• Journal of the Korean Data and Information Science Society
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• 제25권5호
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• pp.971-986
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• 2014

동시에 여러 개의 가설검정 수행시 귀무가설이 참일 경우 귀무가설을 기각할 확률이 커지는 문제가 발생한다. 이러한 다중검정 문제 해결을 위해 여러 연구에서는 가설검정시 필요한 집단별 오류율(FWER; family-wise error rate), 위발견율 (FDR; false discovery rate) 또는 위비발견율 (FNR; false nondiscovery rate) 과 통계량을 고려하여 검정력을 높이고자 하였다. 본 연구에서는 T 통계량, 수정된 T 통계량, 그리고 LPE (local pooled error) 통계량 기반 P값을 이용한 Bonferroni (1960) 방법, Holm (1979) 방법, Benjamini와 Hochberg (1995) 방법과 Benjamini와 Yekutieli (2001) 방법 그리고 Z 통계량 기반 Sun과 Cai (2007) 방법을 고찰하고 모의실험을 통해 다중검정 능력을 비교하였다. 또한 실제 데이터로 애기장대 유전자 발현 데이터에 대해 여러 가지 다중검정법을 통해 유의한 유전자들을 선별하였다.

• Genomics & Informatics
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• 제11권4호
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• pp.245-253
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• 2013

A radioresistant cell line was established by fractionated ionizing radiation (IR) and assessed by a clonogenic assay, flow cytometry, and Western blot analysis, as well as zymography and a wound healing assay. Microarray was performed to profile global expression and to search for differentially expressed genes (DEGs) in response to IR. H460R cells demonstrated increased cell scattering and acidic vesicular organelles compared with parental cells. Concomitantly, H460R cells showed characteristics of increased migration and matrix metalloproteinase activity. In addition, H460R cells were resistant to IR, exhibiting reduced expression levels of ionizing responsive proteins (p-p53 and ${\gamma}$-H2AX); apoptosis-related molecules, such as cleaved poly(ADP ribose) polymerase; and endoplasmic reticulum stress-related molecules, such as glucose-regulated protein (GRP78) and C/EBP-homologous protein compared with parental cells, whereas the expression of anti-apoptotic X-linked inhibitor of apoptosis protein was increased. Among DEGs, syntrophin beta 2 (SNTB2) significantly increased in H460R cells in response to IR. Knockdown of SNTB2 by siRNA was more sensitive than the control after IR exposure in H460, H460R, and H1299 cells. Our study suggests that H460R cells have differential properties, including cell morphology, potential for metastasis, and resistance to IR, compared with parental cells. In addition, SNTB2 may play an important role in radioresistance. H460R cells could be helpful in in vitro systems for elucidating the molecular mechanisms of and discovering drugs to overcome radioresistance in lung cancer therapy.

• Journal of Ginseng Research
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• 제43권4호
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• pp.645-653
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• 2019

Background: Cytochrome P450 enzymes catalyze a wide range of reactions in plant metabolism. Besides their physiological functions on primary and secondary metabolites, P450s are also involved in herbicide detoxification via hydroxylation or dealkylation. Ginseng as a perennial plant offers more sustainable solutions to herbicide resistance. Methods: Tissue-specific gene expression and differentially modulated transcripts were monitored by quantitative real-time polymerase chain reaction. As a tool to evaluate the function of PgCYP736A12, the 35S promoter was used to overexpress the gene in Arabidopsis. Protein localization was visualized using confocal microscopy by tagging the fluorescent protein. Tolerance to herbicides was analyzed by growing seeds and seedlings on Murashige and Skoog medium containing chlorotoluron. Results: The expression of PgCYP736A12 was three-fold more in leaves compared with other tissues from two-year-old ginseng plants. Transcript levels were similarly upregulated by treatment with abscisic acid, hydrogen peroxide, and NaCl, the highest being with salicylic acid. Jasmonic acid treatment did not alter the mRNA levels of PgCYP736A12. Transgenic lines displayed slightly reduced plant height and were able to tolerate the herbicide chlorotoluron. Reduced stem elongation might be correlated with increased expression of genes involved in bioconversion of gibberellin to inactive forms. PgCYP736A12 protein localized to the cytoplasm and nucleus. Conclusion: PgCYP736A12 does not respond to the well-known secondary metabolite elicitor jasmonic acid, which suggests that it may not function in ginsenoside biosynthesis. Heterologous overexpression of PgCYP736A12 reveals that this gene is actually involved in herbicide metabolism.

