GRep: Gene Set Representation via Gaussian Embedding

Molecular interaction networks are our basis for understanding functional interdependencies among genes. Network embedding approaches analyze these complicated networks by representing genes as low-dimensional vectors based on the network topology. These low-dimensional vectors have recently become the building blocks for a larger number of systems biology applications. Despite the success of embedding genes in this way, it remains unclear how to effectively represent gene sets, such as protein complexes and signaling pathways. The direct adaptation of existing gene embedding approaches to gene sets cannot model the diverse functions of genes in a set. Here, we propose GRep, a novel gene set embedding approach, which represents each gene set as a multivariate Gaussian distribution rather than a single point in the low-dimensional space. The diversity of genes in a set, or the uncertainty of their contribution to a particular function, is modeled by the covariance matrix of the multivariate Gaussian distribution. By doing so, GRep produces a highly informative and compact gene set representation. Using our representation, we analyze two major pharmacogenomics studies and observe substantial improvement in drug target identification from expression-derived gene sets. Overall, the GRep framework provides a novel representation of gene sets that can be used as input features to off-the-shelf machine learning classifiers for gene set analysis.