ArticleMethods (San Diego, Calif.)2013
Image analysis and empirical modeling of gene and protein expression.
Article in Methods (San Diego, Calif.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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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.
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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
13 citing papers in PubMed, 22 citations in OpenAlex.
- Article
- Optogenetic manipulation of nuclear Dorsal reveals temporal requirements and consequences for transcription.bioRxiv : the preprint server for biology · 2024Article
- Target gene responses differ when transcription factor levels are acutely decreased by nuclear export versus degradation.Development (Cambridge, England) · 2024Article
- Dynamics of BMP signaling and stable gene expression in the early Drosophila embryo.Biology open · 2024Article
- Target gene responses differ when transcription factor levels are acutely decreased by nuclear export versus degradation.bioRxiv : the preprint server for biology · 2024Article
- SUMOylation of Dorsal attenuates Toll/NF-κB signaling.Genetics · 2022Article
- Mechanism and implications of morphogen shuttling: Lessons learned from dorsal and Cactus in Drosophila.Developmental biology · 2020Article
- Robustness of the Dorsal morphogen gradient with respect to morphogen dosage.PLoS computational biology · 2020Article
- Tools to reverse-engineer multicellular systems: case studies using the fruit fly.Journal of biological engineering · 2019Review
- Analyzing negative feedback using a synthetic gene network expressed in the Drosophila melanogaster embryo.BMC systems biology · 2016Article
- Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories.Integrative biology : quantitative biosciences from nano to macro · 2015Article
- Spatially resolved transcriptomics and beyond.Nature reviews. Genetics · 2015Review
- Size-dependent regulation of dorsal-ventral patterning in the early Drosophila embryo.Developmental biology · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Protein gradients and gene expression patterns are major determinants in the differentiation and fate map of the developing embryo. Here we discuss computational methods to quantitatively measure the positions of gene expression domains and the gradients of protein expression along the dorsal-ventral axis in the Drosophila embryo. Our methodology involves three layers of data. The first layer, or the primary data, consists of z-stack confocal images of embryos processed by in situ hybridization and/or antibody stainings. The secondary data are relationships between location, usually an x-axis coordinate, and fluorescent intensity of gene or protein detection. Tertiary data comprise the optimal parameters that arise from fits of the secondary data to empirical models. The tertiary data are useful to distill large datasets of imaged embryos down to a tractable number of conceptually useful parameters. This analysis allows us to detect subtle phenotypes and is adaptable to any set of genes or proteins with a canonical pattern. For example, we show how insights into the Dorsal transcription factor protein gradient and its target gene ventral-neuroblasts defective (vnd) were obtained using such quantitative approaches.
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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.