ArticleEMBO reports2004
The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model.
Article in EMBO reports, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers, 1 of them a synthesis that pooled it.
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Who cites it
97 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide.Bioinformatics (Oxford, England) · 2009Pooled it
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- Establishing a model composed of immune-related gene-modules to predict tumor immunotherapy response.Scientific reports · 2024Article
- Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data.Bioinformatics (Oxford, England) · 2024Article
- A gene network-driven approach to infer novel pathogenicity-associated genes: application tomSystems · 2023Article
- WMDS.net: a network control framework for identifying key players in transcriptome programs.Bioinformatics (Oxford, England) · 2023Article
- hCoCena: horizontal integration and analysis of transcriptomics datasets.Bioinformatics (Oxford, England) · 2022Article
- Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.Developmental dynamics : an official publication of the American Association of Anatomists · 2022Article
- A globalBMC bioinformatics · 2022Article
- Feature importance network reveals novel functional relationships between biological features inFrontiers in plant science · 2022Article
- Construction and analysis of gene co-expression network in the pathogenic fungusFrontiers in microbiology · 2022Article
- Integrative Metabolomic and Transcriptomic Analyses Uncover Metabolic Alterations and Pigment Diversity inmSystems · 2021Article
- Self-selection of evolutionary strategies: adaptiveHeliyon · 2021Article
- Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions.Frontiers in microbiology · 2021Review
- Evolving complexity: how tinkering shapes cells, software and ecological networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Transdiagnostic Brain Mapping in Developmental Disorders.Current biology : CB · 2020Article
37 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We investigated the gene coexpression network in Saccharomyces cerevisiae, in which genes are linked when they are coregulated. This network is shown to have a scale-free, small-world architecture. Such architecture is typical of biological networks in which the nodes are connected when they are involved in the same biological process. Current models for the evolution of intracellular networks do not adequately reproduce the features that we observe in the network. We therefore derive a new model for its evolution based on the observation that there is a positive correlation between the sequence similarity of paralogues and their probability of coexpression or sharing of transcription factor binding sites (TFBSs). The simple, neutralist's model consists of (1) coduplication of genes with their TFBSs, (2) deletion and duplication of individual TFBSs and (3) gene loss. A network is constructed by connecting genes that share multiple TFBSs. Our model reproduces the scale-free, small-world architecture of the coregulation network and the homology relations between coregulated genes without the need for selection either at the level of the network structure or at the level of gene regulation.
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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.