• 디지털콘텐츠학회 논문지
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• 제19권9호
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• pp.1795-1801
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• 2018

질환의 원인을 규명하기 위해 전장유전체 연관분석 (GWAS; Genome-Wide Association Study) 연구가 활발히 진행되고 유전체 레벨의 단일염기다형성 (SNP; Single-nucleotide polymorphism)이 많이 밝혀지고 있다. 그러나 단일염기다형성의 연관분석을 통해 질환이 발병하는 생물학적 메카니즘을 이해하기 어렵기 때문에 유전자, 생물학적 패스웨이 및 질환 등의 연관성 분석이 이전보다 더욱 중요하다. 본 논문에서는 단일염기다형성과 관련된 유전자와 패스웨이, 질환 정보를 검색하여 통합 분석하는 서비스를 제공하는 PRaDA 웹 시스템을 제안하였다. PRaDA는 사용자로부터 입력받은 유의한 몇몇의 단일염기다형성들과 관련된 유전자 및 패스웨이 뿐만 아니라, 유의하지 않은 다수의 단일염기다형성 집합의 간접적인 영향을 파악하기 위해 기능적으로 근접한 패스웨이를 검색하고 통계적 분석을 실행한다. 사용자들은 PRaDA가 제공하는 통합된 정보를 통해 질병의 전반적인 이해를 할 수 있다.

• 한방안이비인후피부과학회지
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• 제36권1호
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• pp.50-63
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• 2023

Objectives : This study used a network pharmacology approach to explore the active compounds and therapeutic mechanisms of Yijin-tang on Meniere's disease. Methods : The active compounds of Yijin-tang were screened via the TCMSP database and their target proteins were screened via the STITCH database. The GeneCard was used to establish the Meniere's disease-related genes. The intersection targets were obtained through Venny 2.1.0. The related protein interaction network was constructed with the STRING database, and topology analysis was performed through CytoNCA. GO biological function analysis and KEGG enrichment analysis for core targets were performed through the ClueGO. Results : Network analysis identified 126 compounds in five herbal medicines of Yijin-tang. Among them, 15 compounds(naringenin, beta-sitosterol, stigmasterol, baicalein, baicalin, calycosin, dihydrocapsaicin, formononetin, glabridin, isorhamnetin, kaempferol, mairin, quercetin, sitosterol, nobiletin) were the key chemicals. The target proteins were 119, and 7 proteins(TNF, CASP9, PARP1, CCL2, CFTR, NOS2, NOS1) were linked to Meniere's disease-related genes. Core genes in this network were TNF, CASP9, and NOS2. GO/KEGG pathway analysis results indicate that these targets are primarily involved in regulating biological processes, such as excitotoxicity, oxidative stress, and apoptosis. Conclusion : Pharmacological network analysis can help to explain the applicability of Yijin-tang on Meniere's disease.

• 대한한의학방제학회지
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• 제31권4호
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• pp.295-313
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• 2023

Objectives : While treatments for cancer are advancing, the development of effective treatments for cancer metastasis, the main cause of cancer patient death, remains insufficient. Recent studies on Dichroae Radix have revealed that its active ingredients have the potential to inhibit cancer metastasis. This study aimed to investigate the cancer metastasis inhibitory effect of Dichroae Radix using network pharmacological analysis. Methods : The active compounds of Dichroae Radix have been identified using Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. The UniProt database was used to collect each of information of all target proteins associated with the active compounds. To find the bio-metabolic processes associated with each target, the DAVID6.8 Gene Functional classifier tool was used. Compound-Target and Target-Pathway networks were analyzed via Cytoscape 3.40. Results : In total, 25 active compounds and their 62 non-redundant targets were selected through the TCMSP database and analysis platform. The target genes underwent gene ontology and pathway enrichment analysis. The gene list applied to the gene ontology analysis revealed associations with various biological processes, including signal transduction, chemical synaptic transmission, G-protein-coupled receptor signaling pathways, response to xenobiotic stimulus, and response to drugs, among others. A total of eleven genes, including HSP90AB1, CALM1, F2, AR, PAKACA, PTGS2, NOS2, RXRA, ESR1, ESR2, and NCOA1, were found to be associated with biological pathways related to cancer metastasis. Furthermore, nineteen of the active compounds from Dichroae Radix were confirmed to interact with these genes. Conclusions : The results provide valuable insights into the mechanism of action and molecular targets of Dichroae Radix. Notably, Berberine, the main active ingredient of Dichroae Radix, plays a significant role in degrading AR proteins in advanced prostate cancer. Further studies and validations can provide crucial data to advance cancer metastasis prevention and treatment strategies.

