A Comparative Analysis of Metabolic Pathways Based on Metabolic Steady States

• Item type: Trans(1)
• 公開日: 2009-09-24
• タイトル: A Comparative Analysis of Metabolic Pathways Based on Metabolic Steady States
• タイトル / 言語: en
• タイトル: A Comparative Analysis of Metabolic Pathways Based on Metabolic Steady States
• 言語: eng
• キーワード / 主題Scheme: Other
• キーワード / 主題: Original Papers
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_6501
• 資源タイプ: journal article
• 著者所属: Kobe University
• 著者所属: Kobe University
• 著者所属: Kobe University
• 著者所属(英): en
• 著者所属(英): Kobe University
• 著者所属(英): en
• 著者所属(英): Kobe University
• 著者所属(英): en
• 著者所属(英): Kobe University
• 著者名: Yuta, Ashida; Tomonobu, Ozaki; Takenao, Ohkawa
• 著者名(英): Yuta, Ashida; Tomonobu, Ozaki; Takenao, Ohkawa
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: A comparative analysis of organisms with metabolic pathways provides important information about functions within organisms. In this paper, we discuss problem of comparing organisms using partial metabolic structures that contain many biological characteristics and propose a pathway comparison method based on an elementary flux mode (EFM) ―the minimal metabolic pathway that satisfies a steady state. By the extraction of the ‘elementary flux mode,’ we obtain biologically significant metabolic substructures. To compare metabolic pathways based on EFMs, we propose a new pseudo alignment method with a penalty based on the importance of enzymes. The distance among organisms can be calculated based on the pseudo alignment of EFMs. To confirm its effectivity, we apply the proposed method to the pathway datasets from 38 organisms. We successfully reconstructed a “three domain theory” from the aspect of the biological function. Moreover, we evaluated the results in terms of the accuracy of organism classification from the biological function and confirmed that the obtained classification was related deeply to such habitats as aerobe or anaerobe.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: A comparative analysis of organisms with metabolic pathways provides important information about functions within organisms. In this paper, we discuss problem of comparing organisms using partial metabolic structures that contain many biological characteristics and propose a pathway comparison method based on an elementary flux mode (EFM) ―the minimal metabolic pathway that satisfies a steady state. By the extraction of the ‘elementary flux mode,’ we obtain biologically significant metabolic substructures. To compare metabolic pathways based on EFMs, we propose a new pseudo alignment method with a penalty based on the importance of enzymes. The distance among organisms can be calculated based on the pseudo alignment of EFMs. To confirm its effectivity, we apply the proposed method to the pathway datasets from 38 organisms. We successfully reconstructed a “three domain theory” from the aspect of the biological function. Moreover, we evaluated the results in terms of the accuracy of organism classification from the biological function and confirmed that the obtained classification was related deeply to such habitats as aerobe or anaerobe.
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AA12177013
• 書誌情報: IPSJ Transactions on Bioinformatics（TBIO）; 巻 2, 号 4, p. 83-92, 発行日 2009-09-24
• ISSN / 収録物識別子タイプ: ISSN
• ISSN / 収録物識別子: 1882-6679
• 出版者 / 言語: ja
• 出版者: 情報処理学会