• Genomics & Informatics
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• v.5 no.1
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• pp.10-18
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• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1110-1118
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• 2018

Objective: This study was intended to identify genes positively selected in Thoroughbred horses (THBs) that potentially contribute to their running performances. Methods: The genomes of THB and Jeju horses (JH, Korean native horse) were compared to identify genes positively selected in THB. We performed cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio test (XP-CLR) statistical methods for our analysis using whole genome resequencing data of 14 THB and 6 JH. Results: We identified 98 (XP-EHH) and 200 (XP-CLR) genes that are under positive selection in THB. Gene enrichment analysis identified 72 gene ontology biological process (GO BP) terms. The genes and GO BP terms explained some of THB's characteristics such as immunity, energy metabolism and eye size and function related to running performances. GO BP terms that play key roles in several cell signaling mechanisms, which affected ocular size and visual functions were identified. GO BP term Eye photoreceptor cell differentiation is among the terms annotated presumed to affect eye size. Conclusion: Our analysis revealed some positively selected candidate genes in THB related to their racing performances. The genes detected are related to the immunity, ocular size and function, and energy metabolism.

• Genomics & Informatics
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• v.17 no.3
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• pp.31.1-31.7
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• 2019

We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript exerts in a cell as enzyme or protein function after translation. We used the genome-wide association study (GWAS) beta effect and transcription level in RNA-sequencing to estimate TC. The trait was body fat percent and the transcript reads were obtained from the human protein atlas. The assumption was that the GWAS beta effect is the gene's effect and TC was related to the corresponding gene effect and transcript reads. Further, we surveyed gene ontology (GO) in the highest TC and the lowest TC genes. The most frequent GOs with the highest TC were neuronal-related and cell projection organization related. The most frequent GOs with the lowest TC were wound-healing related and embryo development related. We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.

• Molecules and Cells
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• v.21 no.2
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• pp.269-275
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• 2006

A recent report of the Korean Intellectual Property Office(KIPO) showed that the number of biological sequence-based patents is rapidly increasing in Korea. We present biological features of Korean patented sequences though bioinformatic analysis. The analysis is divided into two steps. The first is an annotation step in which the patented sequences were annotated with the Reference Sequence (RefSeq) database. The second is an association step in which the patented sequences were linked to genes, diseases, pathway, and biological functions. We used Entrez Gene, Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Through the association analysis, we found that nearly 2.6% of human genes were associated with Korean patenting, compared to 20% of human genes in the U.S. patent. The association between the biological functions and the patented sequences indicated that genes whose products act as hormones on defense responses in the extra-cellular environments were the most highly targeted for patenting. The analysis data are available at http://www.patome.net

• Journal of Plant Biotechnology
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• v.50
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• pp.127-136
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• 2023

Water scarcity decreases the rate of photosynthesis and, consequently, the yield of banana plants (Musa spp). In this study, transcriptome analysis was performed to identify photosynthesis-related genes in banana plants and determine their expression profiles under water stress conditions. Banana plantlets were in vitro cultured on Murashige and Skoog agar medium with and without 10% polyethylene glycol and marked as BP10 and BK. Chlorophyll contents in the plant shoots were determined spectrophotometrically. Two cDNA libraries generated from BK and BP10 plantlets, respectively, were used as the reference for transcriptome data. Gene ontology (GO) enrichment analysis was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) and visualized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway prediction. Morphological observations indicated that water deficiency caused chlorosis and reduced the shoot chlorophyll content of banana plantlets. GO enrichment identified 52 photosynthesis-related genes that were affected by water stress. KEGG visualization revealed the pathways related to the 52 photosynthesisr-elated genes and their allocations in four GO terms. Four, 12, 15, and 21 genes were related to chlorophyll biosynthesis, the Calvin cycle, the photosynthetic electron transfer chain, and the light-harvesting complex, respectively. Differentially expressed gene (DEG) analysis using DESeq revealed that 45 genes were down-regulated, whereas seven genes were up-regulated. Four of the down-regulated genes were responsible for chlorophyll biosynthesis and appeared to cause the decrease in the banana leaf chlorophyll content. Among the annotated DEGs, MaPNDO, MaPSAL, and MaFEDA were selected and validated using quantitative real-time PCR.

