**450**wrote:

Hi all,

I a read paper about gene regulatory network inference algorithms. they reconstructed GRN with different GRN inference methods and they used first two principal components to see the clusters. Can somebody explain me, what PCA say us about performance of these algorithms ? for me seems that, if different methods produce similar GRN, then the PCA of them should reveal same number and similar clusters. is it right ?

**7.6k**• written 6.3 years ago by jack •

**450**

What did they use the principal components of? The principal component of a network doesn't make any sense in and of itself. I can only assume that they did PCA on the expression data (rather than networks) to see if the genes group into some coherent number of obvious clusters. BTW, this seems like a pretty hand-wavy way to go about assessing performance.

94kthey reconstructed GRN with regression method, Bayesian and mutual information methods. then they used PCA on inferred GRNs by these methods to see how similar the networks are .

450Can you cite the paper?

2.8k