Data repository for: Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression

• DOI: 10.5281/zenodo.6954162
• Publication Date: 2022-08-02
• Authors: Dustin Sokolowski; Jedid Ahn; Lauren Erdman; Huayun Hou; Kai Ellis; Liangxi Wang; Anna Goldenberg; Michael Wilson
• Keywords: Differential Gene Expression; Data Repository; RNA sequencing; Gene Set Enrichment

Updated to include files after review process.<br/>Description adapted from manuscript abstract. RNA sequencing (RNA-seq) followed by differential gene expression analyses is a fundamental approach for making biological discoveries. Ongoing large-scale efforts to systematically process and normalize publicly available gene expression data facilitate rapid reanalyses of specific studies and the development of new methods for querying these public data. However, while several powerful tools can query systematically processed publicly available RNA-seq data at the individual sample level, there are fewer options for querying differentially expressed gene (DEG) lists generated from these experiments. Here, we present the Differential Expression Enrichment Tool (DEET), which allows users to interact with 3162 consistently processed DEG lists curated from 142 RNA-seq datasets obtained from the recount2 database, which contains data from consortiums (GTEx, TCGA) and individual labs (SRA). To establish DEET, we integrated systematically processed human RNA-seq data from recount2 with reported and previously predicted metadata from multiple sources. We then developed a CRAN R package (https://cran.r-project.org/web/packages/DEET/index.html) and Shiny App (https://wilsonlab-sickkids-uoft.shinyapps.io/DEET-shiny/) where users can compare their gene lists against the DEG lists within DEET. Here we present DEET and demonstrate how it can facilitate hypothesis generation and provide biological insight from user-defined differential gene expression results.<br/>