• Genes and Genomics
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• v.40 no.12
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• pp.1331-1338
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• 2018

Although there have been plenty of dominance deviation analysis, few studies have dealt with multiple phenotypes. Because researchers focused on multiple phenotypes (final weight and backfat thickness) of Landrace pigs, the classification of the genes was possible. With genome-wide association studies (GWASs), we analyzed the additive and dominance effects of the single nucleotide polymorphisms (SNPs). The classification of the pig genes into four categories (overdominance in final weight, overdominance in backfat thickness and overdominance in final weight, underdominance in backfat thickness, etc.) can enable us not only to analyze each phenotype's dominant effects, but also to illustrate the gene ontology (GO) analysis with different aspects. We aimed to determine the additive and dominant effect in backfat thickness and final weight and performed GO analysis. Using additive model and dominance deviation analysis in GWASs, Landrace pigs' overdominant and underdominant SNP effects in final weight and backfat thickness were surveyed. Then through GO analysis, we investigated the genes that were classified in the GWASs. The major GO terms of the underdominant effects in final weight and overdominant effects in backfat thickness were ion transport with the SLC8A3, KCNJ16, P2RX7 and TRPC3 genes. Interestingly, the major GO terms in the underdominant effects in the final weight and the underdominant effects in the backfat thickness were the regulation of ion transport with the STAC, GCK, TRPC6, UBASH3B, CAMK2D, CACNG4 and SCN4B genes. These results demonstrate that ion transport and ion transport regulation genes have distinct dominant effects. Through GWASs using the mode of linear additive model and dominance deviation, overdominant effects and underdominant effects in backfat thickness was contrary to each other in GO terms (ion transport and ion transport regulation, respectively). Additionally, because ion transport and ion transport regulation genes are associative with adipose tissue accumulation, we could infer that these two groups of genes had to do with unique fat accumulation mechanisms in Landrace pigs.

• BMB Reports
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• v.57 no.5
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• pp.232-237
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• 2024

This study investigated how adipose tissue-derived mesenchymal stem cells (AT-MSCs) respond to chondrogenic induction using droplet-based single-cell RNA sequencing (scRNA-seq). We analyzed 37,219 high-quality transcripts from control cells and cells induced for 1 week (1W) and 2 weeks (2W). Four distinct cell clusters (0-3), undetectable by bulk analysis, exhibited varying proportions. Cluster 1 dominated in control and 1W cells, whereas clusters (3, 2, and 0) exclusively dominated in control, 1W, and 2W cells, respectively. Furthermore, heterogeneous chondrogenic markers expression within clusters emerged. Gene ontology (GO) enrichment analysis of differentially expressed genes unveiled cluster-specific variations in key biological processes (BP): (1) Cluster 1 exhibited up-regulation of GO-BP terms related to ribosome biogenesis and translational control, crucial for maintaining stem cell properties and homeostasis; (2) Additionally, cluster 1 showed up-regulation of GO-BP terms associated with mitochondrial oxidative metabolism; (3) Cluster 3 displayed up-regulation of GO-BP terms related to cell proliferation; (4) Clusters 0 and 2 demonstrated similar up-regulation of GO-BP terms linked to collagen fibril organization and supramolecular fiber organization. However, only cluster 0 showed a significant decrease in GO-BP terms related to ribosome production, implying a potential correlation between ribosome regulation and the differentiation stages of AT-MSCs. Overall, our findings highlight heterogeneous cell clusters with varying balances between proliferation and differentiation before, and after, chondrogenic stimulation. This provides enhanced insights into the single-cell dynamics of AT-MSCs during chondrogenic differentiation.

• Journal of Physiology & Pathology in Korean Medicine
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• v.38 no.1
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• pp.22-26
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• 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.

• Journal of KIISE:Databases
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• v.34 no.6
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• pp.546-553
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• 2007

As ontologies are used widely, interest for semantic similarity search is also increasing. In this paper, we suggest a query evaluation scheme for k-nearest neighbor query, which retrieves k most similar objects to the query object. We use the best match method to calculate the semantic similarity between objects and use the signature tree to index annotation information of objects in database. The signature tree is usually used for the set similarity search. When we use the signature tree in similarity search, we are required to predict the upper-bound of similarity for a node; the highest similarity value which can be found when we traverse into the node. So we suggest a prediction function for the best match similarity function and prove the correctness of the prediction. And we modify the original signature tree structure for same signatures not to be stored redundantly. This improved structure of signature tree not only reduces the size of signature tree but also increases the efficiency of query evaluation. We use the Gene Ontology(GO) for our experiments, which provides large ontologies and large amount of annotation data. Using GO, we show that proposed method improves query efficiency and present several experimental results varying the page size and using several node-splitting methods.

