• 한국정보과학회논문지:시스템및이론
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• 제36권2호
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• pp.60-67
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• 2009

단백질 상호작용 네트워크는 어떤 단백질들 간에 상호 작용 관계가 있는지를 네트워크 형태로 나타낸 것이며 단백질 상호작용을 발견하거나 분석하는 것은 생명 공학에서 중요한 연구분야이다. 본 논문에서는 방대한 단백질 상호작용 데이터를 유전자 온톨로지와 연계한 시각화를 통하여 효과적으로 직관을 얻을 수 있는 효율적인 단백질 상호작용 네트워크 분석시스템을 다룬다. 단백질 상호작용 네트워크는 데이터 양이 매우 방대하기 때문에 이를 효율적으로 분석하는 방법과 효과적인 시각화 기법이 요구된다. 본 연구에서는 이를 위하여 동적이고 상호작용 가능한 그래프와 관심 노드와 그 주변 노드를 표시하며 점진적으로 탐색할 수 있는 컨텍스트 기반 탐색 기법을 도입하였다. 이 밖에도 특화된 기능으로써 단백질 상호작용과 유전자 온톨로지 간의 빠르고 자유로운 상호참조 기능과 최소 공통 조상을 사용한 유전자 온톨로지 분석 기능 등을 지원한다. 인터페이스 측면에서는 상호참조 기능을 효과적으로 사용하게 하기 위하여 유전자 온톨로지 그래프와 단백질 상호작용의 시각화 결과를 2차원 윈도우로 나란히 보여주는 인터페이스를 디자인 하였다.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2006년도 한국컴퓨터종합학술대회 논문집 Vol.33 No.1 (A)
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• pp.88-90
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• 2006

본 논문에서는 SBML문서를 효율적으로 저장관리 할 수 있는 Gene Ontology 기반의 SBML 문서관리 시스템을 제안한다. SBML은 시스템생물학에서 생화학적 네트워크 데이터의 교환 표준으로 연구 개발되었으며, 다수의 생화학적 네트워크 데이터베이스들이 SBML을 이용하여 데이터를 제공해주고 있다. 이러한 SBML 문서를 통해 서로 다른 데이터베이스 또는 응용 프로그램간 정보를 교환으로 사용되고 있으며, 그 양 또한 급속하게 증가하고 있다. 따라서 본 논문에서는 이러한 대량의 SBML 문서를 효율적으로 저장, 검색 할 수 있는 문서관리시스템을 제안한다. 제안된 시스템은 OODB를 사용하여 효율적으로 SBML 문서를 저장관리하며, Gene Ontology를 기반으로 생화학적 용어의 모호성을 해결하고, SBML문서간의 발생하는 데이터 중복을 제거하여 데이터의 품질을 제고하였다.

• Genomics & Informatics
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• 제4권2호
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• pp.87-93
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• 2006

With the rapid development of MS technologiesy, the demands for a more sophisticated MS interpretation algorithm haves grown as well. We have developed a new protein fingerprinting method using a binomial distribution, (fBIND). With the fBIND, we improved the performance accuracy of protein fingerprinting up to the maximum 49% (more than MOWSE) and 2% than(at a previous binomial distribution approach studied by of Wool et al.) as compared to the established algorithms. Moreover, we also suggest a the statistical approach to define the significance of transcription factors and motifs in the identified proteins based on the Gene Ontology (GO). Abbreviations: fBIND, fingerprinting using binomial distribution; GO, Gene Ontology; MS, Mass Spectrometry; PMF, peptide mass fingerprinting; nr, nonredundant; SGD, Saccharomyces Genome Database

• Journal of Animal Science and Technology
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• 제51권1호
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• pp.1-8
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• 2009

