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stringDB PPI network with Log fold change?

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!

string-db ppi rna-seq
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updated by liux.bio liux.bio • written by abdurehmanb • abdurehmanb

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" )
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written by cpad0112 cpad0112

2 answers

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

• 1 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

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

• 1 views • link
written by liux.bio liux.bio

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