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kegg_network




Select a file   _SAMPLEFILES_




Input sample file: sample_table
Organize the data according to the sample file format, upload and submit.
In the result display, you can modify the network diagram according to your needs.
Input dynamic demonstration: (input once, you can get different types of network diagrams)



1. Normal network diagram:

a) Global modification can adjust the layout, font, font size, whether to use labels and label positions
b) Node modification can adjust shape, transparency, color, size
c) The thickness and color of the node border can be adjusted
d) Line modification can adjust line type, color and thickness
e) The target point line can customize the shape, color, size, etc. of the point line, and also delete the node, which is mainly used to embellish important points and lines.



The last saved result:




2. Complement the network diagram of the connection path:

In the global modification click to supplement the connection path
Other settings are the same as normal network diagram





The last saved result:





3. Supplement the network diagram of adjacent channels:

In the global modification, click to add all adjacent channels
Other settings are the same as normal network diagram





The last saved result:



4. Supplement the network diagram of all channels:

In the global modification, click to supplement the connection pathway and supplement all adjacent pathways
Other settings are the same as normal network diagram





The last saved result:



1. Function:

Network diagram is a visualization method commonly used in bioinformatics to show the direction and degree of association between different nodes. In enrichment analysis, network diagrams are often used to express the interaction between enrichment paths, find upstream and downstream signal paths, find core paths, or supplement interrupted paths, so that users can understand the relationship between network paths from a global perspective. In organisms, different genes coordinate with each other to perform their biological functions. Pathway-based analysis helps to further understand the biological functions of genes.

2. Scope of application:

It is suitable for using the network diagram to understand the relationship between each channel from a global perspective after the KEGG enrichment analysis is done.

3. Input:
The file is a matrix in txt format (the format is as follows, the data must be separated by a tab character (tab), you can choose to open it in Excel, and then save it as a .txt file separated by the tab key.)
1) The first column is the map ID of kegg, which is the ko number
2) The second and third columns are attribute columns. The attribute column is used to define the size and color of the map node. (Note: Only numeric values can be entered in the property file, text types are not supported).

Map_ID

Gene_number

FDR

ko01001

2

0.00001

ko04812

4

0.000003

ko03013

12

1e-10

……

……

……

Note: The input format must have only 3 columns, as shown in the above table, other formats are not supported.

Tip: It is recommended to enter about 10 paths, otherwise there are too many nodes in the graph, which will affect the appearance of the graph; you can choose the path related to the experimental phenomenon or the significant enrichment path that is focused on according to the problems that the experimental design wants to reveal.

4. Parameter settings

(1) Supplementary path connection: select "Yes/No". The network diagram shows the path that can connect the two input kegg paths together (this type of path is not in the input path list, but is supplemented by the KEGG connection path database. The supplementary path is intermediate, so that the input The isolated channels are connected to form a complete network). The default color of this type of path is gray, and the connecting line is a dotted line.

(2) Supplement all adjacent paths: select "Yes/No". Show all supplementary paths adjacent to the input KEGG path in the network diagram (this type of path is not in the input path list, but is supplemented by the KEGG connection path database, supplements all adjacent paths of the input path, so that the network The information is more complete). The default color of this type of pathway is gray, and the connecting line is a dashed line.


(3) Other settings: Some general settings, such as node size, color, connection line style, etc., can be adjusted according to your own needs.


5. Output:
(1) Interactive output file style:

Nodes:

Map_ID

Map_name

Type

Gene number

Degree

FDR

ko04014

Ras signaling pathway

Pathway

41

2

8.56E-83

ko04024

cAMP signaling pathway

pathway

16

6

3.42E-25

ko23120

Add_link

-

-

-

ko00211

Add_link

-

-

-

……

……

……

……

……

……

ko00101

……

Add_Adjacent

-

-

-

ko00112

……

Add_Adjacent

-

-

-

……

……

……

……

……

……

Note: The type column pathway indicates the path entered by the user, Add_link indicates the supplemented connection pathway, and Add_Adjacent indicates the supplemented adjacent pathway; because the supplementary pathway does not have gene number, degree and FDR values, it is represented by "-".


