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The BIOWAY System: A Data Warehouse for Generalized Representation & Visualization of Bio-Pathways.

Min Kyung KIM ; Young Joo SEOL ; Sang Ho LEE ; Eun Ha SONG ; Ho Il LEE ; Chang Shin AHN ; Eun Chung CHOI ; Hyun Seok PARK

Genomics & Informatics.2004;2(4):191-194.

Exponentially increasing biopathway data in recent years provide us with means to elucidate the large-scale modular organization of the cell. Given the existing information on metabolic and regulatory networks, inferring biopathway information through scientific reasoning or data mining of large scale array data or proteomics data get great attention. Naturally, there is a need for a user-friendly system allowing the user to combine large and diverse pathway data sets from different resources. We built a data warehouse - BIOWAY - for analyzing and visualizing biological pathways, by integrating and customizing resources. We have collected many different types of data in regards to pathway information,including metabolic pathway data from KEGG/LIGAND,signaling pathway data from BIND, and protein information data from SWISS-PROT.In addition to providing general data retrieval mechanism, a successful user interface should provide convenient visualization mechanism since biological pathway data is difficult to conceptualize without graphical representations. Still, the visual interface in the previous systems, at best, uses static images only for the specific categorized pathways. Thus, it is difficult to cope with more complex pathways. In the BIOWAY system, all the pathway data can be displayed in computer generated graphical networks, rather than manually drawn image data. Furthermore, it is designed in such a way that all the pathway maps can be expanded or shrinked, by introducing the concept of super node. A subtle graphic layout algorithm has been applied to best display the pathway data.
Data Mining ; Dataset ; Information Storage and Retrieval ; Metabolic Networks and Pathways ; Proteomics

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Five Computer Simulation Studies of Whole-Genome Fragment Assembly: The Case of Assembling Zymomonas mobilis ZM4 Sequences.

Cholhee JUNG ; Jin Young CHOI ; Hyun Seok PARK ; Jeong Sun SEO

Genomics & Informatics.2004;2(4):183-190.

An approach for genome analysis based on assembly of fragments of DNA from the whole genome can be applied to obtain the complete nucleotide sequence of the genome of Zymomonas mobilis. However, the problem of fragment assembly raise thorny computational issues. Computer simulation studies of sequence assembly usually show some abnormal assemblage of artificial sequences containing repetitive or duplicated regions, and suggest methods to correct those abnormalities. In this paper, we describe five simulation studies which had been performed previous to the actual genome assembly process of Zymomonas mobilis ZM4.
Base Sequence ; Computer Simulation* ; DNA ; Genome ; Zymomonas*

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Comparative Statistic Module (CSM) for Significant Gene Selection.

Young Jin KIM ; Hyo Mi KIM ; Sang Bae KIM ; Chan PARK ; Kuchan KIMM ; InSong KOH

Genomics & Informatics.2004;2(4):180-183.

Comparative Statistic Module(CSM) provides more reliable list of significant genes to genomics researchers by offering the commonly selected genes and a method of choice by calculating the rank of each statistical test based on the average ranking of common genes across the five statistical methods, i.e. t-test, Kruskal-Wallis (Wilcoxon signed rank) test, SAM, two sample multiple test, and Empirical Bayesian test. This statistical analysis module is implemented in Perl, and R languages.
Genomics

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Construction of Various Copy Number Plasmid Vectors and Their Utility for Genome Sequencing.

Tae Jin YANG ; Yeisoo YU ; David A FRISCH ; Seunghee LEE ; Hye Ran KIM ; Soo Jin KWON ; Beom Suk PARK ; Rod A WING

Genomics & Informatics.2004;2(4):174-179.

We developed various plasmid cloning vectors that are useful in the construction of genomic and shotgun libraries. Two medium copy vectors, pCUGIblu21(pCb21) and pAGIblu21 (pAb21), which are resistant to kanamycin (KmR) and chloramphenicol (CamR), respectively, are useful for cloning DNA inserts ranging from 5kb to 15kb. Two high copy vectors, pCUGIblu31 (pCb31) and pAGIblu31 (pAb31), containing KmR and CamR, respectively, are useful for DNA inserts less than 5kb. These vectors are well adapted for large-scale genome sequencing projects by providing choice of copy number and selectable marker. The small vector size is another advantage of these vectors. All vectors contain lacZ including multicloning sites that originated from pBluscriptIIsk- for easy cloning and sequencing. Two medium copy vectors contain unique and rare cutting SwaI (ATTTAAAT) restriction enzyme sites for easy determination of insert size. We developed two combined vectors, pC21A31 and pC31A21, which are combinations of (pCb21 + pAb31) and (pCb31 + Ab21),respectively. These two vectors provide four choices of vectors such as KmR and medium, CamR and high, CamR and medium, and KmR and high copy vectors by restriction enzyme cutting, dephosphorylation, and gel purification. These vectors were successfully applied to high throughput shotgun sequencing of rice, tomato, and brassica BAC clones. With an example of extremely biased hydro sheared 3 kb shotgun library of a tomato BAC clone, which is originated from cytogenetically defined peri-centromeric region, we suggest the utility of an additional 10 kb library for sequence assembly of the difficult-to-assemble BAC clone.
Bias (Epidemiology) ; Brassica ; Chloramphenicol ; Clone Cells ; Cloning, Organism ; DNA ; Genetic Vectors ; Genome* ; Kanamycin ; Lycopersicon esculentum ; Plasmids*

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The Atom of Evolution.

