ABOUT GeneSetCart

To facilitate data integration, discovery, and hypothesis generation across diverse Common Fund programs' datasets, highly processed data can be converted into gene-, metabolite- and drug-set libraries. Such abstracted versions of the data facilitate data integration and discovery. GeneSetCart is an interactive web-based application that enables users to fetch gene sets from various Common Fund programs data sources, augment these sets with gene-gene co-expression correlations or protein-protein interactions, perform set operations such as union, consensus, and intersection on multiple sets, visualize and analyze these gene sets in a single session. GeneSetCart provides access to CFDE generated gene sets through a term query interface that returns gene sets related to all biomedical terms sourced from most CFDE DCCs. GeneSetCart also supports the upload of single and multiple user-generated gene sets. Users of GeneSetCart can also 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, CFDE-GSE, Rummagene, RummaGEO, Kinase Enrichment Analysis (KEA3), and Chip-X Enrichment Analysis (ChEA3). All gene sets added or created in a session can be saved to a user account for re-analysis and reproducibility and also shared to others. GeneSetCart also has a GMT Crossing feature where users can cross CF sourced gene set libraries to can find gene sets with a significant number of overlapping genes originated from different CF programs. The crossed pairs are displayed in an interactive table on the CFDE GMT Crossing page . Users can also view a GPT-4-generated hypothesis proposing a possible reason for the high overlap between these sets. Overall, GeneSetCart is a useful resource to facilitate hypothesis generation across CF datasets and programs.
Gene set libraries are regularly updated from the GMT files submitted by CFDE programs on the CFDE Data Portal .
GeneSetCart is actively being developed by the Ma'ayan Lab .