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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
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ChimerDB - Database of Chimeric Sequences in the GenBank
Kim, Namshin ; Shin, Seokmin ; Cho, Kwang-Hwi ; Lee, Sanghyuk ;
Genomics & Informatics, volume 2, issue 2, 2004, Pages 61~66
Fusion proteins resulting from chimeric sequences are excellent targets for therapeutic drug development. We developed a database of chimeric sequences by examining the genomic alignment of mRNA and EST sequences in the GenBank. We identified 688 chimeric mRNA and 20,998 chimeric EST sequences. Including EST sequences greatly expands the scope of chimeric sequences even though it inevitably accompanies many artifacts. Chimeric sequences are clustered according to the ECgene ID so that the user can easily find chimeric sequences related to a specific gene. Alignments of chimeric sequences are displayed as custom tracks in the UCSC genome browser. ChimerDB, available at http://genome.ewha.ac.kr/ECgene/ChimerDB/, should be a valuable resource for finding drug targets to treat cancers.
Changes of Gene Expression in NIH3T3 Cells Exposed to Osmotic and Oxidative Stresses
Lee, Jae-Seon ; Jung, Ji-Hun ; Kim, Tae-Hyung ; Seo, Jeong-Sun ;
Genomics & Informatics, volume 2, issue 2, 2004, Pages 67~74
Cells consistently face stressful conditions, which cause them to modulate a variety of intracellular processes and adapt to these environmental changes via regulation of gene expression. Hyperosmotic and oxidative stresses are significant stressors that induce cellular damage, and finally cell death. In this study, oligonucleotide microarrays were employed to investigate mRNA level changes in cells exposed to hyperosmotic or oxidative conditions. In addition, since heat shock protein 70 (HSP70) is one of the most inducible stress proteins and plays pivotal role to protect cells against stressful condition, we performed microarray analysis in HSP70-overexpressing cells to identify the genes expressed in a HSP70-dependent manner. Under hyperosmotic or oxidative stress conditions, a variety of genes showed altered expression. Downregulation of protein phosphatase1 beta (PP1 beta) and sphingosine-1-phosphate phosphatase 1 (SPPase1) was detected in both stress conditions. Microarray analysis of HSP70-overexpressing cells demonstrated that diverse mRNA species depend on the level of cellular HSP70. Genes encoding Iysyl oxidase, thrombospondin 1, and procollagen displayed altered expression in all tested conditions. The results of this study will be useful to construct networks of stress response genes.
Identification of the Marker-Genes for Dioxin(2, 3, 7, 8- tetradibenzo-p-dioxin)-Induced Immune Dysfunction by Using the High-Density Oligonucleotide Microarray
Kim, Jeong-Ah ; Lee, Eun-Ju ; Chung, In Hye ; Kim, Hyung-Lae ;
Genomics & Informatics, volume 2, issue 2, 2004, Pages 75~80
In a variety of animal species, the perinatal exposure of experimental animals to the 2,3,7,8-tetrachlorodibenzop-dioxin (TCDD) leads to the immune dysfunction, which is more severe and persistent than that caused by adult exposure. We report here the changes of gene expression and the identification of the marker-genes representing the dioxin exposure. The expressions of the transcripts were analyzed using the 11 K oligonucleotidemicroarray from the bone marrow cells of male C57BL/6J mice after an intraperitoneal injection of
TCDD/kg body weight at various time intervals: gestational 6.5 day(G6.5), 13.5 day(G13.5), 18.5 day(G18.5), and postnatal 3 (P3W)and 6 week (P6W). The type of self-organizing maps(SOM) representing the specific exposure dioxin could be identified as follows; G6.5D(C14), G13.5D(C0, C5, C10, C18), G18.5D(7): P3W(C2, C21), and P6W(C4, C15, C20). The candidate marker-genes were restricted to the transcripts, which could be consistently expressed greater than
2-fold in three experiments. The resulting candidates were 85 genes, the characteristics of that were involved in cell physiology and cell functions such as cell proliferation and immune function. We identified the biomarker-genes for dioxin exposure: smc -like 2 from SOM C14 for the dioxin exposure at G6.5D, focal adhesion kinase and 6 other genes from C0, and protein tyrosine phosphatase 4a2 and 3 other genes from C5 for G13.5D, platelet factor 4 from C7 for G18.5D, fos from C2 for P3W.