• 한국정보과학회논문지:데이타베이스
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• 제30권2호
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• pp.168-175
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• 2003

지금까지 문자열 데이타에 대한 선택도 추정은 문자열들의 등장 회수에 대한 정보를 저장하고 있는 '카운트 서픽스 트리'를 생성한 뒤, 이 트리를 이용하여 부분 문자열들의 선택도를 추정하는 방법으로 이루어졌다. 그런데, 문자열 데이타가 생물학 서열처럼 매우 길어질 경우 카운트 서픽스 트리를 생성하는 일은 거의 불가능해진다는 문제점이 발생한다. 이 논문에서는 길이가 q인 부분 문자열들만을 삽입한 '카운트 큐그램 트리'를 제안한다. 카운트 큐그램 트리는 서열 내의 길이가 q 이하인 모든 부분 문자열(큐그램) 들의 정확한 등장 회수를 저장하고 있으며, 문자열의 전체 길이 N에 상관없는 크기로, O(N) 시간에 생성 가능하다. 또한, 이 논문에서는 카운트 큐그램 트리를 이용한 'k번째 최대겹침' 추정 방법을 제시한다. 이 추정 방법은 질의 문자열을 길이 q인 부분 문자열로 나눌 때 부분 문자열들의 겹치는 정도 k를 선택할 수 있도록 한 방법으로 이전 연구에서 제시한 '최대겹침' 방법을 확장하였다. q와 k를 변화시키며 진행한 실험 올 통해 대부분의 경우에 매우 정확하게 선택도를 추정할 수 있음을 확인하였다.

• 환경영향평가
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• 제7권2호
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• pp.103-112
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• 1998

일본에서는 자연친화형 하천사업을 많이 시행하고 있다. 바람직한 수환경을 보전하고 복원하기 위해서는 하천내외의 생태계에 대한 수질기준을 정립하여야 한다. 본 논문에서는 생물학적 지표를 사용한 수질 분류 방법을 개발하여 나가사키현의 혼묘하천에 대하여 적용하였다. 이러한 수질 분류를 위하여, 수정된 오염물 지표 분류법을 제안하였다. 비교적 단순한 방법이지만, 가장 많은 종에 대한 3가지 지표만으로 수질을 효과적으로 평가할 수 있었다. 또한, 하천유역의 통합관리를 위하여 다양한 생태계 자료를 포함하는 종합적인 자료관리시스템을 개발하였다. 본 시스템을 사용하여 건전한 수환경을 보전하기 위한 각종 생태계 자료를 쉽게 취득할 수 있다. 본 연구의 결과를 사용하여 수질자료를 개선하고, 시민들의 의식을 고양하며, 하천관리계획을 세울 수 있을 것이다. 일본에서는, 자연친화적 하천복원사업에 있어서 시민들의 의식 및 행동이 가장 중요한 요소이다.

• 운동영양학회지
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• 제25권3호
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• pp.28-35
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• 2021

[Purpose] As Panax ginseng C. A. Meyer (ginseng) exhibits various physiological activities and is associated with exercise, we investigated the potential active components of ginseng and related target genes through network pharmacological analysis. Additionally, we analyzed the association between ginseng-related genes, such as the G-protein-coupled receptors (GPCRs), and improved exercise capacity. [Methods] Active compounds in ginseng and the related target genes were searched in the Traditional Chinese Medicine Database and Analysis Platform (TCMSP). Gene ontology functional analysis was performed to identify biological processes related to the collected genes, and a compound-target network was visualized using Cytoscape 3.7.2. [Results] A total of 21 ginseng active compounds were detected, and 110 targets regulated by 17 active substances were identified. We found that the active compound protein was involved in the biological process of adrenergic receptor activity in 80%, G-protein-coupled neurotransmitter in 10%, and leucocyte adhesion to arteries in 10%. Additionally, the biological response centered on adrenergic receptor activity showed a close relationship with G protein through the beta-1 adrenergic receptor gene reactivity. [Conclusion] According to bioavailability analysis, ginseng comprises 21 active compounds. Furthermore, we investigated the ginseng-stimulated gene activation using ontology analysis. GPCR, a gene upregulated by ginseng, is positively correlated to exercise. Therefore, if a study on this factor is conducted, it will provide useful basic data for improving exercise performance and health.

