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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 7, Issue 4 - Dec 2009
Volume 7, Issue 3 - Sep 2009
Volume 7, Issue 2 - Jun 2009
Volume 7, Issue 1 - Mar 2009
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RNA Mapping of Mutant Myotonic Dystrophy Protein Kinase 3'-Untranslated Region Transcripts
Song, Min-Sun ; Lee, Seong-Wook ;
Genomics & Informatics, volume 7, issue 4, 2009, Pages 181~186
DOI : 10.5808/GI.2009.7.4.181
Myotonic dystrophy type 1 (DM1), which is a dominantly inherited neurodegenerative disorder, results from a CTG trinucleotide repeat expansion in the 3'-untranslated region (3'-UTR) of the myotonic dystrophy protein kinase (DMPK) gene. Retention of mutant DMPK (mDMPK) transcripts in the nuclei of affected cells has been known to be the main cause of pathogenesis of the disease. Thus, reducing the RNA toxicity through elimination of the mutant RNA has been suggested as one therapeutic strategy against DM1. In this study, we suggested RNA replacement with a trans -splicing ribozyme as an alternate genetic therapeutic approach for amelioration of DM1. To this end, we identified the regions of mDMPK 3'-UTR RNA that were accessible to ribozymes by using an RNA mapping strategy based on a trans-splicing ribozyme library. We found that particularly accessible sites were present not only upstream but also downstream of the expanded repeat sequence. Repair or replacement of the mDMPK transcript with the specific ribozyme will be useful for DM1 treatment through reduction of toxic mutant transcripts and simultaneously restore wild-type DMPK or release nucleus-entrapped mDMPK transcripts to the cytoplasm.
Identification of Polymorphisms in CYP2E1 Gene and Association Analysis among Chronic HBV Patients
Chun, Ji-Yong ; Park, Byung-Lae ; Cheong, Hyun-Sub ; Kim, Jason-Y. ; Park, Tae-Joon ; Lee, Jin-Sol ; Lee, Hyo-Suk ; Kim, Yoon-Jun ; Shin, Hyoung-Doo ;
Genomics & Informatics, volume 7, issue 4, 2009, Pages 187~194
DOI : 10.5808/GI.2009.7.4.187
Cytochrome P450 2E1 (CYP2E1) is a member of the cytochrome P450 superfamily, and it is a key enzyme responsible for the metabolic activation of many smallmolecular-weight compounds such as alcohol, which is classified as a human carcinogen. In this study, we identified 19 single nucleotide polymorphisms (SNPs) in CYP2E1 in Korean population. In these SNPs, we examined possible genetic association of CYP2E1 polymorphisms with HBV clearance and the risk of hepatocellular carcinoma (HCC). Five common polymorphic sites were selected, CYP2E1 polymorphisms at rs381-3867, rs3813870, rs2070673, rs2515641 and rs2480257, considering their allele frequencies, haplotype-tagging status and LDs for genotyping in larger-scale subjects (n=1,092). Statistical analysis demonstrated that CYP2E1 polymorphisms and haplotypes show no significant association with HBV clearance, HCC occurrence and onset age of HCC (p>0.05). Previous studies, however, have shown contradictory findings on associations of CYP2E1 polymorphisms with CYP2E1 activities and HCC risk. Comparing the contrasting results of previous researches suggest that CYP2E1 polymorphism is associated with CYP2E1 activity induced by ethanol, but is not directly associated with HCC risk. CYP2E1 variation/haploype information identified in this study will provide valuable information for future studies on CYP2E1.
Lack of Association of BIRC5 Polymorphisms with Clearance of HBV Infection and HCC Occurrence in a Korean Population
Lee, Jin-Sol ; Kim, Jeong-Hyun ; Park, Byung-Lae ; Cheong, Hyun-Sub ; Kim, Jason-Y. ; Park, Tae-Joon ; Chun, Ji-Yong ; Bae, Joon-Seol ; Lee, Hyo-Suk ; Kim, Yoon-Jun ; Shin, Hyoung-Doo ;
Genomics & Informatics, volume 7, issue 4, 2009, Pages 195~202
DOI : 10.5808/GI.2009.7.4.195
BIRC5 (Survivin) belongs to the inhibitor of apoptosis gene family. The BIRC5 protein inhibits caspases and consequently blocks apoptosis. Thus, BIRC5 contributes to the progression of cancer allowing for continued cell proliferation and survival. In this study, we identified eight sequence variants of BIRC5 through direct DNA sequencing. Among the eight single nucleotide polymorphisms (SNPs), six common variants with frequencies higher than 0.05 were selected for larger-scale genotyping (n=1,066). Results of the study did not show any association between the promoter region polymorphisms and the clearance of hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) occurrence. This is in line with a previous study in which polymorphisms in the promoter region does not influence the function of BIRC5. Initially, we were able to detect a signal with the ＋9194A>G, which disappeared after multiple corrections but led to a change in amino acid. Similarly, we were also able to detect an association signal between two haplotypes (haplotype-2 and haplotype-5) on the onset age of HCC and/or HCC occurrence, but the signals also disappeared after multiple corrections. As a result, we concluded that there was no association between BIRC5 polymorphisms and the clearance HBV infection and/or HCC occurrence. However, our results might useful to future studies.
