Entering edit mode
6.1 years ago
hkarakurt
▴
180
Hello everyone, I need to build a protein-protein interaction network (Mus musculus) with costs. Actually I will use this interaction network for PCSF package of R.
I checked STRING data base. I downloaded Mus musculus data and it has a combined score column. Is it same with cost? Also all protein names have ENSEMBL ID. I need Protein names (GeneSymbol) for node names.
Where can I download this type of network?
P.S: Is there a way to calculate cost from topology of a network? I think costs are experimental values but I thought there has to be a way to calculate it.
Thank you.
What do you mean by "cost?"
With cost I mean edge weight.
Edge weight can be anything you want. StringDB has many scores based on different types of evidence (text-mining, evolution, co-expression, biochemical interaction, etc.), all of these scores represent the confidence in the interaction bewteen the two proteins/genes. To your second question you could use something like edge betweenness but that has a completely different meaning than stringDB's scores.
Thank you for your answer. The "cost" they gave is between 0 and 1. Probably they normalized it. Also, I downloaded coexpression network from GeneMania database and it has its own scores (About 12 million interactions actually so it is hard to manipulate). I hope with cost they meant edge weight.
Thank you again.