ArticleEvolution; international journal of organic evolution2018
The architecture of an empirical genotype-phenotype map.
Article in Evolution; international journal of organic evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Hierarchical genotype networks and incipient ecological speciation in Q[Formula: see text] phage quasispecies.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Shared quasispecies architecture in experimental and natural RNA virus populations.Virus evolution · 2026Article
- Article
- Article
- Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks.Science advances · 2023Article
- Robustness and innovation in synthetic genotype networks.Nature communications · 2023Article
- Article
- Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes.PLoS computational biology · 2022Article
- On the incongruence of genotype-phenotype and fitness landscapes.PLoS computational biology · 2022Article
- Brain Tumor Characterization Using Radiogenomics in Artificial Intelligence Framework.Cancers · 2022Review
- A Family of Fitness Landscapes Modeled through Gene Regulatory Networks.Entropy (Basel, Switzerland) · 2022Article
- Mechanisms of Binding Specificity among bHLH Transcription Factors.International journal of molecular sciences · 2021Review
- Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies.Ecology and evolution · 2021Article
- The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A two-step PCR assembly for construction of gene variants across large mutational distances.Biology methods & protocols · 2021Article
- Neutral components show a hierarchical community structure in the genotype-phenotype map of RNA secondary structure.Journal of the Royal Society, Interface · 2020Article
- Mutation bias interacts with composition bias to influence adaptive evolution.PLoS computational biology · 2020Article
- Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis.PLoS computational biology · 2020Article
- Model genotype-phenotype mappings and the algorithmic structure of evolution.Journal of the Royal Society, Interface · 2019Article
- Adaptive Landscapes in the Age of Synthetic Biology.Molecular biology and evolution · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in high-throughput technologies are bringing the study of empirical genotype-phenotype (GP) maps to the fore. Here, we use data from protein-binding microarrays to study an empirical GP map of transcription factor (TF) -binding preferences. In this map, each genotype is a DNA sequence. The phenotype of this DNA sequence is its ability to bind one or more TFs. We study this GP map using genotype networks, in which nodes represent genotypes with the same phenotype, and edges connect nodes if their genotypes differ by a single small mutation. We describe the structure and arrangement of genotype networks within the space of all possible binding sites for 525 TFs from three eukaryotic species encompassing three kingdoms of life (animal, plant, and fungi). We thus provide a high-resolution depiction of the architecture of an empirical GP map. Among a number of findings, we show that these genotype networks are "small-world" and assortative, and that they ubiquitously overlap and interface with one another. We also use polymorphism data from Arabidopsis thaliana to show how genotype network structure influences the evolution of TF-binding sites in vivo. We discuss our findings in the context of regulatory 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.