Question: How to simultaneously convert gene IDs to Kegg IDs for E. coli
0
gravatar for tpm
6 weeks ago by
tpm10
tpm10 wrote:

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 • 90 views
ADD COMMENTlink modified 6 weeks ago by Kevin Blighe61k • written 6 weeks ago by tpm10
0
gravatar for Kevin Blighe
6 weeks ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

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

ADD COMMENTlink written 6 weeks ago by Kevin Blighe61k

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.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by tpm10

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'

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Kevin Blighe61k

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.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by tpm10

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

ADD REPLYlink written 6 weeks ago by Kevin Blighe61k

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

ADD REPLYlink written 6 weeks ago by tpm10
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