Functional geometry of protein interactomes
Visualitza/Obre
10.1093/bioinformatics/btz146
Inclou dades d'ús des de 2022
Cita com:
hdl:2117/187923
Tipus de documentArticle
Data publicació2019-10-01
EditorOxford University Press (OUP)
Condicions d'accésAccés obert
Tots els drets reservats. Aquesta obra està protegida pels drets de propietat intel·lectual i
industrial corresponents. Sense perjudici de les exempcions legals existents, queda prohibida la seva
reproducció, distribució, comunicació pública o transformació sense l'autorització del titular dels drets
Abstract
Motivation
Protein–protein interactions (PPIs) are usually modeled as networks. These networks have extensively been studied using graphlets, small induced subgraphs capturing the local wiring patterns around nodes in networks. They revealed that proteins involved in similar functions tend to be similarly wired. However, such simple models can only represent pairwise relationships and cannot fully capture the higher-order organization of protein interactomes, including protein complexes.
Results
To model the multi-scale organization of these complex biological systems, we utilize simplicial complexes from computational geometry. The question is how to mine these new representations of protein interactomes to reveal additional biological information. To address this, we define simplets, a generalization of graphlets to simplicial complexes. By using simplets, we define a sensitive measure of similarity between simplicial complex representations that allows for clustering them according to their data types better than clustering them by using other state-of-the-art measures, e.g. spectral distance, or facet distribution distance. We model human and baker’s yeast protein interactomes as simplicial complexes that capture PPIs and protein complexes as simplices. On these models, we show that our newly introduced simplet-based methods cluster proteins by function better than the clustering methods that use the standard PPI networks, uncovering the new underlying functional organization of the cell. We demonstrate the existence of the functional geometry in the protein interactome data and the superiority of our simplet-based methods to effectively mine for new biological information hidden in the complexity of the higher-order organization of protein interactomes.
CitacióMalod Dognin, N.; Pržulj, N. Functional geometry of protein interactomes. "Bioinformatics", 1 Octubre 2019, vol. 35, núm. 19, p. 3727-3734.
ISSN1460-2059
1367-4803
1367-4803
Col·leccions
Fitxers | Descripció | Mida | Format | Visualitza |
---|---|---|---|---|
malod-dognin2019.pdf | 2,000Mb | Visualitza/Obre |