How to identify dysregulated pathways using Support Vector machine (SVM)?

Question

[Chaimaa]

Hello guys,

Does anyone have an idea about how can we identify dysregulated pathways from a pathway network using SVM

What kind of inputs do we need for SVM in this case?

IF anyone can just suggest me?, appreciate that!

[Kevin Blighe]

Did you already search for things to do in relation to this topic? What did you find?

[Chaimaa]

Yes, Kevin, i did that

[Kevin Blighe]

You are not helping too much by not providing information on the data that you currently have.

[Chaimaa]

Ok, Kevin, The data i have is a file with 3 columns path1 path2 score The paper i read is this one: https://www.ias.ac.in/article/fulltext/jgen/097/01/0173-0178

[Chaimaa]

Kevin, you can have a look at this paper, published in 2018

[Kevin Blighe]

It is your job to read the manuscript, not mine.

[Chaimaa]

I already read the manuscript , and I just want to show you from where i got the idea of dysregulated pathways Sorry!

[Kevin Blighe]

I do not see path1 path2 score anywhere in that manuscript; so, I have no idea what you are aiming to do. You should start at the Materials and methods and take it step by step. I am aware that differences in language make this more difficult for you.

[Chaimaa]

@Kevin Blighe Ok, Kevin Thanks! No problem I will try my best to understand how they do that. many thanks for you again!

[Kevin Blighe]

I guess that these 2 threads are also linked? - How to calculate the Pearson correlation coefficients between a list of genes? Let me know how it goes.

[Chaimaa]

@Kevin Blighe Hi, Kevin No the 2 threads are not linked bcz, I built the PIN based on just the overlapped genes and not the coexpression. I tried to text you on GitHub and i can't!?