• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2863-2868
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• 2014

Background: The 765G>C polymorphism in cyclooxygenase-2 (COX-2) gene has been extensively investigated for association with gastric cancer (GC). However, the results of different studies have been inconsistent. The aim of this study is to comprehensively evaluate the genetic risk of -765G>C polymorphism in the COX-2 gene for GC. Materials and Methods: We searched Pubmed, Embase, Medline, CNKI database, Wanfang database, Weipu database, and Chinese Biomedical database, covering all publications (last search been performed on Jan 10, 2014). Statistical analyses were performed using Revman 5.2 and STATA 10.0 software. Results: A total of 1,874 cases and 3,005 controls in 10 case-control studies were included in this meta-analysis. The results indicated that the variant C allele carriers (GC+CC) had a 69% increased risk of GC when compared with the homozygote GG (odds ratio (OR)=1.69, 95% confidence interval (CI), 1.10-2.61 for GC+CC vs GG). In the subgroup analysis by ethnicity, significant elevated risks were associated with C allele carriers in Asians (OR=1.75, 95%CI=1.40-2.18, and p<0.00001) and in Indians (OR=8.38, 95%CI=4.34-16.16, and p<0.00001) but not in Caucasians (OR=1.07, 95%CI=0.81-1.42, and p=0.62) or in Dutch (OR=0.53, 95%CI= 0.33-0.87, and p= 0.01).In the subgroup analysis by Helicobacter pylori (H. pylori) status, a significantly increased risk was identified among H. pylori (+) (OR=3.58, 95%CI=2.33-3.50, and p<0.00001) and H. pylori (-) (OR=2.32, 95%CI=1.46-3.69, and p=0.0004). Conclusions: This meta-analysis suggested that the -765G>C polymorphism in the COX-2 gene could be a risk factor for GC in Asians and Indians.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.24-27
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• 2007

Human cell regulatory mechanism is one of suspicious problems among biologists. Here we tried to uncover the human breast cancer cell regulatory mechanism from gene expression data (Marc J. Van de vijver, et. al., 2002) using a module network algorithm which is suggested by Segal, et. al.(2003) Finally, we derived a module network which consists of 50 modules and 10 tree depths. Moreover, to validate this candidate network, we applied a GO enrichment test and known transcription factor-target relationships from Transfac(R) (V. Matys, et. al, 2006) and HPRD database (Peri, S. et al., 2003).

• Proceedings of the Korea Contents Association Conference
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• 2018.05a
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• pp.549-550
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• 2018

We have developed a web server for the high throughput annotation of gene. This system processes entire data sets with an automated pipeline of 13 analytic services, then deposits the data into the MySQL database and transforms it into three kinds of reports: preprocessing, assembling and annotation.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.457-461
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• 2013

Prostate cancer is a leading cause of death in male populations across the globe. With the advent of gene expression arrays, many microarray studies have been conducted in prostate cancer, but the results have varied across different studies. To better understand the genetic and biologic mechanisms of prostate cancer, we conducted a meta-analysis of two studies on prostate cancer. Eight key genes were identified to be differentially expressed with progression. After gene co-expression analysis based on data from the GEO database, we obtained a co-expressed gene list which included 725 genes. Gene Ontology analysis revealed that these genes are involved in actin filament-based processes, locomotion and cell morphogenesis. Further analysis of the gene list should provide important clues for developing new prognostic markers and therapeutic targets.

• BMB Reports
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• v.37 no.4
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• pp.474-479
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• 2004

The expressed sequence tag (EST) effort in Toxoplasma gondii has generated a substantial amount of gene information. To exploit this valuable resource, we chose to study tgd057, a novel gene identified by a large number of ESTs that otherwise show no significant match to known sequences in the database. Northern analysis showed that tgd057 is transcribed in this tachyzoite. The complete cDNA sequence of tgd057 is 1169 bp in length. Sequence analysis revealed that tgd057 possibly adopts two polyadenylation sites, utilizes the fourth in-frame ATG for translation initiation, and codes for a secretory protein. The longest open reading frame for the tgd057 gene was cloned and expressed as a recombinant protein (rd57) in Escherichia coli. Western analysis revealed that serum against rd57 recognized a molecule of ~21 kDa in the tachyzoite protein extract. This suggests that the tgd057 gene is expressed in vivo in the parasite.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.7
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• pp.3145-3149
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• 2014

Gene expression profiling facilitates the understanding of biological characteristics of gliomas. Previous studies mainly used regression/variance analysis without considering various background biological and environmental factors. The aim of this study was to investigate gene expression differences between grade III and IV gliomas through partial least squares (PLS) based analysis. The expression data set was from the Gene Expression Omnibus database. PLS based analysis was performed with the R statistical software. A total of 1,378 differentially expressed genes were identified. Survival analysis identified four pathways, including Prion diseases, colorectal cancer, CAMs, and PI3K-Akt signaling, which may be related with the prognosis of the patients. Network analysis identified two hub genes, ELAVL1 and FN1, which have been reported to be related with glioma previously. Our results provide new understanding of glioma pathogenesis and prognosis with the hope to offer theoretical support for future therapeutic studies.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.66-72
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• 2003

