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Published on: May 22, 2018
Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology
Chung-Yen Lin1, Chia-Hao Chin, Hsin-Hung Wu
1Institute of Information Science, Academia Sinica, No. 128 Yan-Chiu-Yuan Rd., Sec. 2, Taipei 115, Taiwan.
Nucleic Acids Research
|May 27, 2008
Summary
Hubba identifies essential nodes in biological networks using graph theory. This tool helps discover potential drug targets for diseases by analyzing protein interactions from high-throughput experiments.
Area of Science:
- Bioinformatics
- Systems Biology
- Network Biology
Background:
- Reconstructing proteomic and genomic networks is crucial in the post-genome era.
- Identifying essential nodes (hubs) is key to understanding complex biological pathways and networks.
- These hubs can serve as potential drug targets for diseases like cancer and infectious diseases.
Purpose of the Study:
- To introduce Hub Objects Analyzer (Hubba), a web service for exploring essential nodes in interactome networks.
- To present two novel algorithms, Maximum Neighborhood Component (MNC) and Density of Maximum Neighborhood Component (DMNC), for hub identification.
- To provide a user-friendly platform for analyzing interaction data from various experimental methods.
Main Methods:
- Utilized graph theory to analyze interactome networks.
- Developed and implemented MNC and DMNC algorithms for hub detection.
- Enabled users to submit interaction data in PSI, tab, or tab-with-weights formats.
- Provided email notifications upon completion of analysis, with processing times varying by dataset size.
Main Results:
- Hubba provides a ranked list of essential nodes based on a composite index.
- Results include a manifest graph visualizing hub relationships and links to output files.
- The DMNC || MNC method successfully identified previously unrecognized hubs.
- Validation on yeast protein interactome data showed high accuracy, with 80% of top 10 hubs and over 70% of top 40 hubs reported as essential proteins.
Conclusions:
- Hubba is an effective web-based service for identifying essential nodes in biological networks.
- The developed algorithms (DMNC || MNC) offer a robust approach to discovering critical network components.
- Hubba's topology-based analysis is applicable to diverse biological networks across species.
- The identified hubs represent potential therapeutic targets for human diseases.
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