SCENARIO: Discovery of Similar Aspects for Gene Similarity Explanation from Gene Information Network

Abstract

Gene similarity analysis not only provides information on understanding the biological roles and functions of a gene, but also reveals the relationships among different genes. In this paper, we identify the novel idea of mining similar aspects from gene information network, i.e., given a pair of genes, we want to know, in which aspects (meta paths) the two genes are mostly similar from the perspective of gene information network? We define a similarity metric based on the set of meta paths connecting the query genes in the gene information network, and use the rank of the similarity of a gene pair in a meta path set to measure the similarity significance in the aspect. A minimal set of meta paths where the query gene pair is ranked the best is a similar aspect. Computing the similar aspects of a query gene pair is far from trivial. In this paper, we propose a novel heuristic based-mining method, SCENARIO, to investigate minimal similar aspects. Our empirical study on the gene information network, constructed from seven public gene-related databases, verified that our proposed method is effective, efficient, and useful.