made of / from/ out of/ with

Made of

When we talk about an object that consists of a material that has not be changed in any way, we can use made of.

For example:

The bowl is made of glass.
(Now, the form has changed and so as its function but it's still one hundred per cent glass.)

​Made from

We use this if the object we’re describing and the materials that went into making it are significantly changed in the process of making the object.

For example: 

Cheese and butter are made from milk. 
(Milk as we know it is a liquid that we can drink. Cheese and butter are usually solids that cannot be drank. Therefore the milk was significantly changed in the process.)

​Made out of

When we talk about something that was taken from one form and changed to another, then we can use made out of.

For example:

This candle holder is made out of a wine bottle.
(In this case, the wine bottle has been transformed to be used for something else, a candle holder.)

​

Made with

We use made with most often to talk about the ingredients of food and drink:

This dish is made with beef, red peppers and herbs.