Jonghwa BHAK ; Dan BOLSER ; Daeui PARK ; Yoobok CHO ; Kiesuk YOON ; Semin LEE ; SungSam GONG ; Insoo JANG ; Changbum PARK ; Maryana HUSTON ; Hwanho CHOI

Genomics & Informatics.2004;2(4):167-173.

The main mechanism of evolution is that biological entities change, are selected, and reproduce. We propose a different concept in terms of the main agent or atom of evolution: in the biological world, not an individual object,but its interactive network is the fundamental unit of evolution. The interaction network is composed of interaction pairs of information objects that have order information. This indicates a paradigm shift from 3D biological objects to an abstract network of information entities as the primary agent of evolution. It forces us to change our views about how organisms evolve and therefore the methods we use to analyze evolution.

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Comparative Study of Human and Chimpanzee Genome.

Sang Hang CHOI ; Dae Soo KIM ; Dae Won KIM ; Yong Seok LEE ; Hong Seog PARK

Genomics & Informatics.2004;2(4):163-166.

No abstract available.
Genome* ; Humans* ; Pan troglodytes*

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Current Progress of Next Generation Battery of Toxicology-Cellular and Molecular Toxicology, and Toxicogenomics.

Jae Chun RYU ; Seok joo YOON ; Jong Eun LEE ; Youn Jung KIM

Genomics & Informatics.2004;2(4):153-162.

No abstract available.
Toxicogenetics* ; Toxicology*

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Controlling Linkage Disequilibrium in Association Tests: Revisiting APOE Association in Alzheimer's Disease.

Leeyoung PARK

Genomics & Informatics.2007;5(2):61-67.

The allele frequencies of markers as well as linkage disequilibrium (LD) can be changed in cases due to the LD between markers and the disease allele, exhibiting spurious associations of markers. To identify the true association, classical statistical tests for dealing with confounders have been applied to draw a conclusion as to whether the association of variants comes from LD with the known disease allele. However, a more direct test considering LD using estimated haplotype frequencies may be more efficient. The null hypothesis is that the different allele frequencies of a variant between cases and controls come solely from the increased disease allele frequency and the LD relationship with the disease allele. The haplotype frequencies of controls are estimated using the expectation maximization (EM) algorithm from the genotype data. The estimated frequencies are applied to calculate the expected haplotype frequencies in cases corresponding to the increase or decrease of the causative or protective alleles. The suggested method was applied to previously published data, and several APOE variants showed association with Alzheimer's disease independent from the APOE epsilon4 variant, rs429358, regardless of LD showing significant simulated p-values. The test results support the possibility that there may be more than one common disease variant in a locus.
Alleles ; Alzheimer Disease* ; Apolipoproteins E* ; Gene Frequency ; Genotype ; Haplotypes ; Linkage Disequilibrium*

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Genetic Analysis of TGFA, MTHFR, and IFR6 in Korean Patients Affected by Nonsyndromic Cleft Lip with or without Cleft Palate (CL/P).

Jung Young PARK ; Han Wook YOO ; Youngho KIM

Genomics & Informatics.2007;5(2):56-60.

Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common craniofacial birth defect that is the result of a mixture of genetic and environmental factors. While studies have identified a number of different candidate genes and loci for the etiology of CL/P, the results have not been consistent among different ethnic groups. To study the genetic association of the candidate genes in Korean patients affected by CL/P, we genotyped 97 nonsyndromic CL/P patients and 100 control individuals using single nucleotide polymorphic markers at the MTHFR, TGFA, and IRF6 genes. We report that the T3827C marker at TGFA showed significant association with nonsyndromic CL/P, but all the other markers tested were not significantly associated with nonsyndromic CL/P in Korean patients.
Cleft Lip* ; Cleft Palate* ; Congenital Abnormalities ; Ethnic Groups ; Humans

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Molecular Imaging in the Age of Genomic Medicine.

Jonghoe BYUN

Genomics & Informatics.2007;5(2):46-55.

The convergence of molecular and genetic disciplines with non-invasive imaging technologies has provided an opportunity for earlier detection of disease processes which begin with molecular and cellular abnormalities. This emerging field, known as molecular imaging, is a relatively new discipline that has been rapidly developed over the past decade. It endeavors to construct a visual representation, characterization, and quantification of biological processes at the molecular and cellular level within living organisms. One of the goals of molecular imaging is to translate our expanding knowledge of molecular biology and genomic sciences into good patient care. The practice of molecular imaging is still largely experimental, and only limited clinical success has been achieved. However, it is anticipated that molecular imaging will move increasingly out of the research laboratory and into the clinic over the next decade. Non-invasive in vivo molecular imaging makes use of nuclear, magnetic resonance, and in vivo optical imaging systems. Recently, an interest in Positron Emission Tomography (PET) has been revived, and along with optical imaging systems PET is assuming new, important roles in molecular genetic imaging studies. Current PET molecular imaging strategies mostly rely on the detection of probe accumulation directly related to the physiology or the level of reporter gene expression. PET imaging of both endogenous and exogenous gene expression can be achieved in animals using reporter constructs and radiolabeled probes. As increasing numbers of genetic markers become available for imaging targets, it is anticipated that a better understanding of genomics will contribute to the advancement of the molecular genetic imaging field. In this report, the principles of non-invasive molecular genetic imaging, its applications and future directions are discussed.
Animals ; Biological Processes ; Gene Expression ; Genes, Reporter ; Genetic Markers ; Genomics ; Molecular Biology ; Molecular Imaging* ; Optical Imaging ; Patient Care ; Physiology ; Positron-Emission Tomography

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