• Journal of Ginseng Research
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• v.46 no.1
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• pp.39-53
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• 2022

Ginsenoside Rb₁ (Rb₁), one of the most important ingredients in Panax ginseng Meyer, has been confirmed to have favorable activities, including reducing antioxidative stress, inhibiting inflammation, regulating cell autophagy and apoptosis, affecting sugar and lipid metabolism, and regulating various cytokines. This study reviewed the recent progress on the pharmacological effects and mechanisms of Rb₁ against cardiovascular and nervous system diseases, diabetes, and their complications, especially those related to neurodegenerative diseases, myocardial ischemia, hypoxia injury, and traumatic brain injury. This review retrieved articles from PubMed and Web of Science that were published from 2015 to 2020. The molecular targets or pathways of the effects of Rb₁ on these diseases are referring to HMGB1, GLUT4, 11β-HSD1, ERK, Akt, Notch, NF-κB, MAPK, PPAR-γ, TGF-β1/Smad pathway, PI3K/mTOR pathway, Nrf2/HO-1 pathway, Nrf2/ARE pathway, and MAPK/NF-κB pathway. The potential effects of Rb₁ and its possible mechanisms against diseases were further predicted via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and disease ontology semantic and enrichment (DOSE) analyses with the reported targets. This study provides insights into the therapeutic effects of Rb₁ and its mechanisms against diseases, which is expected to help in promoting the drug development of Rb₁ and its clinical applications.

• The Korean Journal of Applied Statistics
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• v.23 no.4
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• pp.705-713
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• 2010

Predicting survival from microarray data is not easy due to the problem of high dimensionality of data and the existence of censored observations. Also the limitation of individual gene analysis causes the shift of focus to the level of gene sets with functionally related genes. For developing a survival prediction model based on pathway information, the methods for selecting a supergene using principal component analysis and testing its significance for each pathway are discussed. Besides, the performance of gene filtering is compared.

• Biomolecules & Therapeutics
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• v.30 no.1
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• pp.98-116
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• 2022

The small GTPase RhoA has been studied extensively for its role in actin dynamics. In this study, multiple bioinformatics tools were applied cooperatively to the microarray dataset GSE64714 to explore previously unidentified functions of RhoA. Comparative gene expression analysis revealed 545 differentially expressed genes in RhoA-null cells versus controls. Gene set enrichment analysis (GSEA) was conducted with three gene set collections: (1) the hallmark, (2) the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and (3) the Gene Ontology Biological Process. GSEA results showed that RhoA is related strongly to diverse pathways: cell cycle/growth, DNA repair, metabolism, keratinization, response to fungus, and vesicular transport. These functions were verified by heatmap analysis, KEGG pathway diagramming, and direct acyclic graphing. The use of multiple gene set collections restricted the leakage of information extracted. However, gene sets from individual collections are heterogenous in gene element composition, number, and the contextual meaning embraced in names. Indeed, there was a limit to deriving functions with high accuracy and reliability simply from gene set names. The comparison of multiple gene set collections showed that although the gene sets had similar names, the gene elements were extremely heterogeneous. Thus, the type of collection chosen and the analytical context influence the interpretation of GSEA results. Nonetheless, the analyses of multiple collections made it possible to derive robust and consistent function identifications. This study confirmed several well-described roles of RhoA and revealed less explored functions, suggesting future research directions.

• Journal of Korean Academy of Nursing Administration
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• v.8 no.1
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• pp.123-135
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• 2002

Purpose: In this study, the critical pathway for laparoscopic cholecystectomy patients was developed and applied for clinical study. The effectiveness of the critical pathway was analyzed. Method: The subjects with no critical pathway services of this study were 30 laparoscopic cholecystectomy operation patients, who were hospitalized in B General Hospital in Busan from Nov. 28. 2000 to May 2. 2001. The subjects with critical pathway services of this study were 30 laparoscopic cholecystectomy operation patients, who were hospitalized in B General Hospital in Busan from June. 11. 2001 to Oct. 31. 2001. Results: 1. Development for critical pathway Preliminary critical pathway for the laparoscopic cholecystectomy patients was developed though analysis of the reference and 34 case of medical record. The items on the y-axis were assessment, test, treatment, diet, fluid, consult, medication, activity and education and the items on the x-axis were till 3days after operation. The developed critical pathway was applied in clinical field. 2.　Effectiveness of application on developed critical pathwayPost operational complication was not found in neither the critical pathway using Group nor Non-using Group. Hospitalization period mean was 4.63 days for the using Group and 5.93 days for the Non-using Group(P=.001). The mean cost for medical examination and treatment for the using Group was 786,270 won, 117,454 won(12.9%) less than that of the Non-using Group, 903,724 won(P=.000). The degree of satisfaction for the using group was 3.7 points, for the Non-using Group, 3.15 points. The degree of satisfaction for the used Group was 0.55 points higher than that for the Non-using Group and there was a statistically significant difference(P=.000). Concousion: From results of this study, Using the critical pathway in the laparoscopic cholecystectomy operational patients was effective in decreasing the hospitalization period and cost, and increasing the satisfaction about the medical service.

