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enrichR can be installed from Github or soon from CRAN.
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)
## Welcome to enrichR
## Checking connection ...
## Enrichr ... Connection is Live!
## FlyEnrichr ... Connection is Live!
## WormEnrichr ... Connection is Live!
## YeastEnrichr ... Connection is Live!
## FishEnrichr ... Connection is Live!
## OxEnrichr ... Connection is Live!
websiteLive <- getOption("enrichR.live")
if (websiteLive) {
listEnrichrSites()
setEnrichrSite("Enrichr") # Human genes
}
## Enrichr ... Connection is Live!
## FlyEnrichr ... Connection is Live!
## WormEnrichr ... Connection is Live!
## YeastEnrichr ... Connection is Live!
## FishEnrichr ... Connection is Live!
## OxEnrichr ... Connection is Live!
## Connection changed to https://maayanlab.cloud/Enrichr/
## Connection is Live!
Then find the list of all available databases from Enrichr.
## geneCoverage genesPerTerm libraryName
## 1 13362 275 Genome_Browser_PWMs
## 2 27884 1284 TRANSFAC_and_JASPAR_PWMs
## 3 6002 77 Transcription_Factor_PPIs
## 4 47172 1370 ChEA_2013
## 5 47107 509 Drug_Perturbations_from_GEO_2014
## 6 21493 3713 ENCODE_TF_ChIP-seq_2014
## link numTerms
## 1 http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ 615
## 2 http://jaspar.genereg.net/html/DOWNLOAD/ 326
## 3 290
## 4 http://amp.pharm.mssm.edu/lib/cheadownload.jsp 353
## 5 http://www.ncbi.nlm.nih.gov/geo/ 701
## 6 http://genome.ucsc.edu/ENCODE/downloads.html 498
## appyter categoryId
## 1 ea115789fcbf12797fd692cec6df0ab4dbc79c6a 1
## 2 7d42eb43a64a4e3b20d721fc7148f685b53b6b30 1
## 3 849f222220618e2599d925b6b51868cf1dab3763 1
## 4 7ebe772afb55b63b41b79dd8d06ea0fdd9fa2630 7
## 5 ad270a6876534b7cb063e004289dcd4d3164f342 7
## 6 497787ebc418d308045efb63b8586f10c526af51 7
geneCoverage | genesPerTerm | libraryName | numTerms | appyter | categoryId |
---|---|---|---|---|---|
13362 | 275 | Genome_Browser_PWMs | 615 | ea115789fcbf12797fd692cec6df0ab4dbc79c6a | 1 |
27884 | 1284 | TRANSFAC_and_JASPAR_PWMs | 326 | 7d42eb43a64a4e3b20d721fc7148f685b53b6b30 | 1 |
6002 | 77 | Transcription_Factor_PPIs | 290 | 849f222220618e2599d925b6b51868cf1dab3763 | 1 |
47172 | 1370 | ChEA_2013 | 353 | 7ebe772afb55b63b41b79dd8d06ea0fdd9fa2630 | 7 |
47107 | 509 | Drug_Perturbations_from_GEO_2014 | 701 | ad270a6876534b7cb063e004289dcd4d3164f342 | 7 |
21493 | 3713 | ENCODE_TF_ChIP-seq_2014 | 498 | 497787ebc418d308045efb63b8586f10c526af51 | 7 |
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.
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 | 0.0000083 | 0 | 0 | 951.0952 | 16465.833 | KDR;GATA1;RUNX1 |
regulation of myeloid cell differentiation (GO_0045637) | 4/156 | 1.0e-07 | 0.0000083 | 0 | 0 | 261.0789 | 4374.968 | GFI1B;SPI1;GATA1;RUNX1 |
regulation of erythrocyte differentiation (GO_0045646) | 3/36 | 1.0e-07 | 0.0000112 | 0 | 0 | 604.8788 | 9710.235 | GFI1B;SPI1;GATA1 |
positive regulation of myeloid cell differentiation (GO_0045639) | 3/74 | 1.0e-06 | 0.0000762 | 0 | 0 | 280.6056 | 3886.803 | GFI1B;GATA1;RUNX1 |
hemopoiesis (GO_0030097) | 3/95 | 2.1e-06 | 0.0001299 | 0 | 0 | 216.3261 | 2832.846 | KDR;GATA1;RUNX1 |
hematopoietic progenitor cell differentiation (GO_0002244) | 3/106 | 2.9e-06 | 0.0001507 | 0 | 0 | 193.1165 | 2465.031 | SPI1;GATA1;RUNX1 |
Plot Enrichr GO-BP output. (Plotting function contributed by I-Hsuan Lin)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.