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Towards More Biological Mutation Operators in Gene Regulation Studies
Watson, James, Geard, Nicholas and Wiles, Janet (2004-08) Towards More Biological Mutation Operators in Gene Regulation Studies. BioSystems, 76 1-3: 239-248.
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| Name |
Description |
MIMEType |
Size |
Downloads |
BioSys-preprint-.pdf
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BioSys-preprint-.pdf |
application/pdf |
275.02KB |
94 |
| Author(s) |
Watson, James
Geard, Nicholas
Wiles, Janet
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| Title |
Towards More Biological Mutation Operators in Gene Regulation Studies
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| Journal name |
BioSystems
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| Publication date |
2004-08
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| Volume number |
76
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| Issue number |
1-3
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| ISSN |
0303-2647
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| Start page |
239
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| End page |
248
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| Total pages |
10
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| Editor(s) |
Teuscher, Christof
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| Place of publication |
Ireland
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| Publisher |
Elsevier Ireland Ltd.
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| Language |
eng
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| Subject |
280210 Simulation and Modelling
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| Abstract |
Genetic regulation is often viewed as a complex system whose properties emerge from the interaction of regulatory genes. One major paradigm for studying the complex dynamics of gene regulation uses directed graphs to explore structure, behaviour and evolvability. Mutation operators used in such studies typically involve the insertion and deletion of nodes, and the insertion, deletion and rewiring of links at the network level. These network-level mutational operators are sufficient to allow the statistical analysis of network structure, but impose limitations on the way networks are evolved. There are a wide variety of mutations in DNA sequences that have yet to be analysed for their network-level effects. By modelling an artificial genome at the level of nucleotide sequences and mapping it to a regulatory network, biologically grounded mutation operators can be mapped to network level mutations. This paper analyses five such sequence level mutations(single-point mutation, transposition, inversion, deletion and gene duplication) for their effects at the network level. Using analytic and simulation techniques, we show that it is rarely the case that nodes and links are cleanly added or deleted, with even the simplest point mutation causing a wide variety of network-level modifications. As expected, the vast majority of simple (single-point) mutations are neutral, resulting in a neutral plateau from which a range of functional behaviours can be reached. By analysing the effects of sequence-level mutations at the network level of gene regulation, we aim to stimulate more careful consideration of mutation operators in gene regulation models than has previously been given.
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| Keyword(s) |
gene regulation
random Boolean networks
mutation operators
simulation
artificial genome
evolutionary algorithms
molecular evolution
theoretical biology
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| Additional Notes |
Originally published as Watson, J., Geard, N. and Wiles, J., Towards More Biological Mutation Operators in Gene Regulation Studies, BioSystems, 76 (1-3), 239-248. Copyright 2004 Elsevier Science.
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