GOHyperGAll: GO term enrichment analysis for large numbers of gene sets

Description

To test a sample population of genes for over-representation of GO terms, the core function GOHyperGAll computes for all nodes in the three GO networks (BP, CC and MF) an enrichment test based on the hypergeometric distribution and returns the corresponding raw and Bonferroni corrected p-values. Subsequently, a filter function supports GO Slim analyses using default or custom GO Slim categories. Several convenience functions are provided to process large numbers of gene sets (e.g. clusters from partitioning results) and to visualize the results.

Note: GOHyperGAll provides similar utilities as the GOHyperG function in the GOstats package. The main difference is that GOHyperGAll simplifies processing of large numbers of gene sets, as well as the usage of custom array-to-gene and gene-to-GO mappings.

Usage

## Generate gene-to-GO mappings and store as catDB object 
makeCATdb(myfile, lib = NULL, org = "", colno = c(1, 2, 3), idconv = NULL, rootUK=FALSE)
## Enrichment function
GOHyperGAll(catdb, gocat = "MF", sample, Nannot = 2)
## GO slim analysis
GOHyperGAll_Subset(catdb, GOHyperGAll_result, sample = test_sample, type = "goSlim", myslimv)
## Reduce GO term redundancy 
GOHyperGAll_Simplify(GOHyperGAll_result, gocat = "MF", cutoff = 0.001, correct = TRUE)
## Batch analysis of many gene sets
GOCluster_Report(catdb, setlist, id_type = "affy", method = "all", CLSZ = 10, cutoff = 0.001, gocats = c("MF", "BP", "CC"), myslimv = "default", correct = TRUE, recordSpecGO = NULL, ...)
## Bar plot of GOCluster_Report results
goBarplot(GOBatchResult, gocat)

Arguments

myfile

File with gene-to-GO mappings. Sample files can be downloaded from geneontology.org (http://geneontology.org/GO.downloads.annotations.shtml) or from BioMart as shown in example below.

colno

Column numbers referencing in myfile the three target columns containing GOID, GeneID and GOCAT, in that order.

org

Optional argument. Currently, the only valid option is org="Arabidopsis" to get rid of transcript duplications in this particular annotation.

lib

If the gene-to-GO mappings are obtained from a *.db package from Bioconductor then the package name can be specified under the lib argument of the sampleDFgene2GO function.

idconv

Optional id conversion data.frame

catdb

catdb object storing mappings of genes to annotation categories. For details, see ?"SYSargs-class".

rootUK

If the argument rootUK is set to TRUE then the root nodes are treated as terminal nodes to account for the new unknown terms.

sample

character vector containing the test set of gene identifiers

Nannot

Defines the minimum number of direct annotations per GO node from the sample set to determine the number of tested hypotheses for the p-value adjustment.

gocat

Specifies the GO type, can be assigned one of the following character values: "MF", "BP" and "CC".

GOHyperGAll_result

data.frame generated by GOHyperGAll

type

The function GOHyperGAll_Subset subsets the GOHyperGAll results by directly assigned GO nodes or custom goSlim categories. The argument type can be assigned the values goSlim or assigned.

myslimv

optional argument to provide custom goSlim vector

cutoff

p-value cutoff for GO terms to show in result data.frame

correct

If TRUE the function will favor the selection of terminal (informationich) GO terms that have at the same time a large number of sample matches.

setlist

list of character vectors containing gene IDs (or array feature IDs). The names of the list components correspond to the set labels, e.g. DEG comparisons or cluster IDs.

id_type

specifies type of IDs in input, can be assigned gene or affy

method

Specifies analysis type. Current options are all for GOHyperGAll, slim for GOHyperGAll_Subset or simplify for GOHyperGAll_Simplify.

CLSZ

minimum gene set (cluster) size to consider. Gene sets below this cutoff will be ignored.

gocats

Specifies GO type, can be assigned the values "MF", "BP" and "CC".

recordSpecGO

argument to report in the result data.frame specific GO IDs for any of the 3 ontologies disregarding whether they meet the specified p-value cutoff, e.g: recordSpecGO=c("GO:0003674", "GO:0008150", "GO:0005575")

GOBatchResult

data.frame generated by GOCluster_Report

...

additional arguments to pass on

Value

makeCATdb generates catDB object from file.

