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Volcano plot introduction ​

The Volcano plot in Omics Studio serves as a critical analytical tool for visualizing differential expression data. It enables you to quickly identify statistically significant changes in expression levels across conditions or treatments. By plotting log-fold changes(x-axis) against negative log10 p-values(y-axis), the Volcano plot makes it straightforward to evaluate transcripts or proteins of interest based on their expression levels and statistical significance.

In the Volcano plot, the dashed vertical lines represent the threshold for an absolute log2 fold change of one. The horizontal dashed line depicts where the unadjusted p-value is equal to 0.05. Regulations with an absolute log2 fold change of one and a p-value below 0.05 but an adjusted p-value above 0.05 are colored yellow, and regulations with an adjusted p-value below 0.05 are colored red or blue

⚠️ Performance notice

Please be aware that the Volcano plot may respond more slowly than other plots within Omics Studio. Your patience is appreciated. We expect to improve performance in future updates.

When to use the Volcano plot? ​

The Volcano plot provides a strong visual tool, when assessing the differential expression in single or multiple statistical comparisons. In Omics Studio volcano plots are particular usefull, as you can highligt the pathway(s) selected in Pathway graph and compare the statistical conparisons in your dataset.

The Volcano plot is particularly useful when you need to:

  • Assess the overall distribution of differential expression within your dataset.
  • Identify genes or proteins that show significant upregulation or downregulation across comparisons.
  • Prioritize targets for further biological validation based on their statistical significance and fold change.

Get started ​

The Volcano plot feeds directly from statistical information associated to the differential expression analysis. As an alternative to observing the full data, you also have the option to Highligh from Pathway Graph.

  1. Select comparisons: Choose one or more comparisons to include.
  2. Highlight from Pathway Graph: If you enable Highligth from Pathway Graph the nodes associated to the chosen pathway(s) in Pathway graph will be highlighted

From here, use the Volcano plot to analyze.

Select nodes ​

You can select nodes (e.g., proteomics) in the Volcano plot. Selection is as simple as clicking on one or more nodes, or drag select. The filter menu displays your selections by ID, enabling a overview of your selections.

Example

[1] "O15027" "O75396" "P24386" "P49418"

Add selection to My lists: Furthermore, selections from any of these views can be added directly to your My lists with the 📌 Pin button, facilitating a more efficient workflow for managing and analyzing datasets. If you want to learn more about My lists, follow this link.

Tools in the Volcano plot ​

The Volcano plot in Omics Studio is equipped with a suite of interactive tools designed to enhance your data analysis experience:

  • 📸 Download: Capture and save the current view of the plot as a PNG file.
  • 🔍 Zoom: Focus on a specific area of the plot for a closer look.
  • 🍳 Pan: Navigate across the plot by clicking and dragging.
  • 🔲 Box Select: Use a rectangular selection box to highlight specific nodes within the plot.
  • ➕ Zoom In
  • ➖ Zoom Out
  • 🤠 Lasso Select: With the lasso tool, draw freeform shapes to select nodes, offering precision.
  • 💠 Autoscale: Automatically scale the plot view to ensure all nodes are visible.
  • 🏠 Reset Axes: Revert any zoom and pan adjustments to their original state, providing a fresh perspective.