• Genomics & Informatics
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• 제21권2호
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• pp.22.1-22.15
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• 2023

Kidney renal clear cell carcinoma (KIRC) is one of the most aggressive cancer type of the urinary system. Metastatic KIRC patients have poor prognosis and limited therapeutic options. Ankyrin 3 (ANK3) is a scaffold protein that plays important roles in maintaining physiological function of the kidney and its alteration is implicated in many cancers. In this study, we investigated differential expression of ANK3 in KIRC using GEPIA2, UALCAN, and HPA databases. Survival analysis was performed by GEPIA2, Kaplan-Meier plotter, and OS-kirc databases. Genetic alterations of ANK3 in KIRC were assessed using cBioPortal database. Interaction network and functional enrichment analyses of ANK3-correlated genes in KIRC were performed using GeneMANIA and Shiny GO, respectively. Finally, the TIMER2.0 database was used to assess correlation between ANK3 expression and immune infiltration in KIRC. We found that ANK3 expression was significantly decreased in KIRC compared to normal tissues. The KIRC patients with low ANK3 expression had poorer survival outcomes than those with high ANK3 expression. ANK3 mutations were found in 2.4% of KIRC patients and were frequently co-mutated with several genes with a prognostic significance. ANK3-correlated genes were significantly enriched in various biological processes, mainly involved in peroxisome proliferator-activated receptor (PPAR) signaling pathway, in which positive correlations of ANK3 with PPARA and PPARG expressions were confirmed. Expression of ANK3 in KIRC was significantly correlated with infiltration level of B cell, CD8+ T cell, macrophage, and neutrophil. These findings suggested that ANK3 could serve as a prognostic biomarker and promising therapeutic target for KIRC.

• BMB Reports
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• 제41권3호
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• pp.259-265
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• 2008

Three peroxidase (POD) cDNAs were isolated from dehydration-treated fibrous roots of sweetpotato (Ipomoea batatas) plant via the screening of a cDNA library, and their expressions were assessed to characterize functions of each POD in relation to environmental stress. Three PODs were divided into two groups, designated the basic PODs (swpb4, swpb5) and the anionic PODs (swpa7), on the basis of the pI values of mature proteins. Fluorescence microscope analysis indicated that three PODs are secreted into the extracellular space. RT-PCR analysis revealed that POD genes have diverse expression patterns in a variety of plant tissues. Swpb4 was abundantly expressed in stem tissues, whereas the expression levels of swpb5 and swpa7 transcripts were high in fibrous and thick pigmented roots. Swpb4 and swpa7 showed abundant expression levels in suspension cultured cells. Three POD genes responded differently in the leaf and fibrous roots in response to a variety of stresses including dehydration, temperature stress, stress-associated chemicals, and pathogenic bacteria.

• 대한한방부인과학회지
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• 제19권2호
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• pp.214-225
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• 2006

Purpose : This study was aimed to investigate the inhibitory effect of Corydalis Tuber on the proliferation of human uterine leiomyoma cell and the expression of gene related the mechanism of cell apoptosis. Methods : We counted the number of suvival cells treated with indicated concentration of Corydalis Tuber and investigated cell viability by MTS assay. Furthermore, flow cytometric analyis were used to dissect between necrosis and apoptosis related with cell cycle and then we observed the differential gene expression by western blot analysis. Results : 1) The inhibitory effect on the proliferation of uterine leiomyoma cell treated with Corydalis Tuber was increased in a concentration and time proportional. 2) The result of flow cytometry analysis, subG1 phase arrest related cell apoptosis was not investigated in uterine leiomyoma cell treated Corydalis Tuber but showed G2/M phase prolongation. 3) The gene expression of p27, p21 related cell cycle was increased according to increasing concentration, but p53 was not exchanged. 4) The dephosphorylation of pRb gene were increased dependent on treatment concentration and pro-caspase 3, CDK4 were not exchanged. Conclusion : This study showed that Corydalis Tuber have the inhibitory effect on the proliferation of human uterine leiomyoma cell but the effect was thoughted no relationship with apoptosis. The inhibitory effect was suggested that dephosphorylation of pRb gene induced with increasing p21, p27 prolonged cell division in G2/M phase.

