I used GEO datasets against a particular disease. But the common DEGs obtained have varied expression values (LogFC). How can we use these values forward in Cytoscape for representing network based on Differentially expressed?
Looking forward for possible answers.
Here is one method. Cytoscape is very creative regard to apps you can use. For example, you can give the list of your top DEGs to STRING data base to obtian their protein protein interaction scores , and you can then use these data for cytoscape to create a PPI network. Each gene will have a different FC regard to cancer-normal samples.and you might see your DEGs have different fc values in different expression sets you analyze. This is normal. But as much the study has higher number of samples ,these variation will get more normalized. I suggest you to also use other datasets like TCGA if your study id about cancer genomics.
- Badges
- Science topic