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Published on: October 19, 2021
POINeT: protein interactome with sub-network analysis and hub prioritization
Sheng-An Lee1, Chen-Hsiung Chan, Tzu-Chi Chen
1Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan, ROC. d93922005@ntu.edu.tw
BMC Bioinformatics
|April 22, 2009
Summary
POINeT is a new web service that simplifies protein-protein interaction (PPI) network analysis by integrating PPI and tissue-specific expression data. This tool helps identify novel gene markers, such as EXOC4 for schizophrenia, and reveals tissue-specific interactions.
Area of Science:
- Bioinformatics
- Systems Biology
- Computational Biology
Background:
- Protein-protein interactions (PPIs) are fundamental to biological processes.
- Existing PPI network analysis tools often lack spatiotemporal context and face challenges with data reliability.
- An integrated tool is needed to streamline PPI querying and analysis across multiple resources.
Purpose of the Study:
- To develop POINeT, an integrated web service for simplified PPI searching, analysis, and visualization.
- To merge PPI data with tissue-specific expression profiles for context-aware network construction.
- To enhance the identification and ranking of potential novel genes within biological networks.
Main Methods:
- Constructed an integrated web service, POINeT, merging PPI and tissue-specific expression data.
- Implemented user-adjustable filters for tissue-specific PPIs and supporting evidence.
- Integrated network analysis modules, including centrality calculations and a ranking-filtered method (S3).
Main Results:
- POINeT simplifies the process of searching, analyzing, and visualizing PPI networks.
- Tissue-specific PPIs and supporting evidence can be filtered and dynamically updated.
- Analysis of schizophrenia risk markers using POINeT suggested EXOC4 as a potential novel marker.
- A liver-specific PPI network was successfully filtered using adult and fetal liver expression profiles.
Conclusions:
- POINeT offers significantly improved functionalities for PPI network analysis compared to previous versions.
- The tool enables the identification and ranking of potential novel genes in sub-networks.
- Combining POINeT with tissue-specific expression data reveals tissue-specific PPIs.
- POINeT provides a user-friendly interface for efficient PPI search and analysis.
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