Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets

Tintori, Sophia C.; Golden, Patrick; Goldstein, Bob

doi:10.1093/bioinformatics/btz972

Cited by 10 publications

(8 citation statements)

References 8 publications

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“…For comparison we also obtained transcriptional profiles of whole C. elegans bodies at each corresponding condition ( Supplementary file 1 ). An interactive presentation of the dataset using the web tool DrEdGE ( Tintori et al, 2020 ) is available ( Supplementary file 2 ; dredge.bio.unc.edu/BuschLab_eLife) . For 1-day-old animals cultured in 21% O 2 , 7881 genes were differentially expressed in the O 2 -sensing neuron samples when compared to whole-worm transcriptomes, of which 4058 genes were enriched in the O 2 -sensing neurons (at a false discovery rate (FDR) of <0.1 and a minimum fold change of 1.5).…”

Section: Resultsmentioning

confidence: 99%

High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans

Marcu

Palazzo

et al. 2020

eLife

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The ability to learn progressively declines with age. Neural hyperactivity has been implicated in impairing cognitive plasticity with age, but the molecular mechanisms remain elusive. Here, we show that chronic excitation of the Caenorhabditis elegans O2-sensing neurons during ageing causes a rapid decline of experience-dependent plasticity in response to environmental O2 concentration, whereas sustaining lower activity of O2-sensing neurons retains plasticity with age. We demonstrate that neural activity alters the ageing trajectory in the transcriptome of O2-sensing neurons, and our data suggest that high-activity neurons redirect resources from maintaining plasticity to sustaining continuous firing. Sustaining plasticity with age requires the K+-dependent Na+/Ca2+ (NCKX) exchanger, whereas the decline of plasticity with age in high-activity neurons acts through calmodulin and the scaffold protein Kidins220. Our findings demonstrate directly that the activity of neurons alters neuronal homeostasis to govern the age-related decline of neural plasticity and throw light on the mechanisms involved.

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Section: Resultsmentioning

confidence: 99%

High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans

Marcu

Palazzo

et al. 2020

eLife

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“…To visualize actin filament polarity, we endogenously tagged actin filament capping proteins. We used the gene ontology search function on WormBase (Harris et al, 2020) to identify proteins with actin filament capping functions encoded within the C. elegans genome, and we referenced single-cell RNA-sequencing database (Differential Expression Gene Explorer (DrEdGE)) (Tintori et al, 2016(Tintori et al, , 2020 to predict if it would be expressed at detectable levels in the embryo at the time of Ea/Ep internalization.…”

Section: Cap-1 a Barbed-end Capping Protein Is Enriched At Apicolater...mentioning

confidence: 99%

“…Two pointed-end actin filament capping proteins were identified as homologous to tropomodulin: TMD-2 and UNC-94. According to the RNA-sequencing dataset available on DrEdGE (Tintori et al, 2016(Tintori et al, , 2020, tmd-2 is not expressed in the internalizing Ea/Ep cells nor their precursors (E and EMS). Therefore, we focused our efforts on assessing UNC-94 localization.…”

Section: Unc-94 a Pointed-end Capping Protein Exhibits Is Distributed...mentioning

confidence: 99%

Architecture of the cortical actomyosin network driving apical constriction inC. elegans

Zhang

Medwig-Kinney

Goldstein

2023

Preprint

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Apical constriction is a cell shape change that drives key morphogenetic events during development, including gastrulation and neural tube formation. The forces driving apical constriction are primarily generated through the contraction of apicolateral and/or medioapical actomyosin networks. In the Drosophila ventral furrow, the medioapical actomyosin network has a sarcomere-like architecture, with radially polarized actin filaments and centrally enriched non-muscle myosin II and myosin activating kinase. To determine if this is a broadly conserved actin architecture driving apical constriction, we examined actomyosin architecture during C. elegans gastrulation, in which two endodermal precursor cells internalize from the surface of the embryo. Quantification of protein localization showed that neither the non-muscle myosin II NMY-2 nor the myosin-activating kinase MRCK-1 is enriched at the center of the apex. Further, visualization of barbed- and pointed-end capping proteins revealed that actin filaments do not exhibit radial polarization at the apex. Taken together with observations made in other organisms, our results demonstrate that diverse actomyosin architectures are used in animal cells to accomplish apical constriction.

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“…A growing number of software packages (Younesy et al, 2015;Nelson et al, 2016;Su et al, 2017;Harshbarger et al, 2017;Gardeux et al, 2017;Lim et al, 2017;Li and Andrade, 2017;Zhu et al, 2018;Ge et al, 2018;Monier et al, 2018;McDermaid et al, 2018;Schultheis et al, 2018;Kucukural et al, 2019;Choi and Ratner, 2019;Price et al, 2019;Tintori et al, 2020;Su et al, 2019) have been developed to operate on tabular-like summarized expression data, or on formats which might derive from their results (see Additional file 1: Table S1 for a comprehensive list of details on their functionality and characteristics).…”

Section: Introductionmentioning

confidence: 99%

ideal: an R/Bioconductor package for Interactive Differential Expression Analysis

Marini

Linke

Binder

2020

Preprint

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Background: RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking.Results: We developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpretation. ideal is implemented in R using the Shiny framework, and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of the differential expression analysis workflow in an assisted way, and generate a broad spectrum of publication-ready outputs, including diagnostic and summary visualizations in each module, all the way down to functional analysis. ideal also offers the possibility to seamlessly generate a full HTML report for storing and sharing results together with code for reproducibility.Conclusion: ideal is distributed as an R package in the Bioconductor project (http: //bioconductor.org/packages/ideal/), and provides a solution for performing interactive and reproducible analyses of summarized RNA-seq expression data, empowering researchers with many different profiles (life scientists, clinicians, but also experienced bioinformaticians) to make the ideal use of the data at hand.

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Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets

Cited by 10 publications

References 8 publications

High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans

High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans

Architecture of the cortical actomyosin network driving apical constriction inC. elegans

ideal: an R/Bioconductor package for Interactive Differential Expression Analysis

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