I am trying to get a list of genes involved in "metabolism", similar to in this paper - https://www.nature.com/articles/s42003-019-0666-1.
In this paper, they state that they "accessed information of all human metabolic pathways from the Reactome pathways database version 68. Reactome pathways are arranged into several tiers with the Reactome term “metabolism” (Reactome ID: R-HSA-1430728), encompassing 68 different metabolic pathways (see https://reactome.org/PathwayBrowser/#/R-HSA-1430728). The first-tier pathways include sixteen curated metabolic pathways which involve 2325 genes."
How do I do something similar and download a list of all genes involved in metabolism?
Also any explanation of the "tiers" thing would be great! I.e. when the authors talk about "first-tier pathways", what does this actually mean?
To answer this question: How do I do something similar and download a list of all genes involved in metabolism?
My go-to is usually the Comparative Toxicogenomics Database.
You can download the data files here in csv and tsv formats.
If for example you download the csv.gz file. You can extract it (gunzip) and then grep it for your search term using something like this:
grep R-HSA-1430728 your/file/path/here/CTD_genes_pathways.csv | cut -d ',' -f1 | sort | uniq
The command will search for R-HSA-1430728, cut the gene out (cutting the first word detecting commas as the separator), sort the genes alphabetically, and then give only the unique gene names (removes deplicates).
Note: I obtained 2171 unique genes using the command above (not 2325 genes):
grep R-HSA-1430728 your/file/path/here/CTD_genes_pathways.csv | cut -d ',' -f1 | sort | uniq | wc -l
2171
Hope this helps!
Hi Pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-specific. I would appreciate if you have suggestions for an alternative in Mouse data.
My original question is also posted here: Mapping Mouse RNAseq Marker Genes to Reactome Pathways
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