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bioRxiv · 10.1101/2023.04.05.535584

GENI: a web server to identify gene set enrichments in tumor samples

Hayashi, A.·Ruppo, S.·Heilbrun, E. E.·Mazzoni, C.·Adar, S.·Yassour, M.·Abu Rmaileh, A.·Shaul, Y. D.
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Abstract

The Cancer Genome Atlas (TCGA) and other projects provide informative tumor-associated genomic data for the broad research community. Hence, several useful web-based tools have been generated to ease non-expert users with the analysis and characterization of a specific gene behavior in selected tumors. However, none of the existing tools offer the user the means to evaluate the expression profile of a given gene in the context of the whole transcriptome. Currently, such analyses require prior bioinformatic knowledge and expertise. Therefore, we developed GENI (Gene ENrichment Identifier) as a fast, user-friendly tool to analyze the TCGA expression data for gene set enrichments. GENI analyzes large-scale tumor-associated gene expression datasets and evaluates biological relevance, thus offering researchers a simplified means to analyze cancer patient-derived data. Availability and implementationGENI is a freely available fast web-based tool developed using the R programming language. It is accessible via the URL: https://yoavshaul-lab.shinyapps.io/gsea-geni/. The complete script can be found at https://github.com/ArataHayashi/GENI-Gene-ENrichment-Identifier.

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Hayashi, A., Ruppo, S., Heilbrun, E. E., Mazzoni, C., Adar, S., Yassour, M., Abu Rmaileh, A., Shaul, Y. D.. 2023-04-06. GENI: a web server to identify gene set enrichments in tumor samples. https://doi.org/10.1101/2023.04.05.535584

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