• Asian Oncology Nursing
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• v.4 no.2
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• pp.110-123
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• 2004

The purpose of this study was to develop a clinical pathway for the allogeneic bone marrow transplantation donor. For this study, a conceptual framework was developed through a review of the literature including six steps which are using in Jones Hopkins Hospital. USA. The researcher reviewed 129 medical re-cords of donor who had bone marrow donation between January 2002 to January 2004, to identify the overall service contents required by these patients and to make a preliminary clinical pathway. A content validity test was done for the preliminary clinical pathway, a professional group screened 51 medical re-cords and adopted with 3 hospitalization days as the clinical pathway framework. In the fifth step, clinical pathway test was also done to 7 donors from April 28th to July, 2004. After these processes the final clinical pathway was developed. The results of this study are as follows: 1. The vertical axis of the clinical pathway Includes the following 9 items: vital signs, nursing assessment, activity, diet, intervention, medication, test, consultation and patient teaching. The duration of the horizontal axis was 3days from admission to discharge 2. Analysis of the 129 medical records indicated that the average length of stay was 3 4 days. The medical performance according to the vertical axis in the preliminary clinical pathway consisted of 51 items After clinical validity test, it steel consisted of 51 items in the final form. 3. Clinical Validity test was done to 7 bone marrow donors. During these process, The first patient was deleted because he was out of the criteria the investigate set and 6 patients were used, finally The result of this study indicated all of 7 donors were discharged on expected day. 4. Clinical pathway enables to improve the quality of care, multidisciplinary team work It also helps nursing bone marrow donor, effective education to donor or medical member. The results of this study suggest that clinical pathway may be able to improve the quality of nursing care for bone marrow transplantation donors.

• BMB Reports
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• v.44 no.5
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• pp.347-351
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• 2011

The testis is major male gonad responsible for spermatogenesis and steroidogenesis. Much knowledge is still remained to be learned about the control of these events. In this study, we performed a comprehensive bioinformatics analysis on 1,196 mouse testis proteins screened from public protein database. Integrated function and pathway analysis were performed through Database for Annotation, Visualization and Integrated Discovery (DAVID) and ingenuity Pathway Analysis (IPA), and significant features were clustered. Protein membrane organization and gene density on chromosomes were analyzed and discussed. The enriched bioinformatics analysis could provide clues and basis to the development of diagnostic markers and therapeutic targets for infertility and male contraception.

• Molecular & Cellular Toxicology
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• v.5 no.2
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• pp.147-152
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• 2009

This study was conducted to evaluate the inflammatory mechanisms of LPS-stimulated BV-2 microglial cells. The inflammation mechanism was evaluated in BV-2 cells with or without LPS treated using the Affymetrix microarray analysis system. The microarray analysis revealed that B cell receptor signaling pathway, cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, MAPK signaling pathway, Neuro-active ligand-receptor interaction, TLR signaling path-way, and T cell receptor signaling pathway-related genes were up-regulated in LPS stimulated BV-2 cells. Selected genes were validated using real time RTPCR. These results can help an effective therapeutic approach to alleviating the progression of neuro-in-flammatory diseases.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.3905-3909
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• 2012

Ovarian cancer is the fifth leading cause of cancer death in women aged 35 to 74 years. Although there are several popular hypothesis of ovarian cancer pathogenesis, the genetic mechanisms are far from being clear. Recently, systems biology approaches such as network-based methods have been successfully applied to elucidate the mechanisms of diseases. In this study, we constructed a crosstalk network among ovarian cancer related pathways by integrating protein-protein interactions and KEGG pathway information. Several significant pathways were identified to crosstalk with each other in ovarian cancer, such as the chemokine, Notch, Wnt and NOD-like receptor signaling pathways. Results from these studies will provide the groundwork for a combination therapy approach targeting multiple pathways which will likely be more effective than targeting one pathway alone.

• Korean Journal of Clinical Laboratory Science
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• v.55 no.4
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• pp.235-243
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• 2023

As next-generation sequencing has been developed and used widely, RNA-sequencing (RNA-seq) has rapidly emerged as the first choice of tools to validate global transcriptome profiling. With the significant advances in RNA-seq, various types of RNA-seq have evolved in conjunction with the progress in bioinformatic tools. On the other hand, it is difficult to interpret the complex data underlying the biological meaning without a general understanding of the types of RNA-seq and bioinformatic approaches. In this regard, this paper discusses the two main sections of RNA-seq. First, two major variants of RNA-seq are described and compared with the standard RNA-seq. This provides insights into which RNA-seq method is most appropriate for their research. Second, the most widely used RNA-seq data analyses are discussed: (1) exploratory data analysis and (2) pathway enrichment analysis. This paper introduces the most widely used exploratory data analysis for RNA-seq, such as principal component analysis, heatmap, and volcano plot, which can provide the overall trends in the dataset. The pathway enrichment analysis section introduces three generations of pathway enrichment analysis and how they generate enriched pathways with the RNA-seq dataset.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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• v.22 no.3
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• pp.47-62
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• 2009

Glenditsia spina (GS) can resolve carbuncle, relive swelling, dispel wind and destroy parasites. For these reasons, GS has been widely used as dermatologic agent clinically. In this study, the specific pathways of anti-proliferative effect of GS on human derived melanoma cells were identified. The molecular profile was measured using microarray technique to identify up- or down-regulated genes in SK-MEL-2 cell line. Pathway analysis was done by listing percentage of pathway involvement, and the represented pathways were obtained from KEGG. The transcription factor binding sequences were obtained by Transfac database. By the promoter analysis, up-regulated genes by GS were mainly associated with MAPK, Regulation of actin cytoskeleton, Wnt, Focal adhesion and Long term potentiation pathway. Down-regulated genes by GS were mainly associated with MAPK and Antigen processing and presentation pathway. And some of the transcription factors like Sp1 and NF-Y in up-regulated genes and Oct-1 in down-regulated genes by GS also identified.