• 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.

• Journal of Microbiology and Biotechnology
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• v.31 no.4
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• pp.621-629
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• 2021

Shigella flexneri is a facultative intracellular pathogen that causes bacillary dysentery in humans. Infection with S. flexneri can result in more than a million deaths yearly and most of the victims are children in developing countries. Therefore, identifying novel and unique drug targets against this pathogen is instrumental to overcome the problem of drug resistance to the antibiotics given to patients as the current therapy. In this study, a comparative analysis of the metabolic pathways of the host and pathogen was performed to identify this pathogen's essential enzymes for the survival and propose potential drug targets. First, we extracted the metabolic pathways of the host, Homo sapiens, and pathogen, S. flexneri, from the KEGG database. Next, we manually compared the pathways to categorize those that were exclusive to the pathogen. Further, all enzymes for the 26 unique pathways were extracted and submitted to the Geptop tool to identify essential enzymes for further screening in determining the feasibility of the therapeutic targets that were predicted and analyzed using PPI network analysis, subcellular localization, druggability testing, gene ontology and epitope mapping. Using these various criteria, we narrowed it down to prioritize 5 novel drug targets against S. flexneri and one vaccine drug targets against all strains of Shigella. Hence, we suggest the identified enzymes as the best putative drug targets for the effective treatment of S. flexneri.

• BMB Reports
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• v.52 no.2
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• pp.139-144
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• 2019

Breast cancer (BRC) is the most invasive cancer in women. Although the survival rate of BRC is gradually increasing due to improved screening systems, development of novel therapeutic targets for inhibition of BRC proliferation, metastasis and recurrence have been constantly needed. Thus, in this study, we identified overexpression of SETDB1 (SET Domain Bifurcated 1), a histone methyltransferase, in RNA-seq data of BRC derived from TCGA portal. In Gene Ontology (GO) analysis, cell migration-related GO terms were enriched, and we confirmed down-regulation of cell migration/invasion and alteration of EMT /MET markers after knockdown of SETDB1. Moreover, gene network analysis showed that SMAD7 expression is regulated by SETDB1 levels, indicating that up-regulation of SMAD7 by SETDB1 knockdown inhibited BRC metastasis. Therefore, development of SETDB1 inhibitors and functional studies may help develop more effective clinical guidelines for BRC treatment.

• Proceedings of the Korea Information Processing Society Conference
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• 2011.04a
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• pp.333-336
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• 2011

최근 전 세계적으로 소셜 네트워크 서비스의 사용자가 많이 증가하면서 많은 사람들이 소셜 네트워크 서비스를 이용하고 있다. 그리고 소셜 네트워크 서비스를 사용하는 사용자들은 이를 이용하여 많은 정보를 공유하고 있다. 본 논문에서는 소셜 네트워크 서비스 사용자들이 공유하는 정보 중 음악과 관련된 정보와 개방형 API 를 이용하여 MP3 파일의 메타데이터인 ID3 태그 정보를 검색한다. 검색된 결과와 소셜 네트워크 서비스 사용자 정보를 이용하여 ID3 태그 온톨로지를 생성하고 생성된 온톨로지와 온톨로지 추론기를 사용하여 음악과 관련된 다양한 순위 분석 결과와 음악 및 사용자 추천 서비스를 사용자들에게 제공하기 위한 시스템의 설계를 보인다. 본 논문에서 제안한 시스템은 소셜 네트워크 서비스에 실시간으로 등록되는 글을 이용하기 때문에 최근 음악 트렌드를 쉽게 반영한다. 또한 순위 분석을 위해 수동적으로 자료를 수집하는데 들어가는 시간적 비용을 줄여준다. 그리고 제안한 시스템을 사용하여 제공된 정보는 음악 관련 산업에서 마케팅과 사업 전략자료 등 다양한 형태로 활용이 가능하다.

• Journal of KIISE
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• v.44 no.4
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• pp.383-391
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• 2017

As we enter a new era of Big Data, the amount of semantic data has rapidly increased. In order to derive meaningful information from this large semantic data, studies that utilize the SWRL(Semantic Web Rule Language) are being actively conducted. SWRL rules are based on data extracted from a user's empirical knowledge. However, conventional reasoning systems developed on single machines cannot process large scale data. Similarly, multi-node based reasoning systems have performance degradation problems due to network shuffling. Therefore, this paper overcomes the limitations of existing systems and proposes more efficient distributed inference methods. It also introduces data partitioning strategies to minimize network shuffling. In addition, it describes a method for optimizing the incremental reasoning process through data selection and determining the rule order. In order to evaluate the proposed methods, the experiments were conducted using WiseKB consisting of 200 million triples with 83 user defined rules and the overall reasoning task was completed in 32.7 minutes. Also, the experiment results using LUBM bench datasets showed that our approach could perform reasoning twice as fast as MapReduce based reasoning systems.

