Cluster BACTERIA genes in metabolic pathways and functions with gene names

Question

[ecg1g15]

Hi, I have my RNAseq data all annotated already and have done further analysis. I would like to cluster the genes in function or metabolic pathways. Is there a way of generating this clusters/groups with the list of gene names? I have never used KEGG or GO analysis but I think they need the reads files?

My organism is a bacteria whose genome is found in NCBI, but its not common, so it is not found in some useful softwares such as "g:Profiler".

Thanks!

[Friederike]

You should probably add to the title of your question that you're dealing with bacteria.

I personally have no experience with the state of the annotation for bacterial genomes, but a quick google search let to this data base: https://metacyc.org/

Apart from that, if you're able to use R, clusterProfiler is probably the tool you're looking for (if your organism of interest has KEGG annotation)

Answer 1

[davidtmscott]

The link below will download all KEGG pathway data. This is a file containing each pathway and respective KO (gene). You could then filter this list for only the KO you have. You should then have a list of your KO's under their specific pathways.

https://www.kegg.jp/kegg-bin/download_htext?htext=ko00001.keg&format=htext&filedir=

You can also follow this link and select "Download htext": https://www.kegg.jp/kegg-bin/get_htext?ko00001.keg

Hope this helps.