• Title/Summary/Keyword: 대사경로

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2.5D Metabolic Pathway Drawing based on 2-layered Layout (2-계층 레이아웃을 이용한 2.5차원 대사 경로 드로잉)

  • Song, Eun-Ha;Ham, Sung-Il;Lee, Sang-Ho;Park, Hyun-Seok
    • Journal of KIISE:Software and Applications
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    • v.36 no.11
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    • pp.875-890
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    • 2009
  • Metabolimics interprets an organism as a network of functional units and an organism is represented by a metabolic pathway i.e., well-displayed graph. So a software tool for drawing pathway is necessary to understand it comprehensively. These tools have a problem that edge-crossings exponentially increase as the number of nodes grows. To apply automatic graph layout techniques to the genome-scale metabolic flow, it is very important to reduce unnecessary edge-crossing on a metabolic pathway layout. In this paper, we design and implement 2.5D metabolic pathway layout modules. Metabolic pathways are represented hierarchically by making use of the '2-layered layout algorithm' in 3D. It enhances the readability and reduces unnecessary edge-crossings by using 3D layout modules instead of 2D layout algorithms.

On the Construction of an Object-Oriented Metabolic Pathway Database (대사경로 데이터베이스 구축)

  • 안명상;정태성;조완섭;노동현
    • Proceedings of the Korean Information Science Society Conference
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    • 2004.04b
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    • pp.295-297
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    • 2004
  • 유전자의 생물학적 기능을 밝히고 세포 내 상호작용을 이해하는 것은 post-genome era의 가장 중요한 작업 중 하나이다. 이러한 세포 내 상호작용은 복잡한 생화학적 네트워크를 형성하게 되며 그 중 Metabolic pathway(대사 경로)는 생물 시스템을 이해하는데 가장 중요한 부분을 차지하게 된다. 대사 경로를 분석하기 위하여 분자의 기능 및 생화학적 프로세스에 대한 정보를 데이터베이스에 저장.관리해야하고, 사용자의 다양한 질의에 대하여 관련정보를 검색하여 GUI환경에서 제공해야 한다. 이 논문은 대사 경로 정보를 객체 데이타베이스 형태로 모델링하여 구축하고, 사용자가 관심있는 정보를 SBML형태로 제공하는 대사경로 데이타베이스의 설계 및 구현에 관해 다룬다.

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An Algorithm for Drawing Metabolic Pathways based on Structural Characteristics (구조적 특징에 기반한 대사 경로 드로잉 알고리즘)

  • 이소희;송은하;이상호;박현석
    • Journal of KIISE:Software and Applications
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    • v.31 no.10
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    • pp.1266-1275
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    • 2004
  • Bioinformatics is concerned with the creation and development of advanced information and computational technologies for problems in biology. It is divided into genomics, proteomics and metabolimics. In metabolimics, an organism is represented by metabolic pathway, i.e., well-displayed graph, and so the graph drawing tool to draw pathway well is necessary to understand it comprehensively. In this paper, we design an improved drawing algorithm. It enhances the readability by making use of the bipartite graph. Also it is possible to draw large graph properly by considering the facts that metabolic pathway graph is scale-free network and is composed of circular components, hierarchic components and linear components.

Design of an Expert System for Pathway Search (대사경로 탐색용 전문가 시스템 설계)

  • Choi, Young-Sang;Choi, Han-Suk;Yang, Gi-Chul;Kim, Dong-Wook;Cho, Kwang-Moon
    • Proceedings of the KAIS Fall Conference
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    • 2007.11a
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    • pp.233-236
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    • 2007
  • 현재 생물정보학에서는 무수히 많은 생물들에서 엄청난 양의 EST(expressed sequence tag) 정보가 나온다. 본 논문에서는 그런 정보들을 가지고 대사경로를 유추할 수 있는 전문가 시스템을 개발하고자 한다. 현재까지의 대사경로 탐색은 발견해 놓은 데이터를 가지고 전부 수작업으로 이루어진다. 그러한 과정을 자동화 시키고자 하는 연구가 많이 진행되고 있다. 본 논문에서는 전문가 시스템을 활용하여 생물정보학의 EST(expressed sequence tag) 데이터에서 효율적으로 대사경로를 찾을 수 있도록 하는 방안을 제시한다.

