• The Korea Journal of Herbology
• /
• v.38 no.1
• /
• pp.45-53
• /
• 2023

Objectives : Network pharmacology-based research is one of useful tool to predict the possible efficacy and molecular mechanisms of natural materials with multi compounds-multi targeting effects. In this study, we investigated the functional underlying mechanisms of Astragalus membranaceus Bunge (AM) on its anti-obesity effects using a network pharmacology analysis. Methods : The constituents of AM were collected from public databases and its target genes were gathered from PubChem database. The target genes of AM were compared with the gene set of obesity to find the correlation. Then, the network was constructed by Cytoscape 3.9.1. and functional enrichment analysis was conducted to predict the most relevant pathway of AM. Results : The result showed that AM network contained the 707 nodes and 6867 edges, and 525 intersecting genes were exhibited between AM and obesity gene set, indicating that high correlation with the effects of AM on obesity. Based on GO biological process and KEGG Pathway, 'Response to lipid', 'Cellular response to lipid', 'Lipid metabolic process', 'Regulation of chemokine production', 'Regulation of lipase activity', 'Chemokine signaling pathway', 'Regulation of lipolysis in adipocytes' and 'PPAR signaling pathway' were predicted as functional pathways of AM on obesity. Conclusions : AM showed high relevance with the lipid metabolism related with the chemokine production and lipolysis pathways. This study could be a basis that AM has promising effects on obesity via network pharmacology analysis.

• Herbal Formula Science
• /
• v.30 no.3
• /
• pp.175-182
• /
• 2022

Objective : This study aims to investigate the active ingredients and potential mechanisms of the beneficial herb on human cancers such as the liver by employing network pharmacology. Methods : Ingredients and their target information was obtained from various databases such as TM-MC, TTD, and Drugbank. Related protein for liver cancer was retrieved from the Comparative Toxicogenomics Database and literature. A hypergeometric test and gene set enrichment analysis were conducted to evaluate associations between protein targets of red ginseng (Panax ginseng C. A. Meyer) and liver cancer-related proteins and identify related signaling pathways, respectively. Network proximity was employed to identify active ingredients of red ginseng on liver cancer. Results : A compound-target network of red ginseng was constructed, which consisted of 363 edges between 53 ingredients and 121 protein targets. MAPK signaling pathway, PI3K-Akt signaling pathway, p53 signaling pathway, TGF-beta signaling pathway, and cell cycle pathway was significantly associated with protein targets of red ginseng. Network proximity results indicated that Ginsenoside Rg1, Acetic Acid, Ginsenoside Rh2, 20(R)-Ginsenoside Rg3, Notoginsenoside R1, Ginsenoside Rk1, 2-Methylfuran, Hexanal, Ginsenoside Rd, Ginsenoside Rh1 could be active ingredients of red ginseng against liver cancer. Conclusion : This study suggests that network-based approaches could be useful to explore potential mechanisms and active ingredients of red ginseng for liver cancer.

• Herbal Formula Science
• /
• v.31 no.1
• /
• pp.41-51
• /
• 2023

Objectives : Raphani Semen (Raphanus sativus L.) is known for the various beneficial effects in Korean medicine. This study aimed to investigate the effect of Raphani Semen extract (RSE) against arachidonic acid (AA)+iron-induced oxidative stress in cells. Methods : Ingredients, their target information, oxidative stress liver injury-related proteins was obtained from various network pharmacology databases and software. A hypergeometric test and enrichment analysis were conducted to evaluate associations between protein targets of RSE. The cell viability was assessed by MTT assay, and immunoblot analysis was used to confirm the molecular mechanisms. Results : A compound-target network of RSE was constructed, which consisted of 336 edges between 18 ingredients and 123 protein targets. PI3K-Akt signaling pathway, ErbB signaling pathway, HIF-1 signaling pathway, PPAR signaling pathway, and AMPK signaling pathway was significantly associated with protein targets of RSE. RSE protected HepG2 cells against AA+iron-induced oxidative stress as mediated with AMPK signaling. Conclusion : RSE was found to protect the cells against oxidative stress via the AMPK signaling pathway.

• BMB Reports
• /
• v.57 no.6
• /
• pp.299-304
• /
• 2024

Upregulation of PRAME (preferentially expressed antigen of melanoma) has been implicated in the progression of a variety of cancers, including melanoma. The tumor suppressor p53 is a transcriptional regulator that mediates cell cycle arrest and apoptosis in response to stress signals. Here, we report that PRAME is a novel repressive target of p53. This was supported by analysis of melanoma cell lines carrying wild-type p53 and human melanoma databases. mRNA expression of PRAME was downregulated by p53 overexpression and activation using DNA-damaging agents, but upregulated by p53 depletion. We identified a p53-responsive element (p53RE) in the promoter region of PRAME. Luciferase and ChIP assays showed that p53 represses the transcriptional activity of the PRAME promoter and is recruited to the p53RE together with HDAC1 upon etoposide treatment. The functional significance of p53 activation-mediated PRAME downregulation was demonstrated by measuring colony formation and p27 expression in melanoma cells. These data suggest that p53 activation, which leads to PRAME downregulation, could be a therapeutic strategy in melanoma cells.

