This project aims to help users to analyse and procuce good outputs for gene set enrichment analysis.
The enrichment process comes from other R packages like ClusterProfiler and enrichR and here we just work to give a better visualization of the results from these packages.
For an initial step lets select a data set to workthrough.
| log2FoldChange | padj | exp | |
|---|---|---|---|
| DDX11L1 | -1.125993 | 0.0495855 | -1 |
| PLEKHN1 | 1.072670 | 0.0358392 | 1 |
| HES4 | 1.868776 | 0.0058709 | 1 |
| ISG15 | 4.598033 | 0.0000000 | 1 |
| AGRN | 2.391258 | 0.0000000 | 1 |
| RP11-465B22.3 | 1.003380 | 0.0104877 | 1 |
| RP1-140A9.1 | 1.545089 | 0.0149719 | 1 |
| TP73 | 2.360830 | 0.0000276 | 1 |
| AJAP1 | -2.364369 | 0.0000006 | -1 |
| CHD5 | -1.110567 | 0.0356134 | -1 |
Here i'm showing an exemple of an enhichment analysis using the function enrichGO from ClusterProfiler.
library(clusterProfiler)
library(org.Hs.eg.db)
GO_CP <- enrichGO(gene = DE_agudo$symbol, #column from the dataframe with the symbols
OrgDb = org.Hs.eg.db, #orgdb
keyType = "SYMBOL", #type of data
ont = "BP") #especify the GO ontology Here is an example of an enrichment analysis using the enrichR.
library(enrichR)
GO_ER <- enrichr(genes = DE_agudo$symbol, #column from the dataframe with the symbols
databases = "GO_Biological_Process_2018" #database to perform the enrichment analysis
)Uploading data to Enrichr... Done.
Querying GO_Biological_Process_2018... Done.
Parsing results... Done.
This function recevies the output from enrichR or clusterProfiler and adds some information to the dataframe. it creates four columns called "up", "down", "up_genes" and "down_genes", related to # of genes upregulates, # of genes downregulated, a vector of genes up and downregulated, respectively. This function requires the specification of an enrichment type for the input object in enrich.type, choose 1 for clusterProfiler input and 2 for enrichR input.
source("~/Dropbox/Rcodes/cooltable.R")
#creating a vector with upregulated SYMBOL
up_agudo <- subset(DE_agudo$symbol, DE_agudo$log2FoldChange > 0)
#creating a vector with downregulated SYMBOL
down_agudo <- subset(DE_agudo$symbol, DE_agudo$log2FoldChange < 0)
CT_GO_CP <- cool_table(enrichment.obj = GO_CP, #enrichment object from clusterProfiler
enrich.type = 1, #selecting clusterProfiler object as input
up = up_agudo, #vector with upregulated genes
down = down_agudo #vector with downregulated genes
)
head(CT_GO_CP, 6) ID
GO:0006958 GO:0006958
GO:0002455 GO:0002455
GO:0006956 GO:0006956
GO:0016064 GO:0016064
GO:0019724 GO:0019724
