dorsal/arxiv
View SchemaInherent size constraints on prokaryote gene networks due to "accelerating" growth
| Authors | M. J. Gagen, J. S. Mattick |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0312021 |
| URL | https://arxiv.org/abs/q-bio/0312021 |
| Journal | Theory in Bioscience, 123(4), 381-411 (2005) |
Abstract
Networks exhibiting "accelerating" growth have total link numbers growing faster than linearly with network size and can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at particular critical network sizes. However, if for any reason the network cannot tolerate such gross structural changes then accelerating networks are constrained to have sizes below some critical value. This is of interest as the regulatory gene networks of single celled prokaryotes are characterized by an accelerating quadratic growth and are size constrained to be less than about 10,000 genes encoded in DNA sequence of less than about 10 megabases. This paper presents a probabilistic accelerating network model for prokaryotic gene regulation which closely matches observed statistics by employing two classes of network nodes (regulatory and non-regulatory) and directed links whose inbound heads are exponentially distributed over all nodes and whose outbound tails are preferentially attached to regulatory nodes and described by a scale free distribution. This model explains the observed quadratic growth in regulator number with gene number and predicts an upper prokaryote size limit closely approximating the observed value.
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"abstract": "Networks exhibiting \"accelerating\" growth have total link numbers growing\nfaster than linearly with network size and can exhibit transitions from\nstationary to nonstationary statistics and from random to scale-free to regular\nstatistics at particular critical network sizes. However, if for any reason the\nnetwork cannot tolerate such gross structural changes then accelerating\nnetworks are constrained to have sizes below some critical value. This is of\ninterest as the regulatory gene networks of single celled prokaryotes are\ncharacterized by an accelerating quadratic growth and are size constrained to\nbe less than about 10,000 genes encoded in DNA sequence of less than about 10\nmegabases. This paper presents a probabilistic accelerating network model for\nprokaryotic gene regulation which closely matches observed statistics by\nemploying two classes of network nodes (regulatory and non-regulatory) and\ndirected links whose inbound heads are exponentially distributed over all nodes\nand whose outbound tails are preferentially attached to regulatory nodes and\ndescribed by a scale free distribution. This model explains the observed\nquadratic growth in regulator number with gene number and predicts an upper\nprokaryote size limit closely approximating the observed value.",
"arxiv_id": "q-bio/0312021",
"authors": [
"M. J. Gagen",
"J. S. Mattick"
],
"categories": [
"q-bio.MN",
"cond-mat.stat-mech",
"q-bio.GN"
],
"journal_ref": "Theory in Bioscience, 123(4), 381-411 (2005)",
"title": "Inherent size constraints on prokaryote gene networks due to \"accelerating\" growth",
"url": "https://arxiv.org/abs/q-bio/0312021"
},
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