example_DEET_enrich_input

<p>Exon-level DEGs of HAoEC after TNFa treatment for 45 mins
from Alizada et al., 2021. Object is a data.frame with columns
"gene_symbol" "padj" and "coef", which in this case is the
log2Fold-change of differential expression.</p>

datasets

Abstract of Manuscript. Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user’s gene lists, aiding in hypothesis generation and data-driven literature review. Sokolowski, Dustin J., et al. "Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression." Nucleic Acids Research Genomics and Bioinformatics (2023).

Dustin Sokolowski

DEET

Differential Expression Enrichment Tool

Jedid Ahn

Lauren Erdman

Kai Ellis

Huayun Hou

Anna Goldenberg

Michael Wilson

example_DEET_enrich_input function

<p>A data frame with three columns. Rows are genes and it's
populated by the gene symbol, padj of gene expression, and coef (log2Fold-change).</p>

Format

example_DEET_enrich_input — example_DEET_enrich_input

example_DEET_enrich_input: example_DEET_enrich_input

Description

Usage

Arguments

Format

Examples