PlotTwist: A web app for plotting and annotating continuous data

Goedhart, Joachim

doi:10.1371/journal.pbio.3000581

Cited by 64 publications

(55 citation statements)

References 26 publications

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“…All settings that are defined in the user interface can be stored as a URL, as was previously implemented for PlotsOfData and PlotTwist 8,9 . When the data is retrieved from an external online resource, this hyperlink is included in the URL.…”

Section: Sharing Data and Plot Settingsmentioning

confidence: 99%

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots

Goedhart

Luijsterburg

2020

Sci Rep

Self Cite

437

264

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Comparative genome- and proteome-wide screens yield large amounts of data. To efficiently present such datasets and to simplify the identification of hits, the results are often presented in a type of scatterplot known as a volcano plot, which shows a measure of effect size versus a measure of significance. The data points with the largest effect size and a statistical significance beyond a user-defined threshold are considered as hits. Such hits are usually annotated in the plot by a label with their name. Volcano plots can represent ten thousands of data points, of which typically only a handful is annotated. The information of data that is not annotated is hardly or not accessible. To simplify access to the data and enable its re-use, we have developed an open source and online web tool with R/Shiny. The web app is named VolcaNoseR and it can be used to create, explore, label and share volcano plots (https://huygens.science.uva.nl/VolcaNoseR). When the data is stored in an online data repository, the web app can retrieve that data together with user-defined settings to generate a customized, interactive volcano plot. Users can interact with the data, adjust the plot and share their modified plot together with the underlying data. Therefore, VolcaNoseR increases the transparency and re-use of large comparative genome- and proteome-wide datasets.

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Section: Sharing Data and Plot Settingsmentioning

confidence: 99%

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots

Goedhart

Luijsterburg

2020

Sci Rep

Self Cite

437

264

View full text Add to dashboard Cite

show abstract

“…All settings that are defined in the user interface can be stored as a URL, as was previously implemented for PlotsOfData and PlotTwist (Postma and Goedhart, 2019;Goedhart, 2020). When the data is retrieved from an external online resource, this hyperlink is included in the URL.…”

Section: Sharing Data and Plot Settingsmentioning

confidence: 99%

“…Several web apps are available (Singh et al, 2016;Naumov et al, 2017), but these do not generate interactive plots and only have limited options for customization and annotation. Therefore, we decided to generate a web-based online tool for generating volcano plots, similar to previously plotting apps (Goedhart, 2020;Postma and Goedhart, 2019). Here, we report an open source web app for generating, exploring, labeling and sharing Volcano plots.…”

Section: Introductionmentioning

confidence: 99%

VolcaNoseR – a web app for creating, exploring, labeling and sharing volcano plots

Goedhart

Luijsterburg

2020

Preprint

Self Cite

View full text Add to dashboard Cite

Comparative genome-and proteome-wide screens yield large amounts of data. To efficiently present such datasets and to simplify the identification of hits, the results are often presented in a type of scatterplot known as a volcano plot, which shows a measure of effect size versus a measure of significance. The data points with the largest effect size and a statistical significance beyond a userdefined threshold are considered as hits. Such hits are usually annotated in the plot by a label with their name. Volcano plots can represent ten thousands of data points, of which typically only a handful is annotated. The information of data that is not annotated is hardly or not accessible. To simplify access to the data and enable its re-use, we have developed an open source and online web tool with R/shiny. The web app is named VolcaNoseR and it can be used to create, explore, label and share volcano plots (https://huygens.science.uva.nl/VolcaNoseR). When the data is stored in an online data repository, the web app can retrieve that data together with user-defined settings to generate a customized, interactive volcano plot. Users can interact with the data, adjust the plot and share their modified plot together with the underlying data. Therefore, VolcaNoseR increases the transparency and re-use of large comparative genome-and proteome-wide datasets.

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“…Because fluorescent biosensors were abruptly dissipated from the cell when the plasma membrane of the apoptotic cell was collapsed, data after fluorescence values from cells were less than half of the maximum were excluded from the analysis. Single-cell ATP traces were visualized using PlotTwist ( Goedhart, 2020 ). Plots of single-cell ATP changes were generated using PlotsOfData ( Postma and Goedhart, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Single-cell dynamics of pannexin-1-facilitated programmed ATP loss during apoptosis

Imamura

Sakamoto

Yoshida

et al. 2020

eLife

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ATP is essential for all living cells. However, how dead cells lose ATP has not been well investigated. In this study, we developed new FRET biosensors for dual imaging of intracellular ATP level and caspase-3 activity in single apoptotic cultured human cells. We show that the cytosolic ATP level starts to decrease immediately after the activation of caspase-3, and this process is completed typically within 2 hr. The ATP decrease was facilitated by caspase-dependent cleavage of the plasma membrane channel pannexin-1, indicating that the intracellular decrease of the apoptotic cell is a ‘programmed’ process. Apoptotic cells deficient of pannexin-1 sustained the ability to produce ATP through glycolysis and to consume ATP, and did not stop wasting glucose much longer period than normal apoptotic cells. Thus, the pannexin-1 plays a role in arresting the metabolic activity of dead apoptotic cells, most likely through facilitating the loss of intracellular ATP.

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PlotTwist: A web app for plotting and annotating continuous data

Cited by 64 publications

References 26 publications

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots

VolcaNoseR – a web app for creating, exploring, labeling and sharing volcano plots

Single-cell dynamics of pannexin-1-facilitated programmed ATP loss during apoptosis

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