• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.787-789
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• 2003

본 논문에서는 생물체의 세포에 존재하는 방대한 단백질들 사이의 복잡한 상화작용 관계 네트워크를 개념화하기 위한 방법을 제안한다. 일반적으로 하나의 단백질은 세포의 특정한 구성요소로서 몇 개의 생물학적 작용에 참여하며 고유의 분자 기능을 수행하게 된다. 즉, 하나의 상호작용 관계 네트워크에 포함된 각각의 단백질들은 구성요소(Cellular Component), 생물학적 작용(Biological Process), 그리고 분자 기능(Molecular Function) 3가지 특징으로 개념화할 수 있다. 또한, 비슷한 특징으로 개념화되는 단백질들은 서로 클러스터링될 수 있기 때문에 단백질 상호작용 네트워크를 일반적인 의미의 개념 네트워크로 표현할 수 있다. 여기서, 단백질 특징을 개념화하기 위해 사용되는 표준개념과 이 개념들 사이의 관계를 정의하는 유전자 온톨로지(Gene Ontology)가 이용된다.

• Biomolecules & Therapeutics
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• v.27 no.3
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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.

• Journal of KIISE:Computing Practices and Letters
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• v.15 no.5
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• pp.375-379
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• 2009

Protein domain is the conserved unit of compact tree-dimensional structure and evolution, which carries specific function. Domains may appear in patterns in proteins, since they have been conserved through the evolution for functional formation of proteins. In this paper, we propose a formulated method for conservation analysis of domain combination based on association rule. Proposed method measures mutual dependency of domains in a combination, as well as co-occurrence frequency of them, which is conventionally used. Based on the method, we extracted conserve domain combinations in S.cerevisiae proteins and analyzed their functions based on Gene Ontology. From the results, we drew conclusions that domains in S.cerevisiae proteins form patterns whose members are highly affiliated to one another, and that extracted patterns tend to be associated with molecular function. Moreover, the results testified to proposed method superior to conventional ones for identifying domain combinations conserved for functional cooperation.

• Genomics & Informatics
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• v.19 no.2
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• pp.14.1-14.6
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• 2021

Coronavirus disease 2019 (COVID-19) is an on-going pandemic disease infecting millions of people across the globe. Recent reports of reduction in antibody levels and the re-emergence of the disease in recovered patients necessitated the understanding of the pandemic at the core level. The cases of multiple organ failures emphasized the consideration of different organ systems while managing the disease. The present study employed RNA sequencing data to determine the disease associated differentially regulated genes and their related protein interactions in several organ systems. It signified the importance of early diagnosis and treatment of the disease. A map of protein interactions of multiple organ systems was built and uncovered CAV1 and CTNNB1 as the top degree nodes. A core interactions sub-network was analyzed to identify different modules of functional significance. AR, CTNNB1, CAV1, and PIK3R1 proteins were unfolded as bridging nodes interconnecting different modules for the information flow across several pathways. The present study also highlighted some of the druggable targets to analyze in drug re-purposing strategies against the COVID-19 pandemic. Therefore, the protein interactions map and the modular interactions of the differentially regulated genes in the multiple organ systems would incline the scientists and researchers to investigate in novel therapeutics for the COVID-19 pandemic expeditiously.

• Proceedings of the Korean Information Science Society Conference
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• 2008.06a
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• pp.41-42
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• 2008

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.5
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• pp.2273-2278
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• 2014

Purpose: The purpose of our study was to explore the molecular mechanisms in the process of oral squamous cells carcinoma (OSCC) development. Method: We downloaded the affymetrix microarray data GSE31853 and identified differentially expressed genes (DEGs) between OSCC and normal tissues. Then Gene Ontology (GO) and Protein-Protein interaction (PPI) networks analysis was conducted to investigate the DEGs at the function level. Results: A total 372 DEGs with logFCI >1 and P value < 0.05 were obtained, including NNMT, BAX, MMP9 and VEGF. The enriched GO terms mainly were associated with the nucleoplasm, response to DNA damage stimuli and DNA repair. PPI network analysis indicated that GMNN and TSPO were significant hub proteins and steroid biosynthesis and synthesis and degradation of ketone bodies were significantly dysregulated pathways. Conclusion: It is concluded that the genes and pathways identified in our work may play critical roles in OSCC development. Our data provides a comprehensive perspective to understand mechanisms underlying OSCC and the significant genes (proteins) and pathways may be targets for therapy in the future.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.131-131
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• 2017

Though the Platycodon grandiflorum, has a broad range of pharmacologic properties, but the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two-dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}2-fold$) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, the frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). Taken together, the protein profile may provide insight clues for better understanding the characteristics of proteins and its metabolic activities in various explants of this essential medicinal plant P. grandiflorum.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.1
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• pp.97-106
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• 2015

Platycodon grandiflorum, commonly known as Doraji in Korea, has a wide range of pharmacologic properties, such as reducing adiposity and hyperlipidemia, and antiatherosclerotic effects. However, the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}$ 2-fold) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). In that way, the exclusive protein profile may provide insight clues for better understanding the characteristics of proteins and metabolic activity in various explants of the economically important medicinal plant Platycodon grandiflorum.

• Journal of Microbiology and Biotechnology
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• v.19 no.10
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• pp.1103-1108
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• 2009

The human immunodeficiency virus (HIV)-l protein Tat acts as a transcription transactivator that stimulates expression of the infected viral genome. It is released from infected cells and can similarly affect neighboring cells. The nucleocapsid is an important protein that has a related significant role in early mRNA expression, and which contributes to the rapid viral replication that occurs during HIV-1 infection. To investigate the interaction between the Tat and nucleocapsid proteins, we utilized cDNA micro arrays using pTat and flag NC cotransfection in HEK 293T cells and reverse transcription-polymerase chain reaction to validate the micro array data. Four upregulated genes and nine downregulated genes were selected as candidate genes. Gene ontology analysis was conducted to define the biological process of the input genes. A proteomic approach using PathwayStudio determined the relationship between Tat and nucleocapsid; two automatically built pathways represented the interactions between the upregulated and downregulated genes. The results indicate that the up- and downregulated genes regulate HIV-1 replication and proliferation, and viral entry.

• Proceedings of the Korean Information Science Society Conference
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• 2006.06c
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• pp.94-96
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• 2006

단백질 상호작용(Protein-Protein interaction : PPI )은 생명체 내에서 생명현상을 유지하기 위한 단백질 간의 유기적인 반응이다. 생물학 실험 도구의 발달로 현재 대량의 PPI 데이터가 발생하고 있으며 이것을 활용하여 생명체를 시스템 관점에서 이해하기 위한 시도가 진행되고 있다. 하지만 현재 PPI 데이터는 중복의 문제, 생물학자들 간의 용어사용의 불일치성 문제로 인해 데이터의 질이 저하되어 분석결과에 부정적인 영향을 끼치고 있다. 본 논문에서는 현재 인간 PPI 데이터의 문제점을 분석하고 이것을 해결하기 위한 온톨로지 기반의 데이터 정제 방법론을 제시한다. 본 연구를 통해 HPRD내에 존재하고 있던 약 52%의 결함이 있는 데이터를 발견하고 인간 단백질 상호작용 데이터의 품질을 향상시켰다.