DEGs From Microarray experiment

[Nieves del Rocio Colás Ruiz]

Hello,

 

I am a new user in Cytoscape and I have a very basic question, so I apologise in advance if it is a silly one.

 

I have recently performed a Microarray experiment with a custom design array from a non-model marine organism.

 

After obtaining my DEGs I have performed the functional annotation of them and now I have Ensembl Gene and proteins IDs.

 

I would like to perform pathway analysis for these DEGs in order to understand the interaction occurring in my studied organism but I don't know how should be the input file format or what should it contains or even if it is possible with my current data.

 

Many thanks in advance and sorry for the disturbance,

 

I haven't seen a similar question in the discussion so I decided to send mine.

 

Regards.

 

Rocio/

[Alex Pico]

There are lots of pathway analysis tools available that take lists of DEGs and give you lists of pathways with significant overlap. I'd recommend Enrichr as a online tool or clusterProfiler as an R tool, for example.

However, you can also do this in Cytoscape using the STRING app. Check out http://tutorials.cytoscape.org, e.g.,

https://cytoscape.org/cytoscape-tutorials/protocols/differentially-expressed-genes/#/

 - Alex