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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
> Journal Vol & Issue
Genomics & Informatics
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Journal DOI :
Korea Genome Organization
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Volume & Issues
Volume 6, Issue 4 - Dec 2008
Volume 6, Issue 3 - Sep 2008
Volume 6, Issue 2 - Jun 2008
Volume 6, Issue 1 - Mar 2008
Selecting the target year
Development of KHapmap Browser using DAS for Korean HapMap Research
Jin, Hoon ; Kim, Seung-Ho ; Kim, Young-Uk ; Park, Young-Kyu ; Ji, Mi-Hyun ; Kim, Young-Joo ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 57~63
DOI : 10.5808/GI.2008.6.2.057
The Korean HapMap Project has been carried out for the last 5 years since it started in June, 2003. The project generated data for a sum of 1,764,000 Korean SNPs and formally registered the data to the dbSNP of NCBI (The dbSNP website. 2008). We have developed a series of software programs for association studies as well as for the comparison and analysis of Korean HapMap data with four other populations (CEPH, Yoruba, Han Chinese, and Japanese populations). The KHapmap Browser was developed and integrated to provide haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). On that basis, GBrowse was adopted in the KHapmap Browser for inherent Korean genetic data, and a provision of extended services was pledged with the distributed sequence annotation system (DAS). The dynamic linking service of the KHapmap Browser to other tools in our intranetwork environment provides many enhanced functions over GBrowse without DAS. KHapmap Browser is expected to be an invaluable tool for the study of Korean and international Hapmap data.
KRDD: Korean Rice Ds-tagging Lines Database for Rice (Oryza sativa L. Dongjin)
Kim, Chang-Kug ; Lee, Myung-Chul ; Ahn, Byung-Ohg ; Yun, Doh-Won ; Yoon, Ung-Han ; Suh, Seok-Cheol ; Eun, Moo-Young ; Hahn, Jang-Ho ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 64~67
DOI : 10.5808/GI.2008.6.2.064
The Korean Rice Ds-tagging lines Database (KRDD) is designed to provide information about Ac/Ds insertion lines and activation tagging lines using japonica rice. This database has provided information on 18,158 Ds lines, which includes the ID, description, photo image, sequence information, and gene characteristics. The KRDD is visualized using a web-based graphical view, and anonymous users can query and browse the data using the search function. It has four major menus of web pages: (i) a Blast Search menu of a mutant line; Blast from rice Ds-tagging mutant lines; (ii) a primer design tool to identify genotypes of Ds insertion lines; (iii) a Phenotype menu for Ds lines, searching by identification name and phenotype characteristics; and (iv) a Management menu for Ds lines.
J2dpathway: A Global Metabolic Pathway Viewer with Node-Abstracting Features
Song, Eun-Ha ; Ham, Seong-Il ; Yang, San-Duk ; Rhie, A-Rang ; Park, Hyun-Seok ; Lee, Sang-Ho ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 68~71
DOI : 10.5808/GI.2008.6.2.068
The static approach of representing metabolic pathway diagrams offers no flexibility. Thus, many systems adopt automatic graph layout techniques to visualize the topological architecture of pathways. There are weaknesses, however, because automatically drawn figures are generally difficult to understand. The problem becomes even more serious when we attempt to visualize all of the information in a single, big picture, which usually results in a confusing diagram. To provide a partial solution to this thorny issue, we propose J2dpathway, a metabolic pathway atlas viewer that has node-abstracting features.
Functional Role of a Conserved Sequence Motif in the Oxygen-dependent Degradation Domain of Hypoxia-inducible Factor 1α in the Recognition of p53
Chi, Seung-Wook ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 72~76
DOI : 10.5808/GI.2008.6.2.072
is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of
is responsible for the negative regulation of
in normoxia. The interactions of the
ODD domain with partner proteins such as von Hippel-Lindau tumor suppressor (pVHL) and p53 are mediated by two sequence motifs, the N- and C-terminal ODD(NODD and CODD). Multiple sequence alignment with
homologs from human, monkey, pig, rat, mouse, chicken, frog, and zebrafish has demonstrated that the NODD and CODD motifs have noticeably high conservation of the primary sequence across different species and isoforms. In this study, we carried out molecular dynamics simulation of the structure of the
CODD motif in complex with the p53 DNA-binding domain (DBD). The structure reveals specific functional roles of highly conserved residues in the CODD sequence motif of
for the recognition of p53.
Identification of Human LRG1 Polymorphisms and Their Genetic Association with Rheumatoid Arthritis
Jin, Eun-Heui ; Chae, Soo-Cheon ; Shim, Seung-Cheol ; Kim, Hwan-Gyu ; Chung, Hun-Taeg ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 77~83
DOI : 10.5808/GI.2008.6.2.077
Human leucine-rich alpha-2-glycoprotein 1 (LRG1) was first identified as a trace protein in human serum. The primary sequence of LRG1 includes repeated leucine residues and putative membrane-binding domains. But, there is no published information on the genetic variation of this gene. In this study, LRG1 was identified as one of several upregulated genes in RA patients. We examined the expression levels of LRG1 between an RA patient and a healthy control by RT-PCR and validated that LRG1 was highly expressed in RA patients compared with controls. We identified the possible variation sites and single nucleotide polymorphisms (SNPs) in the human LRG1 gene by direct sequencing and analyzed the association of genotype and allele frequencies between RA patients and a control group without RA. We further investigated the relationship between these polymorphisms and the level of RF or anti-CCP in RA patients. We identified a total of three SNPs(g.-678A>G, g.-404C>T and g.1427T>C) and two variation sites (g.-1198delA and g.-893delA) in the LRG1 gene. Our results suggest that polymorphisms of the LRG1 gene are not associated with the susceptibility of RA in the Korean population.
