ReviewDevelopmental biology2009
Modeling the dynamics of transcriptional gene regulatory networks for animal development.
Review in Developmental biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed.
- Constructing the dynamic transcriptional regulatory networks to identify phenotype-specific transcription regulators.Briefings in bioinformatics · 2024Article
- Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons.Genome biology · 2024Article
- Differential sensitivity to longitudinal and transverse stretch mediates transcriptional responses in mouse neonatal ventricular myocytes.American journal of physiology. Heart and circulatory physiology · 2024Article
- Article
- A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networks.Epigenetics · 2021Article
- Review
- Identifying Transcription Factor Combinations to Modulate Circadian Rhythms by Leveraging Virtual Knockouts on Transcription Networks.iScience · 2020Article
- Addressing Non-linear System Dynamics of Single-Strand RNA Virus-Host Interaction.Frontiers in microbiology · 2020Article
- Connecting the molecular function of microRNAs to cell differentiation dynamics.Journal of the Royal Society, Interface · 2019Article
- Effect of temperature on Pi54-mediated leaf blast resistance in rice.World journal of microbiology & biotechnology · 2019Article
- Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges.Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Encounters across networks: Windows into principles of genomic regulation.Marine genomics · 2019Article
- An integrative method to decode regulatory logics in gene transcription.Nature communications · 2017Article
- Article
- Regulatory states in the developmental control of gene expression.Briefings in functional genomics · 2017Review
- Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor-Promoter Interplay.ACS synthetic biology · 2017Article
- Dynamics of the Interaction between Cotton BollwormMolecular & cellular proteomics : MCP · 2017Article
- A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions.BMC systems biology · 2017Article
- A spectrum of modularity in multi-functional gene circuits.Molecular systems biology · 2017Article
- Placental transcriptomes in the common aneuploidies reveal critical regions on the trisomic chromosomes and genome-wide effects.Prenatal diagnosis · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The dynamic process of cell fate specification is regulated by networks of regulatory genes. The architecture of the network defines the temporal order of specification events. To understand the dynamic control of the developmental process, the kinetics of mRNA and protein synthesis and the response of the cis-regulatory modules to transcription factor concentration must be considered. Here we review mathematical models for mRNA and protein synthesis kinetics which are based on experimental measurements of the rates of the relevant processes. The model comprises the response functions of cis-regulatory modules to their transcription factor inputs, by incorporating binding site occupancy and its dependence on biologically measurable quantities. We use this model to simulate gene expression, to distinguish between cis-regulatory execution of "AND" and "OR" logic functions, rationalize the oscillatory behavior of certain transcriptional auto-repressors and to show how linked subcircuits can be dealt with. Model simulations display the effects of mutation of binding sites, or perturbation of upstream gene expression. The model is a generally useful tool for understanding gene regulation and the dynamics of cell fate specification.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.