GENI - Gene Enrichment Identifier - a web-based tool to identify gene set enrichment of the gene of interest in patient data

Arata Hayashi ¹ Shmoel Ruppo ² Elisheva Heilbrun-Katz ³ Sarah Knapp ⁴ Chiara Mazzoni ³ Rotem Einav ¹ Areej Abu Rmaileh ¹ Shirel Lavi ¹ Anees Khatib ¹ Balakrishnan Solaimuthu ¹ Mayur Tanna ¹ Yoav Shaul ¹

¹Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, the Hebrew University of Jerusalem, Israel
²Info-CORE, Bioinformatics Unit of the I-CORE, The Hebrew University of Jerusalem, Israel
³Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Israel
⁴Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Israel

Several informative databases such as The Cancer Genome Atlas (TCGA), that harbor patient data including their gene expression are available. Existing web tools demonstrate correlations between different gene pairs (gene of interest, versus the hit gene). Nevertheless, ranking correlations between a whole gene set (e.g. Hallmark of Epithelial to Mesenchymal transition) with the gene of interest requires prior software/programming experience. Furthermore, in recent years by applying gene-expression analysis, accompanied by functional assays, many genes associated with several cell programs were identified. However, analysis of these genes` correlation with these programs was mainly characterized in cell lines, and a simple tool to determine their expression in patient-derived tumors is missing. Here we present Gene ENrichment Identifier (GENI), a user-friendly, open-source web tool that provides multiple pathway enrichment analysis graphs for the gene of interest. Based on the input, GENI will automatically calculate Spearman`s correlation coefficients for the gene of interest against the whole transcriptome. Then, it subjects these correlation ranks to gene set enrichment analysis (GSEA) and provides the final enrichment graphs.