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
1 answer
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).
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
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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?
Just a simple network, based on the above data. No statistical measure required.
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?
I have changed the question a bit, I hope it makes more sense in generic terms.