Neurodegenerative as well as autoimmune diseases have unclear aetiologies, but 
an increasing number of evidences report for a combination of genetic and 
epigenetic alterations that predispose for the development of disease. This 
review examines the major milestones in epigenetics research in the context of 
diseases and various computational approaches developed in the last decades to 
unravel new epigenetic modifications. However, there are limited studies that 
systematically link genetic and epigenetic alterations of DNA to the aetiology 
of diseases. In this work, we demonstrate how disease-related epigenetic 
knowledge can be systematically captured and integrated with heterogeneous 
information into a functional context using Biological Expression Language 
(BEL). This novel methodology, based on BEL, enables us to integrate epigenetic 
modifications such as DNA methylation or acetylation of histones into a specific 
disease network. As an example, we depict the integration of epigenetic and 
genetic factors in a functional context specific to Parkinson's disease (PD) and 
Multiple Sclerosis (MS).