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Description

Provides an R Interface to 'Enrichr'.

Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.

An R interface to the Enrichr database

Wajid Jawaid 2023-04-12

CRAN_Status_Badge Project Status: Active - The project has reached a stable, usablestate and is being activelydeveloped. CRAN mirrordownloads

Installation

enrichR can be installed from Github or 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 https://maayanlab.cloud/Enrichr/.

By default human genes are selected otherwise select your organism of choice. (This functionality was contributed by Alexander Blume)

library(enrichR)
listEnrichrSites()
#> Enrichr ... Connection is Live!
#> FlyEnrichr ... Connection is available!
#> WormEnrichr ... Connection is available!
#> YeastEnrichr ... Connection is available!
#> FishEnrichr ... Connection is available!
#> OxEnrichr ... Connection is available!
setEnrichrSite("Enrichr") # Human genes
#> Connection changed to https://maayanlab.cloud/Enrichr/
#> Connection is Live!

Then find the list of all available databases from Enrichr.

dbs <- listEnrichrDbs()
head(dbs)
geneCoveragegenesPerTermlibraryNamenumTermsappytercategoryId
13362275Genome_Browser_PWMs615ea115789fcbf12797fd692cec6df0ab4dbc79c6a1
278841284TRANSFAC_and_JASPAR_PWMs3267d42eb43a64a4e3b20d721fc7148f685b53b6b301
600277Transcription_Factor_PPIs290849f222220618e2599d925b6b51868cf1dab37631
471721370ChEA_20133537ebe772afb55b63b41b79dd8d06ea0fdd9fa26307
47107509Drug_Perturbations_from_GEO_2014701ad270a6876534b7cb063e004289dcd4d3164f3427
214933713ENCODE_TF_ChIP-seq_2014498497787ebc418d308045efb63b8586f10c526af517

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]])
TermOverlapP.valueAdjusted.P.valueOld.P.valueOld.Adjusted.P.valueOdds.RatioCombined.ScoreGenes
embryonic hemopoiesis (GO_0035162)3/240.0e+000.000008300951.095216465.833KDR;GATA1;RUNX1
regulation of myeloid cell differentiation (GO_0045637)4/1561.0e-070.000008300261.07894374.968GFI1B;SPI1;GATA1;RUNX1
regulation of erythrocyte differentiation (GO_0045646)3/361.0e-070.000011200604.87889710.235GFI1B;SPI1;GATA1
positive regulation of myeloid cell differentiation (GO_0045639)3/741.0e-060.000076200280.60563886.803GFI1B;GATA1;RUNX1
hemopoiesis (GO_0030097)3/952.1e-060.000129900216.32612832.846KDR;GATA1;RUNX1
hematopoietic progenitor cell differentiation (GO_0002244)3/1062.9e-060.000150700193.11652465.031SPI1;GATA1;RUNX1

Plot Enrichr GO-BP output. (Plotting function contributed by I-Hsuan Lin)

plotEnrich(enriched[[3]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value")

References2

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): W90–97.

Metadata

Version

3.2

License

Unknown

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