ArticlePLoS computational biology2013
From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Inferring cell developmental stage-specific lncRNA regulation in the developing human neocortex with CDSlncR.Frontiers in molecular neuroscience · 2022Article
- Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data.BMC bioinformatics · 2021Article
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- A Molecular Interaction Map ofFrontiers in microbiology · 2021Article
- Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases.In silico biology · 2021Article
- Link clustering explains non-central and contextually essential genes in protein interaction networks.Scientific reports · 2019Article
- Collective influencers in protein interaction networks.Scientific reports · 2019Article
- Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs.Frontiers in plant science · 2018Review
- Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA.Journal of chemical information and modeling · 2016Article
- Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks.BMC bioinformatics · 2016Article
- PTIR: Predicted Tomato Interactome Resource.Scientific reports · 2016Article
- Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network.Scientific reports · 2016Article
- Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics.Frontiers in bioengineering and biotechnology · 2016Article
- Graph theoretic network analysis reveals protein pathways underlying cell death following neurotropic viral infection.Scientific reports · 2015Article
- Determining minimum set of driver nodes in protein-protein interaction networks.BMC bioinformatics · 2015Article
- Essentiality and centrality in protein interaction networks revisited.BMC bioinformatics · 2015Article
- Identification of important interacting proteins (IIPs) in Plasmodium falciparum using large-scale interaction network analysis and in-silico knock-out studies.Malaria journal · 2015Article
- What makes a RAG regeneration associated?Frontiers in molecular neuroscience · 2015Review
- Article
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2 authors.
Funding
Abstract
Numerous studies have suggested that hub proteins in the S. cerevisiae physical interaction network are more likely to be essential than other proteins. The proposed reasons underlying this observed relationship between topology and functioning have been subject to some controversy, with recent work suggesting that it arises due to the participation of hub proteins in essential complexes and processes. However, do these essential modules themselves have distinct network characteristics, and how do their essential proteins differ in their topological properties from their non-essential proteins? We aimed to advance our understanding of protein essentiality by analyzing proteins, complexes and processes within their broader functional context and by considering physical interactions both within and across complexes and biological processes. In agreement with the view that essentiality is a modular property, we found that the number of intracomplex or intraprocess interactions that a protein has is a better indicator of its essentiality than its overall number of interactions. Moreover, we found that within an essential complex, its essential proteins have on average more interactions, especially intracomplex interactions, than its non-essential proteins. Finally, we built a module-level interaction network and found that essential complexes and processes tend to have higher interaction degrees in this network than non-essential complexes and processes; that is, they exhibit a larger amount of functional cross-talk than their non-essential counterparts.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.