五周年,102个工具都降价了
微生物数据分析工具限时免费一天!10月29-30日!
富集工具限时免费一天!10月27-28日!
五周年,102个工具都降价了

kegg_senior_network




Select a file   _SAMPLEFILES_


Select a file   _SAMPLEFILES_




Input sample file:
File 1: sample_table1
File 2: sample_table2

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:



1. Function:
Network diagram is a commonly used visualization method 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 relationship 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, and Show the relationship between pathways and genes. 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. Application scope:
It is suitable for KEGG enrichment analysis. The network diagram is used to present the relationship between the various pathways, and the relationship between pathways and genes is also displayed, so that users can understand the relationship between pathways and pathways, pathways and genes from a global perspective.

3. Input: (The format is as follows, and the data must be separated by a tab character (tab character), you can choose to open it in Excel, and then save it as a .txt file separated by the tab key.)
(1) Channel files: display various channels and attributes
The first column is the map ID of kegg, which is the ko number.

The second and third columns are attribute columns, namely gene number and FDR. 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

……

……

……


(2) Path ko number and gene ID relationship file: used to show the relationship between pathways and genes in the network diagram
The first column is the ko number of the pathway where the gene you want to display is located
The second column is the gene ID. Can be customized, or use the symbol number.

ko number

gene_ID (or symbol

ko04014

gene1

ko04014

gene2

ko04921

gene3

……

……

Note: The tool only reads the format shown in the table, other formats are not read.

4. Parameter setting:
(1) Supplementary connection path: 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 pathway node is gray, and the connecting lines are connected by dashed lines.

(2) Supplement all adjacent paths: select "Yes/No". Show all supplementary channels adjacent to the input KEGG channel in the network diagram. (This type of path is not in the input path list, but is derived from the KEGG connection path database, supplementing adjacent paths, making the network information more complete). The default color of this type of pathway node is gray, and the connecting lines are connected by dashed lines.

(3) Other parameter settings: such as node size, color, character, connection line color, type, etc. can be set according to requirements.

5. Output:

(1) Nodes:

ID

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

-

-

-

……

……

……

……

……

……

-

Unigene0003256(Rasa4)

gene

-

-

-

-

Unigene0003714(B0563.7)

Gene

-

-

-

-

Unigene0005540(GAP1)

Gene

-

-

-

……

……

……

……

……

……

Note: The type column pathway indicates the pathway entered by the user, Add_link indicates the supplemented connection pathway, Add_Adjacent indicates the supplemented adjacent pathway, and gene indicates the gene entered by the user; because supplementary pathways and genes do not have gene number, degree and FDR values, Use "-" to indicate.

(2) Edge:

fromNode_ID

fromNode_name

toNode_ID

toNode_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

……

……

……

……

……

ko_00001

-

Unigene0003256(Rasa4)

Path-gene

ko_00001

-

Unigene0003714(B0563.7)

Path-gene

ko_00001

-

Unigene0005540(GAP1)

Path-gene

……

……

……

……

……

Note: path-path represents the path relationship pair entered by the user; Path-link and Link-path represent the complementary connection path relationship pair; path-Adjacent represents all adjacent complementary path relationship pairs; path-gene represents the path and gene relationship relationship.

(3) Graphics:

Normal network diagram:


Graphic interpretation and description:

The green octagonal node represents the gene, and its size can be adjusted to a single size according to the parameters without a gradient size; the color can also be adjusted to a single color without a gradient.
Other nodes with different colors and sizes represent 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 the KEGG enrichment analysis.
The solid line indicates that there is a connection relationship between pathways and pathways or pathways and genes (Note: 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.



Complementary network diagram of the connection path:




Graphic interpretation and description:

The sky blue circular node represents the gene, and its size can be adjusted to a single size according to the parameters, without gradient size; the color can also be adjusted to a single color, without gradient color.
Other nodes of different colors and sizes represent 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 supplement from the KEGG connection database. The role of pathways 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 indicates the connection between the pathway and the pathway or the pathway and the gene (Note: the KEGG pathway has no upstream and downstream relationship, and it can only be said that there is a relationship between them), and the dotted line indicates the connection line connecting the supplementary pathway and the input pathway. Form a network of relationships.


Complement the network diagram of the adjacent path:




Graphic interpretation and description:

The sky blue octagonal node represents the gene, and its size can be adjusted to a single size according to the parameters, without a gradient size; the color can also be adjusted to a single color without a gradient. The sky blue octagonal node with a bold red border indicates that the gene is more important in this study, and is highlighted in color.
Other nodes of different colors and sizes represent 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 supplement from the KEGG connection database. Adjacent pathways, it allows us to understand the adjacent pathways of the pathways where KEGG is significantly enriched.
The solid line indicates the connection between the pathway and the pathway or the pathway and the gene (Note: the KEGG pathway has no upstream and downstream relationship, and it can only be said that there is a relationship between them), and the dotted line indicates the connection line connecting the supplementary pathway and the input pathway. Form a network of relationships.
According to your experience or looking up the literature, it is found that a certain pathway or gene is very relevant or important to this research. You can highlight the node or connection line through its attributes.




There may be more nodes and connecting lines in all the supplementary paths, resulting in the overall appearance of the graph, which can be done according to your needs.





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