• Genomics & Informatics
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• v.16 no.4
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• pp.39.1-39.3
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• 2018

The rapid increase in genetic dataset volume has demanded extensive adoption of biological knowledge to reduce the computational complexity, and the biological pathway is one well-known source of such knowledge. In this regard, we have introduced a novel statistical method that enables the pathway-based association study of large-scale genetic dataset-namely, PHARAOH. However, researcher-level application of the PHARAOH method has been limited by a lack of generally used file formats and the absence of various quality control options that are essential to practical analysis. In order to overcome these limitations, we introduce our integration of the PHARAOH method into our recently developed all-in-one workbench. The proposed new PHARAOH program not only supports various de facto standard genetic data formats but also provides many quality control measures and filters based on those measures. We expect that our updated PHARAOH provides advanced accessibility of the pathway-level analysis of large-scale genetic datasets to researchers.

• Genomics & Informatics
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• v.18 no.1
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• pp.11.1-11.3
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• 2020

In genome-wide association studies, pathway-based analysis has been widely performed to enhance interpretation of single-nucleotide polymorphism association results. We proposed a novel method of hierarchical structural component model (HisCoM) for pathway analysis of common variants (HisCoM for pathway analysis of common variants [HisCoM-PCA]) which was used to identify pathways associated with traits. HisCoM-PCA is based on principal component analysis (PCA) for dimensional reduction of single nucleotide polymorphisms in each gene, and the HisCoM for pathway analysis. In this study, we developed a HisCoM-PCA software for the hierarchical pathway analysis of common variants. HisCoM-PCA software has several features. Various principle component scores selection criteria in PCA step can be specified by users who want to summarize common variants at each gene-level by different threshold values. In addition, multiple public pathway databases and customized pathway information can be used to perform pathway analysis. We expect that HisCoM-PCA software will be useful for users to perform powerful pathway analysis.

• Journal of Institute of Control, Robotics and Systems
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• v.10 no.12
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• pp.1155-1163
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• 2004

Extracellular signal-regulated kinase (ERK) signaling pathway is one of the mitogen-activated protein kinase (MAPK) signal transduction pathways. This pathway is known as pivotal in many signaling networks that govern proliferation, differentiation and cell survival. The ERK signaling pathway comprises positive and negative feedback loops, depending on whether the terminal kinase stimulates or inhibits the activation of the initial level. In this paper, we attempt to model the ERK pathway by considering both of the positive and negative feedback mechanisms based on Michaelis-Menten kinetics. In addition, we propose a fraction ratio model based on the mass action law. We first develop a mathematical model of the ERK pathway with fraction ratios. Secondly, we analyze the dynamical properties of the fraction ratio model based on simulation studies. Furthermore, we propose a concept of an inhibitor, catalyst, and substrate (ICS) controller which regulates the inhibitor, catalyst, and substrate concentrations of the ERK signal transduction pathway. The ICS controller can be designed through dynamical analysis of the ERK signaling transduction pathway within limited concentration ranges.

• KOGO NEWS
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• v.6 no.1
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• pp.29-33
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• 2006

Gene set analysis is a new concept and method. to analyze and interpret microarray gene expression data and tries to extract biological meaning from gene expression data at gene set level rather than at gene level. Compared with methods which select a few tens or hundreds of genes before gene ontology and pathway analysis, gene set analysis identifies important gene ontology terms and pathways more consistently and performs well even in gene expression data sets with minimal or moderate gene expression changes. Moreover, gene set analysis is useful for comparing multiple gene expression data sets dealing with similar biological questions. This review briefly summarizes the rationale behind the gene set analysis and introduces several algorithms and tools now available for gene set analysis.

• The Korean Journal of Physiology and Pharmacology
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• v.20 no.4
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• pp.367-378
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• 2016

Recently, it was reported that the role of mitochondria-reactive oxygen species (ROS) generating pathway in cisplatin-induced apoptosis is remarkable. Since a variety of molecules are involved in the pathway, a comprehensive approach to delineate the biological interactions of the molecules is required. However, quantitative modeling of the mitochondria-ROS generating pathway based on experiment and systemic analysis using the model have not been attempted so far. Thus, we conducted experiments to measure the concentration changes of critical molecules associated with mitochondrial apoptosis in both human mesothelioma H2052 and their ${\rho}^0$ cells lacking mitochondrial DNA (mtDNA). Based on the experiments, a novel mathematical model that can represent the essential dynamics of the mitochondrial apoptotic pathway induced by cisplatin was developed. The kinetic parameter values of the mathematical model were estimated from the experimental data. Then, we have investigated the dynamical properties of this model and predicted the apoptosis levels for various concentrations of cisplatin beyond the range of experiments. From parametric perturbation analysis, we further found that apoptosis will reach its saturation level beyond a certain critical cisplatin concentration.