• Proceedings of the Korean Information Science Society Conference
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• 2006.10c
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• pp.246-251
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• 2006

마이크로어레이 실험은 수 천에서 수 만개의 유전자 발현 결과를 동시에 측정할 수 있어 질병의 발현 형질 분류 등에 유용하게 이용되고 있다. 그러나 마이크로어레이 실험은 동일한 플랫폼의 실험이라 할지라도 환경 등에 따라 그 실험 결과에 차이가 나는 등 오차를 항상 포함하고 있다. 또한 마이크로어레이 실험은 아직 고가의 실험으로 분류되어 다수의 샘플에 대한 반복 실험 결과를 얻기 어려운 상황이다. 따라서 이종의 플랫폼, 데이터 포맷, 정규화 기법 등이 서로 다른 데이터를 효율적으로 통합하여 유용한 정보를 추출하는 새로운 방식의 개발이 필요하다. 본 논문은 이와 같은 문제를 해결하기 위한 기초 단계 연구 결과이다. 마이크로어레이 실험 데이터로부터 통계적 방법을 이용하여 유의(informative) 유전자를 추출하고 유전자 온톨로지(Gene Ontology : GO)와의 연계를 통하여 유전자 정보의 기능적 분류 결과를 사용자에게 제공하는 유전자 기능 분석 시스템의 설계 및 구현 방안을 보인다. 본 시스템의 실험방법에서는 3-Fold Filtering 기법을 통하여 발현 차가 큰 유전자를 추출하고, t-검정 기법에 의하여 이들 유전자를 순위화 하였으며, 이 중 상위 100개의 유전자를 유의 유전자로 추출하였다. 다음, 이 들 유의 유전자의 t-검정 값을 GO의 유전자 기능을 나타내는 해당 텀 (term)에 가중치로 부과하여 각 유전자들과 기능적으로 연관성이 높은 텀들을 추출한다. 또한 본 연구의 유효성을 검증하기 위하여 본 시스템에 의한 마이크로어레이 데이터 분석 결과를 전문가에 의한 유전자 기능 분석 결과와 비교한다.투명성 있는 서비스를 제공하고 높은 신뢰성과 안정성이 확보될 수 있도록 구성하고자 한다. Query 수행을 여러 서버로 분산처리하게 함으로써 성능에 대한 신뢰성을 향상 시킬 수 있는 Load Balancing System을 제안한다.할 때 가장 효과적인 라우팅 프로토콜이라고 할 수 있다.iRNA 상의 의존관계를 분석할 수 있었다.수안보 등 지역에서 나타난다 이러한 이상대 주변에는 대개 온천이 발달되어 있었거나 새로 개발되어 있는 곳이다. 온천에 이용하고 있는 시추공의 자료는 배제하였으나 온천이응으로 직접적으로 영향을 받지 않은 시추공의 자료는 사용하였다 이러한 온천 주변 지역이라 하더라도 실제는 온천의 pumping 으로 인한 대류현상으로 주변 일대의 온도를 올려놓았기 때문에 비교적 높은 지열류량 값을 보인다. 한편 한반도 남동부 일대는 이번 추가된 자료에 의해 새로운 지열류량 분포 변화가 나타났다 강원 북부 오색온천지역 부근에서 높은 지열류량 분포를 보이며 또한 우리나라 대단층 중의 하나인 양산단층과 같은 방향으로 발달한 밀양단층, 모량단층, 동래단층 등 주변부로 NNE-SSW 방향의 지열류량 이상대가 발달한다. 이것으로 볼 때 지열류량은 지질구조와 무관하지 않음을 파악할 수 있다. 특히 이러한 단층대 주변은 지열수의 순환이 깊은 심도까지 가능하므로 이러한 대류현상으로 지표부근까지 높은 지온 전달이 되어 나타나는 것으로 판단된다.의 안정된 방사성표지효율을 보였다. $^{99m}Tc$-transferrin을 이용한 감염영상을 성공적으로 얻을 수 있었으며, $^{67}Ga$-citrate