ArticleMolecular systems biology2010
Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape.
Article in Molecular systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- SINTER3D: continuous 3D reconstruction of spatial transcriptomics via implicit neural representations.Genome biology · 2026Article
- Somatic gene repression ensures physical segregation of germline and soma in Drosophila embryos.EMBO reports · 2026Article
- Network based simultaneous embedding of cells and marker genes from scRNA-seq studies.Briefings in bioinformatics · 2025Article
- Single-nucleus multiome ATAC and RNA sequencing reveals the molecular basis of thermal acclimation inbioRxiv : the preprint server for biology · 2025Article
- How germ granules promote germ cell fate.Nature reviews. Genetics · 2024Review
- Proteins rather than mRNAs regulate nucleation and persistence of Oskar germ granules in Drosophila.Cell reports · 2023Article
- RNA Helicase Vasa as a Multifunctional Conservative Regulator of Gametogenesis in Eukaryotes.Current issues in molecular biology · 2023Review
- Structural and functional organization of germ plasm condensates.The Biochemical journal · 2022Review
- Selective role of the DNA helicase Mcm5 in BMP retrograde signaling during Drosophila neuronal differentiation.PLoS genetics · 2022Article
- Genomic organization of the autonomous regulatory domain of eyeless locus in Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- HES and Mox genes are expressed during early mesoderm formation in a mollusk with putative ancestral features.Scientific reports · 2021Article
- Spatial molecular profiling: platforms, applications and analysis tools.Briefings in bioinformatics · 2021Review
- Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila.PLoS genetics · 2021Article
- Differential Expression ofFrontiers in cell and developmental biology · 2021Article
- The Epidermal Growth Factor Ligand Spitz Modulates Macrophage Efferocytosis, Wound Responses and Migration Dynamics DuringFrontiers in cell and developmental biology · 2021Article
- Patterning the Drosophila embryo: A paradigm for RNA-based developmental genetic regulation.Wiley interdisciplinary reviews. RNA · 2020Review
- RNA Granules: A View from the RNA Perspective.Molecules (Basel, Switzerland) · 2020Review
- Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis.IEEE transactions on big data · 2020Article
- Germ granules in Drosophila.Traffic (Copenhagen, Denmark) · 2019Review
- Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues ofG3 (Bethesda, Md.) · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Discovery of temporal and spatial patterns of gene expression is essential for understanding the regulatory networks and development in multicellular organisms. We analyzed the images from our large-scale spatial expression data set of early Drosophila embryonic development and present a comprehensive computational image analysis of the expression landscape. For this study, we created an innovative virtual representation of embryonic expression patterns using an elliptically shaped mesh grid that allows us to make quantitative comparisons of gene expression using a common frame of reference. Demonstrating the power of our approach, we used gene co-expression to identify distinct expression domains in the early embryo; the result is surprisingly similar to the fate map determined using laser ablation. We also used a clustering strategy to find genes with similar patterns and developed new analysis tools to detect variation within consensus patterns, adjacent non-overlapping patterns, and anti-correlated patterns. Of the 1800 genes investigated, only half had previously assigned functions. The known genes suggest developmental roles for the clusters, and identification of related patterns predicts requirements for co-occurring biological functions.
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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.