E.coli expression files not recognized

[GoogleCodeExporter]

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.

Original issue reported on code.google.com by omosk...@gmail.com on 19 Aug 2013 at 4:12

[GoogleCodeExporter]

I seem to be having a similar problem, uploaded a tab delimited text file (I 
hope this is the correct format as I couldn't find any hits for "ta separated 
file" in google), for staphylococcus gene expression data using gene symbols as 
the IDs. Loads in fine but no actual pathways are highlighted, even though I 
know there are plenty of KEGG pathways because of my DAVID analysis. Not sure 
if all the settings when loading in are correct as the tutorial has no 
information on what settings to use. Using Mac OSX 10.8

I would very much appreciate any answers from the tool designers, I expect I'm 
putting something in wrong but it's very hard to know without any clearer 
instructions.

Original comment by Jo.Mora...@gmail.com on 21 Aug 2013 at 2:27

[GoogleCodeExporter]

I have the same problem with E.coli dataset using UniProt Identifiers to search 
for pathways doesn´t show any results and only mapped 2 genes of 1900 
identifiers. Maybe only the listed Model Organisms are available which are 
visible in "Repositiory" and "Browse Pathway" Options?
If so, is there a way or work-around to get the Data for other organisms?
What is the default identifier to use?
Help would be appreciated  

Original comment by treit...@gmail.com on 24 Sep 2013 at 8:40

[GoogleCodeExporter]

Hi, I have the same problem with a human data set as Jo.Mora. Did anyone of you 
find a solution? Thanks for any help! 

Original comment by MELLI.LA...@gmail.com on 8 Oct 2013 at 10:48

[GoogleCodeExporter]

CytoKegg does not support gene symbols yet so when the tool tries to map the 
gene ids, no hits are found. I will add an error message for such cases.

Currently, the mapping tool is based on the KEGG API 
(http://www.kegg.jp/kegg/rest/keggapi.html) which does not support gene symbols 
but ncbi-gi, ncbi-geneid and uniprot identifiers.

I would suggest you to map your gene list to one of the identifiers listed 
above.

Original comment by seceval...@gmail.com on 20 Jan 2014 at 2:16