Rapamycin-Induced Abundance Changes in the Proteome of Budding Yeast
Shin, Chun-Shik ; Chang, Yeon-Ji ; Lee, Hun-Goo ; Huh, Won-Ki ;
Genomics & Informatics, volume 7, issue 4, 2009, Pages 203~207
DOI : 10.5808/GI.2009.7.4.203
The target of rapamycin (TOR) signaling pathway conserved from yeast to human plays critical roles in regulation of eukaryotic cell growth. It has been shown that TOR pathway is involved in several cellular processes, including ribosome biogenesis, nutrient response, autophagy and aging. However, due to the functional diversity of TOR pathway, we do not know yet some key effectors of the pathway. To find unknown effectors of TOR signaling pathway, we took advantage of a green fluorescent protein (GFP)-tagged collection of budding yeast Saccharomyces cerevisiae. We analyzed protein abundance changes by measuring the GFP fluorescence intensity of 4156 GFP-tagged yeast strains under inhibition of TOR pathway. Our proteomic analysis argues that 83 proteins are decreased whereas 32 proteins are increased by treatment of rapamycin, a specific inhibitor of TOR complex 1 (TORC1). We found that, among the 115 proteins that show significant changes in protein abundance under rapamycin treatment, 37 proteins also show expression changes in the mRNA levels by more than 2-fold under the same condition. We suggest that the 115 proteins indentified in this study may be directly or indirectly involved in TOR signaling and can serve as candidates for further investigation of the effectors of TOR pathway.
IdMapper: A Java Application for ID Mapping across Multiple Cross-referencing Providers
Lee, Hoo-Keun ; Kim, Hyeon-Jin ; Yu, Ung-Sik ;
Genomics & Informatics, volume 7, issue 4, 2009, Pages 208~211
DOI : 10.5808/GI.2009.7.4.208
We developed an identifier mapping application for bioinformatics research in Java programming language. It is easy to use and provides many usability functionalities that are expected as essentials for a professional application. It supports three widely used mapping services and can convert many ids from one source database into many target databases at once. Id mapping across service providers is possible by remapping the resultant ids. Because it adheres to the NetBeans platform architecture, it can be incorporated into other NetBeans platform applications as an id mapping provider without adaption or modification.
WebChemDB: An Integrated Chemical Database Retrieval System
Hou, Bo-Kyeng ; Moon, Eun-Joung ; Moon, Sung-Chul ; Kim, Hae-Jin ;
Genomics & Informatics, volume 7, issue 4, 2009, Pages 212~216
DOI : 10.5808/GI.2009.7.4.212
WebChemDB is an integrated chemical database retrieval system that provides access to over 8 million publicly available chemical structures, including related information on their biological activities and direct links to other public chemical resources, such as PubChem, ChEBI, and DrugBank. The data are publicly available over the web, using two-dimensional (2D) and three-dimensional (3D) structure retrieval systems with various filters and molecular descriptors. The web services API also provides researchers with functionalities to programmatically manipulate, search, and analyze the data.
ORF Miner: a Web-based ORF Search Tool
Park, Sin-Gi ; Kim, Ki-Bong ;
Genomics & Informatics, volume 7, issue 4, 2009, Pages 217~219
DOI : 10.5808/GI.2009.7.4.217
The primary clue for locating protein-coding regions is the open reading frame and the determination of ORFs (Open Reading Frames) is the first step toward the gene prediction, especially for prokaryotes. In this respect, we have developed a web-based ORF search tool called ORF Miner. The ORF Miner is a graphical analysis utility which determines all possible open reading frames of a selectable minimum size in an input sequence. This tool identifies all open reading frames using alternative genetic codes as well as the standard one and reports a list of ORFs with corresponding deduced amino acid sequences. The ORF Miner can be employed for sequence annotation and give a crucial clue to determination of actual protein-coding regions.