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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 9, Issue 4 - Dec 2011
Volume 9, Issue 3 - Sep 2011
Volume 9, Issue 2 - Jun 2011
Volume 9, Issue 1 - Mar 2011
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The Hairless Gene: A Putative Navigator of Hair Follicle Development
Kim, Jeong-Ki ; Kim, Bong-Kyu ; Park, Jong-Keun ; Choi, Jee-Hyun ; KimYoon, Sung-Joo ;
Genomics & Informatics, volume 9, issue 3, 2011, Pages 93~101
DOI : 10.5808/GI.2011.9.3.93
The Hairless (HR ) gene regulates the expression of several target genes as a transcriptional corepressor of nuclear receptors. The hair follicle (HF), a small independent organ of the skin, resides in the epidermis and undergoes regenerative cycling for normal hair formation. HF development requires many genes and signaling pathways to function properly in time and space, one of them being the HR gene. Various mutations of the HR gene have been reported to cause the hair loss pheno-type in rodents and humans. In recent studies, it has been suggested that the HR gene is a critical player in the regulation of the hair cycle and, thus, HF development. Furthermore, the HR gene is associated with the Wnt signaling pathway, which regulates proliferation and differentiation of cells and plays an essential role in hair and skin development. In this review, we summarize the mutations responsible for human hair disorders and discuss the roles of the HR gene in HF development.
Differentially Expressed Genes by Inhibition of C-terminal Src Kinase by siRNA in Human Vascular Smooth Muscle Cells and Their Association with Blood Pressure
Hong, Kyung-Won ; Shin, Young-Bin ; Kim, Koan-Hoi ; Oh, Berm-Seok ;
Genomics & Informatics, volume 9, issue 3, 2011, Pages 102~113
DOI : 10.5808/GI.2011.9.3.102
C-terminal SRC kinase (CSK) is a ubiquitously expressed, cytosolic enzyme that phosphorylates and inactivates several SRC family protein tyrosine kinases. Recent genomewide association studies have implicated CSK in the regulation of blood pressure. The current study aim is to determine the blood pressure association of the genes regulated by CSK down-regulation. The CSK mRNA expression was downregulated in vascular smooth muscle cells using small interfering RNA (siRNA). CSK mRNA levels fell by 90% in cells that were treated with CSK siRNA; the RNA from these cells was examined by microarray using the Illumina HumanRef-8 v3 platform, which comprises 24,526 reference mRNA probes. On treatment with CSK siRNA, 19 genes were downregulated by more than 2-fold and 13 genes were upregulated by more than 2-fold. Three (CANX, SLC30A7, and HMOX1) of them revealed more than 3 fold differential expression. Interestingly, the HMOX1 SNPs were associated with diastolic blood pressure in the 7551 Koreans using Korea Association REsource data, and the result was supported by the other reports that HMOX1 linked to blood vessel maintenance. Among the remaining 29 differentially expressed genes, seven (SSBP1, CDH2, YWHAE, ME2, PFTK1, G3BP2, and TUFT1) revealed association with both systolic and diastolic blood pressures. The CDH2 gene was linked to blood pressures. Conclusively, we identified 32 differentially expressed genes which were regulated by CSK reduction, and two (HOMX1 and CDH2) of them might influence the blood pressure regulation through CSK pathway.
Association of an Anti-inflammatory Cytokine Gene IL4 Polymorphism with the Risk of Type 2 Diabetes Mellitus in Korean Populations
Go, Min-Jin ; Min, Hae-Sook ; Lee, Jong-Young ; Kim, Sung-Soo ; Kim, Yeon-Jung ;
Genomics & Informatics, volume 9, issue 3, 2011, Pages 114~120
DOI : 10.5808/GI.2011.9.3.114
Chronic inflammation has been implicated as one of the important etiological factors in insulin resistance and type 2 diabetes mellitus (T2DM). To investigate the role of anti-inflammatory cytokines in the development of T2DM, we conducted a case-control study to assess the association between IL4/IL4R polymorphisms and disease risk. We firstly identified single nucleotide poly-morphisms (SNP) at IL4 and IL4RA loci by sequencing the loci in Korean participants. Case-control studies were conducted by genotyping the SNPs in 474 T2DM cases and 470 non-diabetic controls recruited from community-based cohorts. Replication of the associated signals was performed in 1,216 cases and 1,352 controls. We assessed effect of IL4 -IL4RA interaction on T2DM using logistic regression method. The functional relevance of the SNP associated with disease risk was determined using a reporter expression assay. We identified a strong association between the IL4 promoter variant rs2243250 and T2DM risk (OR=0.77; 95% CI, 0.67~0.88; p=
in the meta-analysis). The reporter gene expression assay demonstrated that the presence of rs2243250 might affect the gene expression level with ~1.5-fold allele difference. Our findings contribute to the identification of IL4 as a T2D susceptibility locus, further supporting the role of anti-inflammatory cytokines in T2DM disease development.
