how can we show in Cytoscape the types of interactions among gene-TF

Question

[zizigolu]

Hi,

I have a list of interactions like below, how I can illustrate in Cytoscape whether a gene is being activated or suppressed by a TF?/

TF      gene     interaction

FOXP3   IL2RA   Activation

FOXP3   IL2     Repression

IRF1    FOXP3   Repression

IRF1    IL10    Activation

[zizigolu]

Cytoscape 3.3.0 visualize network with up/down regulated color

Answer 1

[scooter]

Hi Fereshteh, You could read that file in as a network, then use the Cytoscape Style panel (look at the Edge tab) and change the arrow type (or edge color, if you want) to reflect whether it's activation or repression.

-- scooter