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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Genomics & Informatics
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Korea Genome Organization
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Volume & Issues
Volume 8, Issue 4 - Dec 2010
Volume 8, Issue 3 - Sep 2010
Volume 8, Issue 2 - Jun 2010
Volume 8, Issue 1 - Mar 2010
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Bioinformatics Resources of the Korean Bioinformation Center (KOBIC)
Lee, Byung-Wook ; Chu, In-Sun ; Kim, Nam-Shin ; Lee, Jin-Hyuk ; Kim, Seon-Yong ; Kim, Wan-Kyu ; Lee, Sang-Hyuk ;
Genomics & Informatics, volume 8, issue 4, 2010, Pages 165~169
DOI : 10.5808/GI.2010.8.4.165
The Korean Bioinformation Center (KOBIC) is a national bioinformatics research center in Korea. We developed many bioinformatics algorithms and applications to facilitate the biological interpretation of OMICS data. Here we present an introduction to major bioinformatics resources of databases and tools developed at KOBIC. These resources are classified into three main fields: genome, proteome, and literature. In the genomic resources, we constructed several pipelines for next generation sequencing (NGS) data processing and developed analysis algorithms and web-based database servers including miRGator, ESTpass, and CleanEST. We also built integrated databases and servers for microarray expression data such as MDCDP. As for the proteome data, VnD database, WDAC, Localizome, and CHARMM_HM web servers are available for various purposes. We constructed IntoPub server and Patome database in the literature field. We continue constructing and maintaining the bioinformatics infrastructure and developing algorithms.
Comparative Analysis of the Three Classes of Archaeal and Bacterial Ribonucleotide Reductase from Evolutionary Perspective
Pangare, Meenal G. ; Chandra, Sathees B. ;
Genomics & Informatics, volume 8, issue 4, 2010, Pages 170~176
DOI : 10.5808/GI.2010.8.4.170
The Ribonucleotide reductases (RNR) are essential enzymes that catalyze the conversion of nucleotides to deoxynucleotides in DNA replication and repair in all living organisms. The RNRs operate by a free radical mechanism but differ in the composition of subunit, cofactor required and regulation by allostery. Based on these differences the RNRs are classified into three classesclass I, class II and class III which depend on oxygen, adenosylcobalamin and S-adenosylmethionine with an iron sulfur cluster respectively for radical generation. In this article thirty seven sequences belonging to each of the three classes of RNR were analyzed by using various tools of bioinformatics. Phylogenetic analysis, dot-plot comparisons and motif analysis was done to identify a number of differences in the three classes of RNRs. In this research article, we have attempted to decipher evolutionary relationship between the three classes of RNR by using bioinformatics approach.
Genomewide Profiling of Rapamycin Sensitivity in Saccharomyces cerevisiae on Synthetic Medium
Chang, Yeon-Ji ; Shin, Chun-Shik ; Han, Dong-Hun ; Kim, Ji-Yun ; Kim, Kang-In ; Kwon, Yong-Min ; Huh, Won-Ki ;
Genomics & Informatics, volume 8, issue 4, 2010, Pages 177~184
DOI : 10.5808/GI.2010.8.4.177
The target of rapamycin (TOR) signaling pathway is a conserved pathway that regulates eukaryotic cell growth in response to environmental cues. Chemical genomic approaches that profile rapamycin sensitivity of yeast deletion strains have given insights into the function of TOR signaling pathway. In the present study, we analyzed the rapamycin sensitivity of yeast deletion library strains on synthetic medium. As a result, we identified 130 strains that are hypersensitive or resistant to rapamycin compared with wild-type cells. Among them, 36 genes are newly identified to be related to rapamycin sensitivity. Moreover, we found 16 strains that show alteration in rapamycin sensitivity between complex and synthetic media. We suggest that these genes may be involved in part of TOR signaling activities that is differentially regulated by media composition.
Recovery of Genes Epigenetically Altered by the Histone Deacetylase Inhibitor Scriptaid and Demethylating Agent 5-Azacytidine in Human Leukemia Cells
Park, Eun-Kyung ; Jeon, Eun-Hyung ; Kim, In-Ho ; Park, Seon-Yang ;
Genomics & Informatics, volume 8, issue 4, 2010, Pages 185~193
DOI : 10.5808/GI.2010.8.4.185
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.
No Association between PIK3CA Polymorphism and Lung Cancer Risk in the Korean Population
Sung, Jae-Sook ; Park, Kyong-Hwa ; Kim, Seung-Tae ; Seo, Jae-Hong ; Shin, Sang-Won ; Kim, Jun-Suk ; Kim, Yeul-Hong ;
Genomics & Informatics, volume 8, issue 4, 2010, Pages 194~200
DOI : 10.5808/GI.2010.8.4.194
The PIK3CA gene, oncogenic gene located on human chromosome 3q26.3, is an important regulator of cell proliferation, death, motility and invasion. To evaluate the role of PIK3CA gene in the risk of Korean lung cancer, genotypes of the PIK3CA polymorphisms (rs11709323, rs2699895, rs3729679, rs17849074 and rs1356413) were determined in 423 lung cancer patients and 443 normal controls. Statistical analyses revealed that the genotypes and haplotypes in the PIK3CA gene were not significantly associated with the risk of lung cancer in the Korean population, suggesting that these PIK3CA polymorphisms do not contribute to the genetic susceptibility to lung cancer in the Korean population.
