tgodoy / cytokegg Goto Github PK

What steps will reproduce the problem?
1. In pathway selection, any genes could not be mapped on mTOR pathway even 
though part of genes in the list are involved in mTOR pathway entries of KEGG. 
2.
3.

What is the expected output? What do you see instead?
I think at least, the same genes in between my gene list and KEGG entry for 
mTOR pathway should be mapped in cytokegg. 

What version of the product are you using? On what operating system?
Cytokegg 0.0.5 / Cytoscape 3.0.2 / Mac OS X

Please provide any additional information below.
I attached my tab delimited txt file. 

What steps will reproduce the problem?
1. created 2 versions of expression files for E.coli with "b-numbers" or Gene 
Symbols as gene IDs (both of those IDs are present in the KEGG metagdata and 
can be seen in the table panel if we load any E.coli pathway via cytokegg 
plugin)
2. Apps -> Cytokegg -> Find pathways by gene(s) -> Import from file
3. If gene symbols are used as IDs, the dataset is loaded and listed in the 
"Select DataSet" menue but hughlighting it and running "Search" result in no 
response; if b-nmbers are used as IDs, the dataset fails to be recognized at 
all. 

What is the expected output? What do you see instead?
see above; the expression set in question was used successfully with, for 
example, the gage pipeline, with clear overrepresentation results

What version of the product are you using? On what operating system?
ver. 0.05, Debian Linux Squeeze 64-bit


Please provide any additional information below.

What steps will reproduce the problem?
1. Load network is OK
2. Then when I try to find pathways by gene, there is a new window that shows a 
blank pathway selection so I do not know what to do from here?

I am using both files from network and Txt

What is the expected output? What do you see instead?

I was hoping to see pathways ID from the data/network i have.


What version of the product are you using? On what operating system?

3.0.2 on version OS x 10.9.5


Please provide any additional information below.

My email [email protected]

Thanks!!!