GO:0072376 GO:0072376
Description
GO:0006958 complement activation, classical pathway
GO:0002455 humoral immune response mediated by circulating immunoglobulin
GO:0006956 complement activation
GO:0016064 immunoglobulin mediated immune response
GO:0019724 B cell mediated immunity
GO:0072376 protein activation cascade
Term_size p.adjust up down
GO:0006958 137 7.451780e-69 86 0
GO:0002455 149 1.813608e-67 87 1
GO:0006956 170 2.923462e-58 86 0
GO:0016064 212 4.152903e-55 89 3
GO:0019724 213 5.547052e-55 89 3
GO:0072376 194 1.283225e-53 87 0
up_genes
GO:0006958 C1QA/C1QC/C1QB/SERPING1/IGHA2/IGHG4/IGHG2/IGHA1/IGHG1/IGHG3/IGHM/IGHV6-1/IGHV1-3/IGHV2-5/IGHV3-7/IGHV3-11/IGHV3-13/IGHV3-15/IGHV1-18/IGHV3-20/IGHV3-21/IGHV3-23/IGHV1-24/IGHV2-26/IGHV4-28/IGHV3-30/IGHV3-33/IGHV4-34/IGHV4-39/IGHV3-43/IGHV3-48/IGHV3-49/IGHV5-51/IGHV3-53/IGHV1-58/IGHV4-59/IGHV4-61/IGHV3-64/IGHV3-66/IGHV1-69/IGHV2-70/IGHV1-69-2/IGHV3-72/IGHV3-73/IGHV3-74/IGKC/IGKV4-1/IGKV5-2/IGKV1-5/IGKV1-12/IGKV3-15/IGKV1-16/IGKV1-17/IGKV3-20/IGKV2-28/IGKV2-29/IGKV2-30/IGKV1-39/IGKV2-40/IGKV1D-39/IGKV1D-33/IGKV2D-30/IGKV2D-28/IGKV3D-20/IGKV1D-12/IGKV3D-11/IGLV6-57/IGLV1-51/IGLV1-47/IGLV1-44/IGLV7-43/IGLV1-40/IGLV3-27/IGLV3-25/IGLV2-23/IGLV3-21/IGLV3-19/IGLV2-14/IGLV2-11/IGLV2-8/IGLV3-1/IGLL5/IGLC2/IGLC3/IGLC6/IGLC7
GO:0002455 C1QA/C1QC/C1QB/EXO1/SERPING1/IGHA2/IGHG4/IGHG2/IGHA1/IGHG1/IGHG3/IGHM/IGHV6-1/IGHV1-3/IGHV2-5/IGHV3-7/IGHV3-11/IGHV3-13/IGHV3-15/IGHV1-18/IGHV3-20/IGHV3-21/IGHV3-23/IGHV1-24/IGHV2-26/IGHV4-28/IGHV3-30/IGHV3-33/IGHV4-34/IGHV4-39/IGHV3-43/IGHV3-48/IGHV3-49/IGHV5-51/IGHV3-53/IGHV1-58/IGHV4-59/IGHV4-61/IGHV3-64/IGHV3-66/IGHV1-69/IGHV2-70/IGHV1-69-2/IGHV3-72/IGHV3-73/IGHV3-74/IGKC/IGKV4-1/IGKV5-2/IGKV1-5/IGKV1-12/IGKV3-15/IGKV1-16/IGKV1-17/IGKV3-20/IGKV2-28/IGKV2-29/IGKV2-30/IGKV1-39/IGKV2-40/IGKV1D-39/IGKV1D-33/IGKV2D-30/IGKV2D-28/IGKV3D-20/IGKV1D-12/IGKV3D-11/IGLV6-57/IGLV1-51/IGLV1-47/IGLV1-44/IGLV7-43/IGLV1-40/IGLV3-27/IGLV3-25/IGLV2-23/IGLV3-21/IGLV3-19/IGLV2-14/IGLV2-11/IGLV2-8/IGLV3-1/IGLL5/IGLC2/IGLC3/IGLC6/IGLC7
GO:0006956 C1QA/C1QC/C1QB/SERPING1/IGHA2/IGHG4/IGHG2/IGHA1/IGHG1/IGHG3/IGHM/IGHV6-1/IGHV1-3/IGHV2-5/IGHV3-7/IGHV3-11/IGHV3-13/IGHV3-15/IGHV1-18/IGHV3-20/IGHV3-21/IGHV3-23/IGHV1-24/IGHV2-26/IGHV4-28/IGHV3-30/IGHV3-33/IGHV4-34/IGHV4-39/IGHV3-43/IGHV3-48/IGHV3-49/IGHV5-51/IGHV3-53/IGHV1-58/IGHV4-59/IGHV4-61/IGHV3-64/IGHV3-66/IGHV1-69/IGHV2-70/IGHV1-69-2/IGHV3-72/IGHV3-73/IGHV3-74/IGKC/IGKV4-1/IGKV5-2/IGKV1-5/IGKV1-12/IGKV3-15/IGKV1-16/IGKV1-17/IGKV3-20/IGKV2-28/IGKV2-29/IGKV2-30/IGKV1-39/IGKV2-40/IGKV1D-39/IGKV1D-33/IGKV2D-30/IGKV2D-28/IGKV3D-20/IGKV1D-12/IGKV3D-11/IGLV6-57/IGLV1-51/IGLV1-47/IGLV1-44/IGLV7-43/IGLV1-40/IGLV3-27/IGLV3-25/IGLV2-23/IGLV3-21/IGLV3-19/IGLV2-14/IGLV2-11/IGLV2-8/IGLV3-1/IGLL5/IGLC2/IGLC3/IGLC6/IGLC7
