How to start with

[shys...@gmail.com]

Hello,I am a new user of CS. I wanted to visualize interaction between a set of 100 up regulated and 208 down regulated genes found in my RNAseq experiment (arbitrary numbers) in Arabidopsis(ATG numbers) with three GOI of my choice.
I opened Arabidopsis_thaliana mitab file in network, showing interaction between all the proteins. How can I get the interaction network specific for my list?
Also can I selectively visualize up and down regulated genes by color function?
I tried the online tutorial but unable to figure it out.

Please help !!
Thanks

[Scooter Morris]

Welcome to Cytoscape!

First, if the mitab file has as it's name column the ATG numbers, all you would need to do to select the proteins of interest is to create a file with your ATG numbers and then use Select->Nodes->From ID List File...  Alternatively, you could use the stringApp and just enter your ATG numbers in and retrieve a STRING network with just your data.

Second, which online tutorial were you looking at?  You can use File->Import->Table from file to import your data, and then you map your expression values to the color of the node (Fill Color) using a continuous mapping.  Your up and down fold change values need to be in the same column so that you can use that column for the mapping.

-- scooter