• Journal of KIISE:Databases
• /
• v.33 no.5
• /
• pp.526-537
• /
• 2006

The most representative approach for efficient storing of XML data is to store XML data in relational databases. The merit of this approach is that it can easily accept the realistic status that most data are still stored in relational databases. This approach needs to convert XML data into relational data or relational data into XML data. The most important issue in the translation is to reflect structural and semantic relations of RDB to XML schema model exactly. Many studies have been done to resolve the issue, but those methods have several problems: Not cover structural semantics or just support explicit referential integrity relations. In this paper, we propose an algorithm for extracting implicit referential integrities automatically. We also design and implement the suggested algorithm, and execute comparative evaluations using translated XML documents. The proposed algorithm provides several good points such as improving semantic information extraction and conversion, securing sufficient referential integrity of the target databases, and so on. By using the suggested algorithm, we can guarantee not only explicit referential integrities but also implicit referential integrities of the initial relational schema model completely. That is, we can create more exact XML schema model through the suggested algorithm.

• Asian Pacific Journal of Cancer Prevention
• /
• v.14 no.2
• /
• pp.963-968
• /
• 2013

Objective: To study the effect of the antagomiR-27a inhibitor on glioblastoma cells. Methods: The miR-27a expression level in specimens of human glioblastoma and normal human brain tissues excised during decompression for traumatic brain injury was assessed using qRT-PCR; The predicted target gene of miR-27a was screened out through bioinformatics databases, and the predicted gene was verified using genetic report assays; the effect of antagomiR-27a on the invasion and proliferation of glioma cells was analyzed using MTT assays and 5-ethynyl-2'-deoxyuridine (EdU) labeling. A xenograft glioblastoma model in BALB-c nude mice was established to detect the effect of antagomiR-27a on tumour growth. Results: qRT-PCR results showed that miR-27a significantly increased in specimens from glioblastoma comparing with normal human brain tissues. Th miR-27a inhibitor significantly suppressed invasion and proliferation of glioblastoma cells. FOXO3a was verified as a new target of miR-27a by Western blotting and reporter analyzes. Tumor growth in vivo was suppressed by administration of the miR-27a inhibitor. Conclusion: MiR-27a may be up-regulated in human glioblastoma, and antagomiR-27a could inhibit the proliferation and invasion ability of glioblastoma cells.

• Journal of the Korea Society of Computer and Information
• /
• v.10 no.1 s.33
• /
• pp.59-66
• /
• 2005

The organization of the web is progressively more being used to improve search and analysis of information on the web as a large collection of heterogeneous documents. Most people begin at a Web search engine to find information. but the user's pertinent search results are often greatly diluted by irrelevant data or sometimes appear on target but still mislead the user in an unwanted direction. One of the intentional, sometimes vicious manipulations of Web databases is a intentionally biased web page like Google bombing that is based on the PageRank algorithm. one of many Web structuring techniques. In this thesis, we regard the World Wide Web as a directed labeled graph that Web pages represent nodes and link edges. In the Present work, we define the label of an edge as having a link context and a similarity measure between link context and target page. With this similarity, we can modify the transition matrix of the PageRank algorithm. By suggesting a motivating example, it is explained how our proposed algorithm can filter the Web intentionally biased web Pages effective about $60\%% rather than the conventional PageRank.

• The Korea Journal of Herbology
• /
• v.39 no.3
• /
• pp.37-47
• /
• 2024

Objectives : Because predicting the potential efficacy and mechanisms of Korean medicines is challenging due to their high complexity, employing an approach based on network pharmacology could be effective. In this study, network pharmacological analysis was utilized to anticipate the effects of YunPye-Hwan (YPH) in treating Chronic obstructive pulmonary disease (COPD). Methods : Compounds and their related target genes of YPH were gathered from the TCMSP and PubChem databases. These target genes of YPH were subsequently compared with gene sets associated with COPD to assess correlation. Next, core genes were identified through a two-step screening process, and finally, functional enrichment analysis of these core genes was conducted using both Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Results : A total of 15 compounds and 437 target genes were gathered, resulting in a network comprising 473 nodes and 14,137 edges. Among them, 276 genes overlapped with gene sets associated with COPD, indicating a significant correlation between YPH and COPD. Functional enrichment analysis of the 18 core genes revealed biological processes and pathways such as "miRNA Transcription," "Nucleic Acid-Templated Transcription," "DNA-binding Transcription Factor Activity," "MAPK signaling pathway," and "TNF signaling pathway" were implicated. Conclusion : YPH exhibited significant relevance to COPD by modulating cell proliferation, differentiation, inflammation, and cell death pathways. This study could serve as a foundational framework for further research investigating the potential use of YPH in the treatment of COPD.

• Journal of Korea Society of Industrial Information Systems
• /
• v.16 no.5
• /
• pp.107-114
• /
• 2011

The purpose of this paper is to develop a reliability estimation process of agricultural machinery components using field failure data. Estimating the durability is a time-consuming in the product development process. Using the field data of tractor, failures for major parts are investigated and databases are developed. Accelerated life test using the stress analysis could improve Weibull B10 considerably. This estimation process is useful for preparing the design input and planning the durability target.

• Proceedings of the IEEK Conference
• /
• 2002.07a
• /
• pp.62-65
• /
• 2002

The locking is the most widely-used concurrency control mechanism for guaranteeing logical consistency of a database where a number of transactions perform concurrently. In this Paper, we propose a new method for lock management appropriate in main-memory databases. Our method chooses the partition, a fixed-sized container for records. as a unit of locking. and directly keeps lock information within the Partition itself. These make our method enjoy the following advantages: (1) it has freedom in controlling of the trade-off between the system concurrency and the lock processing overhead by considering the characteristics of given target applications. (2) it enhances the overall system performance by eliminating the hashing overhead, a serious problem occurred in the traditional method.