dorsal/arxiv
View SchemaFailed "nonaccelerating" models of prokaryote gene regulatory networks
| Authors | M. J. Gagen, J. S. Mattick |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0312022 |
| URL | https://arxiv.org/abs/q-bio/0312022 |
Abstract
Much current network analysis is predicated on the assumption that important biological networks will either possess scale free or exponential statistics which are independent of network size allowing unconstrained network growth over time. In this paper, we demonstrate that such network growth models are unable to explain recent comparative genomics results on the growth of prokaryote regulatory gene networks as a function of gene number. This failure largely results as prokaryote regulatory gene networks are "accelerating" and have total link numbers growing faster than linearly with network size and so can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at particular critical network sizes. In the limit, these networks can undergo transitions so marked as to constrain network sizes to be below some critical value. This is of interest as the regulatory gene networks of single celled prokaryotes are indeed characterized by an accelerating quadratic growth with gene count and are size constrained to be less than about 10,000 genes encoded in DNA sequence of less than about 10 megabases. We develop two "nonaccelerating" network models of prokaryote regulatory gene networks in an endeavor to match observation and demonstrate that these approaches fail to reproduce observed statistics.
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"abstract": "Much current network analysis is predicated on the assumption that important\nbiological networks will either possess scale free or exponential statistics\nwhich are independent of network size allowing unconstrained network growth\nover time. In this paper, we demonstrate that such network growth models are\nunable to explain recent comparative genomics results on the growth of\nprokaryote regulatory gene networks as a function of gene number. This failure\nlargely results as prokaryote regulatory gene networks are \"accelerating\" and\nhave total link numbers growing faster than linearly with network size and so\ncan exhibit transitions from stationary to nonstationary statistics and from\nrandom to scale-free to regular statistics at particular critical network\nsizes. In the limit, these networks can undergo transitions so marked as to\nconstrain network sizes to be below some critical value. This is of interest as\nthe regulatory gene networks of single celled prokaryotes are indeed\ncharacterized by an accelerating quadratic growth with gene count and are size\nconstrained to be less than about 10,000 genes encoded in DNA sequence of less\nthan about 10 megabases. We develop two \"nonaccelerating\" network models of\nprokaryote regulatory gene networks in an endeavor to match observation and\ndemonstrate that these approaches fail to reproduce observed statistics.",
"arxiv_id": "q-bio/0312022",
"authors": [
"M. J. Gagen",
"J. S. Mattick"
],
"categories": [
"q-bio.MN",
"cond-mat.stat-mech",
"q-bio.GN"
],
"title": "Failed \"nonaccelerating\" models of prokaryote gene regulatory networks",
"url": "https://arxiv.org/abs/q-bio/0312022"
},
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