Common Fund Data Ecosystem (CFDE) Gene Set Enrichment (GSE)

NIH Common Fund (CF) programs have accelerated transformative science by producing massive omics datasets for the research community. A challenge remains in making these data more Findable. Accessible. Interoperable. and Reusable (FAIR), and integrating these datasets to aid researchers in querying data across NIH Common Fund (CF) programs have accelerated transformative science by producing massive omics datasets for the research community. A challenge remains in making these data more Findable, Accessible, Interoperable, and Reusable (FAIR), and integrating these datasets to aid researchers in querying data across CF programs. Here we introduce the Common Fund Data Ecosystem (CFDE) Gene Set Enrichment (GSE) app, a web-based application that serves gene sets extracted from CF programs datasets to provide an integrated cross programs enrichment analysis tool. So far, 10 gene set libraries were created for CFDE-GSE by processing datasets from 8 programs: LINCS, GTEx, Metabolomics, IDG, GlyGen, KOMP2, MoTrPAC, and HuBMAP. To use CFDE-GSE, gene sets obtained from omics experiments by individual investigators can be submitted to the tool using a simple input form. The results produced by CFDE-GSE illuminates connections between the input gene set and various CF gene sets that overlap with the queried gene set. Such analysis enables users to explore CF datasets for further hypothesis generation for their research. Besides enrichment analysis, CFDE-GSE can be used to query the consolidated CF abstracted knowledge by searching for cross-CF dataset associations for a gene or a biological term, for example, a drug, a metabolite, a tissue, a cell type, or a phenotype. This feature of CFDE-GSE discovers connections between entities that may not be obvious. CFDE-GSE is linked to the Data Resource Portal’s search engine, and this provides further analysis of gene sets returned from searches conducted from the CFDE Data Resource Portal. The CFDE-GSE is available from: https://cfde-gskg.dev.maayanlab.cloud/.