An R interface to the Enrichr database

Wajid Jawaid 2019-08-01

CRAN_Status_Badge Project Status: Active - The project has reached a stable, usable state and is being actively developed. CRAN mirror downloads

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

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]])
Term Overlap P.value Adjusted.P.value Old.P.value Old.Adjusted.P.value Odds.Ratio Combined.Score Genes
embryonic hemopoiesis (GO_0035162) 3/24 0.0e+00 0.0001573 0 0 416.66667 7213.540 KDR;GATA1;RUNX1
regulation of myeloid cell differentiation (GO_0045637) 4/156 1.0e-07 0.0001370 0 0 85.47009 1432.245 GFI1B;SPI1;GATA1;RUNX1
regulation of erythrocyte differentiation (GO_0045646) 3/36 1.0e-07 0.0001847 0 0 277.77778 4459.220 GFI1B;SPI1;GATA1
positive regulation of myeloid cell differentiation (GO_0045639) 3/74 1.0e-06 0.0012521 0 0 135.13514 1871.822 GFI1B;GATA1;RUNX1
hemopoiesis (GO_0030097) 3/95 2.1e-06 0.0021339 0 0 105.26316 1378.448 KDR;GATA1;RUNX1
hematopoietic progenitor cell differentiation (GO_0002244) 3/106 2.9e-06 0.0024754 0 0 94.33962 1204.196 SPI1;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.