• Animal Bioscience
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• 제35권6호
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• pp.814-825
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• 2022

Objective: This study was conducted to identify the functional long non-coding RNAs (lncRNAs) for swine lactation by RNA-seq data of mammary gland. Methods: According to the RNA-seq data of swine mammary gland, we screened lncRNAs, performed differential expression analysis, and confirmed the functional lncRNAs for swine lactation by validation of genome wide association study (GWAS) signals, functional annotation and weighted gene co-expression network analysis (WGCNA). Results: We totally identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition, and the expressions of most of lncRNAs were strongly changed from day -2 to day +1. Further, the GWAS signals of sow milk ability trait were significantly enriched in DE lncRNAs. Functional annotation revealed that these DE lncRNAs were mainly involved in mammary gland and lactation developing, milk composition metabolism and colostrum function. By performing weighted WGCNA, we identified 7 out of 12 lncRNA-mRNA modules that were highly associated with the mammary gland at day -14, day -2, and day +1, in which, 35 lncRNAs and 319 mRNAs were involved. Conclusion: This study suggested that 18 lncRNAs and their 20 target genes were promising candidates for swine parturition and colostrum occurrence processes. Our research provided new insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.

• 대한임상검사과학회지
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• 제48권1호
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• pp.8-14
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• 2016

포유류의 난소에서 과립막 세포)는 난포내 난자를 둘러싸고 난자 뿐만 아니라 난포의 발달에 필요한 상태를 만드는데 중요한 역할을 한다, 그리고 협막세포 등의 성장과 분화를 조절하는 매우 복잡한 과정이다. 본 연구의 목적은 성장이 정지되어 있는 원시난포에서 성장이 개시되는 1차난포, 2차난포로 전환하는 동안에 관여하여 발현하는 유전자를 조사하는 것이다. 본 연구에서는 5일자, 12일자 난소로부터 총 리보핵산을 추출하여 동량의 RNA로부터 cDNA를 합성하여 ACP-PCR을 수행하였다. 서로 다르게 발현하는 유전자들 (DEGs)을 클로닝과 BLAST를 통한 염기서열 분석하였다. Anxa11과 Plekha5는 5일자 난소에서 높게 나타났으며 특히 난자핵과 세포질에서 높게 발현하였다. 이에 반해 과립막 세포에서는 난포발달단계에 따라 증가하는 양상을 보였다. 본 연구에서 성공적으로 5일, 12일 난소에서 서로 다르게 발현하는 발현유전자 목록을 일부 찾아 확인하였다. 이들은 막융합을 통해 난소의 난포발달과정에서 시간적-공간적인 조절 기전에 의해 이루어 질 것으로 보인다. 이 유전자 발현 정보는 원시난포의 개시와 성장을 위한 전환에 관여하는 기전을 이해하는 기초정보와 난소기능부전의 기전을 규명하는데 정보를 제공할 것으로 기대된다.

• 동의생리병리학회지
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• 제18권4호
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• pp.1041-1054
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• 2004

Electroacupuncture (EA) has been reported to increase pain threshold, and to enhance the NK cell activity by up-regulation of IFN-γ and endogenous β-endolphin. For the purpose of understanding the molecular mechanism of EA stimulation, we analyzed the gene expression profile of rat hypothalamus, treated on Zusanli (ST36) with EA, in comparison with control group by oligonucleotide chip microarray (Affymetrix GeneChip Rat Neurobiology U34 Array) and real-time RT-PCR. Sprague-Dawley (S-D) male rats were stimulated at the Zusanli (ST36) acupoint in restriction holder. Simultaneously the control group was given only holder stress without EA stimulation. In order to prove the appropriateness of EA treatment, we measured spleen NK cell activity with standard 51Cr release assay. NK cell activity of EA group was significantly increased comparing to control group. The microarray and PCR results show that EA treatment up-regulates expression of genes associated with 1) nerve growth such as NGF induced factor A and VGF, 2) signal transduction such as 5HT3 receptor subunit, AMPA receptor binding protein and Na-dependent neurotransmitter transporter, and 3) anti-oxidation such as superoxide dismutase and glutathione S-transferase. In addition, the activity of the anti-oxidative enzyme, SOD of hypothalamus, liver and RBC was enhanced compared to that of control. The list of differentially expressed genes may implicate further insight on the mechanism of acupuncture effects.

• Animal Bioscience
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• 제37권2호
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• pp.193-202
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• 2024

Objective: Oxidative stress (OS) is a pathological process arising from the excessive production of free radicals in the body. It has the potential to alter animal gene expression and cause damage to the jejunum. However, there have been few reports of changes in the expression of long noncoding RNAs (lncRNAs) in the jejunum in piglets under OS. The purpose of this research was to examine how lncRNAs in piglet jejunum change under OS. Methods: The abdominal cavities of piglets were injected with diquat (DQ) to produce OS. Raw reads were downloaded from the SRA database. RNA-seq was utilized to study the expression of lncRNAs in piglets under OS. Additionally, six randomly selected lncRNAs were verified using quantitative real-time polymerase chain reaction (qRT-PCR) to examine the mechanism of oxidative damage. Results: A total of 79 lncRNAs were differentially expressed (DE) in the treatment group compared to the negative control group. The target genes of DE lncRNAs were enriched in gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathways. Chemical carcinogenesis-reactive oxygen species, the Foxo signaling pathway, colorectal cancer, and the AMPK signaling pathway were all linked to OS. Conclusion: Our results demonstrated that DQ-induced OS causes differential expression of lncRNAs, laying the groundwork for future research into the processes involved in the jejunum's response to OS.

