DAVID functional analysis with clusterProfiler
Some users told me that they may want to use DAVID at some circumstances. I think it maybe a good idea to make clusterProfiler supports DAVID, so that DAVID users can use visualization functions provided by clusterProfiler.
require(DOSE) require(clusterProfiler) data(geneList) gene = names(geneList)[abs(geneList) > 2] david = enrichDAVID(gene = gene, idType="ENTREZ_GENE_ID", listType="Gene", annotation="KEGG_PATHWAY") > summary(david) ID Description GeneRatio BgRatio pvalue hsa04110 hsa04110 Cell cycle 11/68 125/5085 4.254437e-06 hsa04114 hsa04114 Oocyte meiosis 10/68 110/5085 1.119764e-05 hsa03320 hsa03320 PPAR signaling pathway 7/68 69/5085 2.606715e-04 p.adjust qvalue geneID hsa04110 0.0003998379 NA 9133/4174/890/991/1111/891/7272/8318/4085/983/9232 hsa04114 0.0005261534 NA 9133/5241/51806/3708/991/891/4085/983/9232/6790 hsa03320 0.0081354974 NA 4312/2167/5346/5105/3158/9370/9415 Count hsa04110 11 hsa04114 10 hsa03320 7
There are only 5085 human genes annotated by KEGG, this is due to out-of-date DAVID data.
With enrichDAVID, compare DAVID functional profiles among different gene clusters is also supported.
data(gcSample) x=compareCluster(gcSample, fun="enrichDAVID", annotation="KEGG_PATHWAY") plot(x)
As I pointed out in KEGG enrichment analysis with latest online data using clusterProfiler, there are many webservers using out of date data. This may leads to different interpretation of biological results. DAVID’s data is also out of date. DAVID stopped updating database since 2010. This is why I love Bioconductor, almost all the annotation packages are maintained by Bioconductor core team and will be updated biannual. enrichGO and enrichKEGG is more reliable with more updated data than many other tools.
Yu G, Wang L, Han Y and He Q*. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.