Question

stringDB PPI network with Log fold change?

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5.8 years ago

abdurehmanb • 0

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 • 2.3k views

ADD COMMENT • link updated 5.8 years ago by liux.bio ▴ 360 • written 5.8 years ago by abdurehmanb • 0

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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 REPLY • link 5.8 years ago by cpad0112 21k

score 0 · Answer 1 · 2018-06-17

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5.8 years ago

Jean-Karim Heriche 27k

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

ADD COMMENT • link 5.8 years ago by Jean-Karim Heriche 27k

score 0 · Answer 2 · 2018-06-23

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