Entering edit mode
7.8 years ago
seta
★
1.9k
Hi friends,
I came across several papers that used BINGO (the Cytoscape plugin) for KEGG enrichment analysis of differentially expressed genes (DEG). Actually, I have made a transcriptome assembly and annotated against KEGG database, so I 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
Do you say that you do not have gene list but KO ids which are differentially expressed across your conditions? If I am not wrong BINGO accepts gene lists, and in cytoscape if you have gene lists or gene id with your BINGO plugins you have easily perform GO enrichment, or alternatively you can use DAVID (yes it is updated) , ENRICHR, geneSCF for the KEGG enrichment. So I would suggest if you can retrieve your gene list it would be better. Alternatively there is a plugin for cytoscape for KEGG enrichment from gene list which you can use KEGGscape. These should help you to perform your much needed tasks. There is always more than one way to do enrichment analysis!
Thank you for your response. My mean was I have gene list that annotated with KO ids. Regarding your suggestions, ENRICHR is great but just for human and rat, my case is a plant. As far as I know, DAVID and KEGGscape (in Cytoscape) doesn't perform KEGG enrichment analysis. In addition to BiNGO, I know KOBAS (enter link description here also do KEGG enrichment analysis, but my problem with both of them (BiNGO and KOBAS) is what is the right format of the custom background?. Custom background for my enrichment analysis will be whole transcriptome, however, I am not sure about its correct format. Any help would be highly appreciated.
Custom background should be the genes that got expressed across all samples in all conditions once you have the transcriptome abundances. DAVID has KEGG pathways as output. If you check carefully here.
Thank you. Yes, I know the concept of background, but I have a problem with the right format of background that is acceptable by BiNGO and KOBAS programs. If you or anybody have experience with these software, please kindly help me out on this issue.