ArticleScientific reports2015
Module organization and variance in protein-protein interaction networks.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
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- Integrating protein interaction and pathway crosstalk network reveals a promising therapeutic approach for psoriasis through apoptosis induction.Scientific reports · 2024Article
- Inference of single-cell network using mutual information for scRNA-seq data analysis.BMC bioinformatics · 2024Article
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- SWEET: a single-sample network inference method for deciphering individual features in disease.Briefings in bioinformatics · 2023Article
- Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View.Genes · 2022Review
- Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data.Scientific reports · 2021Article
- Highly heterogeneous-related genes of triple-negative breast cancer: potential diagnostic and prognostic biomarkers.BMC cancer · 2021Article
- Systemic Bioinformatic Analyses of Nuclear-Encoded Mitochondrial Genes in Hypertrophic Cardiomyopathy.Frontiers in genetics · 2021Article
- Membrane protein-regulated networks across human cancers.Nature communications · 2019Article
- Functional homogeneity and specificity of topological modules in human proteome.BMC bioinformatics · 2019Article
- Mutational Pleiotropy and the Strength of Stabilizing Selection Within and Between Functional Modules of Gene Expression.Genetics · 2018Article
- Analysis of protein-protein interaction network based on transcriptome profiling of ovine granulosa cells identifies candidate genes in cyclic recruitment of ovarian follicles.Journal of animal science and technology · 2018Article
- Introducing Potential Key Proteins and Pathways in Human Laryngeal Cancer: A System Biology Approach.Iranian journal of pharmaceutical research : IJPR · 2018Article
- Functional diversity of topological modules in human protein-protein interaction networks.Scientific reports · 2017Article
- PTIR: Predicted Tomato Interactome Resource.Scientific reports · 2016Article
- Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules.BMC bioinformatics · 2016Article
- Mining Temporal Protein Complex Based on the Dynamic PIN Weighted with Connected Affinity and Gene Co-Expression.PloS one · 2016Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A module is a group of closely related proteins that act in concert to perform specific biological functions through protein-protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores and interface evolution scores to describe the module elements, including core and ring components. Functions of core components were highly correlated with those of essential genes. In comparison with ring components, core proteins/PPIs were conserved across multiple species. Subsequently, protein/module variance of PPI networks confirmed that core components form dynamic network hubs and play key roles in various biological functions. Based on the analyses of gene essentiality, module variance, and gene co-expression, we summarize the observations of module organization and variance as follows: 1) a module consists of core and ring components; 2) core components perform major biological functions and collaborate with ring components to execute certain functions in some cases; 3) core components are more conserved and essential during organizational changes in different biological states or conditions.
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