Enrichr-KG: bridging enrichment analysis across multiple libraries

Gene and protein set enrichment analysis is a critical step in the analysis of data collected from omics experiments. Enrichr is a popular gene set enrichment analysis web-server search engine that contains hundreds of thousands of annotated gene sets. While Enrichr has been useful in providing enrichment analysis with many gene set libraries from different categories, integrating enrichment results across libraries and domains of knowledge can further hypothesis generation. To this end, Enrichr-KG is a knowledge graph database and a web-server application that combines selected gene set libraries from Enrichr for integrative enrichment analysis and visualization. The enrichment results are presented as subgraphs made of nodes and links that connect genes to their enriched terms. In addition, users of Enrichr-KG can add gene-gene links, as well as predicted genes to the subgraphs. This graphical representation of cross-library results with enriched and predicted genes can illuminate hidden associa-tions between genes and annotated enriched terms from across datasets and resources. Enrichr-KG cur-rently serves 26 gene set libraries from different categories that include transcription, pathways, on-tologies, diseases/drugs, and cell types. To demon-strate the utility of Enrichr-KG we provide several case studies. Enrichr-KG is freely available at: https: //maayanlab.cloud/enrichr-kg.

Automated summary

Enrichr-KG is a knowledge graph database and web-server application that integrates gene set libraries from Enrichr for comprehensive enrichment analysis and visualization. The graphical representation of cross-library results allows users to uncover hidden associations between genes and annotated enriched terms from different datasets and resources. Enrichr-KG currently offers 26 gene set libraries from various categories including transcription, pathways, ontologies, diseases/drugs, and cell types.