to themselves, until the addition of Arcee. The gems tend to be female shaped and use a feminine pronoun to refer to themselves.
Both leaders tend to be the biggest and strongest of them, but also the most cunning/wisest. Both also have universe spanning empires.