• Genomics & Informatics
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• 제19권2호
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• pp.17.1-17.13
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• 2021

Breast cancer is one of the leading causes of cancer in women all over the world and accounts for ~25% of newly observed cancers in women. Epigenetic modifications influence differential expression of genes through non-coding RNA and play a crucial role in cancer regulation. In the present study, epigenetic regulation of gene expression by in-silico analysis of histone modifications using chromatin immunoprecipitation sequencing (ChIP-Seq) has been carried out. Histone modification data of H3K4me3 from one normal-like and four breast cancer cell lines were used to predict miRNA expression at the promoter level. Predicted miRNA promoters (based on ChIP-Seq) were used as a probe to identify gene targets. Five triple-negative breast cancer (TNBC)-specific miRNAs (miR153-1, miR4767, miR4487, miR6720, and miR-LET7I) were identified and corresponding 13 gene targets were predicted. Eight miRNA promoter peaks were predicted to be differentially expressed in at least three breast cancer cell lines (miR4512, miR6791, miR330, miR3180-3, miR6080, miR5787, miR6733, and miR3613). A total of 44 gene targets were identified based on the 3'-untranslated regions of downregulated mRNA genes that contain putative binding targets to these eight miRNAs. These include 17 and 15 genes in luminal-A type and TNBC respectively, that have been reported to be associated with breast cancer regulation. Of the remaining 12 genes, seven (A4GALT, C2ORF74, HRCT1, ZC4H2, ZNF512, ZNF655, and ZNF608) show similar relative expression profiles in large patient samples and other breast cancer cell lines thereby giving insight into predicted role of H3K4me3 mediated gene regulation via the miRNA-mRNA axis.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.197-197
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• 2022

Wheat is highly susceptible to heat stress, which significantly reduces grain yield. In this study, we used RNA-seq technology to analyze the transcript expression at three different time-points after heat treatment in three cultivars differing in their susceptibility to heat stress: Jopum, Keumkang, and Olgeuru. A total of 11,751, 8850, and 14,711; 10,959,7946, and 14,205; and 22,895,13,060, and 19,408 differentially-expressed genes (log2 fold-change > 1 and FDR (padj) < 0.05) were identified in Jopum, Keumkang, and Olgeuru in the control vs. 6-h, in the control vs. 12-h, and in the 6-h vs. 12-h heat treatment, respectively. Functional enrichment analysis showed that the biological processes for DEGs, such as the cellular response to heat and oxidative stress-and including the removal of superoxide radicals and the positive regulation of superoxide dismutase activity-were significantly enriched among the three comparisons in all three cultivars. Furthermore, we investigated the differential expression patterns of reactive oxygen species (ROS)-scavenging enzymes, heat shock proteins, and heat-stress transcription factors using qRT-PCR to confirm the differences in gene expression among the three varieties under heat stress. This study contributes to a better understanding of the wheat heat-stress response at the early growth stage and the varietal differences in heat tolerancea.

• ALGAE
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• 제39권1호
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• pp.17-30
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• 2024

Red macroalga Pyropia yezoensis is a high valuable cultivated marine crop. Its acclimation to cold stress is especially important for long cultivation period across winter in coasts of warm temperate zone in East Asia. In this study, the response of P. yezoensis thalli to low temperature was analyzed on physiology and transcriptome level, to explore its acclimation mechanism to cold stress. The results showed that the practical photosynthesis activity (indicated by Φ_PSII and qP) was depressed and pigment allophycocyanin content was decreased during the cold stress of 48 h. However, the F_v/F_m and non-photochemical quenching increased significantly after 24 h, and the average growth rate of thalli also rebounded from 24 to 48 h, indicating a certain extent of acclimation to cold stress. On transcriptionally, the low temperature promoted the expression of differentially expressed genes (DEGs) related to carbohydrate metabolism and energy metabolism, while genes related to photosynthetic system were depressed. The increased expression of DEGs involved in ribosomal biogenesis and lipid metabolism which could accelerate protein synthesis and enhance the degree of fatty acid unsaturation, might help P. yezoensis thallus cells to cope with cold stress. Further co-expression network analysis revealed differential expression trends along with stress time, and corresponding hub genes play important roles in the systemic acquired acclimation to cold stress. This study provides basic mechanisms of P. yezoensis acclimation to cold temperature and may aid in exploration of functional genes for genetic breeding of economic macroalgae.

