Hello, I have a dataset of scRNA-Seq gene expression with a list of more or less 27.000 genes. What I would like to do is to recover for each gene one of more metabolic pathways in which is involved. I can do so, for instance, with KEGG MAPPER but 21750 genes remain out (thus it is not possible to "cluster" them in the proper pathway). I have tried to convert my gene names in KEGG Id, unsuccessfully (KEGG returns "No data found."). I have also tried with GeneMANIA, and I had the same troubles (genes are not identified thus the network cannot be created). Does anybody have any other idea or is able to improve mine?
Please show code. Anecdotal evidence is hard to debug.
I am sorry, I do not understand what code I should show.
For KEGG I have copy-pasted the list of gene here https://www.genome.jp/kegg/tool/map_pathway.html and then click Exec button. For a subgroup of genes, I am able to get an output, but not for all of them.
For GeneMANIA, I have downloaded Cytoscape, and added the GeneMANIA tool. In the same way, I am not able the get the full network, but just some sub networks for small subgroups of my genoma.
What I need is something like a table:
that associate each gene to a pathway (or more).
Thank you for your comment! :)
What kind of gene IDs do you have? Which species?
@Jean-Karim Heriche sorry, I didn't specify. They are human genes and I have their official gene symbol.
The KEGG reconstruct pathway tool you linked to needs KEGG pathway identifiers. It doesn't do identifier conversion or ID to pathway mapping for you. Check the example input files provided. The KEGG convert ID tool found in this section of the KEGG website (see the left hand side bar) only works with UniProt or NCBI IDs.
Oh, I see. I am quite sure I got lost into KEGG tools and I link the wrong tool, as I think I found a tool that maps properly some of my genes to a path - by ignoring most of them though. This is the tool I was referring to: https://www.kegg.jp/kegg/tool/map_pathway1.html . Do you recommend any tools to do ID to pathway mapping? Thank you!
If you're not stuck with using KEGG, you could try Reactome. The "analyze data" section should do what you want.