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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 7, Issue 4 - Dec 2009
Volume 7, Issue 3 - Sep 2009
Volume 7, Issue 2 - Jun 2009
Volume 7, Issue 1 - Mar 2009
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A New Approach to Find Orthologous Proteins Using Sequence and Protein-Protein Interaction Similarity
Kim, Min-Kyung ; Seol, Young-Joo ; Park, Hyun-Seok ; Jang, Seung-Hwan ; Shin, Hang-Cheol ; Cho, Kwang-Hwi ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 141~147
DOI : 10.5808/GI.2009.7.3.141
Developed proteome-scale ortholog and paralog prediction methods are mainly based on sequence similarity. However, it is known that even the closest BLAST hit often does not mean the closest neighbor. For this reason, we added conserved interaction information to find orthologs. We propose a genome-scale, automated ortholog prediction method, named OrthoInterBlast. The method is based on both sequence and interaction similarity. When we applied this method to fly and yeast, 17% of the ortholog candidates were different compared with the results of Inparanoid. By adding protein-protein interaction information, proteins that have low sequence similarity still can be selected as orthologs, which can not be easily detected by sequence homology alone.
The Effect of Increasing Control-to-case Ratio on Statistical Power in a Simulated Case-control SNP Association Study
Kang, Moon-Su ; Choi, Sun-Hee ; Koh, In-Song ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 148~151
DOI : 10.5808/GI.2009.7.3.148
Generally, larger sample size leads to a greater statistical power to detect a significant difference. We may increase the sample size for both case and control in order to obtain greater power. However, it is often the case that increasing sample size for case is not feasible for a variety of reasons. In order to look at change in power as the ratio of control to case varies (1:1 to 4:1), we conduct association tests with simulated data generated by PLINK. The simulated data consist of 50 disease SNPs and 300 non-disease SNPs and we compute powers for disease SNPs. Genetic Power Calculator was used for computing powers with varying the ratio of control to case (1:1, 2:1, 3:1, 4:1). In this study, we show that gains in statistical power resulting from increasing the ratio of control to case are substantial for the simulated data. Similar results might be expected for real data.
Localization of Quantitative Trait Loci for Bone Mineral Density on Chromosome 13 in the Mongolian Population
Seo, Soo-Hyun ; Lim, Hae-Jeng ; Ahn, Se-Jin ; Lee, Joseph ; Kim, Jong-Il ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 152~158
DOI : 10.5808/GI.2009.7.3.152
Although the genetic basis for bone mineral density (BMD) has been studied by many groups so far, genes responsible for this complex trait has not been completely revealed. In order to localize quantitative trait loci (QTLs) for BMD variation in Asian population, the study was designed using a group of Mongolian population, a genetically closed population with a homogeneous lifestyle. BMD was measured at the left and right wrists and ankles using DEXA in 1,082 participants from 142 families. Genotyping of 13 polymorphic microsatellite markers on chromosome 13 (average spacing 8-9 cM) and two-point and multipoint linkage analysis were performed. In two-point linkage analysis, we identified two markers, D13S175 (6.03 cM) and D13S265 (68.73 cM) that had LOD scores greater than 1 for left ankle (LOD=2.09, LOD=1.49, respectively). We also found a marker D13S175 (6.03 cM) with a high LOD for left wrist (LOD=1.49) and the markers D13S265 (68.73 cM) and D13S217 (17.21 cM) for the right wrist (LOD= 1.82, LOD= 1.62, respectively). Among these significant marker regions, only two regions at 17 cM (13p11) and 65 cM (13q21) for the right wrist overlapped with major QTLs reported in following multipoint linkage analysis (LOD= 1.7549, LOD=1.4462, respectively). This study provides the possible evidence of the presence of QTLs affecting right wrist BMD in Mongolian populations on 13p11 and 13q21. Modest evidence was also found for genes affecting left ankle and left wrist BMD on 13p13.
Detection of hydin Gene Duplication in Personal Genome Sequence Data
Kim, Jong-Il ; Ju, Young-Seok ; Kim, Shee-Hyun ; Hong, Dong-Wan ; Seo, Jeong-Sun ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 159~162
DOI : 10.5808/GI.2009.7.3.159
Human personal genome sequencing can be done with high efficiency by aligning a huge number of short reads derived from various next generation sequencing (NGS) technologies to the reference genome sequence. One of the major obstacles is the incompleteness of human reference genome. We tried to analyze the effect of hidden gene duplication on the NGS data using the known example of hydin gene. Hydin2, a duplicated copy of hydin on chromosome 16q22, has been recently found to be localized to chromosome 1q21, and is not included in the current version of standard human genome reference. We found that all of eight personal genome data published so far do not contain hydin2, and there is large number of nsSNPs in hydin. The heterozygosity of those nsSNPs was significantly higher than expected. The sequence coverage depth in hydin gene was about two fold of average depth. We believe that these unique finding of hydin can be used as useful indicators to discover new hidden multiplication in human genome.