Details

GOHyperGAll_Simplify: The result data frame from GOHyperGAll will often contain several connected GO terms with significant scores which can complicate the interpretation of large sample sets. To reduce this redundancy, the function GOHyperGAll_Simplify subsets the data frame by a user specified p-value cutoff and removes from it all GO nodes with overlapping children sets (OFFSPRING), while the best scoring nodes are retained in the result data.frame.

GOCluster_Report: performs the three types of GO term enrichment analyses in batch mode: GOHyperGAll, GOHyperGAll_Subset or GOHyperGAll_Simplify. It processes many gene sets (e.g. gene expression clusters) and returns the results conveniently organized in a single result data frame.

References

This workflow has been published in Plant Physiol (2008) 147, 41-57.

Examples

Run this code

## Not run: 
# 
# ## Obtain annotations from BioMart
# listMarts() # To choose BioMart database
# m <- useMart("ENSEMBL_MART_PLANT"); listDatasets(m) 
# m <- useMart("ENSEMBL_MART_PLANT", dataset="athaliana_eg_gene")
# listAttributes(m) # Choose data types you want to download
# go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=m)
# go <- go[go[,3]!="",]; go[,3] <- as.character(go[,3])
# write.table(go, "GOannotationsBiomart_mod.txt", quote=FALSE, row.names=FALSE, col.names=FALSE, sep="\t")
# 
# ## Create catDB instance (takes a while but needs to be done only once)
# catdb <- makeCATdb(myfile="GOannotationsBiomart_mod.txt", lib=NULL, org="", colno=c(1,2,3), idconv=NULL)
# catdb
# 
# ## Create catDB from Bioconductor annotation package
# # catdb <- makeCATdb(myfile=NULL, lib="ath1121501.db", org="", colno=c(1,2,3), idconv=NULL)
# 
# ## AffyID-to-GeneID mappings when working with AffyIDs 
# # affy2locusDF <- systemPipeR:::.AffyID2GeneID(map = "ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_ATH1_array_elements-2010-12-20.txt", download=TRUE)
# # catdb_conv <- makeCATdb(myfile="GOannotationsBiomart_mod.txt", lib=NULL, org="", colno=c(1,2,3), idconv=list(affy=affy2locusDF))
# # systemPipeR:::.AffyID2GeneID(catdb=catdb_conv, affyIDs=c("244901_at", "244902_at"))
# 
# ## Next time catDB can be loaded from file
# save(catdb, file="catdb.RData") 
# load("catdb.RData")
# 
# ## Perform enrichment test on single gene set
# test_sample <- unique(as.character(catmap(catdb)$D_MF[1:100,"GeneID"]))
# GOHyperGAll(catdb=catdb, gocat="MF", sample=test_sample, Nannot=2)[1:20,]
# 
# ## GO Slim analysis by subsetting results accordingly
# GOHyperGAll_result <- GOHyperGAll(catdb=catdb, gocat="MF", sample=test_sample, Nannot=2)
# GOHyperGAll_Subset(catdb, GOHyperGAll_result, sample=test_sample, type="goSlim") 
# 
# ## Reduce GO term redundancy in 'GOHyperGAll_results'
# simplifyDF <- GOHyperGAll_Simplify(GOHyperGAll_result, gocat="MF", cutoff=0.001, correct=T)
# # Returns the redundancy reduced data set. 
# data.frame(GOHyperGAll_result[GOHyperGAll_result[,1] 
# 
# ## Batch Analysis of Gene Clusters
# testlist <- list(Set1=test_sample)
# GOBatchResult <- GOCluster_Report(catdb=catdb, setlist=testlist, method="all", id_type="gene", CLSZ=10, cutoff=0.001, gocats=c("MF", "BP", "CC"), recordSpecGO=c("GO:0003674", "GO:0008150", "GO:0005575"))
# 
# ## Plot 'GOBatchResult' as bar plot
# goBarplot(GOBatchResult, gocat="MF")
# 
# ## End(Not run)

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