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An R interface to the Enrichr database

Wajid Jawaid 2019-08-01

Installation

enrichR can be installed from Github or soon from CRAN.

Github

library(devtools)
install_github("wjawaid/enrichR")

CRAN

The package can be downloaded from CRAN using:

install.packages("enrichR")

Usage example

enrichR provides an interface to the Enrichr database [@kuleshov_enrichr:_2016] hosted at http://amp.pharm.mssm.edu/Enrichr.

First find the list of all available databases from Enrichr.

library(enrichR)
dbs <- listEnrichrDbs()
head(dbs)
geneCoveragegenesPerTermlibraryNamelinknumTerms
113362275Genome_Browser_PWMshttp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/615
2278841284TRANSFAC_and_JASPAR_PWMshttp://jaspar.genereg.net/html/DOWNLOAD/326
3600277Transcription_Factor_PPIs290
547107509Drug_Perturbations_from_GEO_2014http://www.ncbi.nlm.nih.gov/geo/701
6214933713ENCODE_TF_ChIP-seq_2014http://genome.ucsc.edu/ENCODE/downloads.html498

View and select your favourite databases. Then query enrichr, in this case I have used genes associated with embryonic haematopoiesis.

dbs <- c("GO_Molecular_Function_2015", "GO_Cellular_Component_2015", "GO_Biological_Process_2015")
enriched <- enrichr(c("Runx1", "Gfi1", "Gfi1b", "Spi1", "Gata1", "Kdr"), dbs)
#> Uploading data to Enrichr... Done.
#>   Querying GO_Molecular_Function_2015... Done.
#>   Querying GO_Cellular_Component_2015... Done.
#>   Querying GO_Biological_Process_2015... Done.
#> Parsing results... Done.

Now view the results table.

enriched[["GO_Biological_Process_2015"]]

You can give many genes.

data(genes790)
length(genes790)
head(enrichr(genes790, c('LINCS_L1000_Chem_Pert_up'))[[1]])
TermOverlapP.valueAdjusted.P.valueOld.P.valueOld.Adjusted.P.valueOdds.RatioCombined.ScoreGenes
embryonic hemopoiesis (GO_0035162)3/240.0e+000.000157300416.666677213.540KDR;GATA1;RUNX1
regulation of myeloid cell differentiation (GO_0045637)4/1561.0e-070.00013700085.470091432.245GFI1B;SPI1;GATA1;RUNX1
regulation of erythrocyte differentiation (GO_0045646)3/361.0e-070.000184700277.777784459.220GFI1B;SPI1;GATA1
positive regulation of myeloid cell differentiation (GO_0045639)3/741.0e-060.001252100135.135141871.822GFI1B;GATA1;RUNX1
hemopoiesis (GO_0030097)3/952.1e-060.002133900105.263161378.448KDR;GATA1;RUNX1
hematopoietic progenitor cell differentiation (GO_0002244)3/1062.9e-060.00247540094.339621204.196SPI1;GATA1;RUNX1

References

Kuleshov, Maxim V., Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, et al. 2016. “Enrichr: A Comprehensive Gene Set Enrichment Analysis Web Server 2016 Update.” Nucleic Acids Res 44 (Web Server issue): W90–W97. https://doi.org/10.1093/nar/gkw377.

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Install

install.packages('enrichR')

Monthly Downloads

2,854

Version

2.1

License

GPL (>= 2)

Maintainer

Last Published

August 29th, 2019

Functions in enrichR (2.1)