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

Abstract

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.

Redefining the Clostridioides difficile σ B Regulon: σ B Activates Genes Involved in Detoxifying Radicals That Can Result from the Exposure to Antimicrobials and Hydrogen Peroxide

“…Our findings are recapitulated in a volcano plot ( 28 ), which clearly shows that genes with lower expression upon sigB induction (in blue) cluster close to the significance threshold, whereas those with increased expression (in red) show a larger fold change ( Fig. 3 ).…”

“…A gene was considered differentially expressed if the log 2 fold change (log 2 FC) was ≤−1.5 or ≥1.5 and the P value was <0.05. Results were visualized in VolcaNoseR ( 28 ) and are available as an interactive graph via the URL contained in Text S1 in the supplemental material.…”

Redefining theClostridioides difficileσBregulon: σBactivates genes involved in detoxifying radicals that can result from the exposure to antimicrobials and hydrogen peroxide

“…Our findings are recapitulated in a volcano plot (27), that clearly shows that genes with lower expression upon sigB induction (in blue) cluster close to the significance threshold whereas those with increased expression (in red) show a larger fold change (Figure 3). We calculated the Manhattan distance for each data point (Dataset S2), and discuss the proteins encoded by the top-10 of the differentially expressed genes below.…”

“…A gene was considered differentially expressed if the log2 foldchange (log2 FC) was ≤ -1.5 or ≥1.5 and the p-value was <0.05. Results were visualized in VolcanoseR (27), and are available as an interactive graph via the URL contained in Text S1.…”

Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes

“…Heatmaps were generated using Morpheus 22 and volcano plots were generated using VolcaNoseR package. 23 Both case and control sequencing data were normalized to counts per million (CPM), which is calculated by normalizing the read counts for a given gene by the total counts per sample. CPM values were used to compare expression between certain genes and violin plots were generated using GraphPad Prism v8.0.…”