Go to the main menu
Skip to content
Go to bottom
REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
> Journal Vol & Issue
Genomics & Informatics
Journal Basic Information
Journal DOI :
Korea Genome Organization
Editor in Chief :
Volume & Issues
Volume 7, Issue 4 - Dec 2009
Volume 7, Issue 3 - Sep 2009
Volume 7, Issue 2 - Jun 2009
Volume 7, Issue 1 - Mar 2009
Selecting the target year
Identification of Genetic Variations in CBL, SORBS1, CRK, and RHOQ, Key Modulators in the CAP/TC10 Pathway of Insulin Signal Transduction, and Their Association with Type 2 Diabetes Mellitus in the Korean Population
Hong, Kyung-Won ; Jin, Hyun-Seok ; Lim, Ji-Eun ; Go, Min-Jin ; Lee, Jong-Young ; Hwang, Sue-Yun ; Park, Hun-Kuk ; Oh, Berm-Seok ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 53~56
DOI : 10.5808/GI.2009.7.2.053
Recent evidence has strongly suggested that the CAP/TC10 pathway is involved in the trafficking, docking, and fusion of vesicles containing the insulin-responsive glucose transporter Glut4 to the plasma membrane. However, little is known about how the genes employed in the CAP/TC10 pathway are associated with the development of type 2 diabetes mellitus. In this study, we sequenced 4 genes of the CAP/TC10 pathway [SORBS1, CBL, CRK, and RHOQ] in 24 individuals to identify genetic variations in these loci. A total of 48 sequence variants were identified, including 23 novel variations. To investigate the possible association with type 2 diabetes mellitus, 3 single nucleotide polymorphisms from SORBS1, 3 from CBL, and 4 from RHOQ were genotyped in 1122 Korean type 2 diabetic patients and 1138 nondiabetic controls. Using logistic regression analysis, 1 significant association between SNP rs1376405 in RHOQ and type 2 diabetes mellitus [OR = 8.714 (C.I. 1.714-44.29), p = 0.009] was found in the recessive model. Our data demonstrate a positive association of the RHOQ gene in the CAP/TC10 pathway with T2DM in the Korean population.
Association between Single Nucleotide Polymorphisms of the Fibrinogen Alpha Chain (FGA) Gene and Type 2 Diabetes Mellitus in the Korean Population
Hwang, Joo-Yeon ; Ryu, Min-Hyung ; Go, Min-Jin ; Oh, Berm-Seok ; Cho, Yoon-Shin ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 57~64
DOI : 10.5808/GI.2009.7.2.057
Fibrinogen alpha chain (FGA), a subunit of fibrinogen, might be a potential player for type 2 diabetes mellitus (T2DM), since the plasma levels of fibrinogen is known to be related to the incidence of T2DM. To elucidate the potential role of FGA in T2DM, we investigated whether FGA genetic variations are relevant in T2DM in the Korean population. Seven FGA single nucleotide polymorphisms (SNPs) were genotyped in Ansung and Ansan cohorts (474 T2DM subjects and 470 normal controls) in Korea. The association between SNPs and T2DM was determined by logistic regression analysis. Genetic relevance of SNPs to T2DM-related phenotypes was investigated by multiple linear regression analysis. Statistical analysis revealed that among seven FGA SNPs, significant associations with T2DM were observed in FGA rs2070011 (p=0.013-0.034, OR=0.72
0.79), rs6050 (p=0.026
1.37), and rs2070022 (p=0.016
0.72). Two SNPs, rs2070011 and rs6050, also showed significant association with T2DM-related phenotypes such as triglyceride (p=0.005
0.011 for rs2070011 and p=0.003
0.008 for rs6050), total cholesterol (p=0.01 for rs2070011 and p=0.024 for rs6050) and fasting glucose (p=0.035
0.036 for rs2070011 and p=0.048 for rs6050) in 470 normal controls. Our association study implies that FGA might be an important genetic factor in T2DM pathogenesis in the Korean population by affecting plasma lipid and glucose levels.
Identification of 1,531 cSNPs from Full-length Enriched cDNA Libraries of the Korean Native Pig Using in Silico Analysis
Oh, Youn-Shin ; Nguyen, Dinh Truong ; Park, Kwang-Ha ; Dirisala, Vijaya R. ; Choi, Ho-Jun ; Park, Chan-Kyu ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 65~84
DOI : 10.5808/GI.2009.7.2.065
Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomics related studies, genome annotation and SNP discovery. We analyzed 7,392 high-quality chromatograms (Phred value
30) obtained from sequencing the 5' ends of clones derived from full-length enriched cDNA libraries of Korean native pigs including brainstem, liver, cerebellum, neocortex and spleen libraries. In addition, 50,000 EST sequence trace files obtained from GenBank were combined with our sequences to identify cSNPs in silico. The process generated 11,324 contigs, of which 2,895 contigs contained at least one SNP and among them 610 contigs had a minimum of one sequence from Korean native pigs. Of 610 contigs, we randomly selected 262 contigs and performed in silico analysis for the identification of cSNPs. From the results, we identified 1,531 putative coding single nucleotide polymorphisms (cSNPs) and the SNP detection frequency was one SNP per 465 bp. A large-scale sequencing result of clones from full-length enriched cDNA libraries and identified cSNPs will serve as a useful resource to functional genomics related projects such as a pig HapMap project in the near future.
