Question: Cluster BACTERIA genes in metabolic pathways and functions with gene names
gravatar for ecg1g15
14 months ago by
ecg1g150 wrote:

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".


rna-seq • 340 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by ecg1g150

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:

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)

ADD REPLYlink written 14 months ago by Friederike6.0k
gravatar for davidtmscott
14 months ago by
davidtmscott80 wrote:

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.

You can also follow this link and select "Download htext":

Hope this helps.

ADD COMMENTlink written 14 months ago by davidtmscott80
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