• Journal of the Korean Data and Information Science Society
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• 제25권5호
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• pp.1151-1160
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• 2014

In DNA microarray studies, the number of genes far exceeds the number of samples and the gene expression measures are highly correlated. Partial least squares regression (PLSR) is one of the popular methods for dimensional reduction and known to be useful for the classifications of microarray data by several studies. In this study, we suggest a modified version of the partial least squares regression to analyze gene expression data with survival information. The method is designed as a new gene selection method using PLSR with an iterative procedure of imputing censored survival time. Mean square error of prediction criterion is used to determine the dimension of the model. To visualize the data, plot for variables superimposed with samples are used. The method is applied to two microarray data sets, both containing survival time. The results show that the proposed method works well for interpreting gene expression microarray data.

• 혜화의학회지
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• 제21권1호
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• pp.11-21
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• 2012

New onset diabetes is a major complication after kidney transplantation. However, the natural course of posttransplantation diabetes mellitus (PTDM) remains unclear. The aim of this study was to demonstrate the detailed natural courses of PTDM according to the onset and persistency of hyperglycemia, and to investigate risk factors for development of different courses of PTDM in renal allograft recipients. The purpose of this study is to develop novel immune suppressants for PTDM using of action mechanism of them. The use of immunosuppressive drugs in transplanted patients is associated with the development of diabetes, possibly due to ${\beta}$-cell toxicity. To better understand the mechanisms leading to post-transplant diabetes, we investigated the actions of prolonged exposure of ${\beta}$-cells to therapeutical levels of tacrolimus (FK506) or cyclosporin A(CsA). The immunosuppressive drug cyclosporine(CsA) is a potent agent widely used after organ transplantations and various autoimmune disorders. After using CsA, some patients suffer severe complications including renal and vascular toxicity. The renal or vascular toxicity is influenced by the degree of the endothelial damage. FK506(tacrolimus) is a widely used immunosuppressive agent in the treatment of various medical conditions, including autoimmune disease, bone marrow and organ transplantations. We found some interesting clusters and confirmed the feasibility of cDNA microarray in the study of Immunosuppressant. In this study, we investigated gene expression patterns induced by Immunosuppressant in RIN-m5F of rat insulinoma cell line. Gene expressions evaluated using cDNA microarry in two clusters were increased or decreased. this study provides comprehensive comparison of the patterns of gene expression changes induced by CsA and FK506 in ${\beta}$-cells. This study could establish that the mode of action mechanism by which currently used insulin inhibitors inducing PTDM could be elucidated at least in part, which raises the possibility that novel immune suppressive PTDM can be developed. The molecular biological study on PTDM will also contribute the progress in diabetes research field as well as in that of PTDM.

• Genomics & Informatics
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• 제8권4호
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• pp.185-193
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• 2010

Histone deacetylation and demethylation are epigenetic mechanisms implicated in cancer. Studies regarding the role of modulation of gene expression utilizing the histone deacetylase inhibitor scriptaid and the demethylating agent 5-azacytidine in HL-60 leukemia cells have been limited. We studied the possibility of recovering epigenetically silenced genes by scriptaid and 5-azacytidine in human leukemia cells by DNA microarray analysis. The first group was leukemia cells that were cultured with 5-azacytidine. The second group was cultured with scriptaid. The other group was cultured with both agents. Two hundred seventy newly developed genes were expressed after the combination of 5-azacytidine and scriptaid. Twenty-nine genes were unchanged after the combination treatment of 5-azacytidine and scriptaid. Among the 270 genes, 13 genes were differed significantly from the control. HPGD, CPA3, CEACAM6, LOC653907, ETS1, RAB37, PMP22, FST, FOXC1, and CCL2 were up-regulated, and IGLL3, IGLL1, and ASS1 were down-regulated. Eleven genes associated with oncogenesis were found among the differentially expressed genes: ETS1, ASCL2, BTG2, BTG1, SLAMF6, CDKN2D, RRAS, RET, GIPC1, MAGEB, and RGL4. We report the results of our leukemia cell microarray profiles after epigenetic combination therapy with the hope that they are the starting point of selectively targeted epigenetic therapy.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제13권1호
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• pp.7-22
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• 2010

