Volcano plot

A volcano plot is a type of scatter-plot that is used to quickly identify changes in large data sets. It plots significance versus fold-change on the y (-log10 of p value) and x axes, respectively. The dashed red line shows where the cutoff of p-value (normally, p = 0.05) with points above the line having p < cutoff and points below the line having p > cutoff. This plot is colored such that those points having a fold-change less than 2 (log2 = 1, users also can customize it) are shown in one color and those having a fold-changes larger than 2 are shown in another color.

In statistics, a volcano plot is a type of scatter-plot that is used to quickly identify changes in large data sets composed of replicate data. [3]

A volcano plot combines a measure of statistical significance from a statistical test (e.g., a p value from an ANOVA model) with the magnitude of the change, enabling quick visual identification of those data-points (genes, etc.) that display large magnitude changes that are also statistically significant.

A volcano plot is constructed by plotting the negative log of the p value on the y axis (usually base 10). This results in data points with low p values (highly significant) appearing toward the top of the plot. The x axis is the log of the fold change between the two conditions. The log of the fold change is used so that changes in both directions appear equidistant from the center. Plotting points in this way results in two regions of interest in the plot: those points that are found toward the top of the plot that are far to either the left- or right-hand sides. These represent values that display large magnitude fold changes (hence being left or right of center) as well as high statistical significance (hence being toward the top).

Additional information can be added by coloring the points according to a third dimension of data (such as signal intensity), but this is not uniformly employed. Volcano plots are also used to graphically display a significance analysis of microarrays (SAM) gene selection criterion, an example of regularization.[4, 5]

As we mentioned above, there are three ways to get into the Volcano plot page.

→ Through the Navigation bar at the Home page, select “Volcano plot” under “Data Analysis”;

→ Go to “Data Analysis” page, then go to “Data visualization” area, select “Volcano plot”;

→ Through the link in the “Link area” at the Home page, go to “Data Analysis” page, then go to “Data visualization” area, select “Volcano plot”.

For “Volcano plot” page, there are five areas:

→ Navigation bar: You can switch to other pages through this navigation bar.

→ Setting area: You can specify genes, cancer types, data types, cutoff values and other parameter details here.

→ Plotting area: The Volcano plot will be plotted in this area.

→ Figure Downloading and DIY area: You can download Volcano plot in a certain format and size. You can also customize line color and so on through the option buttons in this area.

→ Link area: Necessary links are available for you to switch to other pages or websites.

Note: quick help can be available through putting your mouse on the small question marks besides certain options in this pages.

1. It reminds you which kind of plot you are working on.

2. You can select mRNA expression, copy number variation.

3. In TCGA/GDC dataset, non-malignant samples and tumor samples are not both always available for all cancer types. Available sample types vary for different data type even for the same cancer type. For example, for acute myeloid leukemia (LAML) cancer, no non-malignant samples of mRNA expression values are available, but both non-malignant and tumor samples are available for copy number variation data. Different legends are added before cancer names to tell you which kind of samples of the given cancer types can be available.

⚠: without non-malignant which means only tumor samples of this cancer type are available for the data type specified in (4) and (5).

❌: not available which means neither tumor samples nor non-malignant samples of this cancer type are available for the data type specified in (4) and (5).

4. You can specify the first cancer type here through the drop-down list.

5. You can specify the second cancer type through the drop-down list.

Note: It needs samples of two different groups to do the t-test, if you select the same cancer type for the first and second group, please make sure the sample types of them are different. Otherwise, an error information will be displayed in the plotting area and no Manhattan plot will be created.

6. You can input the concern gene symbols here. Then they will be highlighted in Volcano plot in different colors to make it easier to compare. If you want to input more than one gene symbols, a common and a space should be used to separate two gene symbols. Only HUGO (Human Genome Organization) symbols are accepted. For example: EGFR, KRAS, TP63….

Note: small case and big case are all acceptable. For example, kRAS, kras, KRas, KRAS are all treated as the same gene.

7. There is another option available (Log2): You can specify concern transformation type checking this option. Correspondingly, log2 transformation will be applied to the data before Bee-swarm plot (for mRNA expression values, it's log2 transformation; for CNV (copy number variation) values, it's log2(CNV/2) transformation).

8. You can input a cutoff value for p-value to see how many gene's P-values are significantly different for each arm. A line at -10log10(cutoff) will be plotted to show the cutoffs on the Volcano plot.

9. You can input a cutoff value for fold change to see how many genes' amplitudes is greatly variety in two groups. In default, it's 2 (log22=1). Two lines at ±1 will be plotted to show the cutoffs on the Volcano plot.

After setting all these necessary options, click “GO” button at the bottom of this area, the Volcano plot will be created in the plotting area. Because the big data size and the calculating time for t-test, it may take seconds or minutes to do the t-test and to create Volcano plot. The processing time varies according to the Internet transmitting speed and the configuration of your computer.

Volcano plot figures will be shown in this area.

A toolbar will show up at the top right of this plotting area when a Volcano plot is created.

1. Zoom in: Rectangular zoom in tool. This tool allows you to select a region to display at full application size. After clicking this botton, your mouse will turn into a small cross. Then click and hold the left mouse button and drag a rectangle around a portion of the screen and have it zoom in.

2. Zoom out: Zoom back to the status it was a step before by cliking it.

3. Restore: Show the plots in the original portion.

4 .Save as Image: You can click it to swich into a image saving webpage then click right mouse button to save this image. You also can specify the image format and size by selecting the options in the Figure downloading and DIY area.

5 .Data table: If you want to download the sample data in a table, you can click this button. Then a table containing all data will show up in the plotting area like this. You can select and copy the whole table or any part of it into a word or excel file by selecting and clicking right mouse button as you usally do. You can scroll down to see the information of other samples. You also can click the “close” button at the bottom left of this page to close the table page and go back to the default page with the plotting area.

For your convinence, the sample ID and other details of each individual gene will show up when you put your mouse on the corresponding line.

For example: in the above figure, after putting the mouse on a line, a catalog showed up is:

From the left to the right are: gene symbol and p-value of this gene in the corresponding two cancer types. Therefore, in this example: the gene symbol is PHACTR4, the p-value of its copy number variations in lung adenocarcinoma and lung squmous cell carcinoma tumor samples is 9.32e-15 which means it has significantly different copy number variations in these two groups.

You can specify image format (png or jpg) and size/dimensions for the image to download .

You can modify colors and Y-Limits of this figure.

  • volcano.txt
  • Last modified: 2019/07/06 14:18
  • by tongyifan