Question: Weighted Enrichment Analysis For Gene Networks
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gravatar for ncl.lazzarini
5.5 years ago by
United Kingdom
ncl.lazzarini90 wrote:

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

ADD COMMENTlink modified 5.5 years ago by Biojl1.6k • written 5.5 years ago by ncl.lazzarini90
1
gravatar for Biojl
5.5 years ago by
Biojl1.6k
Barcelona
Biojl1.6k wrote:

You may want to take a look at the GeneMania plugin for Cytoscape. They also have a web version but is limited to small sizes.

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Biojl1.6k

It doesn't realize what I need. I want an enrichment analysis which takes in account the interactions between genes.

ADD REPLYlink written 5.5 years ago by ncl.lazzarini90

Read the manual. You can select gene interactions only in the Cytoscape plugin.

ADD REPLYlink written 5.5 years ago by Biojl1.6k

"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.

ADD REPLYlink written 5.5 years ago by ncl.lazzarini90

You can do it. Just select 0 genes to expand the network. You'll get interactions, GO, etc.

ADD REPLYlink written 5.5 years ago by Biojl1.6k

So do you mean: upload my network, de-select all others networks, use the nodes of the network as gene list?

ADD REPLYlink written 5.5 years ago by ncl.lazzarini90

I think you need to clarify what exactly you want to obtain and your personal definition of enrichment analysis.

ADD REPLYlink written 5.5 years ago by Biojl1.6k

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.

ADD REPLYlink written 5.5 years ago by ncl.lazzarini90

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.

ADD REPLYlink written 5.5 years ago by Biojl1.6k
0
gravatar for ncl.lazzarini
5.5 years ago by
United Kingdom
ncl.lazzarini90 wrote:

Nobody ever faced with this problem?

ADD COMMENTlink written 5.5 years ago by ncl.lazzarini90
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