Entering edit mode
10.5 years ago
ncl.lazzarini
▴
130
I'm working on Gene Interactions Networks defined using gene expression dataset. I'd like to enrich the networks I obtained, so I used some tools as David or Bingo. Those tools take as input the gene list (in my case the node list of my network) and execute the analysis on it. I'd like to know if there are some other tools/algorithms which take in account the weighted interactions among genes in the network
It doesn't realize what I need. I want an enrichment analysis which takes in account the interactions between genes.
Read the manual. You can select gene interactions only in the Cytoscape plugin.
"GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data". Even uploading my own networks the idea behind the plugin is to find related genes, not to execute an enrichment analysis.
You can do it. Just select 0 genes to expand the network. You'll get interactions, GO, etc.
So do you mean: upload my network, de-select all others networks, use the nodes of the network as gene list?
I think you need to clarify what exactly you want to obtain and your personal definition of enrichment analysis.
I want to obtain enriched terms associated to my network. This is what I obtain using David: a list of "enriched terms" (GO or KEGG pathways) related to the gene set I upload.
Install the plugin. Select search. Input your genes. Select your desired sources of interaction and limit to 0 new genes. You will get the network and the GO terms.