PPI Network Analysis



The protein-protein interaction network (PPI network) is composed of proteins that interact with each other to participate in all aspects of life processes such as biological signal transmission, energy and material metabolism, gene expression regulation, and cell cycle regulation. Systematic analysis of the interaction of a large number of proteins in biological systems is meaningful 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. In the field of biomedicine, it is helpful to study the molecular mechanism of diseases from a systematic perspective, discover new drug targets, and so on.

An Example of PPI Network Analysis Result

Visualization of protein interaction networks using Reactome plugin in Cytoscape, and the Cathepsin proteases are enriched and form a sub-network.Fig 1. Visualization of protein interaction networks using Reactome plugin in Cytoscape, and the Cathepsin proteases are enriched and form a sub-network. (Lahiru G, et al. 2015)

What We Offer

As one of the global biological information analysis service providers, CD Genomics  provides established, cost-efficient, and rapid turnaround PPI network analysis services for doctors and researchers, aiming to help researchers or doctors study molecular mechanisms of diseases and discover new drug targets from a systematic perspective. CD Genomics provides different software such as Cytoscape, Osprey, PIN, pajek, and other cutting-edge software to perform PPI network analysis and visual analysis for researchers to meet the personalized needs. In addition, you only need to provide us with your original data or data analysis requirements. We will be responsible for all the follow-up matters of the project, and finally provide you with a complete and easy-to-interpret analysis result. We will generate high-quality charts that can be directly used for publication. 

Data Analysis Technical Route

A flow chart showing PPI network analysisFig 2. A flow chart showing PPI network analysis.

PPI Network Analysis Process

1. The STRING database is a commonly used protein interaction network database. It contains predicted and experimentally verified protein-protein interactions from multiple species, including direct physical interactions and indirect functional correlations. Combining the differential expression analysis results and the interaction relationship pairs included in the database, a differentially expressed protein interaction network can be constructed. During the analysis process, the differentially expressed proteins are mapped to the STRING database to obtain information about the interaction relationship of the differentially expressed proteins. Because the STING database contains experimental data, the results of text mining from PubMed abstracts, and the synthesis of other database data, there are also results predicted by bioinformatics methods.

2. Select suitable protein pairs from the above search results, and use appropriate bioinformatics analysis software (such as Cytoscape) to visually analyze the interaction results, and finally generate an intuitive protein interaction network result graph.

3. MCL clustering of proteins with similar functions.

4. Protein function annotation analysis.

Service Process

Before data analysis, the first thing is to get your data ready. For PPI network analysis, the raw input data can be protein sequencing raw data or target protein file, and we will provide appropriate data analysis services based on your data. Our service process is as follows:

  • Upload protein sequencing raw data or target protein file

  • Develop an analysis plan

  • PPI network analysis

  • Generate charts

  • After-sales service

For PPI network analysis, if you have any questions about the data analysis cycle, analysis content and price, please click online inquiry.

What's More 

Biomedical-Bioinformatics, as a division of CD Genomics, provides a one-stop PPI network analysis service for biomedical researchers. With years of experience in biological data analysis, CD Genomics' analysis engineers will provide you with the most appropriate analysis strategy based on your data, and generate high-quality results and charts that can be used for publication. For more detailed information about our data analysis services, please feel free to contact us.


  1. Lahiru G, et al. Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin[J]. Oncotarget. 2015 May 10; 6(13): 11175–11190.
  2.  Athanasios A, et al. Protein-Protein Interaction (PPI) Network: Recent Advances in Drug Discovery[J]. Curr Drug Metab. 2017;18(1):5-10.

* For research use only. Not for use in clinical diagnosis or treatment of humans or animals.

Online Inquiry

Please submit a detailed description of your project. Our industry-leading scientists will review the information provided as soon as possible. You can also send emails directly to for inquiries.