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Comparison of Metabolic Pathways of Less Orthologous Prokaryotes than Mycoplasma genitalium (Mycoplasma genitalium 보다 보존적 유전자 수가 작은 원핵생물들의 대사경로 비교)

  • Lee, Dong-Geun
    • Journal of Life Science
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    • v.28 no.3
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    • pp.369-375
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    • 2018
  • Mycoplasma genitalium has 367 conserved genes and the smallest genome among mono-culturable prokaryotes. Conservative metabolic pathways were examined among M. genitalium and 14 prokaryotes, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans and 13 intracellular eubacteria of plants or insects, with fewer conserved genes than M. genitalium. They have 11 to 71 metabolic pathways, however complete metabolic pathways ranged from 1 to 24. Totally, metabolic pathway hole is very high due to the lack of 45.8% of the enzymes required for the whole metabolic pathways and it could be suggested that the shared metabolic pathway with the host's enzyme would work or the essential substances are host dependent. The number of genes necessary for mass transfer through the cell membrane is also very low, and it may be considered that the simple diffusion or the protein of the host will function in the cell membrane of these prokaryotes. Although the tRNA charging pathway was distributed in all 15 prokaryotes, each has 5-20 tRNA charging genes. This study would give clues to the understanding of the metabolic pathways of intracellular parasitic bacteria of plant and endosymbiotic bacteria of insects, and could provide basic data for prevention of crop damage, development of insect pests and human medicines.

Conserved Genes and Metabolic Pathways in Prokaryotes of the Same Genus (동일한 속 원핵생물들의 보존 유전자와 대사경로)

  • Lee, Dong-Geun;Lee, Sang-Hyeon
    • Journal of Life Science
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    • v.29 no.1
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    • pp.123-128
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    • 2019
  • The use of 16S rDNA is commonplace in the determination of prokaryotic species. However, it has limitations, and there are few studies at the genus level. We investigated conserved genes and metabolic pathways at the genus level in 28 strains of 13 genera of prokaryotes using the COG database (conserved genes) and MetaCyc database (metabolic pathways). Conserved genes compared to total genes (core genome) at the genus level ranged from 27.62%(Nostoc genus) to 71.76%(Spiribacter genus), with an average of 46.72%. The lower ratio of core genome meant the higher ratio of peculiar genes of a prokaryote, namely specific biological activities or the habitat may be varied. The ratio of common metabolic pathways at the genus level was higher than the ratio of core genomes, from 58.79% (Clostridium genus) to 96.31%(Mycoplasma genus), with an average of 75.86%. When compared among other genera, members of the same genus were positioned in the closest nodes to each other. Interestingly, Bacillus and Clostridium genera were positioned in closer nodes than those of the other genera. Archaebacterial genera were grouped together in the ortholog and metabolic pathway nodes in a phylogenetic tree. The genera Granulicella, Nostoc, and Bradyrhizobium of the Acidobacteria, Cyanobacteria, and Proteobacteria phyla, respectively, were grouped in an ortholog content tree. The results of this study can be used for (i) the identification of common genes and metabolic pathways at each phylogenetic level and (ii) the improvement of strains through horizontal gene transfer or site-directed mutagenesis.

Predicting Survival of DLBCL Patients in Pathway-Based Microarray Analysis (DLBCL 환자의 대사경로 정보를 이용한 생존예측)

  • Lee, Kwang-Hyun;Lee, Sun-Ho
    • 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.

Comparison of Dietary Carotenoids Metabolism and Effects to Improve the Body Color of Cultured Fresh-water Fishes and Marine Fishes (양식 담수어 및 해산어의 사료 Carotenoids 대사의 비교와 체색개선에 미치는 영향)

