• 동의생리병리학회지
• /
• 제18권5호
• /
• pp.1291-1300
• /
• 2004

Baicalin, a biologically active flavonoid form the roots of Scutallaria baicalensis (Skullcap), have been reported to not only function as anti-oxidants but also cause anticancer effect. We investigated the mechanism of baicalin-induced cytotoxicity and the macro scale gene expression analysis in leukemia cell line, HL-60 cells. Baicalin (10 μM) were used to treat the cells for 6h, 12h, 24h, 48h and 72h. In a human cDNAchip study of 65,000 genes evaluated 6, 12, 24, 48. 72 hours after treated with Baicalin in HL-60 cells. Hierarchical cluster against the genes which showed expression changes by more than two fold. One hundred one genes were grouped into 6 clusters according to their profile of expression by a hierarchical clustering algorithm. For genes differentially expressed in response to baicalin treatment, we tested functional classes based on Gene Ontology (GO) terms. This study provides the most comprehensive available survey of gene expression changes in response to baicalin treatment in HL-60 cell line.

• 한국한의학연구원논문집
• /
• 제13권2호통권20호
• /
• pp.91-100
• /
• 2007

In this paper, We tried to analyze the patent trend on constitution diagnosis and treatment related technologies. For this, constitution diagnosis and treatment related technologies divided into 16 sub-technology by the advisory committee. And we analyzed patents applied in Korea, Japan, U.S.A., China, and Europe. The 16 sub-technology consist of pulse analyzer, skin diagnosis, tongue analyzer, face and body detector, face analyzer, voice analyzer, intelligence ontology, meridian diagnosis, infrared thermography, electric stimulation, laser, high and low frequency, physical, magnetic, and ultrasound therapy. As a result we found that patents of constitution diagnosis and treatment in Korea has been growing steadily in both quality and quantity since 1980s. The number of patent the pulse analyzer and low frequency therapy are larger than others. But applied relevant international patents, marketability of the patent and Cites per Patent (CPP) index are shown to be very low. In conclusion, to occupy key original technologies of the Oriental medical device, we need to apply more patent of the whole related technology and international patents.

• 대한예방한의학회지
• /
• 제27권2호
• /
• pp.35-48
• /
• 2023

Objective : We studied prognostic biomarkers discovery for lung cancer based on the pattern identification for the personalized Korean medicine. Methods : Using 30 tissue samples, we performed a whole exome sequencing to examine the genetic differences among three groups. Results : The exome sequencing identified among 23,490 SNPs germline variants, 12 variants showed significant frequency differences between Xu and Stasis groups (P<0.0005). As similar, 18 and 10 variants were identified in analysis for Xu vs. Gentleness group and Stasis vs. Gentleness group, respectively (P<0.001). Our exome sequencing also found 8,792 lung cancer specific variants and among the groups identified 6, 34, and 12 variants which showed significant allele frequency differences in the comparison groups; Xu vs. Stasis, Xu vs. Gentleness group, and Stasis vs. Gentleness group. As a result of PCA analysis, in germline data set, Xu group was divided from other groups. Analysis using somatic variants also showed similar result. And in gene ontology analysis using pattern identification variants, we found genes like as FUT3, MYCBPAP, and ST5 were related to tumorigenicity, and tumor metastasis in comparison between Xu and Stasis. Other significant SNPs for two were responsible for eye morphogenesis and olfactory receptor activity. Classification of somatic pattern identification variants showed close relationship in multicellular organism reproduction, anion-anion antiporter activity, and GTPase regulator activity. Conclusions : Taken together, our study identified 40 variants in 29 genes in association with germline difference of pattern identification groups and 52 variants in 47 genes in somatic cancer tissues.

• BMB Reports
• /
• 제45권2호
• /
• pp.120-125
• /
• 2012

We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis. It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results. An intuitive user interface with multiple panels allows for extensive visual scrutiny of analysis results. The program includes many essential and useful features, such as enrichment analysis algorithms, multiple test correction methods, and versatile filtering of enriched GO terms for more focused analyses. A unique graphic interface reflecting the GO tree structure was devised to facilitate comparisons of multiple GO analysis results, which can provide valuable insights for biological interpretation. Additional features to enhance user convenience include built in ID conversion, evidence code-based gene-GO association filtering, set operations of gene lists and enriched GO terms, and user -provided data files. It is available at http://neon.gachon.ac.kr/GoBean/.

