Overview
DoRothEA is a gene regulatory network (GRN) containing signed transcription factor
(TF) - target gene interactions. DoRothEA regulons, the collection of a TF and
its transcriptional targets, were curated and collected from different types of
evidence for both human and mouse. A confidence level was assigned to each
TF-target interaction based on the number of supporting evidence.
These regulons, coupled with any statistical method, can be
used to infer TF activities from bulk or single-cell transcriptomics.
This is an R package for storing the regulons. To infer TF
activities, please check out
decoupleR, available in
R or
python.
Installation
DoRothEA is available in
Bioconductor.
In addition, one can install the development version from the Github repository:
## To install the package from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dorothea")
## To install the development version from the Github repo:
devtools::install_github("saezlab/dorothea")
Updates
Since the original release, we have implemented some extensions in DoRothEA:
-
Extension to mouse:
Originally DoRothEA was developed for the application to human data.
In a benchmark study we showed that DoRothEA is also applicable to mouse data,
as described in
Holland et al., 2019.
Accordingly, we included new parameters to run mouse version of DoRothEA by
transforming the human genes to their mouse orthologs.
-
Extension to single-cell RNA-seq data:
We showed that DoRothEA can be applied to scRNA-seq data, as described in
Holland et al., 2020
-
Extension to other databases
We have released a new literature based GRN with increased coverage and better
performance at identifying perturbed TFs, called CollecTRI.
We encourage users to use CollecTRI instead of DoRothEA. Vignettes on how to
obtain activities are available at the decoupleR package.
License
DoRothEA is intended only for academic use as in contains resources
whose licenses don’t permit commercial use. However, we developed a non-academic
version of DoRothEA by removing those resources (mainly TRED from the curated
databases). You can find the non-academic package with the regulons here.
Citation
If you use the DoRothEA resource, please cite:
Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J.
Benchmark and integration of resources for the estimation of human
transcription factor activities. Genome Research. 2019. DOI: 10.1101/gr.240663.118.
If you infer TF activities, please cite:
Badia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov
D., Müller-Dott S., Taus P., Dugourd A., Holland C.H., Ramirez Flores R.O.
and Saez-Rodriguez J. decoupleR: Ensemble of computational methods to
infer biological activities from omics data. 2022. Bioinformatics Advances.
DOI: 10.1093/bioadv/vbac016
If you use the CollecTRI resource, please cite:
Müller-Dott S., Tsirvouli E., Vázquez M., Ramirez Flores R.O.,
Badia-i-Mompel P., Fallegger R., Lægreid A. and Saez-Rodriguez J.
Expanding the coverage of regulons from high-confidence prior knowledge for
accurate estimation of transcription factor activities. bioRxiv. 2023. DOI:
10.1101/2023.03.30.534849
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