Knowledge-based Fuzzy Adaptive Resonance Theory and Its Application to the Analysis of Gene Expression in Plants(BIOINFORMATICS)

スポンサーリンク

概要

• 論文の詳細を見る

• Gene expression data obtained from DNA microarrays are very useful in revealing the mechanisms that drive life. It is necessary to analyze these data through the use of algorithms, as in clustering and machine-learning. In a previous study, we developed fuzzy adaptive resonance theory (FuzzyART) and applied it to gene expression data, to identify genetic networks. FuzzyART was used as a clustering algorithm that is very suitable for the analysis of biological data; however, although FuzzyART is very useful in the analysis of dozens of gene expression profiles, it is difficult to apply this method to thousands of gene expression profiles, owing to inherent category proliferation and long calculation time. In the present study, we developed a knowledge-based FuzzyART (KB-FuzzyART) to mitigate these problems. We first constructed a gene list-1 from the gene database of Arabidopsis thaliana as knowledge for KB-FuzzyART, because KB-FuzzyART requires any knowledge as input. This method was applied to gene expression data obtained via the microarray analysis of A. thaliana, to identify the downstream genes of ASYMMETRIC LEAVES1 (AS1) and ASYMMETRIC LEAVES2 (AS2), both of which are involved in leaf development. The results of the analysis using KB-FuzzyART showed that the KNAT6 and YABBY5 (YAB5) genes are candidates for downstream factors, after a short calculation time for analysis. These results suggest that our gene list-1 is a very useful database for analyzing the expression profiles of genes that are related to the development of A. thaliana; they also suggest that the KB-FuzzyART has the high potential to function as a new method by which one can select candidate genes from thousands of genes, using gene expression data on mutant strains.

• 社団法人日本生物工学会の論文
• 2008-12-25

著者

• 塚谷 裕一

  基礎生物学研究所

• 塚谷 裕一

  東大 基礎生物学研

• Tsukaya Hirokazu

  Plant Biology Research Center Chubu University:college Of Bioscience And Biotechnology Chubu Univers

• MACHIDA Yasunori

  Division of Biological Science, Graduate School of Science, Nagoya University

• Takahashi Hiro

  Plant Biology Research Center, Chubu University

• Iwakawa Hidekazu

  Plant Biology Research Center, Chubu University

• Nakao Sachiko

  College of Bioscience and Biotechnology, Chubu University

• Ojio Takahiro

  College of Bioscience and Biotechnology, Chubu University

• Morishita Ryo

  College of Bioscience and Biotechnology, Chubu University

• Morikawa Satomi

  College of Bioscience and Biotechnology, Chubu University

• Machida Chiyoko

  Plant Biology Research Center, Chubu University

• Kobayashi Takeshi

  Plant Biology Research Center, Chubu University

• Machida Y

  Nagoya Univ. Nagoya Jpn

• Machida Yasunori

  Division Of Biological Science Graduate School Of Science Nagoya University

• Iwakawa Hidekazu

  Plant Biology Research Center Chubu University

• Machida C

  College Of Bioscience And Biotechnology Chubu University

• Tsukaya H

  Biological Sciences Graduate School Of Science University Of Tokyo

• Nakao Sachiko

  College Of Bioscience And Biotechnology Chubu University

• Morishita Ryo

  College Of Bioscience And Biotechnology Chubu University

• Ojio Takahiro

  College Of Bioscience And Biotechnology Chubu University

• Tsukaya H

  National Institute For Basic Biology/okazaki Institutes For Integrated Bioscience

• Tsukaya Hirokazu

  National Inst. Basic Biology Aichi Jpn

• Morikawa Satomi

  College Of Bioscience And Biotechnology Chubu University

• Tsukaya Hirokazu

  Department Of Biological Sciences Graduate School Of Science The University Of Tokyo

• Tsukaya Hirokazu

  National Institute For Basic Biology/okazaki Institutes For Integrated Bioscience

• Machida Chiyoko

  Divison Of Biological Science Graduate School Of Science Nagoya University

• Tanaka Hirokazu

  Divison Of Biological Science Graduate School Of Science Nagoya University

• Machida Chiyoko

  Div. Biol. Sci. Grad. Sch. Sci. Nagoya Univ.

