enrichR can be installed from Github or soon from CRAN.
library(devtools)
install_github("wjawaid/enrichR")The package can be downloaded from CRAN using:
install.packages("enrichR")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 |
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.