ArticleNature communications2021
Inferring multilayer interactome networks shaping phenotypic plasticity and evolution.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 32 citations in OpenAlex.
- Omnidirectional Interaction Networks Modulating Phenotypic Plasticity in the Gut Microbiota Towards Ulcerative Colitis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Statistical learning of stochastic complex systems via the Yau-Yau nonlinear filter.Innovation (Cambridge (Mass.)) · 2026Article
- Article
- Graph statistics theory of individualized quantitative genetics under haplotype-resolved genome assembly.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- An omnigenic interactome model to chart the genetic architecture of individual plants.Horticulture research · 2026Article
- Network stress: a wiring diagram of whole stress genes.Horticulture research · 2026Article
- A Computational Ecological Genetic Model of Phenotypic Plasticity in Species Interactions.Molecular ecology resources · 2026Article
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- Exploiting light energy utilization strategies in Populus simonii through multitrait-GWAS: insights from stochastic differential models.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Mapping the Influence of Light Intensity on the Transgenerational Genetic Architecture ofCurrent issues in molecular biology · 2024Article
- Genome-Wide Network Analysis of Above- and Below-Ground Co-growth inPlant phenomics (Washington, D.C.) · 2024Article
- Gene redundancy and gene compensation of insulin-like peptides in the oocyte development of bean beetle.PloS one · 2024Article
- Nature-Inspired Intelligent Computing: A Comprehensive Survey.Research (Washington, D.C.) · 2024Review
- The metabolomic physics of complex diseases.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Phytochemical Cue for the Fitness Costs of Herbicide-Resistant Weeds.Plants (Basel, Switzerland) · 2023Article
- Elevated temperature and CONature communications · 2023Article
- Characterization, costs, cues and future perspectives of phenotypic plasticity.Annals of botany · 2022Review
- Review
- Genetic dissection of growth trajectories in forest trees: From FunMap to FunGraph.Forestry research · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phenotypic plasticity represents a capacity by which the organism changes its phenotypes in response to environmental stimuli. Despite its pivotal role in adaptive evolution, how phenotypic plasticity is genetically controlled remains elusive. Here, we develop a unified framework for coalescing all single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) into a quantitative graph. This framework integrates functional genetic mapping, evolutionary game theory, and predator-prey theory to decompose the net genetic effect of each SNP into its independent and dependent components. The independent effect arises from the intrinsic capacity of a SNP, only expressed when it is in isolation, whereas the dependent effect results from the extrinsic influence of other SNPs. The dependent effect is conceptually beyond the traditional definition of epistasis by not only characterizing the strength of epistasis but also capturing the bi-causality of epistasis and the sign of the causality. We implement functional clustering and variable selection to infer multilayer, sparse, and multiplex interactome networks from any dimension of genetic data. We design and conduct two GWAS experiments using Staphylococcus aureus, aimed to test the genetic mechanisms underlying the phenotypic plasticity of this species to vancomycin exposure and Escherichia coli coexistence. We reconstruct the two most comprehensive genetic networks for abiotic and biotic phenotypic plasticity. Pathway analysis shows that SNP-SNP epistasis for phenotypic plasticity can be annotated to protein-protein interactions through coding genes. Our model can unveil the regulatory mechanisms of significant loci and excavate missing heritability from some insignificant loci. Our multilayer genetic networks provide a systems tool for dissecting environment-induced evolution.
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.