• 대한가정학회지
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• 제40권1호
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• pp.135-146
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• 2002

The Purpose of this study was to identify the sensibility elements and the evaluative dimensions of internet fashion shopping mall to supply optimal experience to the customer. First, association words for internet fashion shopping mall by open-ended method and sensibility-expression-adjective feeling as navigating personally 57 shopping mall dealing with fashion products were collected. Collected adjectives were ranked after making index by frequency and diversity. Then, correlation analysis was executed to extract independent adjective and their opposite words. Semantic differential scale was made for internet-fashion-shopping-mall-evaluation. After preliminary investigation with this scale, factor analysis was implemented. 12 sensibility evaluation words were extracted. Then, 200 subjects evaluated satisfaction degree for 8 selected shopping mall. To explain the hierarchy of internet fashion shopping mall, cluster analysis was applied. The understanding of sensibility element and evaluative dimensions of internet fashion shopping mall can be utilized efficiently as basic materials when marketer plans internet shopping mall design and makes marketing strategy.

• Communications for Statistical Applications and Methods
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• 제26권4호
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• pp.411-430
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• 2019

Tumor development is driven by complex combinations of biological elements. Recent advances suggest that molecularly distinct subtypes of breast cancers may respond differently to pathway-targeted therapies. Thus, it is important to dissect pathway disturbances by integrating multiple molecular profiles, such as genetic, genomic and epigenomic data. However, missing data are often present in the -omic profiles of interest. Motivated by genomic data integration and imputation, we present a new statistical framework for pathway significance analysis. Specifically, we develop a new strategy for imputation of missing data in large-scale genomic studies, which adapts low-rank, structured matrix completion. Our iterative strategy enables us to impute missing data in complex configurations across multiple data platforms. In turn, we perform large-scale pathway analysis integrating gene expression, copy number, and methylation data. The advantages of the proposed statistical framework are demonstrated through simulations and real applications to breast cancer subtypes. We demonstrate superior power to identify pathway disturbances, compared with other imputation strategies. We also identify differential pathway activity across different breast tumor subtypes.

• 한국작물학회지
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• 제60권1호
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• pp.114-122
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• 2015

침종 기간과 침종 후 발아의 유무에 따른 단백질 발현을 이차원전기영동을 이용하여 단백질 발현양상을 확인하고 비교 분석한 결과, 침종 기간과 침종 후 발아의 유무에 따른 단백질 발현 양상은 전반적으로 매우 유사하였으며, 주요 단백질의 발현에는 차이가 없었다. 침종 기간에 따른 품종별 단백질 발현 양상은 침종 기간이 길어짐에 따라 단백질 발현정도가 점차 증가되는 것을 확인할 수 있었다. 공시품종들 중 황금콩, 단엽콩, Peking이 다른 품종들에 비하여 침종 4일후에 단백질 발현정도가 급격히 증가하는 것을 알 수 있었다. 침종 후 발아 유무에 따른 단백질 발현양상은 소수의 단백질 spot들을 제외하고는 전반적으로 모든 공시 품종들에서 발아한 종자에서의 단백질 발현정도는 미발아 종자에서보다 높게 확인되었다.

• Asian-Australasian Journal of Animal Sciences
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• 제22권8호
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• pp.1091-1101
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• 2009

In an attempt to understand the biochemical mechanism for the synthesis of the anabolic steroid, 19-nortestosterone, produced by prepubertal boar testes and its physiological role, normalized complementary DNA (cDNA) from boar testes was generated. DNA sequencing of 2,016 randomly selected clones yielded 794,116 base pairs of high quality nucleotide sequence. Computer-assisted assembly of the nucleotide sequence of each clone resulted in 423 contigs and 403 singletons including several genes for steroidogenic enzymes and molecules related to steroid metabolism. Analysis of gene expression pattern by use of the presently-fabricated cDNA microarray identified a number of genes that were differentially expressed during the postnatal development period in boar testes. Two genes of unknown function were identified to be highly expressed in the testis of 2-weeks-old neonatal boar. In addition, the sequencing of open reading frames of these genes revealed their homology with human alpha hemoglobin and Homo sapiens hypothetical LOC643669, transcript variant 1. Moreover, the transcripts of these genes were also detected in porcine muscle and adipocytes, in addition to Leydig cells of pigs.