MAGNET: A web-based application for gene set enrichment analysis using macrophage data sets

Abstract

Characterization of gene lists obtained from high-throughput genomic experiments is an essential task to uncover the underlying biological insights. A common strategy is to perform enrichment analyses that utilize standardized biological annotations, such as GO and KEGG pathways, which attempt to encompass all domains of biology. However, this approach provides generalized, static results that may fail to capture subtleties associated with research questions within a specific domain. Thus, there is a need for an application that can provide precise, relevant results by leveraging the latest research. We have therefore developed an interactive web application, Macrophage Annotation of Gene Network Enrichment Tool (MAGNET), for performing enrichment analyses on gene sets that are specifically relevant to macrophages. Using the hypergeometric distribution, MAGNET assesses the significance of overlapping genes with annotations that were curated from published manuscripts and data repositories. We implemented numerous features that enhance utility and user-friendliness, such as the simultaneous testing of multiple gene sets, different visualization options, option to upload custom datasets, and downloadable outputs. Here, we use three example studies compared against our current database of ten publications on mouse macrophages to demonstrate that MAGNET provides relevant and unique results that complement conventional enrichment analysis tools. Although specific to macrophage datasets, we envision MAGNET will catalyze developments of similar applications in other domains of interest. MAGNET can be freely accessed at the URL https://magnet-winterlab.herokuapp.com. Website implemented in Python and PostgreSQL, with all major browsers supported. The source code is available at https://github.com/sychen9584/MAGNET.