Question: stringDB PPI network with Log fold change?
0
gravatar for abdurehmanb
2.4 years ago by
abdurehmanb0 wrote:

I have a set of ~60 differentially expressed genes and their log fold changes. Is there a way for me to visualize the network, but color the nodes based on their fold-change?

Thank you!

rna-seq string-db ppi • 1.1k views
ADD COMMENTlink modified 2.4 years ago by liux.bio350 • written 2.4 years ago by abdurehmanb0

Please refer to stringdb package manual page 3 on wards (pay attention to the following line in page6):

example1_mapped_pval05 <- string_db$add_diff_exp_color( subset(example1_mapped, pvalue<0.05), logFcColStr="logFC" )
ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by cpad011214k
0
gravatar for Jean-Karim Heriche
2.4 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

You can do this using Cystoscape for example. See this post.

ADD COMMENTlink written 2.4 years ago by Jean-Karim Heriche23k
0
gravatar for liux.bio
2.4 years ago by
liux.bio350
China
liux.bio350 wrote:

If you just want to color the nodes based on their fold-change in just one experimental group, I think Cytoscape mentioned by Jean-Karim Heriche can meet your needs. But if you want to color nodes in multiple groups, I recommend you to use PPIExp. In PPIExp, you can color nodes in multiple groups. Here is an example: enter image description here


PS: I am the author of PPIExp

ADD COMMENTlink modified 23 months ago • written 2.4 years ago by liux.bio350
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