GeneWalk identifies relevant gene functions for a biological context using network representation learning

Abstract

The primary bottleneck in high-throughput genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Existing methods such as Gene Ontology (GO) enrichment analysis provide insight at the gene set level. For individual genes, GO annotations are static and biological context can only be added by manual literature searches. Here, we introduce GeneWalk (github.com/churchmanlab/genewalk), a method that identifies individual genes and their relevant functions under a particular experimental condition. After automatic assembly of an experiment-specific gene regulatory network, GeneWalk quantifies the similarity between vector representations of each gene and its GO annotations through representation learning, yielding annotation significance scores that reflect their functional relevance for the experimental context. We demonstrate the use of GeneWalk analysis of RNA-seq and nascent transcriptome (NET-seq) data from human cells and mouse brains, validating the methodology. By performing gene- and condition-specific functional analysis that converts a list of genes into data-driven hypotheses, GeneWalk accelerates the interpretation of high-throughput genetics experiments.