Deflection plot

As what we mentioned above, Manhattan plot is a widely used plot to display the results of the genome-wide association meta- analysis. Normally, it is used to show the significance difference (p-value of t-test) between two groups of data. But in some cases, the association between the variations (values in tumor samples compared with the non-malignant) is more important. Therefore, we proposed a new plot: Deflection plot.

It's also a genome-wide association meta-analysis for mRNA expression values, copy number variations or methylation values in tumor samples and non-malignant samples for two different cancer types. In Deflection plots, genomic coordinates are displayed along the X-axis. Each line stands for a gene. The amplitude of it stands for the negative logarithm of the association P-value for each gene's mRNA expression values in tumor samples in cancer type1 and cancer type2. Therefore, the stronger the associations between gene values, the higher the Y-axis value. If the bigger variation for a gene is a negative one (median value in tumor samples is smaller than what in non-malignant samples), then the corresponding line would point down, other wise, it would point up. Two default colors are assigned to these two cancer types. Color1 indicates that the deflection (tumor vs. non-malignant samples) is greater for cancer type1, whereas color2 indicates that the deflection is greater for cancer type2. A gap within the individual chromosome data indicates the location of the centrosome. For chromosomes 13, 14, 15, 21, and 22 only genes on the q arm were represented on the microarray. Please see the examples.

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

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

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

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

For “Deflection 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 Deflection plot will be plotted in this area.

→ Figure Downloading and DIY area: You can download Deflection 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 cancer types whose tumor and non-malignant samples are both available, please make sure of it while you are selecting. Otherwise, an error information will be displayed in the plotting area and no Deflection plot will be created.

6. You can specify a concern chromosome here. You also can select to create a Deflection plot for chromosomes 1-22. But due to the big data size for transmitting and for t-test calculating (more than 20,000 genes and dozens or hundreds samples), it may take several minutes. So please bear with it!

7. You can input the concern gene symbols here. Then they will be highlighted in Deflection 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.

8. In Deflection plot, the color of each line is decided by the mean or median values of the corresponding gene in the specified two groups. You can specify 'mean' or 'median' through this drop-down list.

9. 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).

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

After setting all these necessary options, click “GO” button at the bottom of this area, the Deflection 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 Deflection plot. The processing time varies according to the internet transmitting speed and the configuration of your computer.

Deflection plot figures will be shown in this area.

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

1. 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.

2. 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.

Example 1: Plotting Deflection plot of copy number variations on chromosome 1 of lung adenocarcinoma samples vs lung squamous cell carcinoma.

According to this plot, we can see that

→ For most part of P-Arm, LUSC has bigger variations (tumor vs non-malignant), therefore the corresponding color is light blue. The corresponding variations are deletions, therefore, the corresponding lines are pointing down.

→ For the whole Q-Arm, LUAD has the bigger variations, the corresponding color is light red. The corresponding variations are amplification, therefore, the corresponding lines are pointing up.

The corresponding Mountain plot which is shown below just confirm the results.

You may not like the colors plotted in default. Therefore, you can use the Figure DIY options to change the color. The Setting area and the final plot are shown in the following picture.

Example 2: Plotting Deflection plot of copy number variations on chromosome 3 of lung adenocarcinoma samples vs lung squamous cell carcinoma.

According to the corresponding Mountain plot, LUSC has the bigger variations across the whole chromosome, therefore, the Deflection plot is in only color2.

  • deflection.txt
  • Last modified: 2019/07/06 14:19
  • by tongyifan