No Evidence of Association of Interleukin 1A (-889) Genetic Polymorphism with Alzheimer's Disease in Koreans
Jhoo, Jin Hyeong ; Park, Woong Yang ; Kim, Ki Woong ; Lee, Kwang Hyuk ; Lee, Dong Young ; Youn, Jong Chul ; Suh, Young Ju ; Seo, Jeong-Sun ; Woo, Jong Inn ;
Genomics & Informatics, volume 2, issue 2, 2004, Pages 81~85
To examine whether the IL-1A (-889) polymorphism associates with a risk for Alzheimer's disease (AD) and acts interactively with the apolipoprotein (APOE)
4 in the development of AD, we performed genotype analyses of the IL-1A and the APOE of the 102 Korean AD patients and 200 Korean non-demented controls. We failed to detect a significant difference in genotypic and allelic frequencies of IL-1A between the AD group and control group. No overexpression of the IL-1A C/T genotype and IL-1A T allele was found when we analyzed the late-onset and early-onset patients, separately. There was no significant genetic interaction between IL-1A polymorphism and the APOE polymorphism. I n conclusion, the IL-1A polymorphism did not contribute to the development of AD independently or interactively with the APOE
4 allele in Koreans.
High Correlation between Alu Elements and the Conversion of 3' UTR of mRNAs Processed Pseudogenes
An, Hyeong Jun ; Na, Dokyun ; Lee, Doheon ; Lee, Kwang Hyung ; Bhak, Jonghwa ;
Genomics & Informatics, volume 2, issue 2, 2004, Pages 86~91
Even though it represents
of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over
of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about
of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.
An Iterative Normalization Algorithm for cDNA Microarray Medical Data Analysis
Kim, Yoonhee ; Park, Woong-Yang ; Kim, Ho ;
Genomics & Informatics, volume 2, issue 2, 2004, Pages 92~98
A cDNA microarray experiment is one of the most useful high-throughput experiments in medical informatics for monitoring gene expression levels. Statistical analysis with a cDNA microarray medical data requires a normalization procedure to reduce the systematic errors that are impossible to control by the experimental conditions. Despite the variety of normalization methods, this. paper suggests a more general and synthetic normalization algorithm with a control gene set based on previous studies of normalization. Iterative normalization method was used to select and include a new control gene set among the whole genes iteratively at every step of the normalization calculation initiated with the housekeeping genes. The objective of this iterative normalization was to maintain the pattern of the original data and to keep the gene expression levels stable. Spatial plots, M&A (ratio and average values of the intensity) plots and box plots showed a convergence to zero of the mean across all genes graphically after applying our iterative normalization. The practicability of the algorithm was demonstrated by applying our method to the data for the human photo aging study.
PubMiner: Machine Learning-based Text Mining for Biomedical Information Analysis
Eom, Jae-Hong ; Zhang, Byoung-Tak ;
Genomics & Informatics, volume 2, issue 2, 2004, Pages 99~106
In this paper we introduce PubMiner, an intelligent machine learning based text mining system for mining biological information from the literature. PubMiner employs natural language processing techniques and machine learning based data mining techniques for mining useful biological information such as proteinprotein interaction from the massive literature. The system recognizes biological terms such as gene, protein, and enzymes and extracts their interactions described in the document through natural language processing. The extracted interactions are further analyzed with a set of features of each entity that were collected from the related public databases to infer more interactions from the original interactions. An inferred interaction from the interaction analysis and native interaction are provided to the user with the link of literature sources. The performance of entity and interaction extraction was tested with selected MEDLINE abstracts. The evaluation of inference proceeded using the protein interaction data of S. cerevisiae (bakers yeast) from MIPS and SGD.
HapAnalyzer: Minimum Haplotype Analysis System for Association Studies
Jung, Ho-Youl ; Park, Jung-Sun ; Park, Yun-Ju ; Kim, Young-Jin ; Kimm, Kuchan ; Koh, InSong ;
Genomics & Informatics, volume 2, issue 2, 2004, Pages 107~109
HapAnalyzer is an analysis system that provides minimum analysis methods for the SNP-based association studies. It consists of Hardy-Weinberg equilibrium (HWE) test, linkage disequilibrium (LD) computation, haplotype reconstruction, and SNP (or haplotype)-phenotype association assessment. It is well suited to a case-control association study for the unrelated population.