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Inducible LAP-tagged Stable Cell Lines for Investigating Protein Function, Spatiotemporal Localization and Protein Interaction Networks
Published on: December 24, 2016
Global versus local hubs in human protein-protein interaction network
Manjari Kiran1, Hampapathalu Adimurthy Nagarajaram
1Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics , Bldg.7, Gruhakalpa, Nampally, Hyderabad 500 001, Andhra Pradesh, India.
Journal of Proteome Research
|September 21, 2013
Summary
Researchers classified protein hubs into tissue-specific (TSHs), tissue-preferred (TPHs), and housekeeping (HKHs) based on expression breadth. TSHs, distinct from HKHs, are involved in tissue-specific functions and evolve rapidly.
Area of Science:
- Systems Biology
- Network Biology
- Proteomics
Background:
- Protein-protein interaction (PPI) networks are crucial for understanding cellular functions.
- Identifying hub proteins within these networks is key to deciphering biological processes.
- Previous classifications often overlook expression breadth and tissue specificity.
Purpose of the Study:
- To construct and analyze tissue-specific PPI networks for 70 human tissues.
- To classify hub proteins into three categories based on expression breadth: tissue-specific hubs (TSHs), tissue-preferred hubs (TPHs), and housekeeping hubs (HKHs).
- To compare the properties and functions of these distinct hub types.
Main Methods:
- Construction of 70 human tissue-specific PPI networks.
- Identification and classification of hub proteins based on expression breadth (≤10 tissues for TSHs, ≥60 tissues for TPHs/HKHs) and connectivity.
- Comparative analysis of protein properties (length, disorder, evolution rate, centrality, PEST motifs) and functional roles.
Main Results:
- Three distinct hub categories were identified: TSHs (≤10 tissues), TPHs (≥60 tissues, low connectivity), and HKHs (≥60 tissues, high connectivity).
- TSHs are longer, more disordered, rapidly evolving, and less connected than HKHs, with distinct tissue-specific functions (e.g., receptors, signaling).
- TPHs exhibit properties more similar to HKHs, involved in core cellular functions (e.g., transcription, translation).
Conclusions:
- Expression breadth is a significant factor in classifying hub proteins and understanding their distinct roles.
- TSHs represent a unique class of hubs involved in specialized functions and exhibit unique evolutionary and regulatory characteristics.
- This classification provides a new perspective on protein hub diversity and function, potentially informing the 'date' vs. 'party' hub debate.
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