Visualisation Of Interaction

Question

[Dataminer]

Hi!

This might be a very silly question but kindly answer it.

I have ONE files, of two columns, pathway and gene.

The files looks like this:

file 1

Pathway Genes 
MAP2k CACN 
MAP2K NT3/4
MAP2K EGF 
MAP2K TNF
INSULIN SIGNALING PATHWAY INSR

INSULIN SIGNALING BAD

APOPTOSIS P53

APOPTOSIS BAD

INSULIN SIGNALING INS

APOPTOSIS ATM

what is the best way/plugin to visualise this interaction in cytoscape the default mode sets the

Kindly Answer.

Thank you

[Darren J. Fitzpatrick]

Could you clarify - Do you mean interaction in a statistical sense? Are you regressing the presence/absence of genes against some measure for your states and including interaction terms?

[Dataminer]

Just a simple network, based on the above data. No statistical measure required.

[Giovanni M Dall'Olio]

can you make an example of how the network would look like? What would the node will be? Can you make an example of interaction that would appear in the network?

[Dataminer]

I have changed the question a bit, I hope it makes more sense in generic terms.

Answer 1

[Russh]

Just use Cytoscape's table import function: File -> Import -> Network from table; it's described in depth in the Csc manual (Creating networks: Import Fixed-Format Network Files).

You might need to play with the advanced options to ensure that it doesn't split on all whitespace.

This will give you a network of links from a given pathway to the genes in that pathway (this was my understanding of your requirements; if you need to link genes which share a pathway, you'll need to reformat your file).

[Dataminer]

Yes, that what I want, genes exclusive to a pathway and genes shared by the pathway. I got the Network also. but how I can enhance my network from its current look any suggestions.

[Russh]

Try the layout section (force-directed's a good start), try the vizmapper (for changing node/edge visual properties). Ultimately you can either read the manual or play around with cytoscape. I won't be replying to any further subjective visualisation questions, sorry

[Dataminer]

Thank you, i will read the manual :)