• Molecules and Cells
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• v.42 no.8
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• pp.579-588
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• 2019

Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. GSEA may be suboptimal for functional gene sets; however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. We also repurposed FDA-approved drugs using NGSEA and experimentally validated budesonide as a chemical with anti-cancer effects for colorectal cancer. We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. NGSEA is freely available at www.inetbio.org/ngsea.

• Genomics & Informatics
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• v.5 no.3
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• pp.133-136
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• 2007

The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.

• Genomics & Informatics
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• v.18 no.4
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• pp.39.1-39.8
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• 2020

Alzheimer's disease (AD) is a chronic, progressive brain disorder that slowly destroys affected individuals' memory and reasoning faculties, and consequently, their ability to perform the simplest tasks. This study investigated the hub genes of AD. Proteins interact with other proteins and non-protein molecules, and these interactions play an important role in understanding protein function. Computational methods are useful for understanding biological problems, in particular, network analyses of protein-protein interactions. Through a protein network analysis, we identified the following top 10 hub genes associated with AD: PTGER3, C3AR1, NPY, ADCY2, CXCL12, CCR5, MTNR1A, CNR2, GRM2, and CXCL8. Through gene enrichment, it was identified that most gene functions could be classified as integral to the plasma membrane, G-protein coupled receptor activity, and cell communication under gene ontology, as well as involvement in signal transduction pathways. Based on the convergent functional genomics ranking, the prioritized genes were NPY, CXCL12, CCR5, and CNR2.

• Journal of Digital Convergence
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• v.12 no.8
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• pp.423-430
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• 2014

The purpose of this article is to present the environmental enrichment(EE) method used to improve the functional recovery and change of brain plastic in animal experimental models of stroke. In animal experimental models of stroke, the environmental enrichment is effective in altering the morphological, biochemical and behavioral characteristics of the brain and thereby improving the functional outcomes. In this review article, we address the effects of EE in achieving a functional recovery in animal experimental models of stroke, thus attempting to describe them in patients with stroke from both occupational and rehabilitation perspectives.

• Genomics & Informatics
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• v.21 no.4
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• pp.45.1-45.11
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• 2023

Nonalcoholic fatty liver disease (NAFLD) is a common type of chronic liver disease, with severity levels ranging from nonalcoholic fatty liver to nonalcoholic steatohepatitis (NASH). The extent of liver fibrosis indicates the severity of NASH and the risk of liver cancer. However, the mechanism underlying NASH development, which is important for early screening and intervention, remains unclear. Weighted gene co-expression network analysis (WGCNA) is a useful method for identifying hub genes and screening specific targets for diseases. In this study, we utilized an mRNA dataset of the liver tissues of patients with NASH and conducted WGCNA for various stages of liver fibrosis. Subsequently, we employed two additional mRNA datasets for validation purposes. Gene set enrichment analysis (GSEA) was conducted to analyze gene function enrichment. Through WGCNA and subsequent analyses, complemented by validation using two additional datasets, we identified five genes (BICC1, C7, EFEMP1, LUM, and STMN2) as hub genes. GSEA analysis indicated that gene sets associated with liver metabolism and cholesterol homeostasis were uniformly downregulated. BICC1, C7, EFEMP1, LUM, and STMN2 were identified as hub genes of NASH, and were all related to liver metabolism, NAFLD, NASH, and related diseases. These hub genes might serve as potential targets for the early screening and treatment of NASH.

• PNF and Movement
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• v.6 no.2
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• pp.39-50
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• 2008

Purpose : This article reviewed the advances in the understanding of the effect of motor rehabilitation and brain plasticity on functional recovery after CNS damage. Methods : This is literature study with Pubmed, Medline and Science journal. Results : The inability of CNS neurons to regenerate is largely associated with nonneuronal aspects of the CNS environment. Especially, this neuronal growth inhibition is mediated by myelin associated glycoprotein, olygodendrocyte-myelin glycoprotein, and NOGO. Enriched environment, motor learning, forced limb use have been utilized in scientific studies to promote functional reorganization and brain plasticity. Especially, enriched environment and motor enrichment may prime the brain to respond more adaptively to injury, in part by expressed neurotrophic factors. Conclusions : These reviews suggest that activity-induced neural plasticity occur in damaged brain areas in order to functional reorganization, where it could contribute to motor recovery, and represent a target for stroke rehabilitation.