In Vivo Target RNA Specificity of Trans-Splicing Phenomena by the Group I Intron
Song, Min-Sun ; Lee, Seong-Wook ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 84~86
DOI : 10.5808/GI.2008.6.2.084
The Tetrahymena group I intron has been shown to employ a trans-splicing reaction and has been modified to specifically target and replace human telomerase reverse transcriptase (hTERT) RNA with a suicide gene transcript, resulting in the induction of selective cytotoxicity in cancer cells that express the target RNA, in animal models as well as in cell cultures. In this study, we evaluated the target RNA specificity of trans-splicing phenomena by the group I intron in mice that were intraperitoneally inoculated with hTERT-expressing human cancer cells to validate the anti-cancer therapeutic applicability of the group I intron. To this end, an adenoviral vector that encoded for the hTERT-targeting group I intron was constructed and systemically injected into the animal. 5'-end RACE-PCR and sequencing analyses of the trans-spliced cDNA clones revealed that all of the analyzed products in the tumor tissue of the virus-infected mice resulted from reactions that were generated only with the targeted hTERT RNA. This study implies the in vivo target specificity of the trans-splicing group I intron and hence suggests that RNA replacement via a trans-splicing reaction by the group I intron is a potent anti-cancer genetic approach.
An Optimized Strategy for Genome Assembly of Sanger/pyrosequencing Hybrid Data using Available Software
Jeong, Hae-Young ; Kim, Ji-Hyun F. ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 87~90
DOI : 10.5808/GI.2008.6.2.087
During the last four years, the pyrosequencing-based 454 platform has rapidly displaced the traditional Sanger sequencing method due to its high throughput and cost effectiveness. Meanwhile, the Sanger sequencing methodology still provides the longest reads, and paired-end sequencing that is based on that chemistry offers an opportunity to ensure accurate assembly results. In this report, we describe an optimized approach for hybrid de novo genome assembly using pyrosequencing data and varying amounts of Sanger-type reads. 454 platform-derived contigs can be used as single non-breakable virtual reads or converted to simpler contigs that consist of editable, overlapping pseudoreads. These modified contigs maintain their integrity at the first jumpstarting assembly stage and are edited by fragmenting and rejoining. Pre-existing assembly software then can be applied for mixed assembly with 454-derived data and Sanger reads. An effective method for identifying genomic differences between reference and sample sequences in whole-genome resequencing procedures also is suggested.
The Korean HapMap Project Website
Kim, Young-Uk ; Kim, Seung-Ho ; Jin, Hoon ; Park, Young-Kyu ; Ji, Mi-Hyun ; Kim, Young-Joo ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 91~94
DOI : 10.5808/GI.2008.6.2.091
Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and are a resource for mapping complex genetic traits. A genome is covered by millions of these markers, and researchers are able to compare which SNPs predominate in people who have a certain disease. The International HapMap Project, launched in October, 2002, motivated us to start the Korean HapMap Project in order to support Korean HapMap infrastructure development and to accelerate the finding of genes that affect health, disease, and individual responses to medications and environmental factors. A Korean SNP and haplotype database system was developed through the Korean HapMap Project to provide Korean researchers with useful data-mining information about disease-associated biomarkers for studies on complex diseases, such as diabetes, cancer, and stroke. Also, we have developed a series of software programs for association studies as well as the comparison and analysis of Korean HapMap data with other populations, such as European, Chinese, Japanese, and African populations. The developed software includes HapMapSNPAnalyzer, SNPflank, HWE Test, FESD, D2GSNP, SNP@Domain, KMSD, KFOD, KFRG, and SNP@WEB. We developed a disease-related SNP retrieval system, in which OMIM, GeneCards, and MeSH information were integrated and analyzed for medical research scientists. The kHapMap Browser system that we developed and integrated provides haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). It is expected that researchers may be able to retrieve useful information from the kHapMap Browser to find useful biomarkers and genes in complex disease association studies and use these biomarkers and genes to study and develop new drugs for personalized medicine.
A Bio-database Management System for the Monitoring and Automatic FTP of Public Databases
Tae, Hong-Seok ; Han, Jeong-Min ; Ahn, Bu-Young ; Park, Kie-Jung ;
Genomics & Informatics, volume 6, issue 2, 2008, Pages 95~97
DOI : 10.5808/GI.2008.6.2.095
Many bioinformatics sites have managed local bio-databases, including major databases such as GenBank and PIR with update load. We have developed several programs to monitor the update status of these databases and to FTP them automatically. These programs can be used for maintaining local bio-databases as recent versions and providing up-to-date databases through FTP sites. Currently, the program serves major bio-databases and will extend to accommodate many more bio-databases.