The Korean Pharmacogenomic Database at NIFDS: 2008 Update
Kang, T.S. ; Woo, S.W. ; Park, H.J. ; Han, S.Y. ; Park, M.H. ; Chung, M.W. ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 163~167
DOI : 10.5808/GI.2009.7.3.163
Since its first release in 2007, the National Institute of Food and Drug Safety Evaluation (NIFDS) has provided pharmacogenomic and comparative information specific to Koreans to allow regulatory reviewers and researchers to adapt their working practices to pharmacogenomics. The highlights of this year's additions include "Drug Information", "Gene Information" and "Pharmacogenomic information in the drug labels" sections. These new additions provide information on 737 genes, 719 drugs and pharmacogenomic data of the labels or relabels of 253 approved drugs as of November 2008. The latest version of the Korean Pharmacogenomic Database (KPD, release 2.0) has expanded significantly since its previous release. More SNP and haplotype information has been added to the database with the latest version of the KPD containing approximately four times as many SNPs and haplotypes than the previous version (719 vs. 152, and 30 vs. 7 respectively). Through the "SNP" and "Haplotype" sections, the KPD provides unique Korean SNP and haplotype information as well as comparative information of other populations (Japanese, Chinese, European, African) to offer a range of pharmacogenomic data that can help reviewers and the public understand pharmacogenomic information. The quality and quantity of information in the KPD has also been improved considerably. This data can be found at: http://www.nitr.go.kr/nitr/contents/m134700/view.do/.
A Computer-aided Design Tool with Semiautomatic Image-Processing Features for Visualizing Biological Pathways
Ham, Sung-Il ; Yang, San-Duk ; Thong, Chin-Ting ; Park, Hyun-Seok ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 168~170
DOI : 10.5808/GI.2009.7.3.168
The explosion in biological data resulting from high-throughput experiments requires new software tools to manipulate and display pathways in a way that can integrate disparate sources of information. A visual Java-based CAD tool for drawing and annotating biological pathways with semiautomatic image-processing features is described in this paper. The result of the image-editing process is an XML file for the appropriate links. This tool integrates the pathway images and XML file sources. The system has facilities for linking graphical objects to external databases and is capable of reproducing existing visual representations of pathway maps.
J2.5dPathway: A 2.5D Visualization Tool to Display Selected Nodes in Biological Pathways, in Parallel Planes
Ham, Sung-Il ; Song, Eun-Ha ; Yang, San-Duk ; Thong, Chin-Ting ; Rhie, Arang ; Galbadrakh, Bulgan ; Lee, Kyung-Eun ; Park, Hyun-Seok ; Lee, San-Ho ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 171~174
DOI : 10.5808/GI.2009.7.3.171
The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in two- and a-half dimensions (2.5D) as an alternative to three-dimensional (3D) visualizations. Such visualization allows user to display different groups of clustered nodes, in different parallel planes, and to see a detailed view of a group of objects in focus and its place in the context of the whole system. This tool is an extended version of J2dPathway.
WinBioDBs: A Windows-based Integrated Program for Manipulating Major Biological Databases
Nam, Hye-Weon ; Lee, Jin-Ho ; Park, Kie-Jung ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 175~177
DOI : 10.5808/GI.2009.7.3.175
We have developed WinBioDBs with Windows interfaces, which include importing modules and searching interfaces for 10 major public databases such as GenBank, PIR, SwissProt, Pathway, EPD, ENZYME, REBASE, Prosite, Blocks, and Pfam. User databases can be constructed with searching results of queries and their entries can be edited. The program is a stand-alone database searching program on Windows PC. Database update features are supported by importing raw database files and indexing after downloading them. Users can adjust their own searching environments and report format and construct their own projects consisting of a combination of a local databases. WinBioDBs are implemented with VC++ and its database is based on MySQL.
COCAW: A Genome-wide Pattern Search System for Designing Microbial Probes
Ryu, Seung-Hee ; Park, Kie-Jung ; Lee, Do-Hoon ; Kim, Cheol-Min ;
Genomics & Informatics, volume 7, issue 3, 2009, Pages 178~180
DOI : 10.5808/GI.2009.7.3.178
A few bioinformatics tools have been used to find out conserved regions as probes. We have developed a system based on a heuristic method with web interfaces to find out conserved regions against microbial genomes. The system runs in real time by using relative entropy in limited narrow regions and detecting similar regions between pair regions with local alignment. The system could be useful to find out conserved regions as genome-wide scale.