ArticleGenetics2008
A computational approach to the functional clustering of periodic gene-expression profiles.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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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.
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Who cites it
32 citing papers in PubMed.
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- 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 Statistical Mechanics Model to Decode Tissue Crosstalk During Graft Formation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Immunogenic cell death and tertiary lymphoid structures jointly define dysregulated antitumor immune states and therapeutic vulnerability in lung adenocarcinoma.Frontiers in immunology · 2026Article
- idopNetwork Analysis of Salt-Responsive Transcriptomes Reveals Hub Regulatory Modules and Genes inInternational journal of molecular sciences · 2025Article
- Identification of biomarkers and target drugs for melanoma: a topological and deep learning approach.Frontiers in genetics · 2025Article
- A nested reciprocal experimental design to map the genetic architecture of transgenerational phenotypic plasticity.Horticulture research · 2024Article
- A Single-Cell Omics Network Model of Cell Crosstalk during the Formation of Primordial Follicles.Cells · 2022Article
- An eco-evo-devo genetic network model of stress response.Horticulture research · 2022Article
- Review
- Inferring multilayer interactome networks shaping phenotypic plasticity and evolution.Nature communications · 2021Article
- Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis.BioData mining · 2021Article
- A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits.Frontiers in genetics · 2021Article
- Genetic dissection of growth trajectories in forest trees: From FunMap to FunGraph.Forestry research · 2021Review
- Article
- SEGN: Inferring real-time gene networks mediating phenotypic plasticity.Computational and structural biotechnology journal · 2020Article
- An omnidirectional visualization model of personalized gene regulatory networks.NPJ systems biology and applications · 2019Article
- Data- and expert-driven rule induction and filtering framework for functional interpretation and description of gene sets.Journal of biomedical semantics · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA microarray analysis has emerged as a leading technology to enhance our understanding of gene regulation and function in cellular mechanism controls on a genomic scale. This technology has advanced to unravel the genetic machinery of biological rhythms by collecting massive gene-expression data in a time course. Here, we present a statistical model for clustering periodic patterns of gene expression in terms of different transcriptional profiles. The model incorporates biologically meaningful Fourier series approximations of gene periodic expression into a mixture-model-based likelihood function, thus producing results that are likely to be closer to biological relevance, as compared to those from existing models. Also because the structures of the time-dependent means and covariance matrix are modeled, the new approach displays increased statistical power and precision of parameter estimation. The approach was used to reanalyze a real example with 800 periodically expressed transcriptional genes in yeast, leading to the identification of 13 distinct patterns of gene-expression cycles. The model proposed can be useful for characterizing the complex biological effects of gene expression and generate testable hypotheses about the workings of developmental systems in a more precise quantitative way.
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