Up-regulated and down-regulated genes in pathway analysis

Question

[dark_rider_2010]

Hi, I have expression of genes in two different groups of patients, I want to do pathway analysis and know which processes are effected by my genes, I know about enrichr, kegg, reactome and so on. I don't know if I am allowed to share this figure, but I want a figure like this! I searched a lot for it but couldn't find how to draw this chart. Thanks

Answer 1

[Jean-Karim Heriche]

The figure you linked to is just a set of horizontal bar charts. Just plot your counts in each pathway as a bar plot in R using the barplot() function with the horiz = TRUE option. Colour as you need with e.g. col = c("red", "blue").

[dark_rider_2010]

I just don't know how to connect output of kegg (or any other databases) to this.

[Jean-Karim Heriche]

Simply count the number of genes of interest that fall into each pathway. This is usually available from the software with which you've done the enrichment analysis, e.g. the web-based enrichr exported table has this in the overlap column or in the genes column as a list of input genes that fall into the corresponding GO term or pathway.

Answer 2

[EagleEye]

This post might be also useful to you,

Gene ontology comparsion between up- and down-regulated genes