How to simultaneously convert gene IDs to Kegg IDs for E. coli

Hi guys, How do I convert these gene IDs to Kegg IDs for E.coli at the same time. I tried this link but somehow I`m not successful (https://www.genome.jp/kegg/tool/conv_id.html). An example shown are these sample set of genes below:

nupX
psuT
atpE
rnlA
yiiM
zapE
eutC
sapD
dut
rpmJ
tatA
gadB
tdcC
ygcB
flgJ
glcG
marC
moaE

geneid kegg bioconductor

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updated 6.2 years ago by Kevin Blighe

• written 6.2 years ago by tpm •

1 answer

Hey again, you have KEGG IDs from my previous answer (see 'PATH' column): A: What codes do I use to generate gene cluster vectors with entrez gene id on clus

Kevin

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written 6.2 years ago by Kevin Blighe

Hi, thanks Kevin, It seems that keytypes for E coil K12 do not have keggID option. I can't seem to find the keyType for "kegg" option at least for me. From the:

keytype(org.EcK12.eg.db)

I want to perform enrichKEGG on compareCluste. That's why I am kindly asking if there was a way to avoid this problem by having KeggID instead of ENTREZID for example.

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written 6.2 years ago by tpm •

Are you implying that you do not see this output when you run this command [?]:

keytypes(org.EcK12.eg.db)
 [1] "ACCNUM"      "ALIAS"       "ENTREZID"    "ENZYME"      "EVIDENCE"   
 [6] "EVIDENCEALL" "GENENAME"    "GO"          "GOALL"       "ONTOLOGY"   
[11] "ONTOLOGYALL" "PATH"        "PMID"        "REFSEQ"      "SYMBOL"

The KEGG pathway IDs are stored under 'PATH'

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written 6.2 years ago by Kevin Blighe

I do see this output when I run the keytypes(org.EcK12.eg.db) , but I cannot see the KEGG option. In order to perform compareCluster function on clusterProfiler, the IDs should be in KEGG format. Initially at least, I wanted to convert using one of these options.

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written 6.2 years ago by tpm •

For clusterProfiler, you just need Entrez IDs, and you have those via the code that I shared in the previous answer.

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written 6.2 years ago by Kevin Blighe

I will run the code again I suppose. Thanks for the timely responses, much appreciated.

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written 6.2 years ago by tpm •