EpICS: A System for Genome-wide Epistasis and Genetic Variation Analysis using Protein-Protein Interactions

Epistasis usually contributes to many well known diseases making the traits more complex and harder to study. The interactions between multiple genes and their alleles of different loci often mask the effects of a single gene at particular locus resulting in a complex trait. So the analysis of epistasis uncovers the facts about the mechanisms and pathways involved in a disease by analyzing biological interactions between implicated proteins. As the existing tools mainly focus on the single or pair wise variation analysis, a comprehensive tool capable of analyzing interactions among multiple variations located in different chromosomal loci is still of growing importance for genome wide association study. In this paper, we focus on exploring all the protein-protein interactions coded by the genes in the regions of variations of human genome. We introduce a tool called EpICS that helps explore the epistatic effects of genes by analyzing the protein-protein interactions within the regions of different types of genetic variations. It accepts variation IDs, type of variations (Insertion-Deletion/Copy Number Variation/Single Nucleotide polymorphism), PubMed identifiers, or a region of a chromosome as input and then enumerates the variations of the user-specified types as well as the interactions of the proteins coded by the genes in the region. It also provides necessary details for further study of the results. EpICS is available at http://integra.cs.wayne.edu:8080/epics for general use.