• Journal of Plant Biotechnology
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• 제43권2호
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• pp.231-239
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• 2016

담배에서 후성유전관련 유전자의 발현연구를 위해 담배유래 시토신 DNA 탈메틸화 관련 NtROS2a 유전자를 과발현 및 RNAi 식물체를 육성하였다. 이들 형질전환체들은 고염 및 산화 스트레스하에서 내성이 증진되었으며, 다양한 표현형변이를 보였다(Lee et al. 2015). 본연구에서는 선발된 과발현 (OX1), RNAi 식물체(RNAi 13) 및 대조식물체(WT)를 이용하여 Agilent Tobacco 4 X 44K Oligo chip으로 microarray분석을 수행하였다. OX1과 RNAi13 계통을 이용하여 WT과 함께 비교 분석한 결과, 대부분 세포 내 이온 수송, 영양 공급 등과 같은 물질대사와 생물적 비생물적 스트레스 및 methylation과 관련되어 영향을 주는 유전자들에서 up-regulation 되었고, 물질대사관련 유전자와 세포 내 기능유전자의 역할을 담당하는 조효소, 그리고 다양한 스트레스 및 메틸레이션 관련 유전자군에서 또한 down-regulation되었다. 각각의 up-, down-regulation된 유전자들을 WT과 비교하여 qRT-PCR을 수행한 결과, KH domain-containing protein, MADS-box protein 및 Zinc phosphodiesterase ELAC protein 유전자들에서 발현이 높게 나타났으며, 반면에 pentatricopeptide (PPR) repeat-containing protein, histone deacetylase HDAC3 protein 및 protein kinase는 0.4 ~ 1.0-fold 발현양이 감소되었다. 따라서 DNA glycosylase를 암호화하는 NtROS2a 유전자는 demethylation과 관련되어 담배 식물체에서 다양한 전사레벨을 조절하는 것으로 판단된다.

• 생명과학회지
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• 제28권5호
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• pp.615-620
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• 2018

EGCG는 녹차의 카테킨 중의 하나로서 항산화, 항염증 그리고 항암 활성 등 다양한 생리활성을 가지고 있는 물질로 알려져 있다. 본 연구에서는 EGCG를 처리한 HCT116 세포와 p53-null HCT116 세포에서 oligo DNA microarray 실험을 통하여 유전자 발현 변화를 분석하였다. Microarray 실험에서 EGCG를 처리한 HCT116 세포주에서 증가된 유전자 4개(ATF3, CDKN1A, DDIT3, NAG-1)를 선별하여, p53-null HCT116에서의 데이터와 비교하였다. NAG-1을 제외한 3개의 유전자는 p53의 상태와 관계없이 발현이 증가하였고, p53-null HCT116 세포주에서는 EGCG에 의해 NAG-1의 발현이 증가되지 않았다. EGCG의 처리에 의해 ATF3와 NAG-1의 유전자와 단백질의 발현을 확인한 경우 동일한 결과를 보여주었다. 또한, 파이토케미칼 genistein과 resveratrol을 처리한 후 ATF3와 NAG-1의 발현을 연구한 결과 genistein은 p53의 상태와 관계없이 ATF3 발현에 영향을 주지 못하는 반면, NAG-1 단백질은 p53 존재 하에서만 발현이 증가되었다. 이에 반해 resveratrol은 p53의 상태와는 관계없이 ATF3와 NAG-1 단백질의 발현을 증가시켰다. 따라서, 항암 활성을 가진 3 종류의 파이토케미칼이 각각 다른 기전으로 항암 유전자를 발현시키는 것으로 생각된다. 종합적으로 본 연구결과는 파이토케미칼 EGCG, genistein, resveratrol에 의해 매개되는 항암 활성의 기전을 이해하는데 도움을 줄 것으로 생각된다.

• 대한약침학회지
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• 제16권1호
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• pp.30-36
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• 2013

Objective: Panax ginseng is one of the most medicinally used herbal medicines in the world. Wild ginseng is widely accepted to be more active than cultivated ginseng in chemoprevention. However, little has actually been reported on the differences between wild ginseng and cultivated ginseng. Method: To identify wild ginseng-specific genes, we used suppressive subtraction hybridization. Results: We report that one of the clones isolated in this screen was the GAPDH (glyceraldehyde 3-phosphate dehydrogenase) gene (designated pGAPDH-w). DNA BLAST sequence analysis revealed that this pGAPDH-w gene contained novel sequences of 94 bp. RT-PCR results showed that the expression of the pGAPDH-w gene was significantly up-regulated in the wild ginseng as compared with the cultivated ginseng. Conclusion: The pGAPDH-w gene may be one of the important markers of wild ginseng.