An R interface to the Enrichr database

Wajid Jawaid 2017-04-02

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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 et al. 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)
libraryName numTerms geneCoverage genesPerTerm link
1 Genome_Browser_PWMs 615 13362 275 http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/
2 TRANSFAC_and_JASPAR_PWMs 326 27884 1284 http://jaspar.genereg.net/html/DOWNLOAD/
3 Transcription_Factor_PPIs 290 6002 77
5 Drug_Perturbations_from_GEO_2014 701 47107 509 http://www.ncbi.nlm.nih.gov/geo/
6 ENCODE_TF_ChIP-seq_2014 498 21493 3713 http://genome.ucsc.edu/ENCODE/downloads.html

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"]]
Term Overlap P.value Adjusted.P.value Old.P.value Old.Adjusted.P.value Z.score Combined.Score Genes
embryonic hemopoiesis (GO_0035162) 3/24 0.00e+00 0.0000083 1.00e-07 0.0000355 -2.869798 33.56095 KDR;GATA1;RUNX1
regulation of erythrocyte differentiation (GO_0045646) 3/36 1.00e-07 0.0000112 4.00e-07 0.0000395 -2.503155 28.52580 GFI1B;SPI1;GATA1
regulation of myeloid cell differentiation (GO_0045637) 4/156 1.00e-07 0.0000083 2.00e-07 0.0000355 -2.325462 27.19519 GFI1B;SPI1;GATA1;RUNX1
positive regulation of granulocyte differentiation (GO_0030854) 2/10 3.40e-06 0.0001522 9.70e-06 0.0004382 -2.728754 23.98657 GFI1B;RUNX1
regulation of granulocyte differentiation (GO_0030852) 2/17 1.02e-05 0.0002681 2.51e-05 0.0006716 -2.824466 23.22908 GFI1B;RUNX1
granulocyte differentiation (GO_0030851) 2/15 7.90e-06 0.0002484 2.00e-05 0.0006314 -2.779246 23.06870 SPI1;GATA1

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. doi:10.1093/nar/gkw377.