본 연구는 한우의 지방, 간, 등심조직에서 유전자 염기서열을 확보하여 생산된 57,598개의 유전자 발현단편 데이터의 기능규명을 실시하였다. 유전자 발현단편 서열은 Assembly 과정을 통하여 unique한 서열인 4,759 contigs와 7,587 singletons을 확보하였으며, 얻어진 전사체를 이용하여 NCBI의 non-redundant 단백질 데이터베이스에 대하여 서열유사성 검색 (BLAST)을 하여 유전자의 기능을 예측할 수 있었다. 또한 기능에 대한 모호성을 확실히 하기 위해 Gene Ontology 용어를 사용하여 한우의 세 조직에서 확보된 서열들의 생물학적 특성을 기술하였다. Gene Ontology 는 모든 기능이 계층적으로 표현되어 있기 때문에, 각 계층에 대하여 유의적인 기능 여부를 확인하기 위하여 통계 분석인 Pearson's chi-square test를 실시하여 통계적으로 유의한 기능들을 산출할 수 있었다. 그 결과, Molecular function, Biological process, Cellular component 각각의 GO category에서 13, 16, 8개의 유의적인 GO terms이 검출되었다. 또한, 한우의 세 조직에 대하여 조직특이적 유전자의 존재여부를 판단하기 위하여 Audic's test를 실시하여 세 조직에서 각각 조직특이적으로 발현되는 유전자들을 검출할 수 있었다. 이러한 생물정보학적 방법들을 사용하여 한우의 세 조직에서 발현된 대량의 서열들에 대한 기능을 예측할 수 있었으며, 통계 검증을 통하여 유의적으로 검출된 유전자들은 추후에 실험적 검증을 실시하여 충분한 정보를 확보할 수 있을 것으로 사료된다.

• BMB Reports
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• 제47권6호
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• pp.348-353
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• 2014

The speed of sound (SOS) value is an indicator of bone mineral density (BMD). Previous genome-wide association (GWA) studies have identified a number of genes, whose variations may affect BMD levels. However, their biological implications have been elusive. We re-analyzed the GWA study dataset for the SOS values in skeletal sites of 4,659 Korean women, using a gene-set analysis software, GSA-SNP. We identified 10 common representative GO terms, and 17 candidate genes between these two traits (PGS < 0.05). Implication of these GO terms and genes in the bone mechanism is well supported by the literature survey. Interestingly, the significance levels of some member genes were inversely related, in several gene-sets that were shared between two skeletal sites. This implies that biological process, rather than SNP or gene, is the substantial unit of genetic association for SOS in bone. In conclusion, our findings may provide new insights into the biological mechanisms for BMD.

• Molecular & Cellular Toxicology
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• 제2권4호
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• pp.273-278
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• 2006

95 squamous cell lung carcinoma samples (normal tissue: 40 samples, tumor: 55 samples) were analyzed with 8 K cDNA microarray. 1-way ANOVA test was employed to select differentially expressed genes in tumor with FDR<0.01. Among the selected 1,655 genes, final 212 genes were chosen according to the expression fold change and used for following analysis. The expression of up-regulated 64 genes was verified with Reverse Transcription PCR and 10 genes were identified as candidates for SCC markers. In our opinion, those candidates can be exploited as diagnostic or therapeutic purposes. Gene Ontology (GO) based analysis was performed using those 212 genes, and following categories were revealed as significant biological processes: Immune response (GO: 0006955), antigen processing (GO: 0030333), inflammatory response (GO: 0006954), Cell adhesion (GO: 0007155), and Epidermis differentiation (GO: 0008544). Gene set enrichment analysis (GSEA) also carried out on overall gene expression profile with 522 functional gene sets. Glycolysis, cell cycle, K-ras and amino acid biosynthesis related gene sets were most distinguished. These results are consistent with the known characteristics of SCC and may be interconnected to rapid cell proliferation. However, the unexpected results from ERK activation in squamous cell carcinoma gripped our attention, and further studies are under progress.