목 적: Helicobacter pylori (H. pylori)에 감염된 환자에서 나타나는 결절성 위염은 소아에 특징적인 소견이지만, 지금까지 이에 대한 연구가 이루어지지 못 하였다. 본 연구에서는 H. pylori 감염이 없는 소아 환자의 위 점막의 유전자 발현 양상과 H. pylori에 감염에 의한 결절성 위염이 있는 소아 및 결절성 위염이 없는 소아의 위 점막 유전자 발현 양상을 microarray를 이용하여 비교함으로써 H. pylori 감염 시에 소아의 위 점막에 나타나는 유전자 발현 양상의 변화를 규명하고자 하였다. 방 법: 분당서울대학교 소아청소년과에 내원하여 상 부위장관내시경검사에 의한 위 점막 조직검사를 시행받은 12명의 소아청소년을 대상으로 하였다. 이들을 H. pylori 양성이면서 육안적인 병변이 없는 환아 4명의 HP(+)NG(-)군과, 위 전정부에서 결절성 위염 소견이 관찰된 환아 4명의 HP(+)NG(+)군으로 나누고, 연령 및 성별이 일치하는 H. pylori 음성인 4명의 소아를 대조군인 HP(-)NG(-)군으로 분류하였다. $-70^{\circ}C$에 냉동보관한 위 점막 조직에서 RNA를 추출하여 microarray를 시행하고 분석된 결과에 의거하여 발현 정도에 변화가 있는 유전자를 분석하였다. 결 과: 대상 환자 12명(남자 6명, 여자 6명, 평균 연령 9.8세)의 위 점막 조직에서 cDNA microarray 시행하여 H. pylori 감염의 유무에 따라 유전자 발현 정도를 비교하였을때, H. pylori 감염된 위 점막은 감염되지 않은 소아에 비해 182개의 유전자가 과발현 되었으며, 29개의 유전자가 발현이 저하되었다. H. pylori 감염이 확인 된 8명을 결절성 위염의 유무에 따라 유전자 발현 정도를 비교분석하였을 때, 상부위장관 내시경검사에서 H. pylori 감염과 연관된 결절성 위염을 보인 환자의 위 점막은 결절성 위염이 없는 H. pylori 감염 환아의 위 점막조직에 비해 5개의 유전자가 발현이 증가하였으며 5개의 유전자가 발현이 저하되었다. 결 론: 소아의 위 점막은 H. pylori 감염 여부에 따라 뚜렷한 유전자 발현의 차이를 보이며, 결절성 위염이 동반된 H. pylori 감염 환자의 위 점막은 일부 유전자에서 발현의 차이를 보이는 것을 알 수 있었다. 향후 추가적인 연구를 통해 소아에서 H. pylori 감염에 의한 결절성 위염의 발병 기전을 밝히려는 시도가 필요할 것이다.

• Restorative Dentistry and Endodontics
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• 제37권3호
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• pp.142-148
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• 2012

Objectives: We analyzed gene-expression profiles after 14 day odontogenic induction of human dental pulp cells (DPCs) using a DNA microarray and sought candidate genes possibly associated with mineralization. Materials and Methods: Induced human dental pulp cells were obtained by culturing DPCs in odontogenic induction medium (OM) for 14 day. Cells exposed to normal culture medium were used as controls. Total RNA was extracted from cells and analyzed by microarray analysis and the key results were confirmed selectively by reverse-transcriptase polymerase chain reaction (RT-PCR). We also performed a gene set enrichment analysis (GSEA) of the microarray data. Results: Six hundred and five genes among the 47,320 probes on the BeadChip differed by a factor of more than two-fold in the induced cells. Of these, 217 genes were upregulated, and 388 were down-regulated. GSEA revealed that in the induced cells, genes implicated in Apoptosis and Signaling by wingless MMTV integration (Wnt) were significantly upregulated. Conclusions: Genes implicated in Apoptosis and Signaling by Wnt are highly connected to the differentiation of dental pulp cells into odontoblast.

• 한국발생생물학회:학술대회논문집
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• 한국발생생물학회 2005년도 제5회 발생공학 국제심포지엄 및 학술대회
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• pp.109-109
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• 2005

• 한국수정란이식학회:학술대회논문집
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• 한국수정란이식학회 2005년도 제5회 발생공학 국제심포지엄 및 학술대회
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• pp.109-109
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• 2005

• 한국어병학회지
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• 제27권1호
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• pp.1-9
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• 2014

