Question: Cluster BACTERIA genes in metabolic pathways and functions with gene names
0
gravatar for ecg1g15
4 months ago by
ecg1g150
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".

Thanks!

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: 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)

ADD REPLYlink written 4 months ago by Friederike5.2k
0
gravatar for davidtmscott
4 months ago by
davidtmscott80
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.

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.

ADD COMMENTlink written 4 months ago by davidtmscott80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1602 users visited in the last hour