Question: Why Gene Regulatory Network Is Sparse?
3
gravatar for kate
8.2 years ago by
kate90
kate90 wrote:

Why gene regulatory network is sparse? Dose anyone konw some biological/physical explanations? Please provide some suggestions to helping me solve this problem. Thank you so much!

gene network • 2.9k views
ADD COMMENTlink written 8.2 years ago by kate90

What do you mean by sparse?

ADD REPLYlink written 8.2 years ago by Niek De Klein2.5k

Empirical data indicate that biological gene networks are sparsely connected, and that the average number of upstream-regulators per gene is less than two. Theoretical results show that selection for robust gene networks will favor minimally complex, more sparsely connected, networks.

ADD REPLYlink written 8.2 years ago by kate90

http://en.wikipedia.org/wiki/Gene_regulatory_network

ADD REPLYlink written 8.2 years ago by kate90

What was the theory underlying the theoretical results?

ADD REPLYlink written 8.2 years ago by Russh1.2k

It's in the paper that I cited in my answer.

ADD REPLYlink written 8.2 years ago by Niek De Klein2.5k
11
gravatar for Niek De Klein
8.2 years ago by
Niek De Klein2.5k
Netherlands
Niek De Klein2.5k wrote:

The paper (Survival of the sparsest: robust gene networks are parsimonious) cited in that wikipedia article answers the question

This indicates that sparse networks are actually more robust if the costs of complexity are accounted for. If true, then evolution should seek to optimize the costs and benefits of complexity with a parsimonious network structure, a network topology that is sparsely connected and not unnecessarily complex, by seeking an optimal topological ensemble of interactions that best meets the network's functional requirements under its normal range of operating conditions.

When getting information from wikipedia it's always a good idea to read through the citations.

ADD COMMENTlink modified 8.2 years ago by Michael Kuhn5.0k • written 8.2 years ago by Niek De Klein2.5k
1

I want to know some physical explanations.Is it possible to apply phsics to address this problem?

ADD REPLYlink written 8.2 years ago by kate90

Maybe you can find the answer by yourself... Why don't you try to simulate a fully connected regulatory network (directed graph with 20K nodes) and evaluate its fitness/efficiency in regulating GO biological processes ?

ADD REPLYlink written 8.2 years ago by ff.cc.cc1.3k
4
gravatar for Manu Prestat
8.2 years ago by
Manu Prestat4.0k
Lyon, France
Manu Prestat4.0k wrote:

They are not only sparse, according to Barabasi work it's beleived they are also "scale-free", meaning the degree of nodes distribution follows a power law function. Then a lot of nodes have a low connectivity, and some have a high connectivity (they are called "hubs" or "modules").

Here is a review (to start): Barabási and Oltvai. Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) vol. 5 (2) pp. 101-13

ADD COMMENTlink written 8.2 years ago by Manu Prestat4.0k
3

These networks are probably not scale-free in the classical sense - they probably have a scale-free tail to their degree distribution (http://www.cs.unm.edu/~aaron/blog/archives/2008/10/power_laws_in_t_1.htm, http://www.sciencemag.org/content/335/6069/665.full )

ADD REPLYlink written 8.2 years ago by Nathan Harmston1.1k

Very interesting. Thanks.

ADD REPLYlink written 8.2 years ago by Manu Prestat4.0k
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