저수온기만 넙치에 대량 폐사를 일으키는 바이러스성 출혈성 패혈증을 폐사가 발생하는 $15^{\circ}C$, 폐사가 발생하지 않는 $20^{\circ}C$에서 인공감염시켜 넙치의 면역 유전자 발현 profile을 cDNA microarray 분석하였으며, 특히 저수온기에 폐사가 나타나는 원인을 면역 유전자 발현과 관련시켜 알아보고자 하였다. $15^{\circ}C$, $20^{\circ}C$의 감염 세포구에 공통으로 발현되는 유전자는 MHC class I, IL-8, myeloperoxidase 및 endonuclease G-like 유전자로 모든 세포표면에 존재하여 항원을 제시하거나 호중구 주화성을 자극하는 유전자들이었다. 항원 가공 및 제시, 항체 생성에 관여하는 MHC class II, immunoglobulin (Ig)과 retinoblastoma 등의 유전자는 $20^{\circ}C$에서는 발현이 증가하였으나 $15^{\circ}C$에서는 발현이 감소되었다. 이로부터 폐사가 발생하지 않는 $20^{\circ}C$는 바이러스 감염초기의 항원 제시, MHC class I과 II에 의한 항원제시, apoptosis 및 이후의 항체 생산이 정상적으로 이루어져 폐사가 발생하지 않는 것으로 생각되었다. 그러나 폐사가 발생하는 $15^{\circ}C$에서는 MHC class I매개의 항원 제시와 탐식 작용등의 선천 면역은 이루어지나 macrophage에 의한 MHC class II매개의 항원 제시와 apoptosis저하, 항체 생산 관련 유전자의 발현저하가 관찰되어 초기 macrophage에 의한 항원제시의 실패로 적응 면역이 제대로 활성화되지 않아 폐사가 발생한 것으로 사료된다.

• Molecular & Cellular Toxicology
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• 제2권2호
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• pp.141-149
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• 2006

Tamoxifen (TAM), a non-steroidal anti estrogen anticancer drug and chemopreventive agent for breast cancer, have caused cholestasis in liver. The potent hepatocarcinogenicity of this drug has been reported. Methotrexate (MTX) is dihydrofolate reductase inhibitor which interfaces with the synthesis for urine nucleotide and dTMP. And it may cause atrophy, necrosis and steatosis in liver. These two anticancer drug have well-known hepatotoxicity. So, in this study we compare the gene expression pattern of antitumor agent TAM and MTX, using the cDNA microarray. We have used 4.8 K cDNA microarray to identify hepatotoxicity-related genes in 5-week-old male Sprague-Dawley (SD) rats. Confirm the pattern of gene expression, we have used Real time PCR for targeted gene. In the case of MTX, Protease related gene (Ctse, Ctsk) and Protein kinase (Pctk 1) have shown specific expression pattern. And in the case of TAM, apoptosis related gene (Pdcd 8) and signal transduction related gene (kdr) have significantly up regulated during treatment time. Gene related with growth factor, lipid synthesis, chemokins were significantly changed. From the result of this study, the information about influence of TAM and MTX to hepatoxicity will provide.

• Journal of Microbiology
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• 제45권1호
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• pp.21-28
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• 2007

In order to search for specific genotypes related to this unique phenotype, we used whole genomic DNA microarray to characterize the genomic diversity of Helicobacter pylori (H. pylori) strains isolated from clinical patients in China. The open reading frame (ORF) fragments on our microarray were generated by PCR using gene-specific primers. Genomic DNA of H. pylori 26695 and J99 were used as templates. Thirty-four H. pylori isolates were obtained from patients in Shanghai. Results were judged based on In(x) transformed and normalized Cy3/Cy5 ratios. Our microarray included 1882 DNA fragments corresponding to 1636 ORFs of both sequenced H. pylori strains. Cluster analysis, revealed two diverse regions in the H. pylori genome that were not present in other isolates. Among the 1636 genes, 1091 (66.7%) were common to all H. pylori strains, representing the functional core of the genome. Most of the genes found in the H. pylori functional core were responsible for metabolism, cellular processes, transcription and biosynthesis of amino acids, functions that are essential to H. pylori's growth and colonization in its host. In contrast, 522 (31.9%) genes were strain-specific genes that were missing from at least one strain of H. pylori. Strain-specific genes primarily included restriction modification system components, transposase genes, hypothetical proteins and outer membrane proteins. These strain-specific genes may aid the bacteria under specific circumstances during their long-term infection in genetically diverse hosts. Our results suggest 34 H. pylori clinical strains have extensive genomic diversity. Core genes and strain-specific genes both play essential roles in H. pylori propagation and pathogenesis. Our microarray experiment may help select relatively significant genes for further research on the pathogenicity of H. pylori and development of a vaccine for H. pylori.