How to use deseq 2 file for keggscape in cytoscape
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7 days ago

Hello everyone, I have got deseq files for various datasets and have to analyze the pathways, I used genecodis web tool and had various pathways for a dataset, I want to shorten the number of pathways by using keggscape on cytoscape. But there are no tutorials covering this, same type of question has been posted in the forum but no replies to that too. Please let me know whether any tutorial are avaialble or in case it's not there , what are the steps or alternate methods I can do for that. Thank you in advance

RNA-SEQ Visualization Sequencing Cytoscape • 125 views
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7 days ago
Scooter ▴ 30

Greetings. If I understand what you're asking, I'm not sure keggscape can do that. It's main goal is to create a Cytoscape representation of a KEGG pathway. It sounds like what you want to do is to reduce the number of pathways you get from your larger set -- I assume, to reduce overlap? If that's your intent, I would take a look at webgestalt, which provides algorithms to reduce overlap when doing either over-representation or gene set enrichment analysis. If you want to use Cytoscape, stringApp's enrichment analysis provides a very rudimentary way to reduce overlap based on Jaccard similarity.

-- scooter

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Thanks for your comment , do you have any idea of how i can use my deg file for webgealt whenever I upload my gene list, this error pops up "ERROR: For the ranked list, please upload a 'rnk' file with two columns (ids and scores)." what is the rank file they are asking , is it log fc or p value?

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