ArticleScientific reports2014
Dissecting the human protein-protein interaction network via phylogenetic decomposition.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it, 39 citations in OpenAlex.
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
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- Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins.Genome biology · 2024Article
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- Discovery of disease- and drug-specific pathways through community structures of a literature network.Bioinformatics (Oxford, England) · 2020Article
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- The Protein-Protein Interaction Network ofFrontiers in physiology · 2019Article
- A Proteomic Network Approach across the Kidney Stone Disease Reveals Endoplasmic Reticulum Stress and Crystal-Cell Interaction in the Kidney.Oxidative medicine and cellular longevity · 2019Article
- Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant.Nucleic acids research · 2018Article
- How the evolution of multicellularity set the stage for cancer.British journal of cancer · 2018Review
- Non-interacting proteins may resemble interacting proteins: prevalence and implications.Scientific reports · 2017Article
- PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology.PloS one · 2017Article
- Information processing in the CNS: a supramolecular chemistry?Cognitive neurodynamics · 2015Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The protein-protein interaction (PPI) network offers a conceptual framework for better understanding the functional organization of the proteome. However, the intricacy of network complexity complicates comprehensive analysis. Here, we adopted a phylogenic grouping method combined with force-directed graph simulation to decompose the human PPI network in a multi-dimensional manner. This network model enabled us to associate the network topological properties with evolutionary and biological implications. First, we found that ancient proteins occupy the core of the network, whereas young proteins tend to reside on the periphery. Second, the presence of age homophily suggests a possible selection pressure may have acted on the duplication and divergence process during the PPI network evolution. Lastly, functional analysis revealed that each age group possesses high specificity of enriched biological processes and pathway engagements, which could correspond to their evolutionary roles in eukaryotic cells. More interestingly, the network landscape closely coincides with the subcellular localization of proteins. Together, these findings suggest the potential of using conceptual frameworks to mimic the true functional organization in a living cell.
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