DEET_Input_as_Reference

Alternative function to DEET enrich for when the inputted gene
list is unordered. Here, we can increase the statistical rigour of enrichment
by levaraging the p-values of the DEGs within DEET. Specifically, the inputted
DE list is used as the reference and we test each DE list against your reference.
Specifically. We convert your reference into a gmt file before inputting each pairwise
DE list into ActivePathways. This function does not complete correlations or pathway-level
analysis.

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_Input_as_Reference function

<dl><dt>genes</dt>
<dd>A character vector of gene symbols within `DEET_dataset`</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".
It also does not need DEET_gmt_DE.</dd>
<dt>background</dt>
<dd>Character vector of human gene symbols showing all
possible genes. Default value is NULL and the background is generated
as all detected DEGs across any comparison.</dd></dl>

Arguments

Author

DEET_Input_as_Reference — DEET_Input_as_Reference

<dl>

<dt>genes</dt>
<dd>A character vector of gene symbols within `DEET_dataset`</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".
It also does not need DEET_gmt_DE.</dd>


<dt>background</dt>
<dd>Character vector of human gene symbols showing all
possible genes. Default value is NULL and the background is generated
as all detected DEGs across any comparison.</dd>

</dl>

DEET_Input_as_Reference: DEET_Input_as_Reference

Description

Usage

Value

Arguments

Author

References

Examples