Gene linkage in Cytoscape

Question

[fatima]

Is it possible in Cytoscape to import your own list of gene names from an experiment and somehow link all of those genes together to create a network, as seen by many of the samples. Ideally I want to be able to look up each gene I am studying and be able to correlate them to each other through some sort of network. I am having a difficult time doing this on Cytoscape as it only allows me to work with preexisting networks. I would like to work with a list of genes specifically from my experiment. Thank you!

Answer 1

[endretoth]

Hi fatima,

You can link both genes and proteins in Cytoscape. For genes, you need the GeneMANIA app (http://apps.cytoscape.org/apps/genemania) and simple input your list of accessions and done. You need to increase the connections until all your genes are become connected. It is the similar for proteins, to those you need to use STRING (http://apps.cytoscape.org/apps/stringapp). I hope this helps.

Please see the attached printscreen:

https://freeimage.host/i/3fWdyx

Best, Endre