• Molecules and Cells
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• 제40권10호
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• pp.714-730
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• 2017

Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.

• 원예과학기술지
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• 제32권5호
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• pp.684-693
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• 2014

저온, 건조, 염과 같은 비생물적 스트레스는 식물의 생리적 형태적 변화와 수확량 감소를 초래한다. 이러한 이유로 식물체는 불리한 환경을 극복하기 위해 다양한 대사과정에 관련된 유전자들간의 복잡한 상호 관계를 조절함으로써 저항성을 획득한다. 본 연구는 배추에서 염 스트레스에 반응하는 유전자를 다각적으로 분석하기 위해 상호발현 네트워크를 구축하였다. 네트워크를 구축하기 위하여 배추를 염스트레스 조건 하에서 시간 경과에 따라 KBGP-24K 마이크로어레이 분석을 실시한 [BrEMD (Brassica rapa EST and Microarray Database)] 실험 결과를 수집하여 분석하였다. 구축된 네트워크 모델은 1,853개 node, 5,740개 edge, 및 142개 connected component(상관계수 > 0.85)로 구성되었다. 구축된 네트워크 분석 결과, ROS 신호 전달을 통한 N$Na^+$ 수송활성화와 proline 축적이 배추의 염 저항성 획득과 밀접한 연관이 있는 것으로 판단하였다.

• Journal of the Korean Data and Information Science Society
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• 제25권5호
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• pp.999-1009
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• 2014

계층적 군집 분석은 분석 결과를 덴드로그램으로 쉽게 표시할 수 있어서 방대한 양의 마이크로어레이 자료를 탐색하기에 유용하며, 군집된 결과를 이용하여 생물학적 현상을 이해하는데 도움을 준다. 하지만, 계층적 군집방법은 두 군집간의 절대값 거리만을 고려하여 병합하기 때문에 군집 간의 상대적 비유사성은 설명하지 못하는 단점이 있다. 본 연구에서는 상대적 계층적 군집 방법을 소개하고, 마이크로어레이 자료와 같이 다양한 군집의 모양을 가진 모의실험 자료들과 실제 마이크로어레이 자료를 사용하여 상대적 계층적 군집방법과 기존의 계층적 군집 방법을 비교하였다. 두 계층적 군집 방법의 질적 평가는 오분류율, 동질성, 이질성 지표를 이용하여 수행하였다.

• 전자공학회논문지CI
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• 제46권6호
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• pp.44-55
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• 2009

최근 활발히 연구가 진행 중인 마이크로어레이로부터 얻어지는 유전자 발현 데이터를 이용한 질병 진단은, 데이터를 직접적으로 분석하기 힘들기 때문에 일반적으로 기계 학습 알고리즘을 사용하여 이루어져왔다. 그러나 유전자 발현 데이터를 분석함에 있어서 유전자들 간의 상호작용을 고려하는 분석이 필요하다는 최근의 연구 결과들은 기존 기계 학습 알고리즘들을 이용한 분석에 한계가 있음을 의미한다고 볼 수 있다. 본 논문에서는 특징들 사이의 고차원 상관관계를 고려 가능한 하이퍼네트워크 모델을 이용하여 유전자 발현 데이터의 분류를 수행하고 기존의 기계 학습 알고리즘들과 분류 성능을 비교한다. 또한 기존 하이퍼네트워크 모델의 단점을 개선 한 모델을 제안하고, 이를 병렬 프로세서 상에서 구현하여 처리 성능을 비교한다. 실험 결과 제안 된 모델은 기존의 기계 학습 방법들과의 비교에서도 경쟁력 있는 분류 성능을 보여주었고, 기존 하이퍼네트워크 모델 보다 안정적이고 향상된 분류 성능을 보여주었다. 또한 이를 병렬 프로세서 상에서 구현 할 경우 처리 성능을 극대화 할 수 있음을 보였다.

