Why we do native gel electrophoresis and what is the meaning of aggregation?

Answer 1

Care to be more specific?

Native gel electrophoresis doen't disrupt the protein structure and formation of (at least some) complexes. Thus the protein will run on the gel depending on its charge, structure, size and oligomeric state. This can give you more info about the protein.
Also for DNA binding proteins you can run samples of protein+DNA and study the formation of the complex.

Aggregation is when proteins come together and precipitate out of solution. Usually this requires high protein concentrations or that they are denatured (partially or completely)