Question: Cluster BACTERIA genes in metabolic pathways and functions with gene names
gravatar for ecg1g15
4 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 • 154 views
ADD COMMENTlink modified 3 months ago • written 4 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 4 months ago by Friederike5.2k
gravatar for davidtmscott
4 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 4 months ago by davidtmscott80
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