ArticleNature biotechnology2008
Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network.
Article in Nature biotechnology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 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
81 citing papers in PubMed.
- A Function-Centric Framework for Mitochondrial Quality Control.Biomolecules · 2026Review
- Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.The Plant cell · 2025Article
- BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale.PLoS computational biology · 2023Article
- Frequency of change determines effectiveness of microbial response strategies.The ISME journal · 2023Article
- Phenotype similarities in automatically grouped T2D patients by variation-based clustering of IL-1β gene expression.EJIFCC · 2023Article
- Timed Pulses in DNA Strand Displacement Reactions.Journal of the American Chemical Society · 2023Article
- Inferring cell cycle phases from a partially temporal network of protein interactions.Cell reports methods · 2023Article
- Functional network motifs defined through integration of protein-protein and genetic interactions.PeerJ · 2022Article
- Effective connectivity determines the critical dynamics of biochemical networks.Journal of the Royal Society, Interface · 2022Article
- Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress.The ISME journal · 2021Article
- Review
- The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Quorum Sensing-Mediated and Growth Phase-Dependent Regulation of Metabolic Pathways inFrontiers in microbiology · 2021Article
- Using optimal control to understand complex metabolic pathways.BMC bioinformatics · 2020Article
- Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling.Genome research · 2020Article
- Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing.Scientific reports · 2020Article
- Learning causal networks using inducible transcription factors and transcriptome-wide time series.Molecular systems biology · 2020Article
- Reserve Flux Capacity in the Pentose Phosphate Pathway by NADPH Binding Is Conserved across Kingdoms.iScience · 2019Article
- Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome.FEMS yeast research · 2019Article
- Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts.Cell systems · 2018Article
21 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
6 authors.
Funding
Abstract
Significant insight about biological networks arises from the study of network motifs--overly abundant network subgraphs--but such wiring patterns do not specify when and how potential routes within a cellular network are used. To address this limitation, we introduce activity motifs, which capture patterns in the dynamic use of a network. Using this framework to analyze transcription in Saccharomyces cerevisiae metabolism, we find that cells use different timing activity motifs to optimize transcription timing in response to changing conditions: forward activation to produce metabolic compounds efficiently, backward shutoff to rapidly stop production of a detrimental product and synchronized activation for co-production of metabolites required for the same reaction. Measuring protein abundance over a time course reveals that mRNA timing motifs also occur at the protein level. Timing motifs significantly overlap with binding activity motifs, where genes in a linear chain have ordered binding affinity to a transcription factor, suggesting a mechanism for ordered transcription. Finely timed transcriptional regulation is therefore abundant in yeast metabolism, optimizing the organism's adaptation to new environmental conditions.
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.