Cytoscape color code according to own annotations

Hi,

I am trying to do a string network analysis of genes and wonder what the best way is to color-code nodes according to some annotations that I have?

cytoscape enrichment string network

• 1,705 views • link

updated 8.3 years ago by Jean-Karim Heriche

• written 8.3 years ago by frida.danielsson •

1 answer

You put your annotations in a node attribute column as I explained in this post.

• 1 views • link

written 8.3 years ago by Jean-Karim Heriche

More posts like this

How do I color the gene nodes according to their category in cnetplot
written 3.8 years ago by estafana.t98 •

I am trying to color the gene nodes according to the category in the cnetplot, but as far as I understand, only the edges get …
How to view large PPI network in STRING database?
written 5.2 years ago by mathavanbioinfo

Dear all, I am doing RNA seq whole transcriptome analysis. I have got 2100 up regulated genes. I have tried to create PPI network in …
Cytoscape Directed Network Layout
written 5.6 years ago by imaparna27 •

Hi, I am trying to construct a directed network with the help of Cytoscape-3.8.2. My network contains different types of nodes that I am trying …
Adding more nodes to a PPI network?
written 7.0 years ago by mendonca_thiago22 •

Hi everyone. I had to add more nodes to a Protein-Protein Interaction (STRING) network in order to get a better p value, but I'm not …
Cytoscape-gene expression data
written 7.8 years ago by Malgorzata.Wieteska •

Dear All, I have time series expression data. I have visualised their values on the network. However, I'm not sure what is the best approach …
stringDB PPI network with Log fold change?
written 8.1 years ago by abdurehmanb •

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 …
How to color nodes in Cytoscape according to expression of genes? How should the input file look li…
written 8.5 years ago by orzech_mag

Dear Colleagues, I would like to do some visualization of my network in Cytoscape. My file contains genes and their expression values in normal and …
Protein-protein interaction database for human
written 8.6 years ago by Dayna •

Hi everyone Do you know what is the best PPI network data base for human? I have some genes that we doubt they are related …
R - Merge 2 network with different color nodes
written 10.8 years ago by Bioinformatist Newbie

Hi, I want to merge 2 networks but I want different color of their node. For example N1's vertices should be represented with color "Red" …
Cytoscape Edge Filtering
written 14.3 years ago by Sudeep

<p>Hi, I have a protein protein interaction network overlayed with gene expression data in cytoscape. What I am doing is selecting nodes with interaction data …