ArticleMolecular systems biology2009
Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture.
Article in Molecular systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
What it found
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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.
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Who cites it
90 citing papers in PubMed, 176 citations in OpenAlex.
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- LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae.Nucleic acids research · 2024Article
- Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights.BioEssays : news and reviews in molecular, cellular and developmental biology · 2024Review
- TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii.Nucleic acids research · 2024Article
- iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease.PLoS computational biology · 2023Article
- Transcription factor expression levels and environmental signals constrain transcription factor innovation.Microbiology (Reading, England) · 2023Article
- Transcriptome-wide analysis reveals core transcriptional regulators associated with culm development and variation inHeliyon · 2022Article
- Mechanisms behind context-dependent role of glucocorticoids in breast cancer progression.Cancer metastasis reviews · 2022Review
- Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration in mice.Nature communications · 2022Article
- DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data.Science advances · 2022Article
- Functional network motifs defined through integration of protein-protein and genetic interactions.PeerJ · 2022Article
- Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses.Genetics · 2021Article
- DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.Bioinformatics (Oxford, England) · 2021Article
- Bow-tie architecture of gene regulatory networks in species of varying complexity.Journal of the Royal Society, Interface · 2021Article
- How directed is a directed network?Royal Society open science · 2020Article
- LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks.BMC bioinformatics · 2020Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
Although several studies have provided important insights into the general principles of biological networks, the link between network organization and the genome-scale dynamics of the underlying entities (genes, mRNAs, and proteins) and its role in systems behavior remain unclear. Here we show that transcription factor (TF) dynamics and regulatory network organization are tightly linked. By classifying TFs in the yeast regulatory network into three hierarchical layers (top, core, and bottom) and integrating diverse genome-scale datasets, we find that the TFs have static and dynamic properties that are similar within a layer and different across layers. At the protein level, the top-layer TFs are relatively abundant, long-lived, and noisy compared with the core- and bottom-layer TFs. Although variability in expression of top-layer TFs might confer a selective advantage, as this permits at least some members in a clonal cell population to initiate a response to changing conditions, tight regulation of the core- and bottom-layer TFs may minimize noise propagation and ensure fidelity in regulation. We propose that the interplay between network organization and TF dynamics could permit differential utilization of the same underlying network by distinct members of a clonal cell population.
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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.