DeCoaD: determining correlations among diseases using protein interaction networks

BACKGROUND: Disease–disease similarities can be investigated from multiple perspectives. Identifying similar diseases based on the underlying biomolecular interactions can be especially useful, because it may shed light on the common causes of the diseases and therefore may provide clues for possible treatments. Here we introduce DeCoaD, a web-based program that uses a novel method to assign pair-wise similarity scores, called correlations, to genetic diseases. FINDINGS: DeCoaD uses a random walk to model the flow of information in a network within which nodes are either diseases or proteins and links signify either protein–protein interactions or disease–protein associations. For each protein node, the total number of visits by the random walker is called the weight of that node. Using a disease as both the starting and the terminating points of the random walks, a corresponding vector, whose elements are the weights associated with the proteins, can be constructed. The similarity between two diseases is defined as the cosine of the angle between their associated vectors. For a user-specified disease, DeCoaD outputs a list of similar diseases (with their corresponding correlations), and a graphical representation of the disease families that they belong to. Based on a probabilistic clustering algorithm, DeCoaD also outputs the clusters that the disease of interest is a member of, and the corresponding probabilities. The program also provides an interface to run enrichment analysis for the given disease or for any of the clusters that contains it. CONCLUSIONS: DeCoaD uses a novel algorithm to suggest non-trivial similarities between diseases with known gene associations, and also clusters the diseases based on their similarity scores. DeCoaD is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/mn/DeCoaD/.