Question: Up-regulated and down-regulated genes in pathway analysis
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gravatar for dark_rider_2010
2.3 years ago by
dark_rider_201010 wrote:

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

R gene • 1.7k views
ADD COMMENTlink modified 2.3 years ago by EagleEye6.5k • written 2.3 years ago by dark_rider_201010
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gravatar for Jean-Karim Heriche
2.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

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").

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Jean-Karim Heriche21k

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

ADD REPLYlink written 2.3 years ago by dark_rider_201010

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.

ADD REPLYlink written 2.3 years ago by Jean-Karim Heriche21k
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gravatar for EagleEye
2.3 years ago by
EagleEye6.5k
Sweden
EagleEye6.5k wrote:

This post might be also useful to you,

Gene ontology comparsion between up- and down-regulated genes

ADD COMMENTlink written 2.3 years ago by EagleEye6.5k
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