ArticleScientific reports2015
Bridging topological and functional information in protein interaction networks by short loops profiling.
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 9 papers.
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Who cites it
9 citing papers in PubMed.
- Presurgical immune biomarkers associated with pain intensity and pain interference recovery after total knee arthroplasty: findings from the PRIME-KNEE study.medRxiv : the preprint server for health sciences · 2026Article
- Data-dependent visualization of biological networks in the web-browser with NDExEdit.PLoS computational biology · 2022Article
- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks.NAR genomics and bioinformatics · 2021Article
- Functional homogeneity and specificity of topological modules in human proteome.BMC bioinformatics · 2019Article
- Article
- PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks.Bioinformatics (Oxford, England) · 2016Article
- Thermodynamic measures of cancer: Gibbs free energy and entropy of protein-protein interactions.Journal of biological physics · 2016Article
- IRES-dependent translated genes in fungi: computational prediction, phylogenetic conservation and functional association.BMC genomics · 2015Article
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Authors and funding
6 authors.
Funding
Abstract
Protein-protein interaction networks (PPINs) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. In this study we identify fundamental principles of PPIN topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. We compared 30 PPINs with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-validated high-confidence dataset of 622 human protein complexes. We demonstrate that loops are an intrinsic feature of PPINs and that specific cell functions are predominantly performed by loops of different lengths. Topologically, we find that loops are strongly related to the accuracy of PPINs and define a core of interactions with high resilience. The identification of this core and the analysis of loop composition are promising tools to assess PPIN quality and to uncover possible biases from experimental detection methods. More than 96% of loops share at least one biological function, with enrichment of cellular functions related to mRNA metabolic processing and the cell cycle. Our analyses suggest that these motifs can be used in the design of targeted experiments for functional phenotype detection.
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