Protein interaction networks

Ebook "Proteomics and protein-protein interactions: Biology, chemistry, bioinformatics, and drug design" attempts to bridge the two extreme ends of protein science: on one end, systems proteomics, which describes, at a system level, the intricate connection network that proteins form in a cell, and on the other end, protein chemistry and biophysics, which describe the molecular properties of individual proteins and the structural and thermodynamic basis of their interactions within the network.

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Ebook "Power laws, scale-free networks and genome biology" deals with crucial aspects of the theoretical foundations of systems biology, namely power law distributions and scale-free networks which have emerged as the hallmarks of biological organization in the post-genomic era. The chapters in the book not only describe the interesting mathematical properties of biological networks but moves beyond phenomenology, toward models of evolution capable of explaining the emergence of these features.

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Cerebral amyloidosis, neuroinflammation, and tauopathy are key features of Alzheimer’s disease (AD), but interactions among these features remain poorly understood. Our previous multiscale molecular network models of AD revealed TYROBP as a key driver of an immune- and microglia-specific network that was robustly associated with AD pathophysiology.

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The bromodomain containing 1 (BRD1) gene has been implicated with transcriptional regulation, brain development, and susceptibility to schizophrenia and bipolar disorder. To advance the understanding of BRD1 and its role in mental disorders, we characterized the protein and chromatin interactions of the BRD1 isoforms, BRD1-S and BRD1-L.

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Basal cell carcinoma (BCC) of the skin is the most common form of human cancer, with more than 90% of tumours presenting with clear genetic activation of the Hedgehog pathway. However, polygenic risk factors affecting mechanisms such as DNA repair and cell cycle checkpoints or which modulate the tumour microenvironment or host immune system play significant roles in determining whether genetic mutations culminate in BCC development.

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Medulloblastoma (MB) is the most common malignant paediatric brain tumour and a leading cause of cancer-related mortality and morbidity. Existing treatment protocols are aggressive in nature resulting in significant neurological, intellectual and physical disabilities for the children undergoing treatment. Thus, there is an urgent need for improved, targeted therapies that minimize these harmful side effects.

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In ebook "Molecular aspects of the stress response: Chaperones, membranes and networks (Advances in experimental medicine and biology, Volume 594)" the reader will learn the role of chaperone classes such as Hsp27 or Hsp90, the action of highly organized chaperone networks in various cellular compartments such as the ER or mitochondrial/ER networks as well as the molecular details of the signaling mechanisms leading to chaperone induction during stress.

218p tachieuhoa 28-01-2024 3 2   Download

TAP1 is an immunomodulation-related protein that plays different roles in various malignancies. This study investigated the transcriptional expression profile of TAP1 in uveal melanoma (UVM), revealed its potential bio-logical interaction network, and determined its prognostic value.

14p vischultz 20-10-2023 2 1   Download

The aspirin compound (AC) is commonly found to have a wide range of pharmacological activities. This study aimed to investigate the underlying mechanism of the anti-osteoporotic (anti-OP) activity of AC using network pharmacology and molecular docking approaches. First, AC targets were identified using the GeneCards database, and second, OP-related targets were mined using a combination of the GeneCards and DisGeNet databases.

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Lung cancer is the most common malignant tumor, and it has a high mortality rate. However, the study of miRNA-mRNA regulatory networks in the plasma of patients with non-small cell lung cancer (NSCLC) is insufficient.

23p vikolindagrabar 27-07-2022 2 1   Download

The relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated systems-level analysis of brain gene expression data to identify molecular networks disrupted in epilepsy

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Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin assortativity, to integrate the epigenomic landscape of a specific cell type with its chromatin interaction network and thus investigate which proteins or chromatin marks mediate genomic contacts.

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3′-Untranslated regions (3′UTRs) play crucial roles in mRNA metabolism, such as by controlling mRNA stability, translation efficiency, and localization. Intriguingly, in some genes the 3′UTR is longer than their coding regions, pointing to additional, unknown functions.

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Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerating the development of precision cancer medicine protocols.

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Identifying or prioritizing genes for chronic obstructive pulmonary disease (COPD), one type of complex disease, is particularly important for its prevention and treatment. Methods: In this paper, a novel method was proposed to Prioritize genes using Expression information in Protein– protein interaction networks with disease risks transferred between genes (abbreviated as PEP).

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To identify candidate key genes and pathways related to resting mast cells in meningioma and the underlying molecular mechanisms of meningioma. Gene expression profiles of the used microarray datasets were obtained from the Gene Expression Omnibus (GEO) database.

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Pulmonary arterial hypertension (PH) secondary to pulmonary fbrosis (PF) is one of the most common complications in PF patients, it causes severe disease and usually have a poor prognosis. Whether the combination of PH and PF is a unique disease phenotype is unclear.

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Knowledge of the pathogen-host interactions between the species is essentialin order to develop a solution strategy against infectious diseases. In vitro methods take extended periods of time to detect interactions and provide very few of the possible interaction pairs. Hence, modelling interactions between proteins has necessitated the development of computational methods. The main scope of this paper is integrating the known protein interactions between thehost and pathogen organisms to improve the prediction success rate of unknown pathogen-host interactions.

11p thiencuuchu 27-11-2021 11 1   Download

Polyhydroxyalkanoate (PHA) is stored as an important carbon and energy source in bacterial cells. For biomedical applications, gram-positive bacteria can be better sources of PHAs, since they lack outer membrane lipopolysaccharide. Although gram-positive Streptomyces coelicolor A3(2) has been indicated as a high potential PHA producer, phaC gene that encodes the key enzyme PHA synthase in the metabolic pathway is not determined in its genome.

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Recently, researchers have tried to integrate various dynamic information with static protein-protein interaction (PPI) networks to construct dynamic PPI networks. The shift from static PPI networks to dynamic PPI networks is essential to reveal the cellular function and organization. However, it is still impossible to construct an absolutely reliable dynamic PPI networks due to the noise and incompletion of high-throughput experimental data.

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