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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
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Higher Order Knowledge Processing: Pathway Database and Ontologies
Fukuda, Ken Ichiro ;
Genomics & Informatics, volume 3, issue 2, 2005, Pages 47~51
Molecular mechanisms of biological processes are typically represented as 'pathways' that have a graphanalogical network structure. However, due to the diversity of topics that pathways cover, their constituent biological entities are highly diverse and the semantics is embedded implicitly. The kinds of interactions that connect biological entities are likewise diverse. Consequently, how to model or process pathway data is not a trivial issue. In this review article, we give an overview of the challenges in pathway database development by taking the INOH project as an example.
BioCovi: A Visualization Service for Comparative Genomics Analysis
Lee, Jungsul ; Park, Daeui ; Bhak, Jong ;
Genomics & Informatics, volume 3, issue 2, 2005, Pages 52~54
Visualization of the homology information is an important method to analyze the evolutionary and functional meanings of genes. With a database containing model genomes of Homo sapiens, Mus muculus, and Rattus norvegicus, we constructed a webbased comparative analysis tool, BioCovi, to visualize the homology information of mammalian sequences on a very large scale. The user interface has several features: it marks regions whose identity is greater than that specified, it shows or hides gaps from the result of global sequence alignment, and it inverts the graph when total identity is higher than the threshold specified.
Classification of Peroxiredoxin Subfamilies Using Regular Expressions
Chon, Jae Kyung ; Choi, Jongkeun ; Kim, Sang Soo ; Shin, Whanchul ;
Genomics & Informatics, volume 3, issue 2, 2005, Pages 55~60
Peroxiredoxins (Prx's) are a superfamily of peroxidases that are ubiquitous in all super-kingdoms. Previous biochemical and structural studies have suggested that Prx's could be divided into five subfamilies (1-Cys, Typical 2-Cys, Atypical 2-Cys C-, L- and R- types). In this work, we have developed a set of regular expression patterns describing subfamily-specific spatial constraints of the key catalytic residues. Using these patterns, 1,016 Prx's available in public databases were classified into the five subfamilies. Our method performed well for most of the types except for Atypical 2 Cys R type.
Comparative Genomics of T-complex protein 10 like in Humans and Chimpanzees
Kim, Il-Chul ; Kim, Dae-Soo ; Kim, Dae-Won ; Choi, Sang-Haeng ; Choi, Han-Ho ; Chae, Sung-Hwa ; Park, Hong-Seog ;
Genomics & Informatics, volume 3, issue 2, 2005, Pages 61~65
Comparing 231 genes on chimpanzee chromosome 22 with their orthologous on human chromosome 21, we have found that 15 orthologs have indels within their coding sequences. It was rather surprising that significant number of genes have changed by indel, despite the shorter time since their divergence and led us hypothesize that indels and structural changes may represent one of the major mechanism of proteome evolution in the higher primates. Human T-complex protein 10 like (TCP 10L) is a representative having indel within its coding sequence. Gene structure of human TCP10L compared with chimpanzee TCP10L gene showed 16 base pair difference in genomic DNA. As a result of the indel, frame shift mutation occurs in coding sequence (CDS) and human TCP10L express longer polypeptide of 21 amino acid residues than that of chimpanzee. Our prediction found that the indel may affect to dramatic change of secondary protein structure between human and chimpanzee TCP10L. Especially, the structural changes in the C-terminal region of TCP10L protein may affect on the interacting potential to other proteins rather than DNA binding function of the protein. Through these changes, TCP10L might influence gene expression profiles in liver and testis and subsequently influence the physiological changes required in primate evolution.
Aging and UV Irradiation Related Changes of Gene Expression in Primary Human Keratinocytes
Lee, Ok Joo ; Lee, Sung-Young ; Park, Jae-Bong ; Lee, Jae-Yang ; Kim, Jong-Il ; Kim, Jaebong ;
Genomics & Informatics, volume 3, issue 2, 2005, Pages 66~72
The epidermis is a physiological barrier to protect organisms against environment. During the aging process, skin tissues undergo various changes including morphological and functional changes. The transcriptional regulation of genes is part of cellular reaction of aging process. In order to examine the changes of gene expression during the aging process, we used the primary cell culture system of human keratinocytes. Since UV radiation is the most important environmental skin aggressor, causing skin cancer and other problems including premature skin aging, we examined the changes of gene expression in human keratinocytes after UV irradiation using oligonucleotide microarray containing over 10,000 genes. We also compared the gene expression patterns of the senescent and UV treated cells. Expression of the variety of genes related to transcription factors, cell cycle regulation, immune response was altered in human keratinocytes. Some of down-regulated genes are represented in both senescent and UV treated cells. The results may provide a new view of gene expression following UVB exposure and aging process in human keratinocytes.
PrimateDB: Development of Primate Genome DB and Web Service
Woo, Taeha ; Shin, Gwangsik ; Kang, Taewook ; Kim, Byoungchul ; Seo, Jungmin ; Kim, Sang Soo ; Kim, Chang-Bae ;
Genomics & Informatics, volume 3, issue 2, 2005, Pages 73~76
The comparative analysis of the human and primate genomes including the chimpanzee can reveal unique types of information impossible to obtain from comparing the human genome with the genomes of other vertebrates. PrimateDB is an open depository server that provides primate genome information for the comparative genome research. The database also provides an easy access to variable information within/between the primate genomes and supports analyzed information, such as annotation and retroelements and phylogeny. The comparative analyses of more primate genomes are also being included as the long-term objective.
Massive Identification of Cancer-Specific Nucleic Acid Ligands
Lee, Young Ju ; Lee, Seong-Wook ;
Genomics & Informatics, volume 3, issue 2, 2005, Pages 77~80
Targeting of complex system such as human cells rather than biochemically pure molecules will be a useful approach to massively identify ligands specific for the markers associated with human disease such as cancer and simultaneously discover the specific molecular markers. In this study, we developed in vitro selection method to identify nuclease-resistant nucleic acid ligands called RNA aptamers that are specific for human cancer cells. This method is based on the combination of the cell-based selection and subtractive systematic evolution of ligands by exponential enrichment (SELEX) method. These aptamers will be useful for cancer-specific ligands for proteomic research to identify cancer-specific molecular markers as well as tumor diagnosis and therapy.