Cytoscape using string and cluego

[Lucky sardar]

Hello

I wanted create gene function network analysis for that I have tried string and Cluego I dont how we can use both together as in  below image used string and cluego any one suggest me I wanted do GO and pathway analysis for my gene list. or any other method suggestions allso helpfull also tried genemania not able show in function  

please help me 

Thank you

[Scooter Morris]

Greetings.  You say you are using string, but are you using the StringApp in Cytoscape?  If so, it will perform pathway enrichment analysis for you, although the figure you include looks like it's more focused on disease prevalence -- maybe based on GWAS or expression data?  In any case, you can use the StringApp and restrict the enrichment to particular branches of GO or pathways.  Also note that you can use enrichmentMap to get a map of the enriched functions after you complete your stringApp enrichment.

-- scooter

[Júlia Brandão]

Hi everyone!

I found this forum while looking for answers to some questions during my research.  

I’m planning to perform some analysis using the ClueGO plugin in Cytoscape, but I have a few questions:

Do I need to run STRING and MCODE analyses before using ClueGO?

I just want to generate a network that shows interactions between pathways associated with my enriched genes. I don’t want to perform PPI analysis or clustering.

Is that possible, or is it mandatory to run STRING and MCODE first?

Another question: is it acceptable to manually select pathways that are more relevant to the specific context of my research, or is it more appropriate to rely strictly on the statistical enrichment results? Some of the enriched pathways don't align with my research focus. For example, I work with virus–host interactions, but many of the enriched pathways are cancer-related, which doesn't seem biologically meaningful for my analysis.

I look forward to any insights you may have.

[Chris Churas]

Hi,

You should not need to run STRING or MCODE before using ClueGO. 

chris

[Alex Pico]

And regarding enrichment analysis, it is common to select pathways from the results that are worthwhile pursuing or discussing. Enrichment analysis is a simple overlap test. Your domain knowledge about the mechanisms relevant to your area of study is MUCH more important.