Systems biology approach for gene set enrichment and topological analysis of Alzheimer's disease pathway

Author(s):  
Ashwani Kumar ◽  
Tiratha Raj Singh
2021 ◽  
Author(s):  
Jordan Bryan ◽  
Arpita Mandan ◽  
Gauri Kamat ◽  
W. Kirby Gottschalk ◽  
Alexandra Badea ◽  
...  

2020 ◽  
Vol 75 (2) ◽  
pp. 531-545 ◽  
Author(s):  
Bo-Hyun Kim ◽  
Yong-Ho Choi ◽  
Jin-Ju Yang ◽  
SangYun Kim ◽  
Kwangsik Nho ◽  
...  

2010 ◽  
Vol 98 (3) ◽  
pp. 738a ◽  
Author(s):  
Christina R. Kyrtsos ◽  
John S. Baras

2006 ◽  
Vol 14 (7S_Part_19) ◽  
pp. P1015-P1015
Author(s):  
Benjamin A. Logsdon ◽  
Thanneer M. Perumal ◽  
Kenneth Daily ◽  
Solveig K. Sieberts ◽  
Larsson Omberg ◽  
...  

2019 ◽  
Vol 15 ◽  
pp. P612-P613
Author(s):  
Christoph Preuss ◽  
Ravi S. Pandey ◽  
Alexander Fine ◽  
Asli Uyar ◽  
Benjamin A. Logsdon ◽  
...  

2020 ◽  
Vol 21 (6) ◽  
pp. 2071 ◽  
Author(s):  
Jia Xu ◽  
Fang Wang ◽  
Jiejie Guo ◽  
Chunshuang Xu ◽  
Yanzi Cao ◽  
...  

Alpinia oxyphylla Miq. (i.e., A. oxyphylla), a traditional Chinese medicine, can exert neuroprotective effects in ameliorating mild cognitive impairment and improving the pathological hallmarks of Alzheimer’s disease (AD). Here, 50 active compounds and 164 putative targets were collected and identified with 251 clinically tested AD-associated target proteins using network pharmacology approaches. Based on the Gene Ontology/Kyoto Encyclopedia of Genes and Genomes pathway enrichments, the compound-target-pathway-disease/protein–protein interaction network constructions, and the network topological analysis, we concluded that A. oxyphylla may have neuroprotective effects by regulating neurotransmitter function, as well as brain plasticity in neuronal networks. Moreover, closely-related AD proteins, including the amyloid-beta precursor protein, the estrogen receptor 1, acetylcholinesterase, and nitric oxide synthase 2, were selected as the bottleneck nodes of network for further verification by molecular docking. Our analytical results demonstrated that terpene, as the main compound of A. oxyphylla extract, exerts neuroprotective effects, providing new insights into the development of a natural therapy for the prevention and treatment of AD.


2013 ◽  
Vol 11 (05) ◽  
pp. 1342003 ◽  
Author(s):  
CHRISTINA ROSE KYRTSOS ◽  
JOHN S. BARAS

Alzheimer's disease (AD) is the most common form of dementia. Even with its well-known symptoms of memory loss and well-characterized pathology of beta amyloid (Aβ) plaques and neurofibrillary tangles, the disease pathogenesis and initiating factors are still not well understood. To tackle this problem, a systems biology model has been developed and used to study the varying effects of variations in the ApoE allele present, as well as the effects of short term and periodic inflammation at low to moderate levels. Simulations showed a late onset peak of Aβ in the ApoE4 case that lead to localized neuron loss which could be ameliorated in part by application of short-term pro-inflammatory mediators. The model that has been developed herein represents one of the first attempts to model AD from a systems approach to study physiologically relevant parameters that may prove useful to physicians in the future.


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