• The Korean Journal of Applied Statistics
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• v.23 no.4
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• pp.705-713
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• 2010

Predicting survival from microarray data is not easy due to the problem of high dimensionality of data and the existence of censored observations. Also the limitation of individual gene analysis causes the shift of focus to the level of gene sets with functionally related genes. For developing a survival prediction model based on pathway information, the methods for selecting a supergene using principal component analysis and testing its significance for each pathway are discussed. Besides, the performance of gene filtering is compared.

• Journal of Environmental Impact Assessment
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• v.14 no.5
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• pp.291-303
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• 2005

Impact pathway analysis(IPA) is a bottom-up approach to estimates health and environmental risks from emissions of classical pollutants (eg. $PM_{10}$, $SO_2$, $NO_x$ and CO). The model starts from the emission rates of facility, calculates the yearly mean concentrations of pollutants at the ground level using atmospheric dispersion models. After this, proper epidemiological exposure-response functions are applied to determine the impact on the receptors. Finally the methodology can monetise the calculated physical impact on the basis of selected economic evaluation. The aim of this study is to evaluate an external cost of virtual point source in Suwon area using IPA. The results shows minor modification of local input data can make it possible to apply the model to Suwon area.

• The Korean Journal of Pain
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• v.18 no.2
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• pp.99-106
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• 2005

Background: Cyclic guanosine monophosphate (cGMP) and opioid receptors are involved in the modulation of nociception. Although the opioid receptors agonists are active in pain, the effect of an phospodiesterase inhibitor (zaprinast) for increasing the level of cGMP has not been thoroughly investigated at the spinal level. This study examined the effects of intrathecal zaprinast and morphine in a nociceptive test and we also examined the nature of the pharmacological interaction after the coadministration of zaprinast with morphine. The role of the nitric oxide (NO)-cGMP-potassium channel pathway on the effect of zaprinast was further clarified. Methods: Catheters were inserted into the intrathecal space of male SD rats. For the induction of pain, $50{\mu}l$ of 5% formalin solution was applied to the hindpaw. Isobolographic analysis was used for the evaluation of the drug interaction between zaprinast and morphine. Furthermore, NO synthase inhibitor ($_L-NMMA$), guanylyl cyclase inhibitor (ODQ) or a potassium channel blocker (glibenclamide) were intrathecally administered to verify the involvement of the NO-cGMP- potassium channel pathway on the antinociception effect of zaprinast. Results: Both zaprinast and morphine produced an antinociceptive effect during phase 1 and phase 2 in the formalin test. Isobolographic analysis revealed a synergistic interaction after the intrathecal administration of the zaprinast-morphine mixture in both phases. Intrathecal $_L-NMMA$, ODQ and glibenclamide did not reverse the antinociception of zaprinast in either phase. Conclusions: These results suggest that zaprinast, morphine and the mixture of the two drugs are effective against acute pain and they facilitated pain state at the spinal level. Thus, the spinal combination of zaprinast with morphine may be useful for the management of pain. However, the NO-sensitive cGMP-potassium channel pathway did not contribute to the antinocieptive mechanism of zaprinast in the spinal cord.

• Proceedings of the KOSOMBE Conference
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• v.1997 no.11
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• pp.255-259
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• 1997

The essence of meridian collateral and acupoints is an overall physiologic unction with the level of multiple unctional states. However it is a pity that until present, so in this paper described about some experimental results of physical reactions of meridian and acupoints. In order to verify meridian pathway and channel theory of energy in body. It is suppose that substance of meridian is pathway channel of the meridian materials. In basic examination, It was analyzed spectrum of reflection waves after beat or continuos vibrate to meridian point and non-meridian point meridian line and non-meridian line. The characteristics of reflection waves similar to flow channel in hydrodynamic. So it be able to suggest that the meridian is pathway and channel in body.

• Bulletin of the Korean Chemical Society
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• v.33 no.6
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• pp.1934-1938
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• 2012

The reaction mechanism between cyclopropenylidene and formaldehyde has been systematically investigated employing the MP2/6-311+$G^*$ level of theory to better understand the cyclopropenylidene reactivity with carbonyl compound. Geometry optimization, vibrational analysis, and energy property for the involved stationary points on the potential energy surface have been calculated. Energies of all the species are further corrected by the CCSD(T)/6-311+$G^*$ single-point calculations. It was found that one important reaction intermediate (INTa) has been located firstly $via$ a transition state (TSa). After that, the common intermediate (INTb) for the two pathways (1) and (2) has been formed $via$ TSb. At last, two different products possessing three- and four-membered ring characters have been obtained through two possible reaction pathways. In the reaction pathway (1), a three-membered ring alkyne compound has been obtained. As for the reaction pathway (2), it is the formation of the four-membered ring conjugated diene compound. The energy barrier of the ratedetermining step of pathway (1) is lower than that of the pathway (2), and the ultima product of pathway (2) is more stable than that of the pathway (1).