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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
> Journal Vol & Issue
Genomics & Informatics
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Journal DOI :
Korea Genome Organization
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Volume & Issues
Volume 9, Issue 4 - Dec 2011
Volume 9, Issue 3 - Sep 2011
Volume 9, Issue 2 - Jun 2011
Volume 9, Issue 1 - Mar 2011
Selecting the target year
Kim, Sang-Soo ; Bhak, Jong ;
Genomics & Informatics, volume 9, issue 1, 2011, Pages 1~4
DOI : 10.5808/GI.2011.9.1.001
Genome-wide association (GWA) studies are the method of choice for discovering loci associated with common diseases. More than a thousand GWA studies have reported successful identification of statistically significant association signals in human genomes for a variety of complex diseases. In this review, I discuss some of the issues related to the future of GWA studies and their biomedical applications.
Recent Progresses in the Linguistic Modeling of Biological Sequences Based on Formal Language Theory
Park, Hyun-Seok ; Galbadrakh, Bulgan ; Kim, Young-Mi ;
Genomics & Informatics, volume 9, issue 1, 2011, Pages 5~11
DOI : 10.5808/GI.2011.9.1.005
Treating genomes just as languages raises the possibility of producing concise generalizations about information in biological sequences. Grammars used in this way would constitute a model of underlying biological processes or structures, and that grammars may, in fact, serve as an appropriate tool for theory formation. The increasing number of biological sequences that have been yielded further highlights a growing need for developing grammatical systems in bioinformatics. The intent of this review is therefore to list some bibliographic references regarding the recent progresses in the field of grammatical modeling of biological sequences. This review will also contain some sections to briefly introduce basic knowledge about formal language theory, such as the Chomsky hierarchy, for non-experts in computational linguistics, and to provide some helpful pointers to start a deeper investigation into this field.
Genetic Association between Eotaxin Genes and Asthma and Its Relationship to Birth Season in Korean Children
Ahn, In-Sung ; Bae, Se-Eun ; Kim, Jeong-Hee ; Son, Byong-Kwan ; Son, Hyeon-S. ; Cho, Sung-Il ;
Genomics & Informatics, volume 9, issue 1, 2011, Pages 12~18
DOI : 10.5808/GI.2011.9.1.012
Asthma is a chronic disease associated with airway constriction due to inflammation caused by eosinophils, mast cells, and T lymphocytes, leading to serious chronic illness in children. The eotaxin gene family has been shown to play an important role in the pathogenesis of asthma. We hypothesized that the distinctive variations among the four seasons in Korea may affect the expression of eotaxin polymorphisms, especially in children. We examined the possible effects of birth season (spring, March-May; summer, June-August; fall, September-November; and winter, December-February) on the phenotype of asthma in children. All SNP data sets of the eotaxin-2 and eotaxin-3 genes were collected from 78 asthma patients and 101 controls. Here, we investigated the effects of birth season on the expression of eotaxin-2 and eotaxin-3 in Korean children. Using the HAPLOTYPE procedure with the HTR method in SAS/Genetics, we showed that children born in spring and summer show significant haplotypes in both the eotaxin-2 and eotaxin-3 genes. Thus, the expression of polymorphisms in eotaxin-2 and eotaxin-3 may vary by season.
Standard-based Integration of Heterogeneous Large-scale DNA Microarray Data for Improving Reusability
Jung, Yong ; Seo, Hwa-Jeong ; Park, Yu-Rang ; Kim, Ji-Hun ; Bien, Sang Jay ; Kim, Ju-Han ;
Genomics & Informatics, volume 9, issue 1, 2011, Pages 19~27
DOI : 10.5808/GI.2011.9.1.019
Gene Expression Omnibus (GEO) has kept the largest amount of gene-expression microarray data that have grown exponentially. Microarray data in GEO have been generated in many different formats and often lack standardized annotation and documentation. It is hard to know if preprocessing has been applied to a dataset or not and in what way. Standard-based integration of heterogeneous data formats and metadata is necessary for comprehensive data query, analysis and mining. We attempted to integrate the heterogeneous microarray data in GEO based on Minimum Information About a Microarray Experiment (MIAME) standard. We unified the data fields of GEO Data table and mapped the attributes of GEO metadata into MIAME elements. We also discriminated non-preprocessed raw datasets from others and processed ones by using a two-step classification method. Most of the procedures were developed as semi-automated algorithms with some degree of text mining techniques. We localized 2,967 Platforms, 4,867 Series and 103,590 Samples with covering 279 organisms, integrated them into a standard-based relational schema and developed a comprehensive query interface to extract. Our tool, GEOQuest is available at http://www.snubi.org/software/GEOQuest/.
Finding Interesting Genes Using Reliability in Various Gene Expression Models
Lee, Eun-Kyung ; Cook, Dianne ; Hoffman, Heike ;
Genomics & Informatics, volume 9, issue 1, 2011, Pages 28~36
DOI : 10.5808/GI.2011.9.1.028
Most statistical methods for finding interesting genes are focusing on the summary values with large fold-changes or large variations. Very few methods consider the probe level data. We developed a new measure to detect reliability that incorporates the probe level data. This reliability measure is useful for exploring the microarray data without ignoring the probe level data. It is easy to calculate, and it can be used for all the other statistical methods as a good guideline to find real differentially expressed genes. Instead of filtering out genes before the analysis, we use whole genes in the analysis and make decisions with new reliability measures.
ManBIF: a Program for Mining and Managing Biobank Impact Factor Data
Yu, Ki-Jin ; Nam, Jung-Min ; Her, Yun ; Chu, Min-Seock ; Seo, Hyung-Seok ; Kim, Jun-Woo ; Jeon, Jae-Pil ; Park, Hye-Kyung ; Park, Kie-Jung ;
Genomics & Informatics, volume 9, issue 1, 2011, Pages 37~38
DOI : 10.5808/GI.2011.9.1.037
Biobank Impact Factor (BIF), which is a very effective criterion to evaluate the activity of biobanks, can be estimated by the citation information of biobanks from scientific papers. We have developed a program, ManBIF, to investigate the citation information from PDF files in the literature. The program manages a dictionary for expressions to represent biobanks and their resources, mines the citation information by converting PDF files to text files and searching with a dictionary, and produces a statistical report file. It can be used as an important tool by biobanks.
MiRPI: Portable Software to Identify Conserved miRNAs, Targets and to Calculate Precursor Statistics
Vignesh, Dhandapani ; Parameswari, Paul ; Im, Su-Bin ; Kim, Hae-Jin ; Lim, Yong-Pyo ;
Genomics & Informatics, volume 9, issue 1, 2011, Pages 39~43
DOI : 10.5808/GI.2011.9.1.039
MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.