Edge:

Map1_ID

Map1_name

Map2_ID

Map2_name

Relations Type

ko00001

ko00002

Path-path

ko00002

ko00004

Path-path

ko00005

ko00006

Path-path

……

……

……

……

……

ko00007

ko00008

Path-link

ko00008

Ko00006

Link-path

……

……

……

……

……

ko_00001

ko_00342

path-Adjacent

ko_00001

ko_04521

path-Adjacent

ko_00001

ko_12316

path-Adjacent

ko_00001

ko_00121

path-Adjacent

ko_00006

ko_00543

path-Adjacent

ko_00006

ko_00214

path-Adjacent

ko_00007

ko_00953

path-Adjacent

……

……

……

……

……

Note: path-path represents the path relationship pair input by the user; Path-link and Link-path represent the supplemented connection path relationship pair; path-Adjacent represents all adjacent supplementary path relationship pairs.


(2) Plots:

Normal Plots:




Graphic interpretation and description:
Each node in the figure represents the KEGG pathway, the size of the node represents the number of genes enriched in the pathway after KEGG enrichment analysis, and the gradient color of the node represents the Pvalue of KEGG enrichment analysis.
The solid line in the figure indicates that there is a connection relationship between the pathways (Note: the KEGG pathway has no upstream and downstream relationship, it can only be said that they have a relationship with each other).
The isolated nodes in the figure indicate that there is no relationship between the paths.


Network diagram after supplementing the connection path:




Graphic interpretation and description:
Each node in the figure represents the KEGG pathway; the size of the node represents the number of genes enriched in the pathway after KEGG enrichment analysis; the gradient color of the node represents the Pvalue of the KEGG enrichment analysis; the gray node represents the pathway supplemented from the KEGG connection database. The role of is to connect isolated pathways and make KEGG significantly enriched pathways form a complete network, allowing us to explain biological issues from a global perspective and learn more about pathways.
The solid line in the figure indicates that there is a connection relationship between the channels (Note: the KEGG channel has no upstream and downstream relationship, only that there is a relationship between them); the dotted line indicates the connection line connecting the supplementary channel and the input channel to form a relationship network .


Complement the network diagram of the adjacent path:



Graphic interpretation and description:
Each node in the figure represents the KEGG pathway; the size of the node represents the number of genes enriched in the pathway after KEGG enrichment analysis; the gradient color of the node represents the Pvalue of the KEGG enrichment analysis; the gray node represents the adjacent pathway supplemented from the KEGG connection database , It can enable us to understand the adjacent pathways of the pathway where KEGG is significantly enriched.
The solid line in the figure indicates that there is a connection relationship between the channels (Note: the KEGG channel has no upstream and downstream relationship, only that there is a relationship between them); the dotted line indicates the connection line connecting the supplementary channel and the input channel to form a relationship network .



Complement the network diagram of all channels:





Graphic interpretation and description:
Each node in the figure represents the KEGG pathway; the size of the node represents the number of genes enriched in the pathway after KEGG enrichment analysis; the gradient color of the node represents the Pvalue of the KEGG enrichment analysis; the gray node represents the pathway supplemented from the KEGG connection database. The role of is to connect isolated pathways and make KEGG significantly enriched pathways form a complete network, so that we can explain biological problems from a global perspective and learn more about adjacent pathways.
The solid line in the figure indicates that there is a connection relationship between the channels (Note: the KEGG channel has no upstream and downstream relationship, only that there is a relationship between them); the dotted line indicates the connection line connecting the supplementary channel and the input channel to form a relationship network .
The bold black border node in the figure indicates that according to your experience or reading the literature, the path of this node is very relevant to this research, which can explain physiological phenomena or experimental problems.
The purple solid line and the dark red dashed line in the figure indicate that the relationship between the two pathways is very important to this study and can illustrate some important issues.




Results Display      (Click " task ID" to view different analysis results)