GO and Pathway enrichment analyses for genes of interest
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DESCRIPTION
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README.md

README.md

FunEnrich

Gregorio Alanis-Lobato

BP, CC, MF (i.e. Gene Ontology) and REACTOME enrichment analyses for a list of genes of interest, given a list of background genes.

The package supports ENTREZIDs (default), GENE SYMBOLs and UNIPROT accessions.

Installation

  1. Install the devtools package from CRAN if you haven't done so:
install.packages("devtools")
  1. Load the devtools package:
library("devtools")
  1. Install FunEnrich using the install_github function:
install_github("galanisl/FunEnrich")

Usage

To start using FunEnrich, load the package:

library("FunEnrich")

Let's now use the gene-disease associations included in the package. We will use disease.genes as background and genes associated with metabolic disorders as genes of interest (type ?metabolic and ?disease.genes in R for more information about these datasets):

analysis <- fun_enrich(gene.list = metabolic, background = disease.genes, 
                       id.type = "ENTREZID", benjamini = FALSE)

We can now explore, for example, the Molecular Functions enriched in genes that are specifically associated with metabolic disorders...

head(analysis$mf)
##          go.id                                                 term
## 624 GO:0030170                          pyridoxal phosphate binding
## 323 GO:0005159          insulin-like growth factor receptor binding
## 340 GO:0005219 ryanodine-sensitive calcium-release channel activity
## 101 GO:0003924                                      GTPase activity
## 118 GO:0004029                aldehyde dehydrogenase (NAD) activity
## 246 GO:0004806                         triglyceride lipase activity
##             pval
## 624 0.0001081392
## 323 0.0002985053
## 340 0.0002985053
## 101 0.0006422754
## 118 0.0008238455
## 246 0.0008238455

... as well as the enriched REACTOME pathways:

head(analysis$reactome)
##           react.id
## 91   R-HSA-1430728
## 1034   R-HSA-71387
## 702   R-HSA-446193
## 1022   R-HSA-70326
## 180  R-HSA-1660662
## 704   R-HSA-446203
##                                                                                                                                  pathway
## 91                                                                                                              Homo sapiens: Metabolism
## 1034                                                                                           Homo sapiens: Metabolism of carbohydrates
## 702  Homo sapiens: Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
## 1022                                                                                                    Homo sapiens: Glucose metabolism
## 180                                                                                           Homo sapiens: Glycosphingolipid metabolism
## 704                                                                                      Homo sapiens: Asparagine N-linked glycosylation
##              pval
## 91   1.401490e-15
## 1034 2.748917e-10
## 702  1.596449e-08
## 1022 5.894149e-07
## 180  1.425224e-06
## 704  1.744076e-06

It is also possible to generate a bar plot that focuses on the most enriched term of one or all categories:

plot_fun_enrich(enr = analysis, aspect = "ALL", benjamini = F, 
                top = 5, char_per_line = 80)