• Asian Pacific Journal of Cancer Prevention
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• 제13권8호
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• pp.3681-3685
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• 2012

Background: In breast cancer, estrogen receptors have been demonstrated to interact with transcription factors to regulate target gene expression. However, high-throughput identification of the transcription regulation relationship between transcription factors and their target genes in response to estradiol is still in its infancy. Purpose: Thus, the objective of our study was to interpret the transcription regulation network of MCF7 breast cancer cells exposed to estradiol. Methods: In this work, GSE11352 microarray data were used to identify differentially expressed genes (DEGs). Results: Our results showed that the MYB (v-myb myeloblastosis viral oncogene homolog [avian]), PGR (progesterone receptor), and MYC (v-myc myelocytomatosis viral oncogene homolog [avian]) were hub nodes in our transcriptome network, which may interact with ER and, in turn, regulate target gene expression. MYB can up-regulate MCM3 (minichromosome maintenance 3) and MCM7 expression; PGR can suppress BCL2 (B-cell lymphoma 2) expression; MYC can inhibit TGFB2 (transforming growth factor, beta 2) expression. These genes are associated with breast cancer progression via cell cycling and the $TGF{\beta}$ signaling pathway. Conclusion: Analysis of transcriptional regulation may provide a better understanding of molecular mechanisms and clues to potential therapeutic targets in the treatment of breast cancer.

• Molecular & Cellular Toxicology
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• 제1권1호
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• pp.17-25
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• 2005

There are some critical drawbacks in the use of biomarkers for a global assessment of the toxicological impacts many chemicals and environmental pollutants have, primarily due to an individual biomarker's specificity for an explicit chemical or toxicant. In other words, the biomarker-based assessment methodology used to analyze toxicological effects lacks a high-throughput capability. Therefore, eco-toxicogenomics, or the study of toxicogenomics with organisms present within a given environmental locale, has recently been introduced with the advent of the so-called "-omics" era, which began with the creation of microarray technologies. Fish are comparable with humans in their toxicological responses and thus data from toxicogenomic studies performed with fish could be applied, with appropriate tools and implementation protocols, to the evaluation of environments where human or animal health is of concern. At present, there have been very active research streams for developing expression sequence tag (EST) databases (DBs) for zebra fish and rainbow trout. Even though few reports involve toxicogenomic studies with fish, a few groups have successfully fabricated and used cDNA microarrays or oligo DNA chips when studying the toxicological impacts of hypoxia or some toxicants with fish. Furthermore, it is strongly believed that this technology can also be implemented with non-model fish. With the standardization of DNA microarray technologies and ample progress in bioinformatics and proteomic technologies, data obtained from DNA microarray technologies offer not only multiple biomarker assays or an analysis of gene expression profiles, but also a means of elucidating gene networking, gene-gene relations, chemical-gene interactions, and chemical-chemical relationships. Accordingly, the ultimate target of eco-toxicogenomics should be to predict and map the pathways of stress propagation within an organism and to analyze stress networking.

• 한국발생생물학회지:발생과생식
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• 제18권1호
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• pp.1-11
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• 2014

Early growth response 1 (Egr1) is a zinc-finger transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. While it is well-known that Egr1 controls transcription of an array of targets in various cell types, downstream target gene(s) whose transcription is regulated by Egr1 in the uterus has not been identified yet. Thus, we have tried to identify a list of potential target genes of Egr1 in the uterus by performing multi-step in silico promoter analyses. Analyses of mRNA microarray data provided a cohort of genes (102 genes) which were differentially expressed (DEGs) in the uterus between Egr1(+/+) and Egr1(-/-) mice. In mice, the frequency of putative EGR1 binding sites (EBS) in the promoter of DEGs is significantly higher than that of randomly selected non-DEGs, although it is not correlated with expression levels of DEGs. Furthermore, EBS are considerably enriched within -500 bp of DEG's promoters. Comparative analyses for EBS of DEGs with the promoters of other species provided power to distinguish DEGs with higher probability as EGR1 direct target genes. Eleven EBS in the promoters of 9 genes among analyzed DEGs are conserved between various species including human. In conclusion, this study provides evidence that analyses of mRNA expression profiles followed by two-step in silico analyses could provide a list of putative Egr1 direct target genes in the uterus where any known direct target genes are yet reported for further functional studies.

