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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Understanding protein evolutionary rate by integrating gene co-expression with protein interactions
Kaifang Pang1, Chao Cheng, Zhenyu Xuan
1Department of Computer Science and Engineering, Shanghai Jiao Tong University, China.
BMC Systems Biology
|December 31, 2010
Summary
The study introduces co-expressed protein-protein interaction degree (ePPID) as a superior predictor of protein evolutionary rate compared to traditional protein-protein interaction degree (PPID). ePPID accounts for permanent interactions, offering a more robust measure independent of experimental methods.
Area of Science:
- Evolutionary Biology
- Systems Biology
- Bioinformatics
Background:
- Protein evolutionary rate is influenced by various factors, with protein-protein interaction degree (PPID) being a key area of investigation.
- The precise impact of PPID on protein evolution remains debated, partly due to inconsistencies across different protein interaction datasets and experimental methods.
Purpose of the Study:
- To develop a more accurate and robust measure of protein-protein interactions that better predicts protein evolutionary rates.
- To resolve the inconsistencies in previous studies by integrating diverse data types.
Main Methods:
- Integrated protein interaction data with gene co-expression data to derive a novel metric: co-expressed protein-protein interaction degree (ePPID).
- Compared the predictive power and robustness of ePPID against traditional PPID for protein evolutionary rates.
- Analyzed hub proteins within the Structural Interaction Network to validate findings.
Main Results:
- ePPID proved to be a better and more robust predictor of protein evolutionary rate than PPID, irrespective of the experimental method used.
- The influence of ePPID on evolutionary rate was found to be statistically independent of protein expression levels.
- Co-expressed multi-interface hub proteins exhibit slower evolution compared to other hub proteins.
Conclusions:
- Established ePPID as a reliable predictor for protein evolutionary rate, overcoming limitations of previous PPID measures.
- Highlighted the significance of permanent protein interactions in shaping evolutionary trajectories.
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