GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets

Abstract

Converting multiomics datasets into gene sets facilitates data integration that leads to knowledge discovery. Although there are tools developed to analyze gene sets, only a few offer the management of gene sets from multiple sources. GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene coexpression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets, all in one place. GeneSetCart supports the upload of single or multiple gene sets, as well as fetching gene sets by searching PubMed for genes comentioned with terms in publications. Venn diagrams, heatmaps, Uniform Manifold Approximation and Projection (UMAP) plots, SuperVenn diagrams, and UpSet plots can visualize the gene sets in a GeneSetCart session to summarize the similarity and overlap among the sets. Users of GeneSetCart can also perform enrichment analysis on their assembled gene sets with external tools. All gene sets in a session can be saved to a user account for reanalysis and sharing with collaborators. GeneSetCart has a gene set library crossing feature that enables analysis of gene sets created from several National Institutes of Health Common Fund programs. For the top overlapping sets from pairs of programs, a large language model (LLM) is prompted to propose possible reasons for the high overlap. Using this feature, two use cases are presented. In addition, users of GeneSetCart can produce publication-ready reports from their uploaded sets. Text in these reports is also supplemented with an LLM. Overall, GeneSetCart is a useful resource enabling biologists without programming expertise to facilitate data integration for hypothesis generation.

Keywords: Alexander disease; Chrome extension; Geneshot; SuperVenn; UpSet; Venn; aging; exercise; gene set intersection; integrative analysis.