ArticleBMC bioinformatics2009
Core and periphery structures in protein interaction networks.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 66 citations in OpenAlex.
- Core-Periphery Multi-Modality Feature Alignment for Zero-Shot Medical Image Analysis.IEEE transactions on medical imaging · 2025Article
- 'Intelligent' proteins.Cellular and molecular life sciences : CMLS · 2025Review
- Nucleation phenomena and extreme vulnerability of spatial k-core systems.Nature communications · 2024Article
- Dimensions of early life adversity and their associations with functional brain organisation.Imaging neuroscience (Cambridge, Mass.) · 2024Article
- Identifying protein complexes based on an edge weight algorithm and core-attachment structure.BMC bioinformatics · 2019Article
- Multiplex core-periphery organization of the human connectome.Journal of the Royal Society, Interface · 2018Article
- A graph modification approach for finding core-periphery structures in protein interaction networks.Algorithms for molecular biology : AMB · 2015Article
- Modelling the yeast interactome.Scientific reports · 2014Article
- Protein interaction networks as metric spaces: a novel perspective on distribution of hubs.BMC systems biology · 2014Article
- Coral: an integrated suite of visualizations for comparing clusterings.BMC bioinformatics · 2012Article
- Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks.BMC bioinformatics · 2012Article
- Functional annotation of hierarchical modularity.PloS one · 2012Article
- Robust detection of hierarchical communities from Escherichia coli gene expression data.PLoS computational biology · 2012Article
- DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules.BMC systems biology · 2011Article
- Evolution of a derived protein-protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Patterns of positive selection and neutral evolution in the protein-coding genes of Tetraodon and Takifugu.PloS one · 2011Article
- Recent advances in clustering methods for protein interaction networks.BMC genomics · 2010Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
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Abstract
backgroundCharacterizing the structural properties of protein interaction networks will help illuminate the organizational and functional relationships among elements in biological systems.
resultsIn this paper, we present a systematic exploration of the core/periphery structures in protein interaction networks (PINs). First, the concepts of cores and peripheries in PINs are defined. Then, computational methods are proposed to identify two types of cores, k-plex cores and star cores, from PINs. Application of these methods to a yeast protein interaction network has identified 110 k-plex cores and 109 star cores. We find that the k-plex cores consist of either "party" proteins, "date" proteins, or both. We also reveal that there are two classes of 1-peripheral proteins: "party" peripheries, which are more likely to be part of protein complex, and "connector" peripheries, which are more likely connected to different proteins or protein complexes. Our results also show that, besides connectivity, other variations in structural properties are related to the variation in biological properties. Furthermore, the negative correlation between evolutionary rate and connectivity are shown toysis. Moreover, the core/periphery structures help to reveal the existence of multiple levels of protein expression dynamics.
conclusionOur results show that both the structure and connectivity can be used to characterize topological properties in protein interaction networks, illuminating the functional organization of cellular systems.
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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.