Categorizing enrichment results
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5 months ago
yoosefyud ▴ 40

Hello In a multi-omics research project, after combining the data between different omics layers and enriching them, I have 55 pathways. Actually, reporting and discussing such amount of data in an article is impossible. So, I was wondering to know is there a cytoscape App or a criteria in which I can sort and choose the most important pathways for my research?

cytoscape Enrichment Biological Kegg Pathway Omics • 289 views
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Entering edit mode
5 months ago
xanderpico ▴ 470

Enrichment analysis is an exploratory analysis. As such, you can use your domain expertise to decide which of the 55 pathways are relevant to describing and interpreting your results, which are useful in setting up new hypotheses for further study, etc. Just report in your methods that you chose to highlight selected results.

There is no application (in Cytoscape or otherwise) that can apply domain-specific knowledge and make sense of a long list of pathways or GO terms better than a human, imo.

Some tools, however, do support reducing redundancy either by applying a Jaccard distance metric or an emap approach. This can help turn a list of 55 into a list of 15 (maybe), but it still lacks critical judgement. The Jaccard distance tool is supported by the stringApp in Cytoscape. And the EnrichmentMap app makes emaps.

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5 months ago
icemduru ▴ 30

for GO terms: http://revigo.irb.hr/

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