Hi, piyushjo! I have the similar idea with you. I am now doing some analysis on a gene expression data for a CNS disease. I am also going to do WGCNA and Aracne analysis on this dataset.
The difference is that I think this two method are relatively independent and they serve to different aims. WGCNa is mainly designed to find the gene clusters (modules) which perform similar function, while ARACNE intends to detect the regulatory effects of a TF on its target genes.
SO my opinion is that after you get the gene clusters by WGCNA, then you can find out how these gene clusters are regulated through some master regulators. You can also try another algorithm called viper, which is also based on ARACNE and designed to predict the regulator activity changes in different conditions.
I have also found a review paper related to this topic, which I think it's useful to help us better understand these methods. https://academic.oup.com/bib/article/19/4/575/2888441
modified 2.1 years ago
2.1 years ago by
fuyingxue • 10