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 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.

Best regards!
**INPUT DATA**

You need two input files to color your network according to expression values in normal and cancer samples.

First file defines interactions between genes. For example, Excel file (`interactions.xls`):

    Source	Target
    Gene1	Gene2
    Gene1	Gene3
    Gene2	Gene3
    Gene2	Gene4
    Gene3	Gene4
    Gene3	Gene4
    Gene4	Gene5


Second file lists gene names with their expression values in normal and cancer samples. For example, Excel file (`expressions.xls`):

    Gene_name	Normal	Cancer
    Gene1	1.92	1.56
    Gene2	0.56	2.02
    Gene3	0.34	0.01
    Gene4	0.98	0.98
    Gene5	0.02	0.87


**CYTOSCAPE**

1. Open Cytoscape.
2. `File` > `Import` > `Network` > `From file`
3. Load the `interactions.xls` file. Define first column as *Source*, and second as *Target*.
4. Load the `expressions.xls` file.
   - `File` > `Import` > `Table` > `File`. 
   - Label first column as *Gene_name*, second as *Normal* and third as *Cancer*.
5. Color your network according to expression values in the *Normal* column. 
    - `Style` > `Fill color` > `Column`: Normal
    - `Mapping Type`: Continuous
    - `Current mapping`: choose your colors.

**OUTPUT**

![enter image description here][1]

Pozdrawiam:)

  [1]: http://i66.tinypic.com/2dv770k.png