ArticleMolecular systems biology2015
Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome.
Article in Molecular systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed, 38 citations in OpenAlex.
- Phenotyping of a new yeast mapping population reveals differences in the activation of the TORC1 signalling pathway between wild and domesticated yeast strains.Biological research · 2024Article
- Genetic effects on molecular network states explain complex traits.Molecular systems biology · 2023Article
- Signed Distance Correlation (SiDCo): an online implementation of distance correlation and partial distance correlation for data-driven network analysis.Bioinformatics (Oxford, England) · 2023Article
- Article
- TORC1 and PKA activity towards ribosome biogenesis oscillates in synchrony with the budding yeast cell cycle.Journal of cell science · 2022Article
- Article
- SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions.BMC bioinformatics · 2021Article
- Cellular quiescence in budding yeast.Yeast (Chichester, England) · 2021Review
- Article
- Gtr/Ego-independent TORC1 activation is achieved through a glutamine-sensitive interaction with Pib2 on the vacuolar membrane.PLoS genetics · 2018Article
- Real Talk: The Inter-play Between the mTOR, AMPK, and Hexosamine Biosynthetic Pathways in Cell Signaling.Frontiers in endocrinology · 2018Review
- Data Reduction Approaches for Dissecting Transcriptional Effects on Metabolism.Frontiers in plant science · 2018Article
- Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.PLoS computational biology · 2017Article
- Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach.Scientific reports · 2016Article
- Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection.PLoS computational biology · 2016Article
- Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations.Frontiers in bioengineering and biotechnology · 2016Review
- Integration of omics: more than the sum of its parts.Cancer & metabolism · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cells react to nutritional cues in changing environments via the integrated action of signaling, transcriptional, and metabolic networks. Mechanistic insight into signaling processes is often complicated because ubiquitous feedback loops obscure causal relationships. Consequently, the endogenous inputs of many nutrient signaling pathways remain unknown. Recent advances for system-wide experimental data generation have facilitated the quantification of signaling systems, but the integration of multi-level dynamic data remains challenging. Here, we co-designed dynamic experiments and a probabilistic, model-based method to infer causal relationships between metabolism, signaling, and gene regulation. We analyzed the dynamic regulation of nitrogen metabolism by the target of rapamycin complex 1 (TORC1) pathway in budding yeast. Dynamic transcriptomic, proteomic, and metabolomic measurements along shifts in nitrogen quality yielded a consistent dataset that demonstrated extensive re-wiring of cellular networks during adaptation. Our inference method identified putative downstream targets of TORC1 and putative metabolic inputs of TORC1, including the hypothesized glutamine signal. The work provides a basis for further mechanistic studies of nitrogen metabolism and a general computational framework to study cellular processes.
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.