HOW TO REDUCE GENES FOR CYTOSCAPE

Question

[Sky]

Hello everyone, I am new to bioinformatics so I need you guys help. I want to make a network from genes that I added in STRING and after analyzing I downloaded the excel file and created a network. The genes are over 500 and the image is not clear. I want to reduce the genes but I don't know at what standard should I reduce my genes to at least 4000 or 300. That contains the main genes or strongest interactions. So I can make a good clear image of GGI.

I also did top 10 genes for Degree, Beweeness and Centrality so if I do use MCODE the top 10 genes changes. So if anyone knows an article where they reduced the genes or any other method please let me know.

Thank you in advance.

Answer 1

[Mensur Dlakic]

Generally speaking, your list can be reduced by increasing the stringency of the quantity that is used to construct the list. If it is a probability-like quantity, the cutoff should be increased (say, from 0.5 to 0.7). If it is a p-value, then it should be decreased (say, from 0.05 to 0.01 or even 0.001).

[Sky]

Sir Thank you so much but can you let me know from where I can change the stringency of the quantity, I am really sorry I am new in it so I couldn't seem to find it. Thank you again

[Mensur Dlakic]

I don't know how you created the list or from where you got it, but they are usually not just gene names. There should be some other information to indicate the strength of edges (probability, p-value) that connect the nodes (genes).