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In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

How to use clusterProfiler to do GO enrichment analysis with unsupported organisms

Guangchuang Yu

Jinan University

This vignette is an extension for what already exists in the clusterProfiler.pdf vignette. The clusterProfiler provide enrichGO function to do hypergeometric testing with “human”, “mouse” , "zebrafish" and “yeast” organism supported. It is very easy to support other organism provided that the bioconductor annotation package exists.

Most of the software packages for GO enrichment analysis in the Bioconductor project were designed for model organism, and they all rely on the bioconductor annotation packages.

If the organism without annotation package available, it is not easy to employ the existed package to perform such an analysis.

I have extended clusterProfiler to support the unsupported organism.

Here, I will illustrate how to do GO analysis for Streptococcus pyogenes M1 MGAS5005, as an example.

For doing GO analysis, you should have gene and GO mapping data.

I suppose you have nothing in hand, and explain how you get these things in hand.

The whole genome annotation can be downloaded from NCBI. In this example, the M5005 bacteria whole genome annotation file can be downloaded from: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptococcus_pyogenes_MGAS5005_uid58337/

The clusterProfiler package has functions for parsing GFF file. When you have downloaded the gff file, using the following command:

suppressPackageStartupMessages(require(clusterProfiler))
Gff2GeneTable("NC_007297.gff")

## Reading NC_007297.gff: found 3989 rows with classes: character, character, character, integer, integer, character, character, character, character 
## [1] "Gene Table file save in the working directory."

This function will parse the gff file, and extract information to form a data.frame, and save it as “geneTable.rda” in the current working directory.

load("geneTable.rda")
head(geneTable)

##     GeneID     seqname start  end strand GeneName          Locus
## 1  3571011 NC_007297.1   202 1557      +     dnaA M5005_Spy_0001
## 3  3571012 NC_007297.1  1712 2848      +     dnaN M5005_Spy_0002
## 5  3571013 NC_007297.1  2923 3120      +        - M5005_Spy_0003
## 7  3571014 NC_007297.1  3450 4565      +     ychF M5005_Spy_0004
## 9  3571015 NC_007297.1  4635 5204      +      pth M5005_Spy_0005
## 11 3571016 NC_007297.1  5207 8710      +     trcF M5005_Spy_0006

This geneTable is useful for ID mapping, and will be used for mapping GeneID to GeneName if parameter readable is set to TRUE when calling enrichGO.

eg <- geneTable$GeneID

Now you have all GeneID stored in eg, I recommend you using biomaRt package to query GO annotation, and I will demonstrate how to do it.

require(biomaRt)

## Loading required package: biomaRt

bacteria = useMart("bacteria_mart_14")
bac = useDataset("str_22007_gene", mart = bacteria)
gomap <- getBM(attributes = c("entrezgene", "go_accession"), filters = "entrezgene", 
    values = eg, mart = bac)

dim(gomap)

## [1] 4025    2

head(gomap)

##   entrezgene go_accession
## 1    3572098   GO:0043565
## 2    3572008   GO:0006355
## 3    3572008   GO:0006352
## 4    3572008   GO:0016987
## 5    3572008   GO:0003677
## 6    3572008   GO:0003700

You should use other dataset for other bacteria. If the organism is not bacteria, you should use other mart, for instance fungi_mart_13 for fungi.

The gomap only contain GO directly annotation, but undirectly annotation was needed for GO enrichment analysis.

So, clusterProfiler provided another function called buildGOmap, for building gomap files needed for analysis.

buildGOmap(gomap)

## [1] "GO Annotation Mapping files save in the working directory."

After running this command, buildGOmap function generate GO2EG.rda, EG2GO.rda, GO2ALLEG.rda and EG2ALLGO.rda in the working directory.

Providing these files in the working directory. The enrichGO function can perform hypergeometric test for this organism.

Suppose the following genes are of interested.

gene <- c("3572890", "3572609", "3572407", "3572408", "3572333", "3572206", 
    "3572193", "3571922", "3571782", "3571786", "3571624", "3571626", "3571412", 
    "3571413", "3571382", "3571286", "3571289", "3571124", "3571106", "3571029")
mf <- enrichGO(gene, ont = "MF", organism = "M5005", pvalueCutoff = 0.05, qvalueCutoff = 0.1, 
    readable = TRUE)

## Loading required package: GO.db

summary(mf)

##                    ID
## GO:0004312 GO:0004312
## GO:0005515 GO:0005515
## GO:0004427 GO:0004427
## GO:0004807 GO:0004807
## GO:0004360 GO:0004360
## GO:0070548 GO:0070548
## GO:0008886 GO:0008886
## GO:0004585 GO:0004585
## GO:0016990 GO:0016990
## GO:0004316 GO:0004316
## GO:0004356 GO:0004356
## GO:0004618 GO:0004618
## GO:0003938 GO:0003938
##                                                                                Description
## GO:0004312                                                    fatty acid synthase activity
## GO:0005515                                                                 protein binding
## GO:0004427                                                inorganic diphosphatase activity
## GO:0004807                                             triose-phosphate isomerase activity
## GO:0004360              glutamine-fructose-6-phosphate transaminase (isomerizing) activity
## GO:0070548                                           L-glutamine aminotransferase activity
## GO:0008886 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity
## GO:0004585                                         ornithine carbamoyltransferase activity
## GO:0016990                                                     arginine deiminase activity
## GO:0004316                     3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004356                                               glutamate-ammonia ligase activity
## GO:0004618                                                phosphoglycerate kinase activity
## GO:0003938                                                      IMP dehydrogenase activity
##            GeneRatio BgRatio   pvalue  qvalue            geneID Count
## GO:0004312      2/20  6/1286 0.003322 0.08059         fabF/fabG     2
## GO:0005515      3/20 33/1286 0.013039 0.08059 nrdE.2/dnaK/groEL     3
## GO:0004427      1/20  1/1286 0.015552 0.08059              ppaC     1
## GO:0004807      1/20  1/1286 0.015552 0.08059              tpiA     1
## GO:0004360      1/20  1/1286 0.015552 0.08059              glmS     1
## GO:0070548      1/20  1/1286 0.015552 0.08059              glmS     1
## GO:0008886      1/20  1/1286 0.015552 0.08059              gapN     1
## GO:0004585      1/20  1/1286 0.015552 0.08059              arcB     1
## GO:0016990      1/20  1/1286 0.015552 0.08059              arcA     1
## GO:0004316      1/20  1/1286 0.015552 0.08059              fabG     1
## GO:0004356      1/20  1/1286 0.015552 0.08059              glnA     1
## GO:0004618      1/20  1/1286 0.015552 0.08059               pgk     1
## GO:0003938      1/20  1/1286 0.015552 0.08059              guaB     1

You can used other tools provided in clusterProfiler, such as plot to visualize the result, and compareCluster to compare different gene clusters.

YuLab-SMU/clusterProfiler documentation built on Nov. 14, 2024, 3:10 a.m.