Question

kegg enrichment using clusterProfiler could not read KEGG Orthology IDs

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jfo • 0

@jfo-19354

Last seen 5.2 years ago

I wanted to perform the kegg enrichment method. Here's what I did: ran my fasta to kaas to get the KEGG Orthology IDs (K#####) then used these ID to perform enrichKEGG.

An example of the command was performed to test the function.

keggID <- c("K15179", "K03377") x <- enrichKEGG(keggID, organism='ko', keyType='kegg')

--> No gene can be mapped.... --> Expected input gene ID: K10780,K16305,K08093,K14275,K18819,K22554 --> return NULL...

When I use other KO ID like K05164, the program ran without any errors. This could mean that the KEGG IDs (in my example above) could not be mapped because they are not enriched? Also for the IDs that were accepted (e.g. K05164), it didn't have qvalue. I wonder if what I am doing wrong.

My other question is that, are the Kegg orthologous IDs invalid for bitr_kegg() function? I could not convert my K##### IDs. This shows up everytime I try different IDs (except for the example, ofc):

Warning message: In bitr_kegg("K15179", fromType = "kegg", toType = "uniprot", organism = "hsa") : 100% of input gene IDs are fail to map...

This is also true for ncbi protein and geneID. Am I using the wrong organism?

Also, what is the proper way to perform KEGG enrichment for non-model organism? I am really confused as to whether I would just use the closest model organism with available db to perform KEGG or use all available databases?

Thank you for the help!

clusterprofiler • 3.7k views

ADD COMMENT • link updated 5.0 years ago by contact • 0 • written 5.3 years ago by jfo • 0

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ADD REPLY • link 5.0 years ago sophieturner067 • 0

score 0 · Answer 1 · 2019-01-11

keggID <- c("K15179", "K03377") x <- enrichKEGG(keggID, organism='ko', keyType='kegg')

--> No gene can be mapped.... --> Expected input gene ID: K10780,K16305,K08093,K14275,K18819,K22554 --> return NULL...

Usually, this means that you are using the wrong ID.

In your case, you are indeed using the correct ID type. Then such error means that all your input ID have no pathway annotation.

You can verify by visiting the KEGG website.

For example, no pathway annotated in https://www.genome.jp/dbget-bin/www_bget?ko:K15179.

And have pathway annotated for the example ID, https://www.genome.jp/dbget-bin/www_bget?ko:K10780.

Warning message: In bitr_kegg("K15179", fromType = "kegg", toType = "uniprot", organism = "hsa") : 100% of input gene IDs are fail to map...

bitr_kegg is for converting ID within the same species, and K number is not a valid ID type of hsa, albeit that we can find ortholog ID.

Look at the gene session on https://www.genome.jp/dbget-bin/www_bget?ko:K15179, and try:

> bitr_kegg("7469", fromType = "kegg", toType = "uniprot", organism = "hsa")
  kegg    uniprot
1 7469     Q9H3P2
2 7469 A0A0C4DFX9