Cytoscape Tutorial

Cytoscape is a software that focuses on open-source network visualization and analysis. Its core is to provide a basic functional layout and query network, and form a visual network baed on the combination of basic data. Cytoscape is derived from systems biology and is used to integrate biomolecular interaction networks with high-throughput gene expression data and other molecular state information. Its most powerful function is still used for large-scale protein-protein interactions, protein- Analysis of the interaction between DNA and genetics. Through Cytoscape, these biological networks can be integrated with various molecular status information such as gene expression and genotype in a visual environment, and these networks can be linked with functional annotation databases.

Note

Java needs to be installed before Cytoscape installation.

Tutorial

Import network file: file->import->network->file(net.txt)

Cytoscape Tutorial

After importing the file, the following interface appears

Cytoscape Tutorial

Import the node property file: file->import->table->file(node.txt) (here is table instead of network)

Note: node.txt: node attribute file. Four columns, containing three attributes; the first column is the gene id, which is consistent with the network file, the second column is the gene name (symbol), the third column is the molecular type (protein coding gene/lncRNA), and the fourth column is the degree of the node in the network.

Cytoscape Tutorial

The "Target Table Data" information in the red box above indicates that the imported node attribute table is associated with the previous network diagram. The "Network Collection" selects the network file we imported before.

"Preview" in the red box below: gene, name, molecular type, degree.

Set the first column of gene to "Key" to ensure that the gene id is not repeated. The second, third, and fourth columns are all attribute "Attribute". If you need to modify it, click the triangle mark on the right side of the name as well.

After clicking OK, the two columns of molecular type and degree are automatically added in the Table Panel below.

Cytoscape Tutorial

You can set a simple network diagram format through style.

Cytoscape Tutorial

Get the network diagram as following.

Cytoscape Tutorial

Network beautification

Basic style

Cytoscape Tutorial

Node style

Cytoscape Tutorial

Edge style

Click style->edge->stroke color in the network processing panel to set

Column is set to correlation, mapping type is set to continue mapping, current mapping (default is white-black)

Cytoscape Tutorial

Regulate network indicators statistics

Cytoscape Tutorial

Cytoscape provides a lot of external databases. Right-click the corresponding node and select externallinks in the options that appear. There are the following connected databases:

Cytoscape Tutorial

* It should be noted that our service is only used for research, not for clinical use.

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