MeSCoT: the tool for quantitative trait simulation through the mechanistic modeling of genes’ regulatory interactions
Open Access
- 27 April 2021
- journal article
- research article
- Published by Oxford University Press (OUP) in G3 Genes|Genomes|Genetics
- Vol. 11 (7)
- https://doi.org/10.1093/g3journal/jkab133
Abstract
This work represents a novel mechanistic approach to simulate and study genomic networks with accompanying regulatory interactions and complex mechanisms of quantitative trait formation. The approach implemented in MeSCoT software is conceptually based on the omnigenic genetic model of quantitative (complex) trait, and closely imitates the basic in vivo mechanisms of quantitative trait realization. The software provides a framework to study molecular mechanisms of gene-by-gene and gene-by-environment interactions underlying quantitative trait’s realization and allows detailed mechanistic studies of impact of genetic and phenotypic variance on gene regulation. MeSCoT performs a detailed simulation of genes’ regulatory interactions for variable genomic architectures, and generates complete set of transcriptional and translational data together with simulated quantitative trait values. Such data provide opportunities to study, for example, verification of novel statistical methods aiming to integrate intermediate phenotypes together with final phenotype in quantitative genetic analyses, or to investigate novel approaches for exploiting gene-by-gene and gene-by-environment interactions.Keywords
Funding Information
- BovReg (815668)
- European Union’s Horizon 2020
This publication has 49 references indexed in Scilit:
- Genetic Architecture of Complex Traits and Accuracy of Genomic Prediction: Coat Colour, Milk-Fat Percentage, and Type in Holstein Cattle as Contrasting Model TraitsPLoS Genetics, 2010
- Mapping genes for complex traits in domestic animals and their use in breeding programmesNature Reviews Genetics, 2009
- Genetic architecture of quantitative traits in mice, flies, and humansGenome Research, 2009
- Models of transcription factor binding: Sensitivity of activation functions to model assumptionsJournal of Theoretical Biology, 2009
- QMSim: a large-scale genome simulator for livestockBioinformatics, 2009
- Data and Theory Point to Mainly Additive Genetic Variance for Complex TraitsPLoS Genetics, 2008
- Comprehensive Analysis of Combinatorial Regulation using the Transcriptional Regulatory Network of YeastJournal of Molecular Biology, 2006
- Modularity and community structure in networksProceedings of the National Academy of Sciences of the United States of America, 2006
- Quantitative Genetics of reaction normsJournal of Evolutionary Biology, 1990
- The OR control system of bacteriophage lambda: A physical-chemical model for gene regulationJournal of Molecular Biology, 1985