Cytoscape network of upregulate and downregulate transcription factors: how to draw?

Question

[Farbod]

Dear Biostars, Hi

I have a list of zebrafish TFs (both family and members) upregulated in my condition1 and same data for condition2. (I also have a list of all transcription factores showing blastx hit with all my RNA-seq analysis) I want to show them in a network (or maybe two networks).

I saw a similar network created using Cytoscape.

Could you please kindly help me in this issue? how to ready files as cytoscape input? how to create circular network showing each DE TFs in different colour?

or even another package/website for doing this ?

Thanks

NOTE: e.g. of TFs families Up-regulated in my condition 1:

BX649453.2

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gtf2ird1

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PBRM1

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Answer 1

[Leite]

Hey Farbod,

You first need to decide whether to make a protein interaction network or co-expression network.

Then you can use STRING, GeneMANIA or BioGRID to build your network.

Once the network is built, you can import it into Cytoscape and change the layout to circle it, and look the same as the picture you showed.

To change the color or shape of only a few nodes, you can add a new column to your network in cystoscape and for example enumerate only the node of interest, there you can only change the shape and color of that node without changing the other.

Best Regards, Leite

[Farbod]

Dear @Leite Hi and thanks.

I have tried "STRING, GeneMANIA or BioGRID"for drawing (1) two separate networks and (2) a network with both condition TFs DEG representative in it; but I did not think about importing the results in Cytoscape :-)

1- So, you mean that I must draw a network for all my differentially expressed TFs in it in GeneMania and then import that in Cytoscape as a network. Yes?

I have used "Network" as saving the results in GeneMania and import that in Cytoscape as a Network, but it shows an error :

"The network can not be created without selecting the source and the target column" !

2- Can you please kindly help me more about "add a new column to your network in cystoscape" as I am not very familiar with Cytoscape, and Is there any way to select the colors or there are default?

Thanks

[Leite]

Hey Farbod,

1. Yes, you've to put all differentially expressed TFs in it inGeneMANIA or STRING and choice your parameters.

I recommend starting with the STRING because it is easier, export the txt and then import into the cytoscape.

I really recommend you read the cytoscape manual for more information.

Add a new column

Add variables related to their DEGS

Change the colors however you want

free image hosting

Best regards,

Leite

[Farbod]

Thank you Leite for your help, I will use your guidance.

Ah, those images are really wonderful, I call it a "Super-help"!

Q: Should I save the string network as "as simple tabular text output .tsv" file?

As Cytoscape did not accept it :(

[Farbod]

Hi, I import it as network and Cytoscape accept that. thanks

[Leite]

Hey Farbod,

I hope you have succeeded.

Best regards,

Leite

[Farbod]

Hi, I also found this topic helpful:

GeneMANIA in Cytoscape