Search results for "interaction network"
showing 10 items of 39 documents
Topological structure analysis of chromatin interaction networks.
2019
Abstract Background Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify biologically significant features, many questions still remain open, in particular regarding potential biological significance of various topological features that are characteristic for chromatin interaction networks. Results It has been previously observed that promoter capture Hi-C (PCHi-C) interaction networks tend to separate easily into well-defined connected components that can be related to certain biological functionality, however, …
An evolutionary restricted neighborhood search clustering approach for PPI networks
2014
Protein-protein interaction networks have been broadly studied in the last few years, in order to understand the behavior of proteins inside the cell. Proteins interacting with each other often share common biological functions or they participate in the same biological process. Thus, discovering protein complexes made of a group of proteins strictly related can be useful to predict protein functions. Clustering techniques have been widely employed to detect significant biological complexes. In this paper, we integrate one of the most popular network clustering techniques, namely the Restricted Neighborhood Search Clustering (RNSC), with evolutionary computation. The two cost functions intr…
MIPPIE: the mouse integrated protein–protein interaction reference
2020
Abstract Cells operate and react to environmental signals thanks to a complex network of protein–protein interactions (PPIs), the malfunction of which can severely disrupt cellular homeostasis. As a result, mapping and analyzing protein networks are key to advancing our understanding of biological processes and diseases. An invaluable part of these endeavors has been the house mouse (Mus musculus), the mammalian model organism par excellence, which has provided insights into human biology and disorders. The importance of investigating PPI networks in the context of mouse prompted us to develop the Mouse Integrated Protein–Protein Interaction rEference (MIPPIE). MIPPIE inherits a robust infr…
Network Physiology of Cortico–Muscular Interactions
2020
Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure a…
Impact of parasitoid-associated polydnaviruses on plant-mediated herbivore interactions
2022
Insect herbivores interact via plant-mediated interactions in which one herbivore species induces changes in plant quality that affects the performance of a second phytophagous insect that shares the food plant. These interactions are often asymmetric due to specificity in induced plant responses to herbivore attack, amount of plant damage, elicitors in herbivore saliva and plant organ damaged by herbivores. Parasitoids and their symbiotic polydnaviruses alter herbivore physiology and behaviour and may influence how plants respond to parasitized herbivores. We argue that these phenomena affect plant-mediated interactions between herbivores. We identify that the extended phenotype of parasit…
Unveiling the molecular basis of disease co-occurrence: towards personalized comorbidity profiles
2018
AbstractComorbidity is an impactful medical problem that is attracting increasing attention in healthcare and biomedical research. However, little is known about the molecular processes leading to the development of a specific disease in patients affected by other conditions. We present a disease interaction network inferred from similarities in patients’ molecular profiles, which significantly recapitulates epidemiologically documented comorbidities, providing the basis for their interpretation at a molecular level. Furthermore, expanding on the analysis of subgroups of patients with similar molecular profiles, our approach discovers comorbidity relations not previously described, implicat…
Changes in the proteome of sea urchin Paracentrotus lividus coelomocytes in response to LPS injection into the body cavity.
2020
Background The immune system of echinoderm sea urchins is characterised by a high degree of complexity that is not completely understood. The Mediterranean sea urchin Paracentrotus lividus coelomocytes mediate immune responses through phagocytosis, encapsulation of non-self particles, and production of diffusible factors including antimicrobial molecules. Details of these processes, and molecular pathways driving these mechanisms, are still to be fully elucidated. Principal findings In the present study we treated the sea urchin P. lividus with the bacterial lipopolysaccharide (LPS) and collected coelomocytes at different time-points (1, 3, 6 and 24 hours). We have shown, using label-free q…
Identification of Key miRNAs in Regulation of PPI Networks
2020
In this paper, we explore the interaction between miRNA and deregulated proteins in some pathologies. Assuming that miRNA can influence mRNA and consequently the proteins regulation, we explore this connection by using an interaction matrix derived from miRNA-target data and PPI network interactions. From this interaction matrix and the set of deregulated proteins, we search for the miRNA subset that influences the deregulated proteins with a minimum impact on the not deregulated ones. This regulation problem can be formulated as a complex optimization problem. In this paper, we have tried to solve it by using the Genetic Algorithm Heuristic. As the main result, we have found a set of miRNA…
Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods
2014
Abstract Motivation: Protein–protein interaction (PPI) networks are powerful models to represent the pairwise protein interactions of the organisms. Clustering PPI networks can be useful for isolating groups of interacting proteins that participate in the same biological processes or that perform together specific biological functions. Evolutionary orthologies can be inferred this way, as well as functions and properties of yet uncharacterized proteins. Results: We present an overview of the main state-of-the-art clustering methods that have been applied to PPI networks over the past decade. We distinguish five specific categories of approaches, describe and compare their main features and …
Complex Detection in Protein-Protein Interaction Networks: A Compact Overview for Researchers and Practitioners
2012
The availability of large volumes of protein-protein interaction data has allowed the study of biological networks to unveil the complex structure and organization in the cell. It has been recognized by biologists that proteins interacting with each other often participate in the same biological processes, and that protein modules may be often associated with specific biological functions. Thus the detection of protein complexes is an important research problem in systems biology. In this review, recent graph-based approaches to clustering protein interaction networks are described and classified with respect to common peculiarities. The goal is that of providing a useful guide and referenc…