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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 2, Issue 4 - Dec 2004
Volume 2, Issue 3 - Sep 2004
Volume 2, Issue 2 - Jun 2004
Volume 2, Issue 1 - Mar 2004
Selecting the target year
Current Status and Future Clinical Applications of Array-based Comparative Genomic Hybridization
Yim, Seon-Hee ; Chung, Yeun-Jun ;
Genomics & Informatics, volume 2, issue 3, 2004, Pages 113~120
Application of Decision Tree for the Classification of Antimicrobial Peptide
Lee, Su Yeon ; Kim, Sunkyu ; Kim, Sukwon S. ; Cha, Seon Jeong ; Kwon, Young Keun ; Moon, Byung-Ro ; Lee, Byeong Jae ;
Genomics & Informatics, volume 2, issue 3, 2004, Pages 121~125
The purpose of this study was to investigate the use of decision tree for the classification of antimicrobial peptides. The classification was based on the activities of known antimicrobial peptides against common microbes including Escherichia coli and Staphylococcus aureus. A feature selection was employed to select an effective subset of features from available attribute sets. Sequential applications of decision tree with 17 nodes with 9 leaves and 13 nodes with 7 leaves provided the classification rates of
against E. coli and S. aureus, respectively. Angle subtended by positively charged face and the positive charge commonly gave higher accuracies in both E. coli and S. aureusdatasets. In this study, we describe a successful application of decision tree that provides the understanding of the effects of physicochemical characteristics of peptides on bacterial membrane.
STAT6 Gene Polymorphisms in Allergic Rhinitis
Kim, Jeong Joong ; Kim, Min Su ; Lee, Jung Hun ; Choi, Tae Wook ; Choi, Sang Heon ; Lee, Jae Hoon ; Chung, Hun Taeg ;
Genomics & Informatics, volume 2, issue 3, 2004, Pages 126~130
T helper-type 2 cytokines, such as IL-4 and IL-13, may play a central role in allergic diseases. The protein known as signal transducers and activators of transcription 6 (STAT6) is a key transcription factor involved in both IL-4- and -13-mediated biological responses. Two polymorphisms of the STAT 6 gene (exon 1 and G2964A variant) have been found. We investigated whether these STAT6 gene polymorph isms were associated with allergic rhinitis. Blood samples for genetic analysis were obtained from 285 individuals with allergic rhinitis and from 271 healthy subjects without atopic disease. The G2964A variant of the STAT6 gene was genotyped using PCR-RFLP analysis. The GT repeat polymorphism in exon 1 of the STAT6 gene was genotyped by fragment analysis. There was no association between the 2964A variant and GT repeat polymorphism in exon 1 of the STAT6 and allergic rhinitis in a Korean population (both p > 0.05). Our results suggest that a combination of STAT6 gene polymorphisms is not a useful marker for predicting allergic rhinitis.
MediScore: MEDLINE-based Interactive Scoring of Gene and Disease Associations
Cho, Hye-Young ; Oh, Bermseok ; Lee, Jong-Keuk ; Kim, Kuchan ; Koh, InSong ;
Genomics & Informatics, volume 2, issue 3, 2004, Pages 131~133
MediScore is an information retrieval system, which helps to search for the set of genes associated with a specific disease or the set of diseases associated with a specific gene. Despite recent improvement of natural language processing (NLP) and other text mining approaches to search for disease associated genes, many false positive results come out due to diversity of exceptional cases as well as ambiguities in gene names. In order to overcome the weak points of current text mining approaches, MediScore introduces statistical normalization based on binomial to normal distribution approximation which corrects inaccurate scores caused by common words not representing genes and interactive rescoring by the user to remove the false positive results. Interactive rescoring includes individual alias scoring for each gene to remove false gene synonyms, referring MEDLINE abstracts, and cross referencing between OMIM and other related information.
In silica Prediction of Angiogenesis-related Genes in Human Hepatocellular Carcinoma
Kang, Seung-Hui ; Park, Jeong-Ae ; Hong, Soon-Sun ; Kim, Kyu-Won ;
Genomics & Informatics, volume 2, issue 3, 2004, Pages 134~141
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and a typical hypervascular tumor. Therefore, it is important to find factors related to angiogenesis in the process of HCC malignancy. In order to find angiogenesis-related factors in HCC, we used combined methods of in silico prediction and an experimental assay. We analyzed 1457 genes extracted from cDNA microarray of HCC patients by text-mining, sequence similarity search and domain analysis. As a result, we predicted that 16 genes were likely to be involved in angiogenesis and then the effects of these genes were confirmed by hypoxia response element(HRE)-luciferase assay. For instant, we classified osteopontin into a potent angiogenic factor and coagulation factor XII into a significant antiangiogenic factor. Collectively, we suggest that using a combination of in silico prediction and experimental approaches, we can identify HCC-specific angiogenesisrelated factors effectively and rapidly.
Web Services Based Biological Data Analysis Tool
Kim, Min Kyung ; Choi, Yo Hahn ; Yoo, Seong Joon ; Park, Hyun Seok ;
Genomics & Informatics, volume 2, issue 3, 2004, Pages 142~146
Biological data and analysis tools are accumulated in distributed databases and web servers. For this reason, biologists who want to find information from the web should be aware of the various kinds of resources where it is located and how it is retrieved. Integrating the data from heterogeneous biological resources will enable biologists to discover new knowledge across the specific domain boundaries from sequences to expression, structure, and pathway. And inevitably biological databases contain noisy data. Therefore, consensus among databases will confirm the reliability of its contents. We have developed WeSAT that integrates distributed and heterogeneous biological databases and analysis tools, providing through Web Services protocols. In WeSAT, biologists are retrieved specific entries in SWISS-PROT/EMBL, PDB, and KEGG, which have annotated information about sequence, structure, and pathway. And further analysis is carried by integrated services for example homology search and multiple alignments. WeSAT makes it possible to retrieve real time updated data and analysis from the scattered databases in a single platform through Web Services.
MitGEN: Single Nucleotide Polymorphism DB Browser for Human Mitochondrial Genome
Park, Hyun Seok ; Lee, Seung Uk ;
Genomics & Informatics, volume 2, issue 3, 2004, Pages 147~148
Recently completed mitochondrial genome databses from public resources provide us with a better understanding of individual mitochondrial genomes for population genomics. By determining the substitution rate of the genomic sequences, it is plausible to derive dates on the phylogenetic tree and build a chronology of events in the evolution of human species. MitGEN is specially designed as a mitochondrial genome browser for analyzing, comparing and visualizing single nucleotide polymorphism for human mitochondrial genomes between human races for comparative genomics. It is a standalone application and is available free for non-commercial work.