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_enrichr:_2016] hosted at http://amp.pharm.mssm.edu/Enrichr.
First find the list of all available databases from Enrichr.
library(enrichR)## Welcome to enrichR
## Checking connection ... Connection is Live!dbs <- listEnrichrDbs()if (is.null(dbs)) websiteLive <- FALSE
if (websiteLive) 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")
if (websiteLive) 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.
if (websiteLive) enriched[["GO_Biological_Process_2015"]]| 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 |
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.