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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 3, Issue 4 - Dec 2005
Volume 3, Issue 3 - Sep 2005
Volume 3, Issue 2 - Jun 2005
Volume 3, Issue 1 - Mar 2005
Selecting the target year
DNA Pooling as a Tool for Case-Control Association Studies of Complex Traits
Ahn, Chul ; King, Terri M. ; Lee, Kyusang ; Kang, Seung-Ho ;
Genomics & Informatics, volume 3, issue 1, 2005, Pages 1~7
Case-control studies are widely used for disease gene mapping using individual genotyping data. However, analyses of large samples are often impractical due to the expense of individual genotyping. The use of DNA pooling can significantly reduce the number of genotyping reactions required; hence reducing the cost of large-scale case-control association studies. Here, we discuss the design and analysis of DNA pooling genetic association studies.
Gene Expression Analysis of Megakaryocytes Derived from Human Umbilical Cord
Cells by Thrombopoietin
Kim, Jeong-Ah ; Kim, Hyung-Lae ;
Genomics & Informatics, volume 3, issue 1, 2005, Pages 8~14
Although much is known about the molecular biology of platelets, the megakaryocytes' (MKs) molecular biology was not understood so well because of their rareness. By the cloning and characterization of thrombopoietin (TPO), which is the principal regulator of the growth and development of the MKs, researches on the MKs have been growing rapidly. To understand megakaryocytopoiesis, we investigated the gene expression profile of the MKs using oligonucleotide microarray where 10,108 unique genes were spotted. Comparing the fluorescence intensities of which ratio is
, 372 genes were up-regulated and 541 genes were down-regulated in MKs. For confirmatory expression, RNase protection assay (RPA) establishing abundant apoptotic gene expression was carried out. In MKs, many of the known genes, including several platelet related genes, GATA binding protein were highly expressed. Particularly, TGF beta, clusterin (complement lysis inhibitor), and thymosin beta 4 (actin-sequestering molecules) were expressed highly in MKs. As MKs specific expressed genes may regulate normal and pathologic platelet (and/or MK) functions, the transcript profiling using microarray was useful on molecular understanding of MKs,
Identification of Caenorhabditis elegans MicroRNA Targets Using a Kernel Method
Lee, Wha-Jin ; Nam, Jin-Wu ; Kim, Sung-Kyu ; Zhang, Byoung-Tak ;
Genomics & Informatics, volume 3, issue 1, 2005, Pages 15~23
Background MicroRNAs (miRNAs) are a class of noncoding RNAs found in various organisms such as plants and mammals. However, most of the mRNAs regulated by miRNAs are unknown. Furthermore, miRNA targets in genomes cannot be identified by standard sequence comparison since their complementarity to the target sequence is imperfect in general. In this paper, we propose a kernel-based method for the efficient prediction of miRNA targets. To help in distinguishing the false positives from potentially valid targets, we elucidate the features common in experimentally confirmed targets. Results The performance of our prediction method was evaluated by five-fold cross-validation. Our method showed 0.64 and 0.98 in sensitivity and in specificity, respectively. Also, the proposed method reduced the number of false positives by half compared with TargetScan. We investigated the effect of feature sets on the classification of miRNA targets. Finally, we predicted miRNA targets for several miRNAs in the Caenorhabditis elegans (C. elegans) 3' untranslated region (3' UTR) database. Condusions The targets predicted by the suggested method will help in validating more miRNA targets and ultimately in revealing the role of small RNAs in the regulation of genomes. Our algorithm for miRNA target site detection will be able to be improved by additional experimentalknowledge. Also, the increase of the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection.
Cloning of Xenopus laevis TRPV2 by Gene Prediction
Lee, Jung Youn ; Shim, Won Sik ; Oh, Uhtaek ;
Genomics & Informatics, volume 3, issue 1, 2005, Pages 24~29
TRPV2 is a non-specific cation channel expressed in sensory neurons, and activated by noxious heat. Particularly, TRPV2 has six transmembrane domains and three ankyrin repeats. TRPV2 has been cloned from various species such as human, rat, and mouse. Oocytes of Xenopus laevis - an African clawed frog have been widely used for decades in characterization of various receptors and ion channels. The functional property of rat TRPV2 was also identified by this oocyte expression system. However, no TRPV2 orthologue of Xenopus laevis has been reported so far. Hence, we have focused to clone a TRPV2 orthologue of Xenopus laevis with the aid of bioinformatic tools. Because the genome sequence of Xenopus laevis is not available until now, a genome sequence of Xenopus tropicalis - a close relative species of Xenopus laevis - was used. After a number of bioinformatic searches in silico, a predicted full-length sequence of TRPV2 orthologue of Xenopus tropicalis was found. Based on this predicted sequence, various approaches such as RT-PCR and 5' -RACE technique were applied to clone a full length of Xenopus laevis TRV2. Consequently, a full-length Xenopus laevis TRPV2 was cloned from heart cDNA.
Supervised Model for Identifying Differentially Expressed Genes in DNA Microarray Gene Expression Dataset Using Biological Pathway Information
Chung, Tae Su ; Kim, Keewon ; Kim, Ju Han ;
Genomics & Informatics, volume 3, issue 1, 2005, Pages 30~34
Microarray technology makes it possible to measure the expressions of tens of thousands of genes simultaneously under various experimental conditions. Identifying differentially expressed genes in each single experimental condition is one of the most common first steps in microarray gene expression data analysis. Reasonable choices of thresholds for determining differentially expressed genes are used for the next-stap-analysis with suitable statistical significances. We present a supervised model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are trying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful structure from microarray datasets.
BioSubroutine: an Open Web Server for Bioinformatics Algorithms and Subroutines
Lee, Joowon ; Kim, Hana ; Lee, Wonhye ; Chung, Dongil ; Bhak, Jong ;
Genomics & Informatics, volume 3, issue 1, 2005, Pages 35~38
We present BioSubroutine, an open depository server that automatically categorizes various subroutines frequently used in bioinformatics research. We processed a large bioinformatics subroutine library called Bio.pl that was the first Bioperl subroutine library built in 1995. Over 1000 subroutines were processed automatically and an HTML interface has been created. BioSubroutine can accept new subroutines and algorithms from any such subroutine library, as well as provide interactive user forms. The subroutines are stored in an SQL database for quick searching and accessing. BioSubroutine is an open access project under the BioLicense license scheme.
Xperanto: A Web-Based Integrated System for DNA Microarray Data Management and Analysis
Park, Ji Yeon ; Park, Yu Rang ; Park, Chan Hee ; Kim, Ji Hoon ; Kim, Ju Ha ;
Genomics & Informatics, volume 3, issue 1, 2005, Pages 39~42
DNA microarray is a high-throughput biomedical technology that monitors gene expression for thousands of genes in parallel. The abundance and complexity of the gene expression data have given rise to a requirement for their systematic management and analysis to support many laboratories performing microarray research. On these demands, we developed Xperanto for integrated data management and analysis using user-friendly web-based interface. Xperanto provides an integrated environment for management and analysis by linking the computational tools and rich sources of biological annotation. With the growing needs of data sharing, it is designed to be compliant to MGED (Microarray Gene Expression Data) standards for microarray data annotation and exchange. Xperanto enables a fast and efficient management of vast amounts of data, and serves as a communication channel among multiple researchers within an emerging interdisciplinary field.