• Kobayashi Takeshi

  Plant Biology Research Center Chubu University:college Of Bioscience And Biotechnology Chubu Univers

• Takahashi Hiro

  Plant Biology Research Center Chubu University

• Tsukaya Hirokazu

  National Institute For Basic Biology/okazaki Institute For Integrated Bioscience

• Kobayashi Takeshi

  Plant Biology Research Center Chubu University

関連論文

• 双子葉植物の葉の形態形成 : モデル植物, アラビドプシスを用いた遺伝学的アプローチ
• 日本産ヘクソカズラにおける葉型の多様性 : 宮島産コバノヘクソカズラの再検討
• 日本産ネジバナSpiranthes sinensis(ラン科)の分子マーカーから見た多型:開花期多型と屋久島産矮小型(f. gracilis)の分類学的扱い
• Ara4 GTPase AND ITS INTERACTANTS
• ANALYSES OF ARA FAMILY, THE SMALL GTPase FROM Arabidopsis thaliana
• 葉の形態形成と植物ホルモン
• オオバコ矮小化に関する形態学的・分子系統学的解析、特にヤクシマオオバコの分類学的扱いについて
• FTAカードを用いたフィールドでの植物DNA採集法
• ジャワ島及びボルネオ島産ツリフネソウ属植物(ツリフネソウ科)の細胞分類学的研究
• 葉の形態形成 (発生システムのダイナミクス) -- (組織・器官形成)
• 雲南省西北部及びチベット東・中部で1999年から2001年にかけて採集されたベンケイソウ科・キク科・イグサ科・ホシクサ科・ラン科植物集覧
• 葉の形とサイズは環境に応じて変化する--葉形の可塑性と進化 (特集 発生学・生態学・進化学の融合)
• セーター植物と温室植物:そのかたちとはたらき (特集 高山植物研究の現在--アルプスからヒマラヤへ)
• Regulation of the biosynthesis of plant hormones by cytochrome P450s
• The Leaf Index : Heteroblasty, Natural Variation, and the Genetic Control of Polar Processes of Leaf Expansion
• 葉の形成--葉の長さ,幅,大きさを決める遺伝子制御 (植物の形づくり--遺伝子からみた分子メカニズム) -- (器官形成と分裂組織の役割)
• 植物の発生メカニズム 後生動物の発生とどれだけ違うのか (特集 発生進化の分子機構 動物と植物の共通性と多様性)
• アラビドプシスの葉細胞の極性伸長を司る遺伝子ROTUNDIFOLIA3の分子遺伝学的解析
• 生物の形の多様性と進化(4)葉の形の多様性とその遺伝子的背景
• Monophyllaea属の子葉における競合器官形成
• 低分子量GTPase Ara4と機能的に相互作用する因子の探索
• 子葉と本葉のアイデンティティー -アラビドプシスにおける遺伝的解析-
• シロイヌナズナをモデル植物とした葉形態形成の発生遺伝学的解析
• シロイヌナズナの変異体を用いた葉身の極性伸長制御機構に関する発生遺伝学的解析
• アラビドプシスにおける葉身非対称性変異体の解析
• ROLES OF PROLINE IN OSMOTIC STRESS TOLERANCE AND MORPHOGENESIS OF Arabidopsis
• 形態進化の実験的モデル植物・シロイヌナズナ (特集・植物の形の進化)
• REGULATION OF CELL PROLIFERATION IN TOBACCO : INTERACTION OF NPK1 (MAPKKK) AND NAK1 (KINESIN-LIKE PROTEIN)
• Transient Gene Expression in Plant Cells Mediated by Agrobacterium tumefaciens: Application for the Analysis of Virulence Loci
• Knowledge-based Fuzzy Adaptive Resonance Theory and Its Application to the Analysis of Gene Expression in Plants(BIOINFORMATICS)
• ホシザキシャクジョウ(ヒナノシャクジョウ科)の18S rDNA配列情報に基づく系統的位置
• Molecular evidences for allopolyploid origins of Plantago asiatica var. densiuscula and P. formosana
• Receptor-like kinases that are essential for protoderm formation in Arabidopsis thaliana
• Arabidopsis Mutants by Activation Tagging in which Photosynthesis Genes are Expressed in Dedifferentiated Calli
• Gravitropism in Leaves of Arabidopsis thaliana (L.) Heynh.
• The Different Growth Responses of the Arabidopsis thaliana Leaf Blade and the Petiole during Shade Avoidance are Regulated by Photoreceptors and Sugar
• Cell division and cell enlargement in isolated Cucurbita cotyledons grown in darkness and in light
• Thermal insulation and accumulation of heat in the downy inflorescences of Saussurea medusa (Asteraceae) at high elevation in Yunnan, China
• The ASYMMETRIC LEAVES2 Gene of Arabidopsis thaliana, Required for Formation of a Symmetric Flat Leaf Lamina, Encodes a Member of a Novel Family of Proteins Characterized by Cysteine Repeats and a Leucine Zipper
