Graph theory is a pivotal branch of mathematics with extensive applications across various disciplines, including computer science, biology, social sciences and more. Graph Theory is used in many areas of Biology. It can be used in drug target identification, determining a protein’s function, gene’s function. It is also used in studying the structures of DNA and RNA. In this case study, we concentrate on the features of biological networks. We demonstrate approaches, models and methods from the graph theory universe and we discuss ways in which they can be used to reveal hidden properties and features of a network. This network profiling combined with knowledge extraction will help us to better understand the biological significance of the system.