PPI analysis (GeNets database)

created at 06-28-2021 views: 4

Protein-protein interaction network

Protein-Protein Interaction Networks (PPI) are composed of proteins that interact with each other to participate in all aspects of life processes such as biological signal transmission, gene expression regulation, energy and material metabolism, and cell cycle regulation. Systematic analysis of the interaction relationship between a large number of proteins in biological systems is useful for understanding the working principles of proteins in biological systems, understanding the reaction mechanism of biological signals and energy substance metabolism under special physiological conditions such as diseases, and understanding the functional connections between proteins Significance.

Commonly used PPI analysis databases include STRING and bioGRID, but their functions also have certain limitations during analysis.

The database name used in this article is called GeNets. This database can analyze the differential genes through machine learning methods to find their key genes and signal pathways; it can also cluster the differential genes found by clustering.

plot

1. Open and register GeNets

2. Import data

3. start plot

4. Adjustment

Remove the Not Assigned gene.

1. Download node information data

2. Delete the Not Assigned gene

3.Paste the remaining genes back and re-analyze.

5. Set up and export

Set the picture. Everyone will know what each project means by doing it. I won’t go into details here. I will talk about the details in the video later.

6. understand the diagram

For protein interaction network diagram:

  • Nodes represent proteins,
  • lines between nodes indicates that there is an interaction between proteins,
  • The color of the node indicates the clustering of genes
  • The color of the line reflects the type of interaction, including experimentally verified or predicted, as well as direct physical interaction, co-expression, gene fusion and other relationships.
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