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2.0 years ago
OST
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Hello!
How did this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372280/pdf/elife-41930.pdf) categorize the pathways in figure 2D (see below)? Are the categorizations of the pathways (Signaling, Immune Response, etc) determined by a particular package in R (GAGE itself?), or is it something the authors did manually? Thank you!
I think that it's not uncommon for categorization such as this to be manually curated.
However my best guess is that the authors of this paper leveraged the KEGG pathway map groupings in which pathways are grouped into different categories such as Metabolism of Amino Acids, Translation, Replication and Repair.
For more details see https://www.genome.jp/kegg/pathway.html
I see, thank you so much! Would you know if there is something similar to GO-BP Pathways? Like a GOBP Pathway map groupings?
For something comparable to the KEPP pathway mappings see: http://amigo.geneontology.org/amigo/dd_browse
This is extremely helpful. Thank you so much! Is there a way to have these GOBP Pathway mappings in R?
I suggest browsing Bioconductor for gene ontology packages that can assist you in this work.