Background The use of high throughput technologies has provided us with large amounts of data for Huntington's disease (HD), especially at the gene and protein levels. As phenotypic changes in HD may not just be due to the activity of individual genes but interrelated alterations of whole molecular networks, it is important to systematically analyse and represent accumulated data in a network based approach.

Aim To establish, analyse and visualise protein interaction networks through a dedicated database to HD. This approach will not only help to understand molecular mechanisms better but also help in identifying potential molecular markers involved in HD.

Methods A HD specific protein–protein database interaction with additional gene expression information obtained from high throughput gene expression experiments has been constructed. We further identified both pathways as well as gene ontology (GO) annotations that are enriched in HD and constructed networks of the pathways and enriched GO annotations.

Results Our integrative network based methodology helped us to identify pathways and networks that are specific to the HD and may lead to the identification of novel molecular targets. Follow-up analyses of molecular changes will distinguish between potential causes and effects in HD.

Conclusions Our study demonstrates that network approaches can greatly facilitate the interpretation of large biological data sets and can support the elucidation of the molecular mechanisms underlying HD. We hope that the constructed database will help researchers worldwide to find a cure for HD.