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In order to solve the problem of how to mark genes in the road map by color pathway, this article introduces the corresponding analysis and answer in detail, hoping to help more partners who want to solve this problem to find a simpler and easier way.

For the visualization of the results of pathway analysis, the most commonly used way of presentation is to highlight the enriched genes in the pathway. Kegg provides online services on Color Pathway, which can easily accomplish this task.

This tool is easy to use and is divided into four steps:

Enter the pathway ID you want to mark in the Select KEGG pathway map input box

Enter the gene to be tagged and the corresponding information in Enter data, or upload the corresponding file by selecting the file button

Select the operation in Option that matches the file format entered in the previous step

Click the Exec button to submit the task

As can be seen from the screenshot above, this tool provides three ways of marking. Let's take the hsa05200 path as an example to take a look at the actual usage.

Mark genes with a specified color

The format of the input file is as follows:

The first is the gene or KO that needs to be tagged, and the other is the corresponding foreground color and background color. The background color is simply the filling color of the box, and the foreground color is the color of the border and text.

Each column is separated by\ t, and when you specify a color, you can write it in two ways, the first way is to write a column with only one color, which represents the background color, such as 1630 blue; the second way to write a column with two colors, the two colors are connected with a comma, then the first color is the background color and the second color is the foreground color, such as 1630 blue,red. When specifying a color, you can use a commonly used color name or hexadecimal code. Note that there must be a comment line that begins with # and specify a name for each column, which can be defined by yourself.

Example:

# hsa highlight1630 blue,red836 blue842 # 00cc3326060 # ff3366999 # 3366ff

The effect of the tag is as follows:

Mark genes with gene expression

When using gene expression, it is necessary to specify a color range and map the value to the color range, which is suitable to show the gradual relationship of expression.

The input file consists of two columns, the first is the gene ID, and the second is the gene expression (of course, the expression can be any value, as long as it is the data you want to represent, such as the length of the gene and the folg change value), and there must be a header starting with #.

Example

# hsa counthsa:25 678hsa:861 26hsa:867 13

The effect of the tag is as follows

Express genes in the form of barplot

The input file format is exactly the same as the second method, and the final output is a web page that converts the value to the height of the column, as shown below:

Through color pathway, we can mark our genes in many ways in the road map, we can specify the color directly, and we can map the numerical information such as expression amount to the map.

For each input format, there must be a comment line that begins with #.

Color pathway can only mark one road map at a time, which is not suitable for large-scale marking.

This is the answer to the question about how color pathway marks genes in the road map. I hope the above content can be of some help to you. If you still have a lot of doubts to be solved, you can follow the industry information channel for more related knowledge.

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