• ACR4, a Putative Receptor Kinase Gene of Arabidopsis thaliana, that is Expressed in the Outer Cell Layers of Embryos and Plants, is Involved in Proper Embryogenesis
• The ASYMMETRIC LEAVES2 gene of A. thaliana regulates the establishment of midvein as the longitudinal axis of leaf symmetry
• MOLECULAR-GENETIC ANALYSIS OF THE AS2 GENE ON THE MECHANISM OF SYMMETRICAL LEAF DEVEL OPMENT IN Arabidopsis thaliana
• Study on the Role of ATCR4,the Arabidopsis Homolog of Maize CRINKLY4 in Epidermis Differentiation
• The ALE1 gene is involved in endosperm development and epidermal differentiation in arabidopsis
• The role of the ASYMMETRIC LEAVES 2(AS2)gene of Arabidopsis thaliana in leaf development
• Characterization of a member of the AN subfamily, IAN, from Ipomoea nil
• 核内倍加による細胞肥大と植物のサイズ制御
• Taxonomic Notes on Cayratia tenuifolia (Wight & Arn.) Gagnep., Vitaceae
• Intra-specific Polyploidy and Possible Occurrence of Some Genetic Types for Pollen Development in Cayratia japonica, Vitaceae.
• A Mitogen-activated Protein Kinase NtMPK4 Activated by SIPKK is Required for Jasmonic Acid Signaling and Involved in Ozone Tolerance via Stomatal Movement in Tobacco
• Microarray analysis of compensated cell enlargement in angustifolia3
• Effect of the WUS (JAM) gene on the regulation of leaf identity in Arabidopsis thaliana
• THE LANCEOLATUSI AND THE MACROPHYLLA GENES INVOLVED IN THE LEAF DEVELOPMENT -AN ONTOGENIC ANALYSIS USING Arabidopsis thaliana.
• ISOLATIONS AND ANALYSES OF MORPHOLOGICAL MUTANTS OF COTYLEDONS IN Arabidopsis thaliana
• Genetic Control of Petiole Length in Arabidopsis thaliana
• Characterization of a dehydrogenase motif and an uORF in Arabidopsis ANGUSTIFOLIA gene
• 腐生植物Monotropastrum humile var. glaberrimumの菌根菌の分子マーカーによる同定
• A novel feature of structural variegation in leaves of the tropical plant Schismatoglottis calyptrata
• Brassinosteroids Control the Proliferation of Leaf Cells of Arabidopsis thaliana
• Morphological, Physiological and Molecular Genetic Characterization of Arabidopsis himalaica, with Reference to A. thaliana
• Compensated cell enlargement occurs post-mitotically and is achieved by several different mechanisms
• Classification of compensated cell enlargement by the extra-small sisters mutations
• Dissection of Enhanced Cell Expansion Processes in Leaves Triggered by a Defect in Cell Proliferation, with Reference to Roles of Endoreduplication
• Coordination of cell proliferation and cell expansion in the control of leaf size in Arabidopsis thaliana
• Morphological and molecular variation in Mitchella undulata, with special reference to the systematic treatment of the dwarf from Yakushima
• GENETIC DISSECTION OF THE ELONGATION PROCESSES IN LEAF DEVELOPMENT-A REGULATION THROUGH CORTICAL MICROTUBULES ORIENTATION-
• ESTABLISHMENT OF MODEL SYSTEM FORANALYZING INTRACELLULAR TRANSPORT OF THE PLANT CELLS
• Analyses of transgenic or mutant plants with altered leaf thickness
• ギンリョウソウ(Monotropastrum humile)の分類的位置の再検討--glaberrimum変種に注目して
• Chromosome Observations in Species of Cayratia (Vitaceae). II. Intraspecific Polyploidy in C. trifolia
• ネパール・ムスタンにおける野生植物種の大規模DNAコレクション