• Biomolecules & Therapeutics
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• 제27권3호
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• pp.302-310
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• 2019

Melanoma cells have been shown to respond to BRAF inhibitors; however, intrinsic and acquired resistance limits their clinical application. In this study, we performed RNA-Seq analysis with BRAF inhibitor-sensitive (A375P) and -resistant (A375P/Mdr with acquired resistance and SK-MEL-2 with intrinsic resistance) melanoma cell lines, to reveal the genes and pathways potentially involved in intrinsic and acquired resistance to BRAF inhibitors. A total of 546 differentially expressed genes (DEGs), including 239 up-regulated and 307 down-regulated genes, were identified in both intrinsic and acquired resistant cells. Gene ontology (GO) analysis revealed that the top 10 biological processes associated with these genes included angiogenesis, immune response, cell adhesion, antigen processing and presentation, extracellular matrix organization, osteoblast differentiation, collagen catabolic process, viral entry into host cell, cell migration, and positive regulation of protein kinase B signaling. In addition, using the PAN-THER GO classification system, we showed that the highest enriched GOs targeted by the 546 DEGs were responses to cellular processes (ontology: biological process), binding (ontology: molecular function), and cell subcellular localization (ontology: cellular component). Ingenuity pathway analysis (IPA) network analysis showed a network that was common to two BRAF inhibitorresistant cells. Taken together, the present study may provide a useful platform to further reveal biological processes associated with BRAF inhibitor resistance, and present areas for therapeutic tool development to overcome BRAF inhibitor resistance.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2004년도 봄 학술발표논문집 Vol.31 No.1 (B)
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• pp.292-294
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• 2004

최근 pathway 정보의 중요성에 점점 커지고 있다. 하지만 이런 정보를 이용하기에 많은 문제점이 발생하고 있다. 이런 문제점의 해결 방법으로 웹 서비스가 도입되고 있다. 이 논문에서는 주요 pathway 데이터베이스 중 하나인 BIND와 체계적인 개념으로 유전자 용어를 정리한 Gene Ontology(GO)에 대한 웹 서비스를 개발하였다. 개발자들은 이 웹 서비스를 이용하여 BIND와 GO 데이터를 보다 쉽게 이용할 수 있을 것이다.

• Journal of Plant Biotechnology
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• 제43권2호
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• pp.189-203
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• 2016

Brassica oleraceae var capitata is a member of the Brassicaceae family and is widely used as an horticultural crop. In the present study, transcriptome analysis of B. oleraceae L. var capitata was done for the first time using eight-week old seedlings treated with $50{\mu}m$ MeJA, versus mock-treated samples. The complete transcripts for both samples were obtained using the GS-FLX sequencer. Overall, we obtained 275,570 and 266,457 reads from seedlings treated with or without $50{\mu}m$ MeJA, respectively. All the obtained reads were annotated using biological databases and functionally classified using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomics (KEGG). By using GO analyses, putative transcripts were examined in terms of biotic and abiotic stresses, cellular component organization, biogenesis, and secondary metabolic processes. The KEGG pathways for most of the transcripts were involved in carbohydrate metabolism, energy metabolism, and secondary metabolite synthesis. In order to double the sequenced data, we randomly chose two putative genes involved in terpene biosynthetic pathways and studied their transcript patterns under MeJA treatment. This study will provide us a platform to further characterize the genes in B. oleracea var capitata.

• Molecular & Cellular Toxicology
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• 제5권3호
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• pp.179-186
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• 2009

Hexachlorobenzene (HCB) is a bioaccumulative, persistent, and toxic pollutant. HCB is one of the 12 priority of Persistent Organic Pollutants (POPs) intended for global action by the United Nations Environment Program (UNEP) Governing Council. POPs are organic compounds that are resistant to environmental degradation through chemical, biological, and photolytic processes. Some of HCB is ubiquitous in air, water, soil, and biological matrices, as well as in major environmental compartments. HCB has effects on various organs such as thyroid, bone, skin, kidneys and blood cells and especially, revealed strong toxicity to liver. In this study, we identified genes related to hepatotoxiciy induced by HCB in human hepatocellular carcinoma (HepG2) cells using microarray and gene ontology (GO) analysis. Through microarray analysis, we identified 96 up- and 617 down-regulated genes changed by more than 1.5-fold by HCB. And after GO analysis, we determined several key pathways which known as related to hepatotoxicity such as metabolism of xenobiotics by cytochrome P450, complement and coagulation cascades, and tight junction. Thus, our present study suggests that genes expressed by HCB may provide a clue for hepatotoxic mechanism of HCB and gene expression profiling by toxicogenomic analysis also affords promising opportunities to reveal potential new mechanistic markers of toxicity.