The Gene Expression Omnibus (GEO) is a major open biomedical research repository for transcriptomics and other omics datasets. It currently contains millions of gene expression samples from tens of thousands of studies collected by many biomedical research laboratories from around the world. While users of the GEO repository can search the metadata describing studies and samples for locating relevant studies, there is currently no method or resource that facilitates global search of GEO at the data level. To address this shortcoming, we developed RummaGEO, a webserver application that enables gene expression signature search against all human and mouse RNA-seq studies deposited into GEO. To enable such a search engine, we performed offline automatic identification of conditions from uniformly aligned GEO studies available from ARCHS4, and then computed differential expression signatures to extract gene sets from these signatures. In total, RummaGEO currently contains 178,975 human and 203,427 mouse gene sets from 30,576 GEO studies. Overall, RummaGEO provides an unprecedented resource for the biomedical research community enabling hypotheses generation for many future studies.