• 생명과학회지
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• 제22권4호
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• pp.492-498
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• 2012

파이토케미칼이 암 세포 성장에 미치는 영향을 확인하기 위하여, 대장암 세포주 HCT116에 네 종류의 파이토케미칼을 각각 25 ${\mu}M$의 농도로 처리하였다. 처리한 파이토케미칼 중 curcumin이 가장 강력하게 세포 성장을 억제하였다. 또한 curcumin은 농도의존적으로 세포 성장을 억제하였다. Curcumin에 의한 대장암 세포주 성장 저해 활성에 대한 분자생물학적 기전을 연구하기 위하여 oligo DNA microarray 실험을 수행하였다. 그 결과, 25 ${\mu}M$ curcumin 처리에 의해 2배 이상 발현이 증가된 유전자 137개, 발현이 감소된 유전자 141개를 선별하였다. 발현이 증가된 유전자 중, 세포사멸과 밀접한 관련이 있는 것으로 알려진 유전자 3개를 선택하여, RT-PCR을 통해 이들 유전자의 발현이 감소됨을 확인하였다. 처리한 파이토케미칼 중 curcumin은 가장 강력한 ATF3의 유도자였으며, 농도의존적으로 ATF3의 발현을 증가시켰다. 흥미롭게도, curcumin에 의한 성장 저해는 ATF3-siRNA에 의한 ATF3 유전자 발현감소에 의해 성장이 회복되었다. 또한, ATF3 유전자의 과대발현 후 발현이 변화되는 유전자를 선별한 결과, 세포사멸과 관련된 많은 유전자들이 증가됨을 확인하였다. 결론적으로, 대장암 세포주에서 curcumin에 의한 항 성장활성에 있어서 ATF3 유전자가 중요한 역할을 할 것으로 생각된다.

• Genomics & Informatics
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• 제1권2호
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• pp.94-100
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• 2003

Motivation: Many have observed a nonlinear relationship between the signal intensity and the transcript abundance in microarray data. The first step in analyzing the data is to normalize it properly, and this should include a correction for the nonlinearity. The commonly used linear normalization schemes do not address this problem. Results: Nonlinearity is present in both cDNA and oligonucleotide arrays, but we concentrate on the latter in this paper. Across a set of chips, we identify those genes whose within-chip ranks are relatively constant compared to other genes of similar intensity. For each gene, we compute the sum of the squares of the differences in its within-chip ranks between every pair of chips as our statistic and we select a small fraction of the genes with the minimal changes in ranks at each intensity level. These genes are most likely to be non-differentially expressed and are subsequently used in the normalization procedure. This method is a generalization of the rank-invariant normalization (Li and Wong, 2001), using all available chips rather than two at a time to gather more information, while using the chip that is least likely to be affected by nonlinear effects as the reference chip. The assumption in our method is that there are at least a small number of non­differentially expressed genes across the intensity range. The normalized expression values can be substantially different from the unnormalized values and may result in altered down-stream analysis.

• BMB Reports
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• 제42권8호
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• pp.493-499
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• 2009

MicroRNAs (miRs) are a family of small noncoding RNAs that regulate gene expression by targeting mRNAs in a sequence specific manner, inducing translational repression or mRNA degradation. In this paper we have first analyzed by microarray the miR-profile in erythroid precursor cells from one normal and two thalassemic patients expressing different levels of fetal hemoglobin (one of them displaying HPFH phenotype). The microarray data were confirmed by RT-PCR analysis, and allowed us to identify miR-210 as an highly expressed miR in the erythroid precursor cells from the HPFH patient. When RT-PCR was performed on mithramycin-induced K562 cells and erythroid precursor cells, miR-210 was found to be induced in time-dependent and dose-dependent fashion, together with increased expression of the fetal $\gamma$-globin genes. Altogether, the data suggest that miR-210 might be involved in increased expression of $\gamma$-globin genes in differentiating erythroid cells.