Kegg Api Matlab Anomalies, How To Identify Pathways And Recruited Genes In An Organism?

Question

[Dhruv Sakalley]

Hi,

I am trying to use MATLAB to identify from a set of KEGG genes (KO ids), which pathways they get recruited into, and for each of these pathways which KEGG genes (KO ids) are present. I need this to conduct a odds ratio calculation. So I create a kegg object, and create a string of tab separated ko ids in the format say: str ='ko:K02313 ko:K02338 ko:K03629 ko:K12972 ko:K13896'; and then use MATLAB to create a link to KEGG as per established protocol, and use the method

getpathwaysby_kos(kegg,str,'bov')%bov refering to organism name from which these ids are %derived I get null

when I use getpathwaysby_kos(kegg,{str},'bov') i still get null, however

getpathwaysby_kos(kegg,{'ko:K02338'},'bov')

ans =

path:bov03030

This confuses me in more than one ways, first why a single entry produces results and combined string does not?

Also, the pathway returned does not correspond to regular pathway id usually beginning with a ko identifier. I might be asking a very basic question here, but I cannot find adequate documentation for any of this. Please advise.

Answer 1

[Sven Mesecke]

I cannot verify it right now, but I think you can only use get_pathways_by_kos with a single string 'ko:K02338' in MATLAB. If you want to apply the method to several pathway ids, you have to use a cell array and cellfun.

Answer 2

[Khader Shameer]

KEGG was recently moved to a subscription model (See the plea here), but they promised to provide support for existing web service calls (See last paragraph). I am not a MatLab user, you may write to KEGG directly to see why you are not able to get response.

Also you may consider other open-access resources with APIs like WikiPathways or Pathway Commons for your genome-wide pathway analysis.