• Journal of the Korea Institute of Information and Communication Engineering
• /
• v.12 no.2
• /
• pp.315-320
• /
• 2008

Nowadays, a lot of related data obtained from these research could be given a new present meaning to accomplish the original purpose of the whole research as a human genome project. In such a thread, construction of gene expression analysis system and a basis rank analysis system is being watched newly. Recently, being identified fact that particular sub-class of tumor be related with particular chromosome, microarray started to be used in diagnosis field by doing cancer classification and predication based on gene expression information. In this thesis, we used cDNA microarrays of 3840 genes obtained from neuronal differentiation experiment of cortical stem cells on white mouse with cancer, created system that can extract informative gene list through normalization separately and proposed combination method for selecting more significant genes. And possibility of proposed system and method is verified through experiment. That result is that PC-ED combination represent 98.74% accurate and 0.04% MSE, which show that it improve classification performance than case to experiment after generating gene list using single similarity scale.

• Proceedings of the Korea Contents Association Conference
• /
• 2003.11a
• /
• pp.343-346
• /
• 2003

To predict and analyze genes, many methods and tools are already developed in Bioinformatics field which is being more important in future. And many biologists have now performed the research with them. Although it is possible to identify gene and to analyze its function efficiently without experimental methods, it is still hard work. In this paper, we propose a method that make gene list on the initial stage of Genome project. It is difficult to obtain detailed gene list in the initial stage of Genome project. but proposed system provides gene information as much as possible even in the initial stage.

• The Science & Technology
• /
• no.2 s.405
• /
• pp.8-9
• /
• 2003

외계생명체 유입설 증거 발견/ 오래된 종이 보관법 개발/ 우리 은하계 주변에 반지 모양의 성운/ 냄새 맡는 폭발물 탐지 장치 개발/ 해왕성에서 위성 3개 새로 발견/ 지구 생물종 목록 25년 내 완성/ 아인슈타인 가설, 사실로 확인 / 멍게 유전자 지도 완성

• 한국생물공학회:학술대회논문집
• /
• 2003.04a
• /
• pp.649-652
• /
• 2003

• Proceedings of the Korea Society of Environmental Biology Conference
• /
• 2005.12a
• /
• pp.22-35
• /
• 2005

내분비계 장애물질 (Endocrine Disruptors: EDs)이란 ‘내분비 기능에 변화를 일으켜, 생체 또는 그 자손의 건강에 위해한 영향을 미치는 외인성 물질’로서 세계야생생물보호기금 (World Wildife Fund: WWF)의 목록에는 67 여종, 일본 후생성에서는 142 여종의 물질을 내분비계 장애물질로 분류하고 있다. 이렇게 분류된 내분비계장애물질 가운데에는 많은 종류의 농약이 포함되어 있으며, 이들이 자연상태계에 미치는 영향에 대한 많은 보고가 있다. 양서류는 먹이연쇄의 중위포식자로 내분비계 장애물질의 순환 및 생채축적 회로에서 중요한 위치를 갖는다. 또한 농경지나 계류 등에 서식하며 산란하는 습성이 있다. 이러한 서식지는 농약 등에 노출받기 쉬우므로 환경오염평가 대상동물로 중요하다. 본 연구에서는 국내에서 사용되고 있는 제초제, 살충제 등이 양서류 발생에 미치는 영향을 평가하고, 이들 물질에 의한 노출을 평가할 수 있는 biomarker 유전자를 발굴하고자 하였다. 우리나라 전역에 많이 분포하는 무당개구리(Bombina orientalis)의 초기 배아발생 과정에서 이들 농약을 처리하였을 때, 물질의 종류에 따라 정도의 차이는 있으나 농도 의존적으로 배아 및 올챙이의 치사율이 높게 나타났다. 또한 농약은 배아 및 올챙이의 기형을 유발하였다. 기형의 종류는 농약에 따라 서로 상이한 형태로도 나타났으나, 특히 몸통휨 또는 꼬리휨등의 척추골 기형이 많이 나타났다. 환경 위해성 평가 biomarker 유전자로서 골격계 형성에 관여하는 Sox9 유전자를 선택하였다. 무당개구리에서 처음으로 Sox9 유전자를 동정하였으며, 농약을 처리한 실험군에서의 Sox9 유전자의 발현 양상은 대조군에 비하여 높게 나타났다. 본 연구결과 생태계에서 내분비계 장애물질의 위해성 평가를 위해 양서류 초기배아의 치사 및 기형의 정도를 관찰하는 방법이 유효할 것으로 사료된다. 또한 야생동물의 biomarker 유전자를 발굴과 이를 이용한 위해성 평가는 더욱 정밀한 평가법으로 유용할 것이다.

• Clinical and Experimental Reproductive Medicine
• /
• v.33 no.2
• /
• pp.125-132
• /
• 2006

Objective: In the previous study, we complied the differentially expressed genes during early folliculogenesis. Objective of the present study was to identify downstream target genes of transcription factors (TFs) using bioinformatics for selecting the target TFs among the gene lists for further functional analysis. Materials & Methods: By using bioinformatics tools, constituent domains were identified from database searches using Gene Ontology, MGI, and Entrez Gene. Downstream target proteins/genes of each TF were identified from database searches using TF database ($TRANSFAC^{(R)}$ 6.0) and eukaryotic promoter database (EPD). Results: DNA binding and trans-activation domains of all TFs listed previously were identified, and the list of downstream target proteins/genes was obtained from searches of TF database and promoter database. Based on the known function of identified downstream genes and the domains, 3 (HNF4, PPARg, and TBX2) out of 26 TFs were selected for further functional analysis. The genes of wee1-like protein kinase and p21WAF1 (cdk inhibitor) were identified as potential downstream target genes of HNF4 and TBX2, respectively. PPARg, through protein-protein interaction with other protein partners, acts as a transcription regulator of genes of EGFR, p21WAF1, cycD1, p53, and VEGF. Among the selected 3 TFs, further study is in progress for HNF4 and TBX2, since wee1-like protein kinase and cdk inhibitor may involved in regulating maturation promoting factor (MPF) activity during early folliculogenesis. Conclusions: Approach used in the present study, in silico analysis of downstream target genes, was useful for analyzing list of TFs obtained from high-throughput cDNA microarray study. To verify its binding and functions of the selected TFs in early folliculogenesis, EMSA and further relevant characterizations are under investigation.

