Microrna-gene network creation

Question

[paulapetronelagroza]

Hello everyone. I am new in the field of bioinformatics and I really need you help. I want to design 2 types of networks - gene - gene interactions and microRNA-gene interactions. I have 60 gene in my research and I want to select common microRNA for all of them and then create a network or a pathway graph. The problem is I don't really know how to get the dataset for the program to work. I need an XML document or cuffdiff. I want to use Navigator too. How am i supposed to create the nodes? I was thinking about using the mirSVR score that http://www.microrna.org/ provides. And make a table with microRNA and the corresponding mirSVR score for each gene. I guess the microRNA would be my nodes, but the genes must also be nodes right? So I don't know if using the mirSVR score will be relevant for the network. Any suggestions? Thank you very much! Wonderful day to everyone! Paula

Answer 1

[Asaf]

The network you want to draw depends on your research question. If you're trying to link genes according to common miRs then you might want to have only genes as nodes and put an edge between two genes that are regulated by the same miR. I think it will make the network simpler. You have to think about the desired output from the network you'll build, e.g. measuring distance between pairs of genes, clustering genes etc. You'll have to do some technical work but I think that you'll manage to do most of it in simple tools like excel. I recommend working on the network with cystoscape.

[paulapetronelagroza]

Thank you Asaf! :) i will try to see if it works, i mean if i make it right.