Hello Everyone! I am wondering if there is any valid method that could be used to virtually knock out a gene from a gene-gene network and study its effect in the whole network? I am aware of this: https://apps.cytoscape.org/apps/interference
Some background information We have performed bulk RNA-Seq of around 36 different samples and performed co-expression module analysis to obtain gene clusters. We were interested in a particular module, say module 1 that has around 200 genes altogether with many functionally relevant genes. Now we are asking the question: of all 200 genes which genes could be playing a potential role. Also is there any machine learning approach that could be used to identify most influencing gene? I am open to all sorts of suggestions :)
Have a look at this tutorial: Identification and classification of the most influential nodes and the related manuscript.