• 생명과학회지
• /
• 제22권11호
• /
• pp.1552-1557
• /
• 2012

Pipernonaline은 후추나무과에 속하는 필발(Piper longum Linn.)의 유도체로서 전립선 암세포에 대한 항암활성이 보고되고 있다. 하지만 실제 암세포 내에서 생물학적 정보를 가진 수 많은 유전자들에 대한 발현이 어떻게 이루어지고 있는지 알려진 바가 없다. 본 연구에 사용된 microarray 분석은 동시에 수 만개 이상의 유전자 발현양상을 한번에 관찰할 수 있는 기술로서 특정 질병의 유전학적 특성과 기전 연구를 더 광범위하게 연구 할 수 있는 기술이다. 본 연구에서는 전립선 암세포인 PC-3 세포에 pipernonaline을 처리하여 cDNA microarray를 실시하였다. 이후, DAVID database를 이용하여 gene ontology의 Biological Process를 분석하여 세포사멸과 세포주기, 세포성장 및 증식에 관련된 유전자들을 우선적으로 분석하였다. 그 결과, 세포주기관련 256개, 세포사멸관련 197개, 세포성장 및 증식관련에 154개의 유전자가 확인 되었다. 이러한 결과는 pipernonaline은 전립선 암세포 내에 존재하는 생물학적 신호전달체계에 관련된 유전자 발현을 조절함으로써 항암활성을 나타내 것을 알 수 있었고, 이후 이러한 microarray의 추가적인 분석은 암세포 내 새로운 유전자의 탐색 및 메커니즘을 규명하는데 유용하게 사용할 수 있을 것으로 사료된다.

• 대한의생명과학회지
• /
• 제18권3호
• /
• pp.313-318
• /
• 2012

Acanthamoeba is an opportunistic pathogen known to cause granulomatous amoebic encephalitis and amebic keratitis. Acanthamoeba exhibits life cycle consisting of trophozoite and cyst, and the cyst is highly resistant to variable antibiotics and therapeutic agents. To understand the encystation mechanism of Acanthamoeba, the expression profiles of trophozoite and cyst were compared by gene ontology (GO) analysis. Ribosomal proteins and cytoskeletal proteins were highly expressed in trophozoite. In cyst, various protease, and signal transduction - and protein turnover - related proteins were highly expressed. These results correlated with eukaryotic orthologous groups (KOG) assignment and microarray analysis of Acanthamoeba trophozoite and cyst ESTs. The information of differential expression profiles of trophozoite and cyst would provide important clues for research on encystation mechanism of cyst forming protozoa including Acanthamoeba.

• 동의생리병리학회지
• /
• 제34권4호
• /
• pp.184-190
• /
• 2020

This study was performed to find antibacterial substances contained in Scutellariae Radix (SR) using a systems pharmacological analysis method and to establish an effective strategy for the prevention and treatment of infectious diseases. Analysis of the main active ingredients of SR was performed using Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database and Analysis Platform. 36 active compounds were screened by the parameter values of Drug-Likeness (DL), Oral Bioavailability (OB), and Caco-2 permeability (Caco-2), which were based on the drug absorption, distribution, metabolism, and excretion indicators. The UniProt database was used to obtain information on 159 genes associated with active compounds. The main active compounds with antibacterial effects were wogonin, β-sitosterol, baicalein, acacetin and oroxylin-A. Target proteins associated with the antibacterial action were chemokine ligand 2, interleukin-6, tumor necrosis factor, caspase-8,9 and mitogen-activated protein kinase 14. In the future, systems pharmacological analysis of traditional medicine will be able to make it easy to find the important mechanism of action of active substances present in natural medicines and to optimize the efficacy of medicinal effects for combinations of major ingredients to help treat certain diseases.

