Hello,
I have multiple pathways that are being studied due to single-cell sequencing. What is the best way to represent pathways or specifically KEGG pathways for a manuscript?
Other than heatmap, or putting the entire pathway, is there any other representation of the data?
Thank you.
Regards,
Shweta
Hi Shweta
you can test StringDb with your list of genes and the multi proteins option (https://string-db.org/cgi/input?sessionId=bZL2FPazSgGv&input_page_active_form=multiple_identifiers) to see if the results fit to what you're waiting for.
all the best
fred
You can also use a table to show your significant pathways (Path way name, ids, FDR etc) and show one or two pathway using PathView that can map the significant proteins on the actual KEGG pathway for easier visualization.
Bioconductor - pathview
You can search pathview in google to see the output of this package.
You can show the colored maps (gene boxes colored by differential expression).
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