title: "An R interface to the Enrichr database" author: "Wajid Jawaid" email: "wj241@cam.ac.uk" date: "2019-07-18" bibliography: ./vignettes/enrichr.bib output: github_document
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) 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"]]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