clusterProfiler for Zebrafish (Danio rerio)
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@niranjanshirgaonkar-15284
Last seen 6.1 years ago

Hi

I was trying to do KEGG and GO analysis in R using clusterProfiler.

rm(list = ls())
dev.off()

library(clusterProfiler)
library(org.Hs.eg.db)

x <- "ENSG00000183733"
# human figla
x.df <- bitr(x, fromType = "ENSEMBL",
                toType = c("ENSEMBL", "ENTREZID", "SYMBOL"),
                OrgDb = org.Hs.eg.db)

gene1 <- x.df$ENTREZID

ggo <- groupGO(gene     = gene1,
               OrgDb    = org.Hs.eg.db,
               ont      = "CC",
               level    = 3,
               readable = TRUE)
# This works great.

###########
###########

y <- "ENSDARG00000087166"
# zebrafish figla
y.df <- bitr(y, fromType = "ENSEMBL",
                toType = c("ENSEMBL", "ENTREZID", "SYMBOL"),
                OrgDb = org.Hs.eg.db)

Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.

Does the same method not work with Zebrafish? Please guide me.

clusterprofiler • 1.8k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 28 days ago
China/Guangzhou/Southern Medical Univer…

How can you expect the org.Hs.eg.db (annotation of homo sapiens and only works for human) works with zebrafish?

What you need is org.Dr.eg.db.

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Apologies and thank you!

Here is the list of all annotation packages http://bioconductor.org/packages/3.6/data/annotation/ for anyone like me who might have problems with this.

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