Genome-wide Association Study Identified TIMP2 Genetic Variant with Susceptibility to Osteoarthritis
Keam, Bhum-Suk ; Hwang, Joo-Yeon ; Go, Min-Jin ; Heo, Jee-Yeon ; Park, Mi-Sun ; Lee, Ji-Young ; Kim, Nam-Hee ; Park, Miey ; Oh, Ji-Hee ; Kim, Dong-Hyun ; Jeong, Jin-Young ; Lee, Jong-Young ; Han, Bok-Ghee ; Lee, Ju-Young ;
Genomics & Informatics, volume 9, issue 3, 2011, Pages 121~126
DOI : 10.5808/GI.2011.9.3.121
Osteoarthritis (OA) is the most common degenerative joint disorder in the elderly population. To identify OA-associated genetic variants and candidate genes, we conducted a genome-wide association study (GWAS). A total 3,793 samples (476 cases: wrist + knee and 3317 controls) from a community-based epidemiological study were genotyped using the Affymetrix SNP 5.0. An intronic SNP (rs4789934) in the TIMP2 (tissue inhibitor of metalloproteinase-2) showed the most significance with OA (odd ratio [OR] = 2.06, 95% confidence interval [CI] = 1.52-2.81, p =
). Furthermore, a poly-morphism (rs1352677) in the NKAIN2 (
transporting ATPase interacting 2) was suggestively associated with OA (OR = 1.43, CI = 1.22-1.66, p =
). The present study provides new insights into the identification of genetic predisposing factors for OA.
Optimized Internal Control and Gene Expression Analysis in Epstein-Barr Virus-Transformed Lymphoblastoid Cell Lines
Nam, Hye-Young ; Kim, Hye-Ryun ; Shim, Sung-Mi ; Lee, Jae-Eun ; Kim, Jun-Woo ; Park, Hye-Kyung ; Han, Bok-Ghee ; Jeon, Jae-Pil ;
Genomics & Informatics, volume 9, issue 3, 2011, Pages 127~133
DOI : 10.5808/GI.2011.9.3.127
The Epstein-Barr virus-transformed lymphoblastoid cell line (LCL) is one of the major genomic resources for human genetics and immunological studies. Use of LCLs is currently extended to pharmacogenetic studies to investigate variations in human gene expression as well as drug responses between individuals. We evaluated four common internal controls for gene expression analysis of selected hematopoietic transcriptional regulatory genes between B cells and LCLs. In this study, the expression pattern analyses showed that TBP (TATA box-binding protein) is a suitable internal control for normalization, whereas GAPDH (glyceraldehyde-3-phosphate dehydrogenase) is not a good internal control for gene expression analyses of hematopoiesis-related genes between B cells and LCLs at different subculture passages. Using the TBP normalizer, we found significant gene expression changes in selected hematopoietic transcriptional regulatory genes (downregulation of RUNX1, RUNX3, CBFB, TLE1, and NOTCH2 ; upregulation of MSC and PLAGL2) between B cells and LCLs at different passage numbers. These results suggest that these hematopoietic transcriptional regulatory genes are potential cellular targets of EBV infection, contributing to EBV-mediated B-cell transformation and LCL immortalization.
Implementation of a Particle Swarm Optimization-based Classification Algorithm for Analyzing DNA Chip Data
Han, Xiaoyue ; Lee, Min-Soo ;
Genomics & Informatics, volume 9, issue 3, 2011, Pages 134~135
DOI : 10.5808/GI.2011.9.3.134
DNA chips are used for experiments on genes and provide useful information that could be further analyzed. Using the data extracted from the DNA chips to find useful patterns or information has become a very important issue. In this paper, we explain the application developed for classifying DNA chip data using a classification method based on the Particle Swarm Optimization (PSO) algorithm. Considering that DNA chip data is extremely large and has a fuzzy characteristic, an algorithm that imitates the ecosystem such as the PSO algorithm is suitable to be used for analyzing such data. The application enables researchers to customize the PSO algorithm parameters and see detail results of the classification rules.
A Visualization Tool for Computational Analysis of DNA Methylation Level Using Bisulfite Sequencing Data
Tae, Hong-Seok ;
Genomics & Informatics, volume 9, issue 3, 2011, Pages 136~137
DOI : 10.5808/GI.2011.9.3.136
Methylation of cytosine is a post-synthesis modification that does not affect the primary DNA sequence but greatly influences gene expression level and phenotypes of an organism. As high-throughput sequencing of bisulfite-treated DNA is the most efficient method to identify methylated sites, several tools to map sequencing reads on a reference are available. But tools to visualize and to interpret the methylation level of methylation sites are currently insufficient. Herein, we present a novel tool to visualize the methylation level of CpG sites.
A Program for Efficient Phasing of Three-Generation Trio SNP Genotype Data
Song, Sang-Hoon ; Kim, Sang-Soo ;
Genomics & Informatics, volume 9, issue 3, 2011, Pages 138~141
DOI : 10.5808/GI.2011.9.3.138
Here, we report a computer program written in Python, which phases SNP genotypes and infers inherited deletions based on the pattern of Mendelian inheritance within a trio pedigree. When tiered trio genotypes that encompass three generations are available, it narrows a recombination event down to a region between two consecutive heterozygous markers. In addition, the phase information that is inferred from the upper trio that is formed by one of the parents and grandparents can be propagated to phase the genotypes of the lower trio that is formed by the parents and an offspring.