Question: Clustering Gene Regulatory Networks
2
gravatar for Diana
6.8 years ago by
Diana750
Germany
Diana750 wrote:

Does anyone have any suggestions as to which clustering technique is best for producing gene regulatory networks from expression data and why is it best?

clustering • 2.2k views
ADD COMMENTlink written 6.8 years ago by Diana750
1
gravatar for Sudeep
6.8 years ago by
Sudeep1.6k
.
Sudeep1.6k wrote:

Have you tried WGCNA?

ADD COMMENTlink written 6.8 years ago by Sudeep1.6k
1
gravatar for Manu Prestat
6.8 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

First, I think that you want to infer genetic regulatory networks from expression data (that is actually not "clustering"). If I'm not wrong, you can start with these articles:

  • de Jong. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol (2002) vol. 9 (1) pp. 67-103
  • Werhli et al. Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics (2006) vol. 22 (20) pp. 2523-31

Most of these methods are not so trivial and do not come from the same fields/"phylosophies". Dig into one of them (are your data kinetics, i.e. do you need a dynamic/static method?...)

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Manu Prestat3.9k

Thanks Manu, I didn't realize its inferring rather than clustering. We want to identify groups of genes from expression assays that have a similar expression pattern and I thought that would involve clustering. I am sorry I didn't make it clear from my Question. But we also want to build up a gene regulatory network. I'll check the papers you suggested. I'm not sure what you mean by dynamic/static. We have expression profiles for 3 different time points.

ADD REPLYlink written 6.8 years ago by Diana750

Ok, so actually, you want to do both: [1] clustering your samples according to their expression profiles, and [2] infer the genetic regulatory network. For the second step, you have to think about dealing your time condition, if you want to modelize that explicitly (dynamic model, e.g. Dynamic Bayesian Network) or not (static model, e.g. Correlation/Mutual Information Based Networks, Bayesian Networks...etc). Unfortunately, I'm not familiar with dynamic ones...

ADD REPLYlink written 6.8 years ago by Manu Prestat3.9k
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