GO:0016064 C1QA/C1QC/C1QB/IL10/EXO1/IRF7/SERPING1/IGHA2/IGHG4/IGHG2/IGHA1/IGHG1/IGHG3/IGHM/IGHV6-1/IGHV1-3/IGHV2-5/IGHV3-7/IGHV3-11/IGHV3-13/IGHV3-15/IGHV1-18/IGHV3-20/IGHV3-21/IGHV3-23/IGHV1-24/IGHV2-26/IGHV4-28/IGHV3-30/IGHV3-33/IGHV4-34/IGHV4-39/IGHV3-43/IGHV3-48/IGHV3-49/IGHV5-51/IGHV3-53/IGHV1-58/IGHV4-59/IGHV4-61/IGHV3-64/IGHV3-66/IGHV1-69/IGHV2-70/IGHV1-69-2/IGHV3-72/IGHV3-73/IGHV3-74/IGKC/IGKV4-1/IGKV5-2/IGKV1-5/IGKV1-12/IGKV3-15/IGKV1-16/IGKV1-17/IGKV3-20/IGKV2-28/IGKV2-29/IGKV2-30/IGKV1-39/IGKV2-40/IGKV1D-39/IGKV1D-33/IGKV2D-30/IGKV2D-28/IGKV3D-20/IGKV1D-12/IGKV3D-11/IGLV6-57/IGLV1-51/IGLV1-47/IGLV1-44/IGLV7-43/IGLV1-40/IGLV3-27/IGLV3-25/IGLV2-23/IGLV3-21/IGLV3-19/IGLV2-14/IGLV2-11/IGLV2-8/IGLV3-1/IGLL5/IGLC2/IGLC3/IGLC6/IGLC7
GO:0019724 C1QA/C1QC/C1QB/IL10/EXO1/IRF7/SERPING1/IGHA2/IGHG4/IGHG2/IGHA1/IGHG1/IGHG3/IGHM/IGHV6-1/IGHV1-3/IGHV2-5/IGHV3-7/IGHV3-11/IGHV3-13/IGHV3-15/IGHV1-18/IGHV3-20/IGHV3-21/IGHV3-23/IGHV1-24/IGHV2-26/IGHV4-28/IGHV3-30/IGHV3-33/IGHV4-34/IGHV4-39/IGHV3-43/IGHV3-48/IGHV3-49/IGHV5-51/IGHV3-53/IGHV1-58/IGHV4-59/IGHV4-61/IGHV3-64/IGHV3-66/IGHV1-69/IGHV2-70/IGHV1-69-2/IGHV3-72/IGHV3-73/IGHV3-74/IGKC/IGKV4-1/IGKV5-2/IGKV1-5/IGKV1-12/IGKV3-15/IGKV1-16/IGKV1-17/IGKV3-20/IGKV2-28/IGKV2-29/IGKV2-30/IGKV1-39/IGKV2-40/IGKV1D-39/IGKV1D-33/IGKV2D-30/IGKV2D-28/IGKV3D-20/IGKV1D-12/IGKV3D-11/IGLV6-57/IGLV1-51/IGLV1-47/IGLV1-44/IGLV7-43/IGLV1-40/IGLV3-27/IGLV3-25/IGLV2-23/IGLV3-21/IGLV3-19/IGLV2-14/IGLV2-11/IGLV2-8/IGLV3-1/IGLL5/IGLC2/IGLC3/IGLC6/IGLC7
GO:0072376 C1QA/C1QC/C1QB/SERPING1/IGHA2/IGHG4/IGHG2/IGHA1/IGHG1/IGHG3/IGHM/IGHV6-1/IGHV1-3/IGHV2-5/IGHV3-7/IGHV3-11/IGHV3-13/IGHV3-15/IGHV1-18/IGHV3-20/IGHV3-21/IGHV3-23/IGHV1-24/IGHV2-26/IGHV4-28/IGHV3-30/IGHV3-33/IGHV4-34/IGHV4-39/IGHV3-43/IGHV3-48/IGHV3-49/IGHV5-51/IGHV3-53/IGHV1-58/IGHV4-59/IGHV4-61/IGHV3-64/IGHV3-66/IGHV1-69/IGHV2-70/IGHV1-69-2/IGHV3-72/IGHV3-73/IGHV3-74/IGKC/IGKV4-1/IGKV5-2/IGKV1-5/IGKV1-12/IGKV3-15/IGKV1-16/IGKV1-17/IGKV3-20/IGKV2-28/IGKV2-29/IGKV2-30/IGKV1-39/IGKV2-40/IGKV1D-39/IGKV1D-33/IGKV2D-30/IGKV2D-28/IGKV3D-20/IGKV1D-12/IGKV3D-11/IGLV6-57/IGLV1-51/IGLV1-47/IGLV1-44/IGLV7-43/IGLV1-40/IGLV3-27/IGLV3-25/IGLV2-23/IGLV3-21/IGLV3-19/IGLV2-14/IGLV2-11/IGLV2-8/IGLV3-1/IGLL5/IGLC2/IGLC3/IGLC6/IGLC7/GP9
down_genes
GO:0006958
GO:0002455 HLA-DQB1
GO:0006956
GO:0016064 TNFSF4/IL4/HLA-DQB1
GO:0019724 TNFSF4/IL4/HLA-DQB1
GO:0072376