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 11, Issue 4 - Dec 2013
Volume 11, Issue 3 - Sep 2013
Volume 11, Issue 2 - Jun 2013
Volume 11, Issue 1 - Mar 2013
Selecting the target year
Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era
Kim, Mincheol ; Lee, Ki-Hyun ; Yoon, Seok-Whan ; Kim, Bong-Soo ; Chun, Jongsik ; Yi, Hana ;
Genomics & Informatics, volume 11, issue 3, 2013, Pages 102~113
DOI : 10.5808/GI.2013.11.3.102
Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances of sequencing techniques. The massive data production and substantial cost reduction in next-generation sequencing have led to the rapid growth of metagenomic research both quantitatively and qualitatively. It is evident that metagenomics will be a standard tool for studying the diversity and function of microbes in the near future, as fingerprinting methods did previously. As the speed of data accumulation is accelerating, bioinformatic tools and associated databases for handling those datasets have become more urgent and necessary. To facilitate the bioinformatics analysis of metagenomic data, we review some recent tools and databases that are used widely in this field and give insights into the current challenges and future of metagenomics from a bioinformatics perspective.
Bioprospecting Potential of the Soil Metagenome: Novel Enzymes and Bioactivities
Lee, Myung Hwan ; Lee, Seon-Woo ;
Genomics & Informatics, volume 11, issue 3, 2013, Pages 114~120
DOI : 10.5808/GI.2013.11.3.114
The microbial diversity in soil ecosystems is higher than in any other microbial ecosystem. The majority of soil microorganisms has not been characterized, because the dominant members have not been readily culturable on standard cultivation media; therefore, the soil ecosystem is a great reservoir for the discovery of novel microbial enzymes and bioactivities. The soil metagenome, the collective microbial genome, could be cloned and sequenced directly from soils to search for novel microbial resources. This review summarizes the microbial diversity in soils and the efforts to search for microbial resources from the soil metagenome, with more emphasis on the potential of bioprospecting metagenomics and recent discoveries.
Comparative Viral Metagenomics of Environmental Samples from Korea
Kim, Min-Soo ; Whon, Tae Woong ; Bae, Jin-Woo ;
Genomics & Informatics, volume 11, issue 3, 2013, Pages 121~128
DOI : 10.5808/GI.2013.11.3.121
The introduction of metagenomics into the field of virology has facilitated the exploration of viral communities in various natural habitats. Understanding the viral ecology of a variety of sample types throughout the biosphere is important per se, but it also has potential applications in clinical and diagnostic virology. However, the procedures used by viral metagenomics may produce technical errors, such as amplification bias, while public viral databases are very limited, which may hamper the determination of the viral diversity in samples. This review considers the current state of viral metagenomics, based on examples from Korean viral metagenomic studies-i.e., rice paddy soil, fermented foods, human gut, seawater, and the near-surface atmosphere. Viral metagenomics has become widespread due to various methodological developments, and much attention has been focused on studies that consider the intrinsic role of viruses that interact with their hosts.
Genome-Wide Association Study of Orthostatic Hypotension and Supine-Standing Blood Pressure Changes in Two Korean Populations
Hong, Kyung-Won ; Kim, Sung Soo ; Kim, Yeonjung ;
Genomics & Informatics, volume 11, issue 3, 2013, Pages 129~134
DOI : 10.5808/GI.2013.11.3.129
Orthostatic hypotension (OH) is defined by a 20-mm Hg difference of systolic blood pressure (dtSBP) and/or a 10-mm Hg difference of diastolic blood pressure (dtDBP) between supine and standing, and OH is associated with a failure of the cardiovascular reflex to maintain blood pressure on standing from a supine position. To understand the underlying genetic factors for OH traits (OH, dtSBP, and dtDBP), genome-wide association studies (GWASs) using 333,651 single nucleotide polymorphisms (SNPs) were conducted separately for two population-based cohorts, Ansung (n = 3,173) and Ansan (n = 3,255). We identified 8 SNPs (5 SNPs for dtSBP and 3 SNPs for dtDBP) that were repeatedly associated in both the Ansung and Ansan cohorts and had p-values of <
in the meta-analysis. Unfortunately, the SNPs of the OH case control GWAS did not pass our p-value criteria. Four of 8 SNPs were located in the intergenic region of chromosome 2, and the nearest gene (CTNNA2) was located at 1 Mb of distance. CTNNA2 is a linker between cadherin adhesion receptors and the actin cytoskeleton and is essential for stabilizing dendritic spines in rodent hippocampal neurons. Although there is no report about the function in blood pressure regulation, hippocampal neurons interact primarily with the autonomic nervous system and might be related to OH. The remaining SNPs, rs7098785 of dtSBP trait and rs6892553, rs16887217, and rs4959677 of dtDBP trait were located in the PIK3AP1 intron, ACTBL2-3' flanking, STAR intron, and intergenic region, respectively, but there was no clear functional link to blood pressure regulation.
Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset
Kim, Jihye ; Kwon, Ji-Sun ; Kim, Sangsoo ;
Genomics & Informatics, volume 11, issue 3, 2013, Pages 135~141
DOI : 10.5808/GI.2013.11.3.135
Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (
< 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.
Structure and Expression Analyses of SVA Elements in Relation to Functional Genes
Kwon, Yun-Jeong ; Choi, Yuri ; Eo, Jungwoo ; Noh, Yu-Na ; Gim, Jeong-An ; Jung, Yi-Deun ; Lee, Ja-Rang ; Kim, Heui-Soo ;
Genomics & Informatics, volume 11, issue 3, 2013, Pages 142~148
DOI : 10.5808/GI.2013.11.3.142
SINE-VNTR-Alu (SVA) elements are present in hominoid primates and are divided into 6 subfamilies (SVA-A to SVA-F) and active in the human population. Using a bioinformatic tool, 22 SVA element-associated genes are identified in the human genome. In an analysis of genomic structure, SVA elements are detected in the 5′ untranslated region (UTR) of HGSNAT (SVA-B), MRGPRX3 (SVA-D), HYAL1 (SVA-F), TCHH (SVA-F), and ATXN2L (SVA-F) genes, while some elements are observed in the 3′UTR of SPICE1 (SVA-B), TDRKH (SVA-C), GOSR1 (SVA-D), BBS5 (SVA-D), NEK5 (SVA-D), ABHD2 (SVA-F), C1QTNF7 (SVA-F), ORC6L (SVA-F), TMEM69 (SVA-F), and CCDC137 (SVA-F) genes. They could contribute to exon extension or supplying poly A signals. LEPR (SVA-C), ALOX5 (SVA-D), PDS5B (SVA-D), and ABCA10 (SVA-F) genes also showed alternative transcripts by SVA exonization events. Dominant expression of HYAL1_SVA appeared in lung tissues, while HYAL1_noSVA showed ubiquitous expression in various human tissues. Expression of both transcripts (TDRKH_SVA and TDRKH_noSVA) of the TDRKH gene appeared to be ubiquitous. Taken together, these data suggest that SVA elements cause transcript isoforms that contribute to modulation of gene regulation in various human tissues.
Genome-Wide Association Study of Liver Enzymes in Korean Children
Park, Tae-Joon ; Hwang, Joo-Yeon ; Go, Min Jin ; Lee, Hye-Ja ; Jang, Han Byul ; Choi, Youngshim ; Kang, Jae Heon ; Park, Kyung Hee ; Choi, Min-Gyu ; Song, Jihyun ; Kim, Bong-Jo ; Lee, Jong-Young ;
Genomics & Informatics, volume 11, issue 3, 2013, Pages 149~154
DOI : 10.5808/GI.2013.11.3.149
Liver enzyme elevations, as an indicator of liver function, are widely associated with metabolic diseases. Genome-wide population-based association studies have identified a genetic susceptibility to liver enzyme elevations and their related traits; however, the genetic architecture in childhood remains largely unknown. We performed a genome-wide association study to identify new genetic loci for liver enzyme levels in a Korean childhood cohort (n = 484). We observed three novel loci (rs4949718, rs80311637, and rs596406) that were multiply associated with elevated levels of alanine transaminase and aspartate transaminase. Although there are some limitations, including genetic power, additional replication and functional characterization will support the clarity on the genetic contribution that the ST6GALNAC3, ADAMTS9, and CELF2 genes have in childhood liver function.
Protein Backbone Torsion Angle-Based Structure Comparison and Secondary Structure Database Web Server
Jung, Sunghoon ; Bae, Se-Eun ; Ahn, Insung ; Son, Hyeon S. ;
Genomics & Informatics, volume 11, issue 3, 2013, Pages 155~160
DOI : 10.5808/GI.2013.11.3.155
Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.