• Journal of Animal Science and Technology
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• v.54 no.6
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• pp.383-394
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• 2012

Microarray analyses provide information that can be used to enhance the efficiency of livestock production. For example, microarray profiling can potentially identify the biological processes responsible for the phenotypic characteristics of porcine liver. We performed transcriptome profiling to identify differentially expressed genes (DEGs) in liver of pigs from two breeds, the Korean native pigs (KNP) and Yorkshire pigs. We correctly identified expected DEGs using factor analysis for robust microarray summarization (FARMS) and robust multi-array average (RMA) strategies. We identified 366 DEGs in liver (p<0.05, fold-change>2). We also performed functional analyses, including gene ontology and molecular network analyses. In addition, we identified the regulatory relationship between DEGs and their transcription factors using in silico and qRT-PCR analysis. Our findings suggest that DEGs and their transcription factors may have a potential role in adipogenesis and/or lipid deposition in liver tissues of two pig breeds.

• Journal of Intelligence and Information Systems
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• v.10 no.2
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• pp.1-13
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• 2004

This paper presents a method for the multilingual product retrieval agent through XML and the semantic networks in e-commerce. Retrieval for products is an important process, since it represents interfaces of the customer contact to the e-commerce. Keyword-based retrieval is efficient as long as the product information is structured and organized. But when the product information is expressed across many online shopping malls, especially when it is expressed in different languages with cultural backgrounds, buyers' product retrieval needs language translation with ambiguities resolved in a specific context. This paper presents a RDF modeling case that resolves semantic problems in the representation of product information and across the boundaries of language domains. With adoption of UNSPSC code system, this paper designs and implements an architecture for the multilingual product retrieval agents. The architecture is based on the central repository model of product catalog management with distributed updating processes. It also includes the perspectives of buyers and suppliers. And the consistency and version management of product information are controlled by UNSPSC code system. The multilingual product names are resolved by semantic networks, thesaurus and ontology dictionary for product names.

• The KIPS Transactions:PartD
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• v.18D no.2
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• pp.89-100
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• 2011

The CNV (Copy Number Variation) which is one of the genetic structural variations in human genome is closely related with the function of gene. In particular, the genome-wide association studies for genetic diseased persons have been researched. However, there have been few studies which infer the genetic function of CNV with normal human. In this paper, we propose the analysis method to reveal the functional relationship between common CNV and genes without considering their genomic loci. To achieve that, we propose the data integration method for heterogeneity biological data and novel measurement which can calculate the correlation between common CNV and genes. To verify the significance of proposed method, we has experimented several verification tests with GO database. The result showed that the novel measurement had enough significance compared with random test and the proposed method could systematically produce the candidates of genetic function which have strong correlation with common CNV.

• Journal of KIISE:Software and Applications
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• v.36 no.1
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• pp.92-108
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• 2009

The Princeton WordNet (PWN), which was developed during last 20 years since the mid 80, aimed at representing a mental lexicon inside the human mind. Its potentiality, applicability and portability were more appreciated in the fields of NLP and KE than in cognitive psychology. The semantic and knowledge processing is indispensable in order to obtain useful information using human languages, in the CMC and HCI environment. The PWN is able to provide such NLP-based systems with 'concrete' semantic units and their network. Referenced to the PWN, about 50 wordnets of different languages were developed during last 10 years and they enable a variety of multilingual processing applications. This paper aims at describing PWN-referenced Korean Wordnet, KorLex 1.5, which was developed from 2004 to 2007, and which contains currently about 130,000 synsets and 150,000 word senses for nouns, verbs, adjectives, adverbs, and classifiers.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.290-296
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• 2019

Objective: Pigs share many physiological, anatomical and genomic similarities with humans, which make them suitable models for biomedical researches. Understanding the genetic status of Yucatan miniature pigs (YMPs) and their association with human diseases will help to assess their potential as biomedical model animals. This study was performed to identify non-synonymous single nucleotide polymorphisms (nsSNPs) in selective sweep regions of the genome of YMPs and present the genetic nsSNP distributions that are potentially associated with disease occurrence in humans. Methods: nsSNPs in whole genome resequencing data from 12 YMPs were identified and annotated to predict their possible effects on protein function. Sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 analyses were used, and gene ontology (GO) network and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. Results: The results showed that 8,462 genes, encompassing 72,067 nsSNPs were identified, and 118 nsSNPs in 46 genes were predicted as deleterious. GO network analysis classified 13 genes into 5 GO terms (p<0.05) that were associated with kidney development and metabolic processes. Seven genes encompassing nsSNPs were classified into the term associated with Alzheimer's disease by referencing the genetic association database. The KEGG pathway analysis identified only one significantly enriched pathway (p<0.05), hsa04080: Neuroactive ligand-receptor interaction, among the transcripts. Conclusion: The number of deleterious nsSNPs in YMPs was identified and then these variants-containing genes in YMPs data were adopted as the putative human diseases-related genes. The results revealed that many genes encompassing nsSNPs in YMPs were related to the various human genes which are potentially associated with kidney development and metabolic processes as well as human disease occurrence.