can i add my own gene list of a pathway to do enrichment with go-elite?

[medicalet]

Hi, Nathan. I have a question about GOElite and may need your help. We
are interested in the question of whether a list of target genes from
a pathway(1000 genes, from a publication by other group) is
significantly enriched in our result(about 3000 genes). How can we do
this since your method is based on GO term hierarchical tree? And can
we add this target gene list manually by your software? Thank you for
your kind reply.

[Nathan Salomonis]

Greetings,

 

Good question. As you alluded to, the 1000 genes represent a custom pathway, which is simple to add in GO-Elite. In addition to GO terms, GO-Elite extracts pathways from WikiPathways.org which are also in GenMAPP. These relationships are stored in a local text file. If you are working in human, for example, open up the GO-Elite directory:

GO-Elite_119beta\Databases\Hs\gene-mapp

There will be two files, "Ensembl-MAPP.txt" and "EntrezGene-MAPP.txt". If you open these files in a text editor and paste into Excel you'll see three columns: ID, SystemCode and MAPP. The ID is the gene ID for that system (e.g., Ensembl), the system code is the code found in the file:

GO-Elite_119beta\Config\source_data.txt

and the pathway is the name of the pathway your looking at. I would recommend that you open one of these files (which ever gene system you have identifiers for) and add those identifiers to the existing file, save this over the existing and run GO-Elite.

 

Does this sound OK?

Best,

Nathan

 

[wang donghai]

Thank you very much, Nathan.

 

I will use your method, which in my understanding is to add my own list of genes associated with the pathway of interest to your default MAPP.txt file, with new pathway name assigned to these genes. After saving, we run the program and will get the enrichment result including my favorite pathway. Is that right?  

 

All the best

 

Donghai

 

[Nathan Salomonis]

That's correct. Of course, the only issues that usually
present occur with weird formatting changes to the text
file that can cause odd errors. I will add a request for a
new feature in the next version of GO-Elite that allows
the user to import new pathway-gene associations without
having to manually change these files.

Best,
Nathan

[wang donghai]

Your kind help is greatly appreciated. Thanks a lot.