DEET_enrich_genesonly

Altered version of the function of DEET where 
an input weighted human gene list will be queried to DEETs 
library of studies. This version does not include pathway 
enrichments.

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

DEET_enrich_genesonly function

<dl><dt>DEG_list</dt>
<dd>Data frame or matrix of gene symbols with corresponding padj
and log2FC values (3 columns in total). Can also be a character vector of
gene symbols only. colnames of genes: c("gene_symbol", "padj", "coef")
The rownames of the dataframe are also the gene symbols.</dd>
<dt>DEET_dataset</dt>
<dd>The databank of the differential expression enrichment tool.
Appropriate inputs here are "DEET_example_data" stored within DEET, the "DEET_combined.rda" file
from the DEET stable repositoy found at X, and the DEET database developmental repository found at Y.
The DEET_dataset is a named list where details of it's structure can be found ?DEET_example_data.
Unlike in DEET_enrich, this dataset does not require the pathway-relevant elements
of the DEET_dataset list, namely "gmt_BP", or "gmt_TF" "DEET_gmt_BP", "DEET_gmt_TF".</dd>
<dt>ordered</dt>
<dd>Boolean value specifying whether DEG_list is a character
vector of gene symbols that is ordered. Default value is FALSE.</dd>
<dt>background</dt>
<dd>Character vector of human gene symbols showing all
possible genes. Default value is NULL.</dd></dl>

Arguments

Author

DEET_enrich_genesonly — DEET_enrich_genesonly

<dl>

<dt>DEG_list</dt>
<dd>Data frame or matrix of gene symbols with corresponding padj
and log2FC values (3 columns in total). Can also be a character vector of
gene symbols only. colnames of genes: c("gene_symbol", "padj", "coef")
The rownames of the dataframe are also the gene symbols.</dd>


<dt>DEET_dataset</dt>
<dd>The databank of the differential expression enrichment tool.
Appropriate inputs here are "DEET_example_data" stored within DEET, the "DEET_combined.rda" file
from the DEET stable repositoy found at X, and the DEET database developmental repository found at Y.
The DEET_dataset is a named list where details of it's structure can be found ?DEET_example_data.
Unlike in DEET_enrich, this dataset does not require the pathway-relevant elements
of the DEET_dataset list, namely "gmt_BP", or "gmt_TF" "DEET_gmt_BP", "DEET_gmt_TF".</dd>


<dt>ordered</dt>
<dd>Boolean value specifying whether DEG_list is a character
vector of gene symbols that is ordered. Default value is FALSE.</dd>


<dt>background</dt>
<dd>Character vector of human gene symbols showing all
possible genes. Default value is NULL.</dd>

</dl>

DEET_enrich_genesonly: DEET_enrich_genesonly

Description

Usage

Value

Arguments

Author

References

Examples