  • Ha, Bong-Seuk;Kweon, Moon-Jeong;Park, Mi-Yeon;Baek, Sung-Han;Kim, Soo-Young;Baek, In-Ok;Kang, Seok-Joong
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.26 no.2
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    • pp.270-284
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    • 1997
  • Effects of dietary carotenoids were investigated on the metaboβsm and body pigmentation of rainbow trout(Salmo gairdneri), masu salmon(Oncorhynchus macrostomos), eel(Anguilla japonica), rock fish(Sebastes inermis) and black rock fish(Sebastes schlegeli). Three weeks later after depletion, these fishes were fed diet supplemented with ${\beta}-carotene$, lutein, canthaxanthin', astaxanthin or ${\beta}-apo-8'-carotenal$ for 4 to 5 weeks, respectively. Carotenoids distributed to and changed in integument were analyzed. In the integument of rainbow trout. zeaxanthin, ${\beta}-carotene$ and canthaxanthin were found to be the major carotenoids, while lutein, isocryptoxanthin and salmoxanthin were the minor carotenoids. In the integument of masu salmon, zeaxanthin was found to be the major carotenoids, while triol, lutein, tunaxanthin, ${\beta}-carotene$, ${\beta}-cryptoxanthin$ and canthaxanthin were the minor carotenoids. In the integument of eel, ${\beta}-carotene$ was found to be the major carotenoids, while lutein, zeaxanthin and ${\beta}-cryptoxanthin$ were the minor carotenoids. In the integument of rock fish, zeaxanthin, ${\beta}-carotene$, tunaxanthin$(A{\sim}C)$ and lutein were found to be the major carotenoids, while ${\beta}-cryptoxanthin$, ${\alpha}-cryptoxanthin$ and astaxanthin were the minor carotenoids. Likely in the integument of black rock fish, ${\beta}-carotene$, astaxanthin and zeaxanthin were found to be the major carotenoids, whereas ${\alpha}-cryptoxanthin$, ${\beta}-cryptoxanthin$, lutein and canthaxanthin were the minor contributor. The efficacy of body pigmentation by the accumulation of carotenoids in the integument of rainbow trout and masu salmon were the most effectively shown in the canthaxanthin group and of eel, rock fish and black rock fish were the most effectively shown in the lutein group. Based on these results in the integument of each fish, dietary carotenoids were presumably biotransformed via oxidative and reductive pathways. In the rainbow trout, ${\beta}-carotene$ was oxidized to astaxanthin via successively isocryptoxanthin, echinenone and canthaxanthin. Lutein was oxidized to canthaxanthin. Canthaxanthin was reduced to ${\beta}-carotene$ via isozeaxanthin, and astaxanthin was reduced to zeaxanthin via triol. In the masu salmon, ${\beta}-carotene$ was oxidized to zeaxanthin. Lutein was reduced to zeaxanthin via tunaxanthin. Canthaxanthin was reduced to zeaxanthin via ${\beta}-carotene$. and astaxanthin was reduced to zeaxanthin via triol. In the eel, ${\beta}-carotene$ and lutein were directly deposited but canthaxanthin was reduced to ${\beta}-carotene$, and cholesterol lowering effect by Meju supplementation might be resulted from the modulation of fecal axanthin, astaxanthin and ${\beta}-apo-8'-carotenal$ were oxidized and reduced to tunaxanthin via zeaxanthin. In the black roch fish, ${\beta}-carotene$ was oxidized to ${\beta}-cryptoxanthin$. Lutein was reduced to ${\beta}-carotene$ via ${\alpha}-cryptoxanthin$. Canthaxanthin was reduced to ${\alpha}-cryptoxanthin$ via successively ${\beta}-cryptoxanthin$ and zeaxanthin. Astaxanthin converted to tunaxanthin via isocryptoxanthin and zeaxanthin, and ${\beta}-apo-8'-carotenal$ was reduced to ${\alpha}-cryptoxanthin$ via ${\beta}-cryptoxanthin$ and zeaxanthin.

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Reconstruction of Metabolic Pathway for the Chicken Genome (닭 특이 대사 경로 재확립)

  • Kim, Woon-Su;Lee, Se-Young;Park, Hye-Sun;Baik, Woon-Kee;Lee, Jun-Heon;Seo, Seong-Won
    • Korean Journal of Poultry Science
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    • v.37 no.3
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    • pp.275-282
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    • 2010
  • Chicken is an important livestock as a valuable biomedical model as well as food for human, and there is a strong rationale for improving our understanding on metabolism and physiology of this organism. The first draft of chicken genome assembly was released in 2004, which enables elaboration on the linkage between genetic and metabolic traits of chicken. The objectives of this study were thus to reconstruct metabolic pathway of the chicken genome and to construct a chicken specific pathway genome database (PGDB). We developed a comprehensive genome database for chicken by integrating all the known annotations for chicken genes and proteins using a pipeline written in Perl. Based on the comprehensive genome annotations, metabolic pathways of the chicken genome were reconstructed using the PathoLogic algorithm in Pathway Tools software. We identified a total of 212 metabolic pathways, 2,709 enzymes, 71 transporters, 1,698 enzymatic reactions, 8 transport reactions, and 1,360 compounds in the current chicken genome build, Gallus_gallus-2.1. Comparative metabolic analysis with the human, mouse and cattle genomes revealed that core metabolic pathways are highly conserved in the chicken genome. It was indicated the quality of assembly and annotations of the chicken genome need to be improved and more researches are required for improving our understanding on function of genes and metabolic pathways of avian species. We conclude that the chicken PGDB is useful for studies on avian and chicken metabolism and provides a platform for comparative genomic and metabolic analysis of animal biology and biomedicine.

A Distributed Path-Finding Algorithm for Distributed Metabolic Pathways (분산된 대사경로네트워크에 대한 경로검색을 위한 분산알고리즘)

  • Lee, Sun-A;Lee, Keon-Myung;Lee, Seung-Joo
    • Journal of the Korean Institute of Intelligent Systems
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    • v.15 no.4
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    • pp.425-430
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    • 2005
  • Many problems can be formulated in terms nf graphs and thus solved by graph-theoretic algorithms. This paper is concerned with finding paths between nodes over the distributed and overlapped graphs. The proposed method allows multiple agents to cooperate to find paths without merging the distributed graphs. For each graph there is a designated agent which is charged of providing path-finding service for hot graph and initiating the path-finding tasks of which path starts from the graph. The proposed method earlier on constructs an abstract graph so-called viewgraph for the distributed overlapped graphs and thus enables to extract the information about how to guide the path finding over the graphs. The viewgraph is shared by all agents which determine how to coordinate other agents for the purpose of finding paths. Each agent maintains the shortest path information among the nodes which are placed in different overlapped subgraphs of her graph. Once an agent is asked to get a path from a node on her graph to another node on another's graph, she directs other agents to provide the necessary information for finding paths.