Procedure of fundamental graph analysis

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Here, we will describe the procedures to construct a pipeline that reads a network from a file (e.g. http://xip.hgc.jp/samples/sampleGeneNetwork.tsv), plot and analyze the network. This sample file is composed of two columns. Both columns are gene names and the pair of genes displayed in each row represent that there is an edge between them.

The contents of the sample data text file
A B
B C
C D
C E
C F
F G
D F
C G
G H
H I
I J
J K
K L
L I
I M
I K
M N
M L
N AA
I S
S AF
I X
I Q
G Q
G V
Q O
O P
Q R
Q T
Q U
Q W
Q V
R V
V U
V T
O V
V W
V X
Q X
R AH
X AH
V AH
V Y
V Z
X Z
X AI
V AF
G AF
AF AH
AF AB
AF AC
AF AD
AF AE
AE AG
AB AC

Contents

Load and display a gene network from a data text file

In order to facilitate to handle graphs in a text format, the CSML format is used. The main components used here are the Input edge file as CSML and the Display on CSML viewer.

‎left

XML file of the entire pipeline

Assembling pipeline

As illustrated above, the Input edge file as CSML, CSML layout, and Display on CSML viewer are positioned in the canvas and connected. The component CSML layout is used to layout the nodes of the network. The parameters of each component are illustrated below.

Inputting of the parameters to each component

Run and Result

Input edge file as CSML View.png

The gene network composed of 35 genes A to AI is displayed.

Graph-layout

Then, the uploaded network will be displayed using the organic layout. The component that will be used is the CSML layout.

CSML layout.png

XML file of the entire pipeline

Assembling pipeline

One more component namely, CSML layout is inserted between the already displayed components CSML layout and Display on CSML viewer. The parameters of each component are displayed below.

Inputting of the parameters to each component

Run and Result

CSML layout View.png

Now, the layout changed to a simpler format. The result layout is modified at each execution of the pipeline.

Graph analysis

Then, a simple graph analysis is performed. For each graph node, there are several properties. For example: Betweenness Centrality, Node Degree, etc. Here, the Node Degree (the number of edges connected to a node) is added to the "property" field of each node. The main component to add this property is the JJGraph basic analyzer.

‎left

XML file of the entire pipeline

Assembling pipeline

Here, we will insert the following components Export CSML to undirected JJGraph, JJGraph basic analyzer, and Export JJGraph to CSML between the components CSML layout and Display on CSML viewer. The parameters of each component are displayed below.

Inputting of the parameters to each component

Run and Result

JJGraph basic analyzer View.png


The layout of the graph is displayed by executing the pipeline. The difference between the previous pipeline and this one is the fact that now, there is the Node Degree in the properties. The information about the node degree is shown by moving the cursor on the node. In the figure, the node degree of node Q is 9.

Reflecting the properties to the view

In the previous step, the information about the Node Degree was added. Now, we will modify the size of each node proportional to the Node Degree. The component to be added is the Size mapping.

‎left

XML file of the entire pipeline

Assembling pipeline

The component Size mapping is added between the components Export JJGraph to CSML and Display on CSML viewer. The parameters of each component are displayed below.

Inputting of the parameters to each component

Run and Result

Size mapping View.png

Running the pipeline, it is possible to notice that the size of the node is proportional to the Node Degree.

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