• Parasites, Hosts and Diseases
• /
• 제59권1호
• /
• pp.67-76
• /
• 2021

Legionella pneumophila is an opportunistic pathogen that survives and proliferates within protists such as Acanthamoeba spp. in environment. However, intracellular pathogenic endosymbiosis and its implications within Acanthamoeba spp. remain poorly understood. In this study, RNA sequencing analysis was used to investigate transcriptional changes in A. castellanii in response to L. pneumophila infection. Based on RNA sequencing data, we identified 1,211 upregulated genes and 1,131 downregulated genes in A. castellanii infected with L. pneumophila for 12 hr. After 24 hr, 1,321 upregulated genes and 1,379 downregulated genes were identified. Gene ontology (GO) analysis revealed that L. pneumophila endosymbiosis enhanced hydrolase activity, catalytic activity, and DNA binding while reducing oxidoreductase activity in the molecular function (MF) domain. In particular, multiple genes associated with the GO term 'integral component of membrane' were downregulated during endosymbiosis. The endosymbiont also induced differential expression of various methyltransferases and acetyltransferases in A. castellanii. Findings herein are may significantly contribute to understanding endosymbiosis of L. pneumophila within A. castellanii.

• 한국정보과학회:학술대회논문집
• /
• 한국정보과학회 2007년도 가을 학술발표논문집 Vol.34 No.2 (C)
• /
• pp.195-199
• /
• 2007

Tim Berners-Lee가 웹을 만든 이후 인터넷은 정보유통에 혁명적인 변화를 가져왔다. 이들 변화중 한가지는 개인이 접촉할 수 있는 정보의 양은 무한이 많아지게 되었다는 것이다. 이렇게 많아진 데이터에서 사용자들이 원하는 지식 정보를 정확하고 빠르게 검색하는 것이 중요한 이슈로 부각되었다. 그 해결책의 일환으로 시맨틱 웹(Semantic Web)이 많은 주목을 받고 있는데 이는 웹 정보에 잘 정의된 "의미 정보"를 부여하고 자동화 에이전트나 검색 엔진 등과 같은 소프트웨어들이 이용하게 한 것이다. 한국 한의학 연구원에서 운영하고 있는 한의학 지식 정보자원 중 약재들에 관한 데이터도 그 수에 있어서 매해 증가하고 있다. 따라서 사용자들에게 정확한 정보를 제공해주기 위해 기존의 검색 시스템에 시맨틱 웹을 사용하였다. 시맨틱 웹의 핵심 기술인 온톨로지를 사용하여 데이터를 구축하고 관리하는 시스템을 개발함으로써 사용자가 원하는 정보를 정확하게 제공하면서 또한 한의학 지식 자체를 전달할 수 있게 되었다. 뿐만 아니라 자원의 현대화는 물론 고급화된 자원의 효율적 가치 활용도를 높일 수 있다.

• 동의생리병리학회지
• /
• 제38권1호
• /
• pp.22-26
• /
• 2024

The purpose of this study was to identify the applicability, main compounds, and target genes of Cnidii Fructus (CF) in the treatment of gastritis using network pharmacology. The compounds in CF were searched in Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine (TM-MC). The target gene information of the compounds was collected from pubchem and cross-compared with the gastritis-related target gene information collected from Genecard to derive the target genes. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed on the derived target genes. Afterwards, network analysis between compounds and disease target genes was performed using cytoscape. We identified 121 active compounds and 139 target genes associated with gastritis. Pathways derived from the GO biological process and KEGG pathway DB primarily focus on target genes related to inflammation (IL-6, IL-8, TNF production, NF-κB transcription factor activity, and NF-κB signaling pathway) and cell death (PI3K-Akt, FoxO). Major targets for CF treatment of gastritis include TP53, TNF, BCL2, EGFR, NFKB1, ABCB1, PPARG, PTGS2, IL6, IL1B, and SOD1, along with major compounds such as coumarin, osthol, hexadecanoic acid, oleic acid, linoleic acid, and stigmasterol. This study provided CF's applicability for gastritis, related compounds, and target information. Evaluating CF's effectiveness in a preclinical gastritis model suggests its potential use in clinical practice for digestive system diseases.