Question: Visualizing Up/Down Regulation Of Genes Based On Fold Change
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gravatar for gundalav
7.9 years ago by
gundalav310
La La Land
gundalav310 wrote:

Given list of genes and the fold-change value is there a way I can visualize them like this?

gene visualization microarray • 4.4k views
ADD COMMENTlink modified 7.8 years ago by Ying W4.0k • written 7.9 years ago by gundalav310
3
gravatar for Sean Davis
7.9 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

I'm not entirely clear what your figure is showing, but take a look at cytoscape.

ADD COMMENTlink written 7.9 years ago by Sean Davis26k
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gravatar for Jelena Aleksic
7.9 years ago by
Cambridge, UK
Jelena Aleksic920 wrote:

Also, do consider using a heatmap for visualising the fold-change values. For example the ggplot package in R does this, though there may be Cytoscape modules available if you definitely want to present your data as a network.

ADD COMMENTlink written 7.9 years ago by Jelena Aleksic920
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gravatar for Ying W
7.8 years ago by
Ying W4.0k
South San Francisco, CA
Ying W4.0k wrote:

That figure looks like something made by IPA network explorer. It will look up all of your genes/molecules and assign different shapes based on known function (receptor/kinase/etc). You will need a license to use this software, if you want a free alternative you can use Cytoscape. Both software have a bit of a learning curve. What IPA can do is show all up regulated genes in one color (such as green) and all down regulated genes in another color (often red) and form connections between genes based on literature, it is often useful for hypothesis generation after a genome wide expression study. This is an example

ADD COMMENTlink modified 7.8 years ago • written 7.8 years ago by Ying W4.0k
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