I would like to do some visualization of my network in Cytoscape. My file contains genes and their expression values in normal and tumor samples. The visualization of interest would be the same network colored according to A) expression in normal samples and B) expression in tumor samples.
Honestly, I completely do not know how should be prepared the input file with such annotation. Basic input file to create network in Cytoscape looks like:
Gene A - Gene B (and some additional annotations).
Some example of such analysis shown in Cytoscape tutorial indicates that such input file should look like this:
GENE COMMON gal1RG gal1RG gal80R
YHR051W COX6 -0.034 -0.034 -0.304
YHR124W NDT80 -0.090 -0.090 -0.348
YKL181W PRS1 -0.167 -0.167 0.112
YGR072W UPF3 0.245 0.245 0.787
(unfortunately, it is not described how the values were obtained).
The above arises in my question: what these values are related to? If in my file I will put expression values for genes only in first columns, then I won't be able to color genes from second column. Moreover, in Cytoscape I can use only one column as such annotation, so there is no chance to provide two columns with expression values for both nodes (start and end).
I would appreciate any suggestion how to solve such issue. Maybe there is some mathematical solution how to calculate "something" that I could possibly use as representation of expression or maybe there is some other software that would be able to do something like this?
Thanks in advance.