ArticlePlant physiology2011
Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis.
Article in Plant physiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed.
- Cross-kingdom sRNA Ta_sRNA1 silences PRIM2 to fine-tune Arabidopsis immunity during symbiosis with Trichoderma atroviride.The New phytologist · 2026Article
- The post-fertilization archegonium gene network of seedless plants contributed to the origin of seeds.Nature communications · 2026Article
- Identifying new players of gynoecium development using tissue-specific transcriptome data of Arabidopsis.Planta · 2025Article
- A spatio-temporal transcriptomic and proteomic dataset of developing Brassica napus seeds.Scientific data · 2025Article
- Comparative transcriptomic and evolutionary analysis of FAD-like genes of Brassica species revealed their role in fatty acid biosynthesis and stress tolerance.BMC plant biology · 2023Article
- Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat.Genome biology · 2023Article
- Spatiotemporal Transcriptomic Atlas of Developing Embryos and Vegetative Tissues in Flax.Plants (Basel, Switzerland) · 2022Article
- Review
- Weighted Gene Correlation Network Analysis (WGCNA) ofInternational journal of genomics · 2022Article
- Conserved, divergent and heterochronic gene expression during Brachypodium and Arabidopsis embryo development.Plant reproduction · 2021Article
- An Optimized Method for the Construction of a DNA Methylome from Small Quantities of Tissue or Purified DNA fromMolecules and cells · 2021Article
- Gene expression variation in Arabidopsis embryos at single-nucleus resolution.Development (Cambridge, England) · 2021Article
- Developmental and genomic architecture of plant embryogenesis: from model plant to crops.Plant communications · 2021Review
- Integrative Modeling of Gene Expression and Metabolic Networks ofFrontiers in plant science · 2021Article
- Analysis of Spatio-Temporal Transcriptome Profiles of Soybean (International journal of molecular sciences · 2020Article
- The R-Loop Atlas of Arabidopsis Development and Responses to Environmental Stimuli.The Plant cell · 2020Article
- Article
- The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development.The Plant cell · 2019Article
- Transcriptional Activation of Arabidopsis Zygotes Is Required for Initial Cell Divisions.Scientific reports · 2019Article
- The SMO1 Family of Sterol 4α-Methyl Oxidases Is Essential for Auxin- and Cytokinin-Regulated Embryogenesis.Plant physiology · 2019Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
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Abstract
Embryogenesis is central to the life cycle of most plant species. Despite its importance, because of the difficulty associated with embryo isolation, global gene expression programs involved in plant embryogenesis, especially the early events following fertilization, are largely unknown. To address this gap, we have developed methods to isolate whole live Arabidopsis (Arabidopsis thaliana) embryos as young as zygote and performed genome-wide profiling of gene expression. These studies revealed insights into patterns of gene expression relating to: maternal and paternal contributions to zygote development, chromosomal level clustering of temporal expression in embryogenesis, and embryo-specific functions. Functional analysis of some of the modulated transcription factor encoding genes from our data sets confirmed that they are critical for embryogenesis. Furthermore, we constructed stage-specific metabolic networks mapped with differentially regulated genes by combining the microarray data with the available Kyoto Encyclopedia of Genes and Genomes metabolic data sets. Comparative analysis of these networks revealed the network-associated structural and topological features, pathway interactions, and gene expression with reference to the metabolic activities during embryogenesis. Together, these studies have generated comprehensive gene expression data sets for embryo development in Arabidopsis and may serve as an important foundational resource for other seed plants.
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