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Analyze yours: Manhattan plot

Normally, for instance in genome-wide association studies (GWAS), a Manhattan plot is a type of scatter plot, usually used to display data with a large number non-zero amplitude data-points. It gains its name from the similarity of such a plot to the Manhattan skyline. In GWAS Manhattan plots, genomic coordinates are displayed along the X-axis. The negative logarithm of the association P-value for each single nucleotide polymorphism (SNP) are displayed on the Y-axis. Therefore, the stronger the associations between SNP, the larger the Y-axis value. To improve the feasibility and transmitting speed of our global website service and to serve the gene targeting research as best as possible, we did several modifications to the original

Manhattan plot:

→ For gene targeting research, we plot Manhattan plot for genes rather than for SNPs which means the P-value are calculated for genes in two different group samples.

→ To improve the transmitting speed, we used line rather than spots in the original Manhattan plot.

→ For more options, you can plot Manhattan plot by chromosomes besides by genome.

→ Besides regular Manhattan plot, we provided another option to show more information in this plot: Directional Manhattan plot. If the median value of the gene in group is smaller than that in group2, the corresponding line points down from the base line (normally, it's zero line). Please see below for the details.

As we mentioned above, there are two ways to get into the Manhattan plot page.

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

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

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

→ Figure Downloading and DIY area: You can download Manhattan 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 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 Manhattan 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 are two other options here:

→ Directional Manhattan: if you select this option, the directional Manhattan plot will be created in the plotting area. In some cases, except for the difference between the samples of two groups, it is also good to know which group is bigger. Therefore, we compare the median values of samples in each group. If the median value of each gene

→ 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).

7. 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 cutoff on the Manhattan plot. For Directional Manhattan plot, two lines will be plotted at -10log10(cutoff) and 10log10(cutoff).

8. You can upload your data in two files through the dialog box here. Only 'xlsx' files are acceptable. Please make sure all data are in the first sheet of these files.

Note: It needs samples of two different groups to do the t-test, please make sure to put them into two different files.

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

Manhattan 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 Manhattan 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, after putting the mouse on a line, a catalog showed up like this:

From the left to the right are: gene symbol and p-value of this gene in the corresponding two groups. Therefore, in this example: the gene symbol is AIM1L, the p-value of it's copy number variations in the two group samples uploaded by the user is 4.18e-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.

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 Mountain plot.

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

Plotting Directional Directional Manhattan plot of copy numbers in the example files with 0.05 as the cutoff of p-value. Then change the color of P-are lines into red. The corresponding Directional Manhattan plot, the setting area and Figure DIY area are shown below.

From the figure below, we can see that almost the whole chromosome genes whose copy number variations in these two groups are significantly different.

Since the Directional Manhattan box is checked, the positive y-axis values of them means the mean values of the copy numbers of genes in group are all bigger than what in group2.

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  • Last modified: 2019/07/06 15:08
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