Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications

About this Class

Every week, thousands of biomedical research papers are published with a portion of them containing supporting tables with data about genes, transcripts, variants, and proteins. For example, supporting tables may contain differentially expressed genes and proteins from transcriptomics and proteomics assays, targets of transcription factors from ChIP-seq experiments, hits from genome-wide CRISPR screens, or genes identified to harbor mutations from GWAS studies. Because these gene sets are commonly buried in the supplemental tables of research publications, they are not widely available for search and reuse.  
Rummagene is a web server application that provides access to hundreds of thousands of human and mouse gene sets extracted from supporting materials of publications listed on PubMed Central (PMC). 

Rummagene can be used to find surprising relationships between unexpected biological processes, concepts, and named entities. By overlaying the Rummagene gene set space with the Enrichr gene set space we can discover areas of biological and biomedical knowledge unique to each resource.