Single Nucleotide Polymorphism in the Promoter Region of H1 Histone Family Member N, Testis-specific (H1FNT) and Its Association Study with Male Infertility
Yang, Seung-Hee ; Lee, Jin-U ; Lee, Su-Man ;
Genomics & Informatics, volume 8, issue 4, 2010, Pages 201~205
DOI : 10.5808/GI.2010.8.4.201
The H1 histone family, member N, testis-specific (H1FNT) is exclusively expressed in the testis, and had its possible role for sperm chromatin formation. The purpose of this study is to investigate any genetic association of H1FNT gene with male infertility, especially at the promoter region. We examined the promoter single nucleotide polymorphisms (SNP) of H1FNT gene which is located within transcription factor binding site for its association with male infertility. The statistical analysis showed that the -1129A>T polymorphism was present at a statistically significance in male infertility (p=0.0059 and 0.0349 for hetero and risk type, respectively). The dual-luciferase promoter assay was performed to examine the polymorphic effect of this promoter SNP by the cloning of promoter region (1700bp fragment) into pGL3-basic vector. In our plasmid based reporter system, there is no big difference between wild and risk type. In conclusion, H1FNT -1129A>T promoter SNP is statistically significant with male infertility, especially with subfertile (non-azoospermia) group. Further analysis of its functional polymorphic effect in vivo may provide the biological significance of testis-specific histone with spermatogenesis.
A Promoter SNP (rs1800682, -670C/T) of FAS Is Associated with Stroke in a Korean Population
Kang, Sung-Wook ; Chung, Joo-Ho ; Kim, Dong-Hwan ; Yun, Dong-Hwan ; Yoo, Seung-Don ; Kim, Hee-Sang ; Seo, Wan ; Yoon, Jee-Sang ; Baik, Hyung-Hwan ;
Genomics & Informatics, volume 8, issue 4, 2010, Pages 206~211
DOI : 10.5808/GI.2010.8.4.206
The Fas (TNF receptor superfamily, member 6) (FAS)/FAS ligand (FASLG) interaction plays a central role in the regulation of programmed cell death. FAS and FASLG polymorphisms in promoter regions affect transcriptional activities. To investigate whether FAS and FASLG polymorphisms are associated with the development and clinical phenotypes of stroke, 2 promoter single nucleotide polymorphisms (SNPs) in FAS (rs1800682, -670C/T) and FASLG (rs763110, -844C/T) were selected and genotyped by direct sequencing in 220 stroke patients [107 ischemic stroke (IS), 77 intracerebral hemorrhage (ICH), and 36 subarachnoid hemorrhage (SAH)] and 369 control subjects. For the analysis of clinical symptoms, all stroke patients were divided into 3 clinical phenotypes according to the respective results of the National Institutes of Health Stroke Survey (NIHSS) and the Modified Barthel Index (MBI) and the presence or absence of complex regional pain syndrome (CRPS). The SNPStats, SNPAnalyzer, and Helixtree programs were used to analyze the genetic data. Multiple logistic regression models (codominant, dominant, and recessive) were used to estimate odds ratios (ORs), 95% confidence intervals (CIs), and p-values. The promoter SNP rs1800682 was associated with stroke in the codominant (OR=0.48, 95% CI=0.25-0.94, p=0.04) and dominant models (OR=0.51, 95% CI=0.30-0.87, p=0.011). However, a FASLG SNP (rs763110) was not in Hardy-Weinberg equilibrium (p<0.05). In the analysis of stroke types, rs1800682 was associated with IS in the codominant (OR=0.30, 95% CI=0.12-0.74, p=0.025), dominant (OR=0.44, 95% CI=0.23-0.88, p=0.018), and recessive models (OR=0.45, 95% CI=0.21-0.99, p=0.042). The genotype frequencies of rs1800682 were different between ICH and controls in the dominant model (OR=0.49, 95% CI=0.26-0.94, p=0.031) but not between SAH and controls. In the analysis of clinical symptoms, however, rs1800682 was not related to the 3 clinical phenotypes (NIHSS, MBI, and CRPS). These results suggest that a promoter SNP (rs1800682, -670C/T) in FAS may be associated with the development of stroke in the Korean population.
Nomogram for Predicting Survival for Oral Squamous Cell Carcinoma
Kim, Ki-Yeol ; Li, Sheng-Jin ; Cha, In-Ho ;
Genomics & Informatics, volume 8, issue 4, 2010, Pages 212~218
DOI : 10.5808/GI.2010.8.4.212
An accurate system for predicting the survival of patients with oral squamous cell carcinoma (OSCC) will be useful for selecting appropriate therapies. A nomogram for predicting survival was constructed from 96 patients with primary OSCC who underwent surgical resection between January 1994 and June 2003 at the Yonsei Dental Hospital in Seoul, Korea. We performed univariate and multivariate Cox regression to identify survival prognostic factors. For the early stage patients group, the nomogram was able to predict the 5 and 10 year survival from OSCC with a concordance index of 0.72. The total point assigned by the nomogram was a significant factor for predicting survival. This nomogram was able to accurately predict the survival after treatment of an individual patient with OSCC and may have practical utility for deciding adjuvant treatment.