KEGG enrichment analysis by BINGO

[setar...@gmail.com]

Hi all,

I came across several papers that used BINGO for KEGG enrichment analysis of differentially expressed genes (DEG). Actually, I have made a transcriptome assembly and annotated against KEGG database, so we have KO numbers. Then, I got DEGs by the differential expression analysis, which would like to expose to KEGG enrichment analysis. Could you please let me know how to do KEGG enrichment analysis by BINGO?

Thank you

[alex.pico]

Hello.

BiNGO performs GO enrichment analysis. I'm not exactly sure how to do KEGG enrichment with BiNGO. You could contact the authors of the papers you mentioned. But I can't think of an approach that wouldn't require a license, given KEGG's restrictions on bulk analysis.

I know of an alternative tool that can perform pathway enrichment analysis called PathVisio. It makes use of the open access content at WikiPathways, which can subsequently be viewed and styled in Cytoscape, post-analysis.

Here's a tutorial: http://www.pathvisio.org/documentation/tutorials/tutorial-2/


***Disclosure: I'm a co-creator of WikiPathways and, in general, shamelessly promote open source and open access resources :)


On Monday, June 20, 2016 at 1:42:20 PM UTC-7:

[setar...@gmail.com]

Hi Alex,

 

Thank you for your response and introducing Pathvisio. It sounds great; I tried it by the tutorial data. However, I need some extra information to apply it to my own data; it will be great if you help me out in this regard. I am working on plants, so based on tutorial; I downloaded the “Gene products/protein databases” of Arabidopsis thaliana as well as “Pathways” for Arabidopsis thaliana. As I found that my gene identifier should be Ensemble format, so I converted my original gene format, which was TAIR, into Ensemble format, but there is still an error that says that “Error: Could not look up this identifier in the identifier mapping database”. Could you please advise me the right format of input data?

 

Another issue, I downloaded the “Pathways” for Arabidopsis, but there are just 23 pathways in this folder that not don’t cover all KEGG pathways. Could you please kindly tell me if it is possible to load all KEGG pathways of Arabidopsis into Pathvisio and visualize differentially expressed genes on these pathways?

 

 

Thank you for your help and time in advance.

Best regards,

Mary