'Made of' / 'Made from'?

Let's start by looking at some examples - I might say: 

"This shirt is made of cotton"
"This house is made of bricks" OR
"The keyboard I use on my computer is made of plastic."

On the other hand, we might say:
"Paper is made from trees."
"Wine is made from grapes." OR
"This cake is made from all natural ingredients."

So, if you think about the first group of examples, you'll notice that there's a common theme - a common pattern.

The cotton in the shirt is still cotton - it hasn't changed its form and become something else. In the same way, the bricks in the walls of the house - they're still bricks. They didn't stop being bricks when the house was made.
And the plastic in my computer keyboard is still plastic.

So we say: 
"The shirt is made of cotton."
"The house is made of bricks."
"The keyboard is made of plastic."

On the other hand, the trees in the example where we say:
"The paper is made from trees."
These trees are not trees anymore - they stopped being trees when they became paper.

And if we say: 
"Wine is made from grapes."
The grapes are no longer grapes - they've been changed into a different type of stuff - a different type of substance - in this case, wine.

And the flour and the eggs and the sugar in the example about the cake; these have all changed their forms as well when they became cake.

So this is the rule: 
If something keeps its form, we use 'made of''
But if the form is changed during the process of making, then we use 'made from'.