Hi
I used blast2go in order to find similar genes to my transcriptome profile,
How can I identify significant kegg pathways for these genes(Profile)? And, is there any software to get visualized pathways like DAVID Bioinformatics output?
I heard that I have to use commercial software for high throughput Kegg pathways analysis.
Thanks
5 answers
I recommend you read the following blog post and use clusterProfiler which now supports using the latest online version of KEGG.
KEGG enrichment analysis with latest online data using clusterProfiler
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Guangchuang Yu
You can also try iPathwayGuide. It's a very simple tool that will provide analysis for DE genes, predited miRNAs, GO analysis, Next-gen Pathway analysis, and disease analysis.
It's free to use and the databases are updated at least every 6 months.
http://www.advaitabio.com/ipathwayguide.html
Here's a brief introductory video:
I used this workflow to do kegg pathway analysis. See if it can help you.
Our approach is unfortunately not in the article that seninp mentioned. But you can use PathVisio to analyse and visualise expression data on the WikiPathways curated pathway collection, the Reactome pathway set in WikiPathways format or a combination of both.
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Chris Evelo
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This article may help you. It has a table of tools and approaches. I am not affiliated with these guys.
It's a great paper thank you so much
Thanks for the link to the paper.
One of the suggestions in that paper is the use of topology-based pathway analysis. iPathwayGuide uses the latest in topology-based pathway analysis approaches. It's completely free to use with some minor restrictions (no downloading of images and tables for free accounts). Feel free to give it a try.