Analysis of Gene Expression in Mouse Spinal Cord-derived Neural Precursor Cells During Neuronal Differentiation
Ahn, Joon-Ik ; Kim, So-Young ; Ko, Moon-Jeong ; Chung, Hye-Joo ; Jeong, Ho-Sang ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 85~96
DOI : 10.5808/GI.2009.7.2.085
The differentiation of neural precursor cells (NPCs) into neurons and astrocytes is a process that is tightly controlled by complicated and ill-defined gene networks. To extend our knowledge to gene networks, we performed a temporal analysis of gene expression during the differentiation (2, 4, and 8 days) of spinal cord-derived NPCs using oligonucleotide microarray technology. Out of 32,996 genes analyzed, 1878 exhibited significant changes in expression level (fold change>2, p<0.05) at least once throughout the differentiation process. These 1878 genes were classified into 12 groups by k-means clustering, based on their expression patterns. K-means clustering analysis revealed that the genes involved in astrogenesis were categorized into the clusters containing constantly upregulated genes, whereas the genes involved in neurogenesis were grouped to the cluster showing a sudden decrease in gene expression on Day 8. Functional analysis of the differentially expressed genes indicated the enrichment of genes for Pax6- NeuroD signaling.TGFb-SMAD and BMP-SMAD.which suggest the implication of these genes in the differentiation of NPCs and, in particular, key roles for Nova1 and TGFBR1 in the neurogenesis/astrogenesis of mouse spinal cord.
High-concentration Epigallocatechin Gallate Treatment Causes Endoplasmic Reticulum Stress-mediated Cell Death in HepG2 Cells
Ahn, Joon-Ik ; Jeong, Kyoung-Ji ; Ko, Moon-Jeong ; Shin, Hee-Jung ; Chung, Hye-Joo ; Jeong, Ho-Sang ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 97~106
DOI : 10.5808/GI.2009.7.2.097
Epigallocatechin gallate (EGCG), a well-known antioxidant molecule, has been reported to cause hepatotoxicity when used in excess. However, the mechanism underlying EGCG-induced hepatotoxicity is still unclear. To better understand the mode of action of EGCG-induced hepatotoxicity, we examined the effect of EGCG on human hepatic gene expression in HepG2 cells using microarrays. Analyses of microarray data revealed more than 1300 differentially expressed genes with a variety of biological processes. Upregulated genes showed a primary involvement with protein-related biological processes, such as protein synthesis, protein modification, and protein trafficking, while downregulated genes demonstrated a strong association with lipid transport. Genes involved in cellular stress responses were highly upregulated by EGCG treatment, in particular genes involved in endoplasmic reticulum (ER) stress, such as GADD153, GADD34, and ATF3. In addition, changes in genes responsible for cholesterol synthesis and lipid transport were also observed, which explains the high accumulation of EGCG-induced lipids. We also identified other regulatory genes that might aid in clarifying the molecular mechanism underlying EGCG-induced hepatotoxicity.
Investigation of Genetic Evidence for Sasang Constitution Types in South Korea
Lee, Mi-Kyeong ; Jang, Eun-Su ; Sohn, Ho-Young ; Park, Jeong-Yeon ; Koh, Byung-Hee ; Sung, Joo-Hon ; Kim, Jong-Il ; Kim, Jong-Yeol ; Seo, Jeong-Sun ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 107~110
DOI : 10.5808/GI.2009.7.2.107
In Sasang constitutional medicine, both disease susceptibility and drug response are considered to be related to the characteristics of an individual's physiology and psychology: a theory which is central to traditional Korean medicine. Based on such observable characteristics, Sasang constitutional medicine classifies people into four constitutional types. Genetic studies of Sasang constitution would help reveal the inheritance patterns and models of the typological traits and, moreover, help with traditional medical diagnosis and treatment. To investigate the heritable aspect of Sasang constitution, we collected various pedigrees from South Korea. The study population has 101 pedigrees composed of 593 individuals. The determination of the Sasang constitution type of each individual was performed by doctors who diagnose the Sasang constitutional type of individuals as part of their professional practice. We calculated estimates of familial correlation and heritability. Parent-Offspring pairs showed the strongest familial correlation of Sasang constitutional type, with the correlation values of 0.21 and 0.28, followed by sibling pairs with the value ranging between 0.14 and 0.25. From the heritability analysis conducted with the Variance-Component method, the heritability of TE (Tae-Eum) type, SY (So-Yang) type, and SE (So-Eum) type were 55%, 41%, and 47%, respectively. This pattern of heritability was consistent with different set of analyses, which suggest the robustness of our result. Our result clearly shows that the Sasang constitution type is heritable, and further genetic analysis based on our result will shed light on the biological mechanism of Sasang constitution.
