Hi I have list of DE genes obtained from RNASeq DE analysis, is it possible to visualize them in cytoscape as inter-connected networks?
You can either map your data onto a protein-protein interaction network (e.g. obtained from public databases like STRING), or generate a gene correlation network from your data (e.g. google for the Weighted Gene Correlation Network Analysis method). In both cases, you can import your network into Cytoscape from a tab-delimited two-column interaction list text-file.
You can use, among the others, the GeneMANIA plugin of Cytoscape (link below). It is as simple as copying and pasting the DE genes in the plugin form and selecting the databases which you want Cytoscape will get evidences of interactions from.
I used this simple tool several times. For example read the NAR paper linked below.
http://pages.genemania.org/cytoscape-app/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2971582/
http://nar.oxfordjournals.org/content/44/9/4025
I have the same problem. Dear Enrico, would you tell me how can map a list of genes interacting pairs onto a database of protein-protein interactions?
I'm trying but I can't. I have also tried Genemania, but with no success.
Arindam Ghosh you have first to build the network (String, Genemania, etc) and then import a table with the values you want into that network (beware of gene IDs, should match) and then apply those values to the network. Another way is to import a network file where source, targets and connectrs values are identified (much more difficult)
you have to first build the network using String App in cytoscape or online string. after that import the csv file in cytoscape from string network . u can also try public database in cytoscape .
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