• The Mechanism of Cell Cycle Arrest Front Progression Explained by a KLUH/CYP78A5-dependent Mobile Growth Factor in Developing Leaves of Arabidopsis thaliana
• Agrobacterium-mediated transformation of the wild orchid species Phalaenopsis amabilis
• The transposition pattern of the Ac element in tobacco cultured cells
• ANALYSES OF THE FUNCTIONS OF AS1 AND AS2 IN ARABIDOPSIS
• ANALYSIS OF THE EXPRESSION PATTERN OF GENES WHICH ARE RELATED TO THE LEAF DEVELOPMENT
• The bHLH Transcription Factor SPATULA Controls Final Leaf Size in Arabidopsis thaliana
• HINKEL kinesin, ANP MAPKKKs and MKK6/ANQ MAPKK, which phosphorylates and activates MPK4 MAPK, constitute a pathway that is required for cytokinesis in Arabidopsis thaliana
• A MAP Kinase Cascade That Controls Plant Cytokinesis
• The Expression Pattern of the Gene for NPK1 Protein Kinase Related to Mitogen-Activated Protein Kinase Kinase Kinase (MAPKKK) in a Tobacco Plant : Correlation with Cell Proliferation
• Arabidopsis AUXIN RESPONSE FACTOR6 and 8 Regulate Jasmonic Acid Biosynthesis and Floral Organ Development via Repression of Class 1 KNOX Genes
• Chromosome observations in Cayratia, Vitaceae
• Chemical Identity of a Rotting Animal-Like Odor Emitted from the Inflorescence of the Titan Arum (Amorphophallus titanum)
• Interaction between Agrobacterium tumefaciens oncoprotein 6b and a tobacco nucleolar protein that is homologous to TNP1 encoded by a transposable element of Antirrhinum majus
• ASYMMETRIC LEAVES2, ASYMMETRIC LEAVES1 and Histone Deacetylases Are Involved in the Spatial Regulation of microRNA in Arabidopsis
• Oncogene 6b from Agrobacterium tumefaciens Induces Abaxial Cell Division at Late Stages of Leaf Development and Modifies Vascular Development in Petioles
• ANALYSES OF THE FUNCTIONAL REGION OF 6b PROTEIN ON T-DNA OF A.tumefaciens AND THE ROLE OF ITS INTERACTING PROTEINS
• Mutual interactions among the genesresponsible for leaf development -- an ontogenetic analysis usingArabidopsis thaliana
• アラビドプシスを用いた葉形態形成の発生遺伝学的解析
• シュ-ト形態形成の遺伝学的背景 (エボル-ション) -- (発生)
• ASYMMETRIC LEAVES2 and Elongator, a Histone Acetyltransferase Complex, Mediate the Establishment of Polarity in Leaves of Arabidopsis thaliana
• ANGUSTIFOLIA3 Plays Roles in Adaxial/Abaxial Patterning and Growth in Leaf Morphogenesis
• ROTUNDIFOLIA4 Regulates Cell Proliferation Along the Body Axis in Arabidopsis Shoot
• A hypothesis on the origin of genetic heterozygosity in diploids and triploids in Japanese Cayratia japonica species complex (Vitaceae)
• Leaf adaxial-abaxial polarity specification and lamina outgrowth : evolution and development
• Flowering phenology of the nine-year plant, Strobilanthes cernua (Acanthaceae)
• A hypothesis on the origin of genetic heterozygosity in diploids and triploids in Japanese Cayratia japonica species complex (Vitaceae)
• How do 'housekeeping' genes control organogenesis? : unexpected new findings on the role of housekeeping genes in cell and organ differentiation
• Leaf adaxial-abaxial polarity specification and lamina outgrowth : evolution and development
• Knowledge-based Fuzzy Adaptive Resonance Theory and Its Application to the Analysis of Gene Expression in Plants

もっと見る 閉じる

スポンサーリンク