• Asian Pacific Journal of Cancer Prevention
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• 제13권10호
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• pp.5263-5272
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• 2012

Background: Gastric cancer (GC) is one of the most common cancers in China. Adjuvant chemotherapy (AC) is a routine auxiliary treatment for GC recommended by the guidelines issued in 2011 by the Ministry of Health of the People's Republic of China, but the relevant credible consequences in China have been insufficient because of China's late start and ethical concerns. Methods: A series of databases, including Cochrane Library, MEDLINE, EMBASE, the Chinese database of the National Knowledge Infrastructure and the VIP database, were searched by 2 reviewers independently for studies investigating AC for GC through March 2012. The retrieved literature was screened according to the eligibility criteria. Results: A total of 35 randomized control trials (RCTs) were subjected to the final analysis, including 4,043 patients in treatment group and 3,884 in the control group, as well as 4 clinical-control trials (CCTs), which accessed the final analysis with 238 and 252 patients, respectively. AC reduced the risk of death as a protective treatment with statistical significance (HR=0.91, 95%CI: [0.85, 0.97], P=0.002), and it seemed more effective for Asian than non-Asian patients. The effects of AC were not influenced by the starting time (P>0.05). D2 lymphadenectomy-based chemotherapy was effective (HR=0.89, 95%CI: [0.80, 0.99], P=0.04). Oral S-1 40 mg/m2 after D2 lymphadenectomy might be a better choice for Asians with advanced GC and might result in a greater reduction of adverse events than in non-Asian patients. GRADE quality assessment determined that the strength of the evidence from foreign studies from Europe, the United States and Asian countries other than China was high, while it was moderate for Chinese studies. Conclusion: AC was effective or even curative in Chinese patients in general, although it is still necessary to optimize a targeted AC scheme for Chinese patients with GC.

• Animal cells and systems
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• 제5권3호
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• pp.243-246
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• 2001

Human endoqenous retroviral long terminal repeats (LTRs) have been found to be coexpressed with sequences of genes closely located nearby. It has been suggested that the LTR elements have contributed to structural changes or genetic variations of human genome connected to various diseases and evolution. Using cDNA library derived from placenta tissue, we performed PCR amplification and identified five new HERV-W LTR elements. Those LTR elements showed a high degree of sequence similarity (98-99%) with HERV-W LTR (AF072500). A phylogenetic tree obtained by the neighbor-joining method revealed that HERV-W LTR elements could be mainly divided into two groups through evolutionary divergence. Five new HERV-W LTR elements (pla-1, 4, 5, 6, 7) belonged to the group I with AX000960, AF072504, and AF072506 from GenBank database. The data suggest that several copy numbers of the HERV-W LTR elements are transcribed in placenta and may contribute to the understanding of biological function such as human placental morphogenesis.

• 생명과학회지
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• 제29권2호
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• pp.181-190
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• 2019

시스템 약리학적 분석을 통해 대회향(Anisi Stellati Fructus)의 활성성분 스크리닝, 표적유전자 확보 및 관련 질병과의 네트워크를 구축한 후 대회향의 항균작용을 중점적으로 분석하였다. Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database 와 Analysis Platform을 통해 대회향의 잠재적 활성성분 49개를 확보하였으며, 그 중 설정한 조건에 부합하는 9개 활성성분을 스크리닝 하였다. TCMSP Database는 활성성분의 약물 동태학적 특성 및 약물-표적-질병 간의 관련성을 네트워크 수준에서 파악할 수 있는 획기적인 in silico적 접근을 가능하게 해준다. 활성성분과 반응하는 201개의 유전자 정보를 UniProt database를 통해 확인하고, 취합한 유전자들이 관여하는 348개의 생물학적 과정을 David 6.8 Gene Functional Classification Tool에서 확보하였다. Chemokine ligand 2, Interleukin-10, Interleukin-6, Tumor Necrosis Factor를 포함한 총 47개의 유전자가 항균작용에 관여하였고 이들을 표적으로 하는 luteolin, kaempferol, quercetin 등이 대표적 항균 관련 활성성분이었다. 이와 같이 확보된 데이터는 연구 재료 선정에 정확성과 시간, 노력, 비용 절감의 효과를 제공함과 더불어 추후 실험적 증명으로 이어져 감염병의 예방과 치료 전략에 과학적인 근거를 제시할 수 있을 것이다.

• Journal of Ecology and Environment
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• 제38권4호
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• pp.541-544
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• 2015

We report the status of wetland vascular plant species in Korea including the whole peninsula and its adjacent islands. This analysis was based on database from our previous categorized list. In all, 4,050 taxa have been reported, including 3,769 native and 281 naturalized. Of these, 479 taxa (12%) are considered as wetland vascular indicator species: 240 obligate wetland plants (OBW) and 239 facultative upland plants (FACW). Approximately 31% of those 479 taxa, i.e., 149 taxa, are labelled as aquatic macrophytes. Wetland plants, mostly herbaceous but some woody, inhabit aquatic bodies and wet meadows. Except for two OBW and six FACW taxa, the rest of the plants are summer-green only. The information provided here is valuable for making assessments of wetland ecosystem health, as well as for developing management plans to preserve and restore wetlands and their resident plant species while also creating artificial wetland environments.