Evolutionary Signature of Information Transfer Complexity in Cellular Membrane Proteomes
Kim, Jong-Min ; Kim, Byung-Gee ; Oh, S.-June ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 111~121
DOI : 10.5808/GI.2009.7.2.111
Cell membrane proteins play crucial roles in the cell's molecular interaction with its environment and within itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, and enzymes. Membrane proteomes of cellular organisms reveal some characteristics in their global topological distribution according to their evolutionary positions, and show their own information transfer complexity. Predicted transmembrane segments (TMSs) in membrane proteomes with HMMTOP showed near power-law distribution and frequency characteristics in 6-TMS and 7-TMS proteins in prokaryotes and eukaryotes, respectively. This reaffirms the important roles of membrane receptors in cellular communication and biological evolutionary history.
Integrative Analysis of Microarray Data with Gene Ontology to Select Perturbed Molecular Functions using Gene Ontology Functional Code
Kim, Chang-Sik ; Choi, Ji-Won ; Yoon, Suk-Joon ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 122~130
DOI : 10.5808/GI.2009.7.2.122
A systems biology approach for the identification of perturbed molecular functions is required to understand the complex progressive disease such as breast cancer. In this study, we analyze the microarray data with Gene Ontology terms of molecular functions to select perturbed molecular functional modules in breast cancer tissues based on the definition of Gene ontology Functional Code. The Gene Ontology is three structured vocabularies describing genes and its products in terms of their associated biological processes, cellular components and molecular functions. The Gene Ontology is hierarchically classified as a directed acyclic graph. However, it is difficult to visualize Gene Ontology as a directed tree since a Gene Ontology term may have more than one parent by providing multiple paths from the root. Therefore, we applied the definition of Gene Ontology codes by defining one or more GO code(s) to each GO term to visualize the hierarchical classification of GO terms as a network. The selected molecular functions could be considered as perturbed molecular functional modules that putatively contributes to the progression of disease. We evaluated the method by analyzing microarray dataset of breast cancer tissues; i.e., normal and invasive breast cancer tissues. Based on the integration approach, we selected several interesting perturbed molecular functions that are implicated in the progression of breast cancers. Moreover, these selected molecular functions include several known breast cancer-related genes. It is concluded from this study that the present strategy is capable of selecting perturbed molecular functions that putatively play roles in the progression of diseases and provides an improved interpretability of GO terms based on the definition of Gene Ontology codes.
Comparison of Exon-boundary Old and Young Domains during Metazoan Evolution
Lee, Byung-Wook ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 131~135
DOI : 10.5808/GI.2009.7.2.131
Domains are the building blocks of proteins. Exon shuffling is an important mechanism accounting for combination of a limited repertoire of protein domains in the evolution of multicellular species. A relative excess of domains encoded by symmetric exons in metazoan phyla has been presented as evidence of exon shuffling, and symmetric domains can be divided into old and new domains by determining the ages of the domains. In this report, we compare the spread, versatility, and subcellular localization of old and new domains by analyzing eight metazoan genomes and their respective annotated proteomes. We found that new domains have been expanding as multicellular organisms evolved, and this expansion was principally because of increases in class 1-1 domains amongst several classes of domain families. We also found that younger domains have been expanding in membranes and secreted proteins along with multi-cellular organism evolution. In contrast, old domains are located mainly in nuclear and cytoplasmic proteins. We conclude that the increasing mobility and versatility of new domains, in contrast to old domains, plays a significant role in metazoan evolution, facilitating the creation of secreted and transmembrane multidomain proteins unique to metazoa.
A Scheme for Filtering SNPs Imputed in 8,842 Korean Individuals Based on the International HapMap Project Data
Lee, Ki-Chan ; Kim, Sang-Soo ;
Genomics & Informatics, volume 7, issue 2, 2009, Pages 136~140
DOI : 10.5808/GI.2009.7.2.136
Genome-wide association (GWA) studies may benefit from the inclusion of imputed SNPs into their dataset. Due to its predictive nature, the imputation process is typically not perfect. Thus, it would be desirable to develop a scheme for filtering out the imputed SNPs by maximizing the concordance with the observed genotypes. We report such a scheme, which is based on the combination of several parameters that are calculated by PLINK, a popular GWA analysis software program. We imputed the genotypes of 8,842 Korean individuals, based on approximately 2 million SNP genotypes of the CHB＋JPT panel in the International HapMap Project Phase II data, complementing the 352k SNPs in the original Affymetrix 5.0 dataset. A total of 333,418 SNPs were found in both datasets, with a median concordance rate of 98.7%. The concordance rates were calculated at different ranges of parameters, such as the number of proxy SNPs (NPRX), the fraction of successfully imputed individuals (IMPUTED), and the information content (INFO). The poor concordance that was observed at the lower values of the parameters allowed us to develop an optimal combination of the cutoffs (IMPUTED
0.9 and INFO
0.9). A total of 1,026,596 SNPs passed the cutoff, of which 94,364 were found in both datasets and had 99.4% median concordance. This study illustrates a conservative scheme for filtering imputed SNPs that would be useful in GWA studies.