Why Gene Regulatory Network Is Sparse?
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12.2 years ago
kate ▴ 100

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 • 4.4k views
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What do you mean by sparse?

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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.

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What was the theory underlying the theoretical results?

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

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12.2 years ago
Niek De Klein ★ 2.6k

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.

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

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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 ?

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12.2 years ago

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

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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 )

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Very interesting. Thanks.

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