ArticleBioinformatics (Oxford, England)2015
Topology-function conservation in protein-protein interaction networks.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 88 citations in OpenAlex.
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- SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment.NPJ systems biology and applications · 2022Article
- Linear functional organization of the omic embedding space.Bioinformatics (Oxford, England) · 2021Article
- Computationally Reconstructed Interactome ofInternational journal of molecular sciences · 2021Article
- Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates.Scientific reports · 2021Article
- Characterization of the Potential Role of NTPCR in Epithelial Ovarian Cancer by Integrating Transcriptomic and Metabolomic Analysis.Frontiers in genetics · 2021Article
- Prediction of Human-Bioinformatics and biology insights · 2021Article
- Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.BMC genomics · 2020Article
- Chromatin network markers of leukemia.Bioinformatics (Oxford, England) · 2020Article
- Functional geometry of protein interactomes.Bioinformatics (Oxford, England) · 2019Article
- Towards a data-integrated cell.Nature communications · 2019Article
- Network Medicine in the Age of Biomedical Big Data.Frontiers in genetics · 2019Review
- Higher-order molecular organization as a source of biological function.Bioinformatics (Oxford, England) · 2018Article
- Network enhancement as a general method to denoise weighted biological networks.Nature communications · 2018Article
- Overlapping functional modules detection in PPI network with pair-wise constrained non-negative matrix tri-factorisation.IET systems biology · 2018Article
- Grasping frequent subgraph mining for bioinformatics applications.BioData mining · 2018Review
- Functional diversity of topological modules in human protein-protein interaction networks.Scientific reports · 2017Article
- Identification of protein complexes by integrating multiple alignment of protein interaction networks.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationProteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species.
resultsTo improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms.
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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.