GeneSetCart

GeneSetCart is an interactive web-based application that enables users to fetch gene sets from various sources, augment these sets with gene-gene co-expression or protein-protein interactions, perform set operations such as union, consensus, and intersection, and visualize and analyze these gene sets in a single session. GeneSetCart supports the uploading of single or multiple gene sets. Users of GeneSetCart can obtain gene sets by searching PubMed for genes co-mentioned with any term in publications. Visualizations of gene sets from the various sources can be generated in the form of publication-ready Venn diagrams, heatmaps, UMAP, SuperVenn diagrams, and UpSet plots that summarize the overlap and similarity between sets. Users can also perform functional enrichment analysis of their assembled gene sets through external links to gene set analysis tools such as Enrichr, Rummagene, RummaGEO, Kinase Enrichment Analysis 3 (KEA3), and Chip-X Enrichment Analysis 3 (ChEA3). All gene sets added or created in a session can be saved to a user account for re-analysis and reproducibility or to be shared with others. Overall, GeneSetCart is a useful resource to facilitate hypothesis generation and knowledge integration.