Toxicogenomics is now emerging as one of the most important genomics application because the toxicity test based on gene expression profiles is expected more precise and efficient than current histopathological approach in pre-clinical phase. One of the challenging points in Toxicogenomics is the construction of intelligent database management system which can deal with very heterogeneous and complex data from many different experimental and information sources. Here we present a new Toxicogenomics database developed as a part of 'Toxicogenomics for Efficient Safety Test (TEST) project'. The TEST database is especially focused on the connectivity of heterogeneous data and intelligent query system which enables users to get inspiration from the complex data sets. The database deals with four kinds of information; compound information, histopathological information, gene expression information, and annotation information. Currently, TEST database has Toxicogenomics information fer 12 molecules with 4 efficacy classes; anti cancer, antibiotic, hypotension, and gastric ulcer. Users can easily access all kinds of detailed information about there compounds and simultaneously, users can also check the confidence of retrieved information by browsing the quality of experimental data and toxicity grade of gene generated from our toxicology annotation system. Intelligent query system is designed for multiple comparisons of experimental data because the comparison of experimental data according to histopathological toxicity, compounds, efficacy, and individual variation is crucial to find common genetic characteristics .Our presented system can be a good information source for the study of toxicology mechanism in the genome-wide level and also can be utilized fur the design of toxicity test chip.

• The Journal of the Korea Contents Association
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• v.10 no.6
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• pp.49-54
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• 2010

As information on gene sequences is not only diverse but also extremely huge in volume, high-performance computer and information technology techniques are required to build and analyze gene sequence databases. This has given rise to the discipline of bioinformatics, a field of research where computers are utilized to collect, to manage, to save, to evaluate, and to analyze biological data. In line with such continued development in bioinformatics, the Korea Institute of Science and Technology Information (KISTI) has built an infrastructure for the biological information, based on the information technology, and provided the information for researchers of bioscience. This paper analyzes the reference fields of Genbank, the most frequently used gene database by the global researchers among the life information databases, and proposes the interface method to NDSL which is the science and technology information integrated service provided by KISTI. For these, after collecting Genbank data from NCBI FTP site, we rebuilt the database by separating Genbank text files into the basic gene data and the reference data. So new tables are generated through extracting the paper and patent information from Genbank reference fields. Then we suggest the method of connection with the paper DB and the patent DB operated by KISTI.

• The Plant Pathology Journal
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• v.24 no.4
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• pp.384-391
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• 2008

Rice blast disease, caused by the pathogenic fungus Magnaporthe grisea, is a serious issue in rice (Oryza sativa L.) growing regions of the world. Transcript profiling in rice inoculated with the fungus has been investigated using the transcriptomics technology, serial analysis of gene expression (SAGE). Short sequence tags containing sufficient information which are ten base-pairs representing the unique transcripts were identified by SAGE technology. We identified a total of 910 tag sequences via the GenBank database, and the resulting genes were shown to be up-regulated in all functional categories under the fungal biotic stress. Compared to the compatible interaction, the stress and defense genes in the incompatible interaction appear to be more up-regulated. Particularly, thaumatin-like gene (TLP) was investigated in determining the gene and protein expression level utilizing Northern and Western blotting analyses, resulting in an increase in both the gene and the protein expression level which arose earlier in the incompatible interaction than in the compatible interaction.

• Journal of Embryo Transfer
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• v.30 no.2
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• pp.99-107
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• 2015

The aim of the present study was to identify coat color associated genes that are differentially expressed in mature Korean brindle cattle (KBC) with different coat colors and in Hanwoo cows. KBC calves, before and after coat color appearance, were included. Total cellular RNA was isolated from the tail hair cells and used for microarray. The number of expressed coat color associated genes/probes was 5813 in mature KBC and Hanwoo cows. Among the expressed coat color associated genes/probes, 167 genes were the coat color associated genes listed in the Gene card database and 125 genes were the pigment and melanocyte genes listed in the Gene ontology_bovine database. There were 23 genes/probes commonly listed in both databases and their expressions were further studied. Out of the 23 genes/probes, MLPH, PMEL, TYR and TYRP1 genes were expressed at least two fold higher (p<0.01) levels in KBC with brindle color than either Hanwoo or KBC with brown color. TYRP1 expression was 22.96 or 19.89 fold higher (p<0.01) in KBC with brindle color than either Hanwoo or KBC with brown color, respectively, which was the biggest fold difference. The hierarchical clustering analysis indicated that MLPH, PMEL, TYR and TYRP1 were the highly expressed genes in mature cattle. There were only a few genes differentially expressed after coat color appearance in KBC calves. Studies on the regulation and mechanism of gene expression of highly expressed genes would be next steps to better understand coat color determination and to improve brindle coat color appearance in KBC.