• Mass Spectrometry Letters
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• v.7 no.4
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• pp.85-90
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• 2016

Post-translational modifications (PTMs) of proteins regulate self-renewal and differentiation in embryonic stem cells (ESCs). Nitration of tyrosine residues of proteins in ESCs modulates their downstream pathways, which can affect self-renewal and differentiation. However, protein tyrosine nitration (PTN) in ESCs has been rarely studied. We reviewed 23 nitrated sites in stem cell proteins. Functional enrichment analysis showed that these nitrated proteins are involved in signal transduction, cell adhesion and migration, and cell proliferation in ESCs. Comparison between the nitrated and known phosphorylated sites revealed that 7 nitrated sites had overlapping phosphorylated sites, indicating functional links of PTNs to their associated signaling pathways in ESCs. Therefore, nitrated proteome provides a basis for understanding potential roles of PTN in self-renewal and differentiation of ESCs.

• Food Science of Animal Resources
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• v.42 no.1
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• pp.34-45
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• 2022

Spirulina platensis was included at 2.5%, 5%, and 7.5% of the diet as a phytobiotic either as a crude preparation or after enrichment by a biosorption process and fed to 126 Japanese quail and the eggs collected and examined for 6 weeks. Assessments were made of physical and chemical characteristics of the eggs. All treatments with added Spirulina increased unsaturated fatty acids and decreased saturated fatty acids with the largest responses for linolenic (omega 3) and oleic (omega 9) acids. The changes in fatty acids were greater with enriched than crude Spirulina. These results suggest that eggs from quail fed with Spirulina may have positive effects on human health.

• The Journal of Korean Physical Therapy
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• v.19 no.1
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• pp.33-44
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• 2007

Purpose: To investigate and analyze effects of environmental enrichment(EE) and nerve stimulation that follows in application times with change of functional recovery(1, 3, 7 and 14 days). Methods: Focal ischemic brain injury was produced in 100 Sprauge-Dawley rats through middle cerebral artery occlusion(MCAO). Neurobehavioral assessment were selected, such as tilting plane testing, horizontal wire testing, vestibulomotor function testing and complex neuromotor function test, then they were randomly divided into five groups; Group I : Sham group, Group II: MCAO group, Group III: MCAO and ES group, Group IV: MCAO and EE group, Group V: MCAO and EE and ES group. Results: In neurobehavioral assessment, group V were significantly difference from other groups on between-subject effects. Conclusion: Our findings suggest that in focal ishemic brain injury, combined environmental enrichment and peripheral nerve electrical stimulation is more improved that the improvement of exercise function recovery than non treatment group.

• International Journal of Computer Science & Network Security
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• v.22 no.11
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• pp.255-259
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• 2022

The new social reality emerging amid the global rise of communication links and integration processes acutely emphasizes the problems of communication in large and small social systems. The method of their communication becomes one of the keys to ensuring global security. It has become the mission of humanitarian education to prepare the younger generations for life in a changing world with no image of the future and increasing uncertainty. In psychological and pedagogical research, there is a growing scientific interest in the problems of interaction of the individual with the social environment. The mental trace of a person's practice in society shapes the experience of social interaction, which constitutes simultaneously the source, tool, and condition for the emergence and development of personality. The study outlines the methodological foundations for the study of individual experiences of social interaction. A hypothesis about the productivity of the functional matrix method is tested. Materials for the training of specialists in the humanities include interdisciplinary approaches to the study and transformation of the experience of social interaction and systematic methodology for the study of complex objects. Fundamental to the study is the systematic-dialectical method, and the matrix method is employed as the instrumental-technological method. The paper presents the results of a multidisciplinary overview of scientific literature concerning the essential characteristics and functions of social interaction and the respective experience. The overview points to the fragmented nature of scientific understanding of the elements of experience outside its integrity and systemic properties. Based on the formula "personality interacts with the social environment", the study presents an algorithm for the application of a systematic methodology for the study of complex objects, which made it possible to identify the system parameters of experience at three levels of cognition and develop the reference structural and functional matrices for the didactic system of its pedagogical enrichment.