analyze_yours_deflection

Analyze yours: 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 two ways to get into the Deflection plot page.

1) Through the Navigation bar at the Home page, select “Deflection plot” under “Analyze yours”;

2) Go to “Analyze yours” page, then select “Deflection plot”;

For “Deflection plot” page, there are six 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.

→ Example area: Examples of the upload files are given here. You can download them through the link.

→ 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 need to specify the datatype here to tell us how to do log transformation (for mRNA expression values, it's log2 transformation; for CNV (copy number variation) values, it's log2(CNV/2) transformation).

3. You need to specify the chromosome through this drop-down list to provide us the necessary information about the location of the centromere. Now only 1-22 chromosomes are available.

4. You can specify concern gene here by inputting gene symbols. Only symbols provided in your files are accepted. If you want to input more than one gene symbols, a common and a space should be used to separate two gene symbols.

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

5. 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.

6. 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 plotting (for mRNA expression values, it's log2 transformation; for CNV (copy number variation) values, it's log2(CNV/2) transformation).

7. 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.

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.

8. According to the definition of the Deflection plot, it takes four groups of samples to create it (group, group_reference, group2, group2_reference). You can select the corresponding four files through the dialog boxes here.

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.

The 'Save as Image' button will show up at the top right of this plotting area when a Deflection plot is created. 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.

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, aftering 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 GLRX2, the p-value of its copy number variations in two groups is 1.38e-10 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.

Only 'xlsx' file type is acceptable! The default sheet is the first sheet of each '*.xlsx' file. This area shows the table format for you to arrange your data. You also can download the example files and use them to try the functions provided in this page.

→ Please make sure that per group per '*.xlsx' file.

→ Please put gene symbols of each group in the first column. If you don't have them, please use numbers or something as symbols. In Mountain plot, the corresponding gene symbol will show up when you put your mouse on any markers. If there are more than one groups, only genes that are common in all groups will be plotted. Therefore, they are necessary information for creating the plot.

→ Please put the start location for the genes in the second column. They will be used as the x-axis values in the Deflection plot.

→ Please put the values in the rest of the table.

  • analyze_yours_deflection.txt
  • Last modified: 2019/07/06 13:11
  • by tongyifan