Genotype Components as Predictors of Phenotype in Model Gene Regulatory Networks.
1Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA. sy.garte@rutgers.edu.
Acta Biotheoretica
|July 10, 2019
Summary
Gene regulatory network (GRN) models reveal that quantitative genotype parameters predict phenotypes when topological genotype effects are weak. However, dynamic network properties like oscillations depend heavily on topology, defying simple quantitative prediction.
Area of Science:
- Computational biology
- Systems biology
- Genetics
Background:
- Gene regulatory networks (GRNs) are crucial for understanding complex biological control systems.
- Non-Boolean network models offer a framework for simulating GRN dynamics.
Purpose of the Study:
- To investigate the relationship between genotypic parameters and dynamic phenotypes in simulated GRNs.
- To quantify the impact of topological genotype effects (TGE) on phenotypic outcomes.
- To determine the predictability of phenotypes based on genotype parameters.
Main Methods:
- Simulated non-Boolean gene regulatory networks with varying genotypic parameters.
- Generated dynamic phenotypes as a function of genotypic and topological parameters.
- Quantified the strength of topological genotype effects (TGE) on phenotypes.
Main Results:
- Predictive relationships were found between quantitative genotype parameters and phenotypes when TGE was low.
- Phenotypic outcomes were accurately predicted using quantitative genotype parameters for phenotypes with low TGE.
- Dynamic network properties, including oscillations, were highly dependent on genotype topology and not easily predicted by quantitative parameters.
Conclusions:
- The predictability of phenotypes in GRNs depends on the influence of topological genotype.
- Quantitative genotype parameters can predict outcomes for some phenotypes, but not for topology-dependent dynamic behaviors.
- Further research is needed to ascertain the applicability of these findings to biological GRNs.
Related Concept Videos
02:02Cis-regulatory Sequences
11.6K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.6K
02:02Cis-regulatory Sequences
4.0K
4.0K
02:07Organization of Genes
73.2K
Overview
73.2K
02:26Protein Networks
4.5K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.5K
01:42What is Gene Expression?
195.1K
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
195.1K
02:18Network Covalent Solids
16.1K
Network covalent solids contain a three-dimensional network of covalently bonded atoms as found in the crystal structures of nonmetals like diamond, graphite, silicon, and some covalent compounds, such as silicon dioxide (sand) and silicon carbide (carborundum, the abrasive on sandpaper). Many minerals have networks of covalent bonds.
To break or to melt a covalent network solid, covalent bonds must be broken. Because covalent bonds are relatively strong, covalent network solids are typically...
To break or to melt a covalent network solid, covalent bonds must be broken. Because covalent bonds are relatively strong, covalent network solids are typically...
16.1K