• Horticultural Science & Technology
• /
• v.31 no.5
• /
• pp.598-606
• /
• 2013

Anther is the major organ of flower in responsible to reproduction and outward appearance. From anther-specific cDNA library of Lilium Oriental Hybrid 'Acapulco', 2000 expressed sequence tags were selected randomly. Differential slot blot analysis with cDNA probes from the anther and leaf was used to get anther-expressed clone and 570 non-redundant ESTs were obtained and sequenced. Compared to the GenBank database using BLASTX algorithm, 191 clones showed significant similarity but others (66.5%) did not measured to known sequence. Functional categories according to gene ontology (GO) annotation included sequence representing a significant portion of protein in cell and cell part respectively. A transcriptional analysis at 7 different organs and developmental stage was performed using northern blot with thirty ESTs as putative anther specific gene. This report suggest that selection of anther expressed clone using differential slot blot was considered as very effective tool and our current study can provide fundamental information on the lily anther including pollen furthermore.

• Journal of the Korea Institute of Information and Communication Engineering
• /
• v.11 no.10
• /
• pp.1924-1929
• /
• 2007

Nowadays, a lot of related data obtained from these research could be given a new present meaning to accomplish the original purpose of the whole research as a human project. The method of tumor classification based on microarray could contribute to being accurate tumor classification by finding differently expressing gene pattern statistically according to a tumor type. Therefore, the process to select a closely related informative gene with a particular tumor classification to classify tumor using present microarray technology with effect is essential. In this thesis, we used cDNA microarrays of 3840 genes obtained from neuronal differentiation experiment of cortical stem cells on white mouse with cancer, constructed accurate tumor classification model by extracting informative gene list through normalization separately and then did performance estimation by analyzing and comparing each of the experiment results. Result classifying Multi-Perceptron classifier for selected genes using Pearson correlation coefficient represented the accuracy of 95.6%.

• Development and Reproduction
• /
• v.7 no.2
• /
• pp.127-136
• /
• 2003

The present study was conducted to investigate gene expression profile of mouse ovaries during the primordial-primary follicle transition. We isolated total RNA from mouse ovaries at day1(contains only primordial follicles) and day5(contains both primordial and primary follicles) and synthesized cDNA using annealing control primers(ACP, Seegene, Inc., Seoul, Korea). Using 80 different ACPs for PCR, we cloned, sequenced, and analyzed identities of 41 differentially expressed genes(DEGs). According to BLAST analysis, sequences of 33 clones significantly matched database entries, 4 clones were novel, and 4 clones were ESTs. We selected 8 DEGs with interesting functions, Anx11 and Pepp2-Pending highly expressed in day1 ovary, while Apg3/Autlp-like, BPOZ, Ches1, Kcmf1, NHE3, Nid2, Ninj1, SENP3, Suil-rsl, and TIAP/m-survivin highly expressed in days ovary, and confirmed their different expression between day1 ovaries and days ovaries using semi-quantitative RT-PCR. There was no false positive result. Using in situ hybridization, we found that almost all of genes studied were expressed in the oocyte from primordial follicle stage but expression decreased from primary follicle stage. Meanwhile their expression was increased in cuboidal granulosa cells. Different expression of BPOZ and TIAP/m-survivin between primordial and primary follicles was confirmed by using laser capture microdissection followed by real-time PCR BPOZ and TIAP/m-survivin expressed 4.5 and 3.4 fold higher in primary than primordial follicles, respectively. List of genes obtained from the present study will provide insights for the study of mechanism regulating primordial-primary follicle transition.

• Development and Reproduction
• /
• v.7 no.2
• /
• pp.119-126
• /
• 2003

In the previous study, we obtained list of differentially expressed genes between postnatal day 1 and day 5 mouse ovaries using suppression subtractive hybridization(SSH) and found that MT Oansposon-like element, clone MTi7(MTi7) was one of the highly expressed genes in the day 5 mouse ovary(Park et at., 2002). Results of in situ hybridization and RNA interference revealed that the expression of MTi7 is oocyte-specific in the ovary and may be involved in the regulation of oocyte maturation(Park et at., 2003). At present, MTi7 sequence has been known only in the mouse. Therefore, the present study was accomplished 1) to identify MTi7 sequence in the other mammalian species, such as bovine, porcine, rat, and human, and 2) to evaluate the flanking sequence of the mouse MTi7 since it has transposon characteristics. Using ovarian cDNAs derived from low different species, we cloned and identified new MTi7 sequence showing a high degree of sequence homology with the mouse MTi7(87∼98%). By using inverse PCR, we found that the mouse MTi7 may intercalated the beta-carotene 15, 15'-monooxygenase(Bcdo) gene and/or serine protease inhibitor, Kunitz Dpe I(Spint 1) gene. By finding the MTi7 sequences in the other mammalian species and the flanking gene of the MTi7 in mouse, it is expected to reveal the role(s) of MTi7 in the oogenesis as well as folliculogenesis in the near future.