Speaking of interactive network diagrams, everyone is familiar with it. When reading the literature, we often see interaction network diagrams showing the targeting relationship of circRNA-miRNA or the competitive network relationship of ceRNA. Let’s take a look at a few pictures first:

CircRNA-miRNA network maps the interaction relationship between circRNAs and miRNAs [1]

miRNA-ceRNA network. Upregulated circRNAs/miRNAs ceRNA network. [ 2]

The network diagram visually displays the connections between them, adding a bit of elegance to the article. These beautiful and clear network diagrams are all drawn by the amazing software Cytoscape. Don’t think that the network diagram looks so complicated, and the use of the software will also be complicated. Let me give you a brief introduction on how to use cytoscape to turn the analyzed data into a network diagram.

The steps are as follows:

First, install the ****cytoscape**** software. The software installation is relatively simple, so I won’t go into details here.

Second, organize the data to be drawn. Suppose that I did circRNA sequencing at Gisei Biotechnology and screened out some circRNA molecules with differential expression. I want to select the circRNAs to be studied and their target miRNAs to make a network diagram.

We will get 2 tables, the table of circRNA-miRNA line attributes (netedges) and point (nodes) attributes:

Example of netedges table

Example diagram of nodes table

Third, first import the target relationship ****netedges**** table into ****cytoscape****:

Then set the is the miRNA source node, and circRNA is set as the target node:

Then click OK to import the data and generate a preliminary network diagram:

Next, everyone can Beautified it. Generally, the expression of circRNA and which miRNAs it binds to are marked by setting different colors, shapes, sizes, etc. of the dots.

Fourth, first import the ****nodes**** table as ****Table****, and import the attributes of each point:

Then, Set the desired style on the Style tab, such as marking up-regulated circRNAs in red, down-regulated circRNAs in green, predicted miRNAs in blue, and adjust the Fill Color according to attributes. Or you can click on a certain point to adjust.

After some coloring and shaping, the network diagram becomes like this:

This kind of diagram looks okay, but if you want to adjust the graphic style, make It has to be the same as the picture at the beginning, and can be changed through the Layout tab.

Finally, we got a beautiful circRNA-miRNA network diagram:

The above briefly introduces some basic functions of Cytoscape, mainly connecting Nodes through Edges to form a Network, and importing Table pairs Annotate the Nodes in the Network to get the effect we want. Of course, the miRNA-mRNA network diagram and the protein-protein interaction network diagram (PPI) can also be visualized through this software. If you want to study the popular circRNA-miRNA-mRNA competitive network, you can also draw the predicted targeting relationship into a network diagram. According to the principle of ceRNA competitive network, there is a negative correlation between the expression levels of miRNA and targeting ceRNA, and a positive correlation between the expression levels of ceRNA pairs; combined with the experimental results, delete those that do not conform to the principle of ceRNA competitive network. relationship and improve the circRNA-miRNA-mRNA network.

In addition, the Cytoscape software also has some small plug-ins that can build larger and clearer network diagrams. This software is far more than the functions introduced in this article. There is no limit to learning and trust in life, and we look forward to exploring it with you.

References:

[1] Xingjie Bao , Shuying Zheng , Shuqi Mao , Tianlun Gu , Shike Liu , Jihan Sun , Lina Zhang.A potential risk factor of essential hypertension in case -control study_ Circular RNA hsa_circ_0037911. Biochemical and Biophysical Research Communications, March 2018; DOI: 10.1016/j.bbrc.2018.03.059.

[2] CHUN FENG, YUXIAO LI, YAN LIN, XIANBAO CAO, DONGDONG LI, HONGLEI ZHANG and XIAOGUANG HE. CircRNA-associated ceRNA network reveals ErbB and Hippo signaling pathways in hypopharyngeal cancer. INTERNATIONAL JOURNAL OF MOlecular medicine 43: 127-142, 2019; DOI: 10.3892/ijmm.2018.3942.