Question: GeneMANIA in Cytoscape
1
gravatar for dgrayson
3.5 years ago by
dgrayson10
dgrayson10 wrote:

I have a genelist that I've analyzed in GENEmania and I would like to import this data into Cytoscape 3.0. It seems like I can only save GENEmania output as an SVG file so I cant import this into Cytoscape. I've also tried using the GENEmania app that I downloaded into Cytoscape and I can't make heads or tails of that either. Does anyone have any suggestions?

rna-seq • 2.1k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by dgrayson10
3
gravatar for Jean-Karim Heriche
3.5 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

Not sure why you can't export your GeneMANIA network as text file. From the Cytoscape Web plugin on the GeneMANIA web site, I can do File > Save network as text and get a tab-delimited file.

The Cytoscape GeneMANIA app allows you to do the same thing as on the GeneMANIA web site but you have to install the network data first. Assuming you've already installed the app in Cytoscape 3.2, you go Apps > GeneMANIA > Choose another data set, check the most recent data and check 'core' (or 'all') then download data for the relevant species. Once you've installed the data, you can now query them like on the GeneMANIA web site by Apps > GeneMANIA > Search. If you installed data for multiple organisms, select the relevant one then input your query genes. Select the networks to mine and weighting scheme under Advanced options. Click on Start when ready.

ADD COMMENTlink written 3.5 years ago by Jean-Karim Heriche20k
0
gravatar for dgrayson
3.5 years ago by
dgrayson10
dgrayson10 wrote:

Thanks I got it to work. Where do I go from here. Any suggestions on a good tutorial for this type o f analysis. thanks, Dennis

ADD COMMENTlink written 3.5 years ago by dgrayson10

GeneMANIA returns a ranked list of genes that are functionally related to your query genes. I use this type of approach for candidate gene selection (for an example, see my paper here). You could also explore the contribution of different data sources. For example, if you're interested in protein complexes, you might want to know which are the links coming from protein interaction data. Or you could be interested in finding which other functions are linked to the function represented by your query. It really depends on what you're interested in.

ADD REPLYlink written 3.5 years ago by Jean-Karim Heriche20k
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