Development of a novel integrated data mining that facilitates functional analysis in the post-genomic era -- Exploring novel gene coexpression --

2012 Fiscal Year Final Research Report

• Project/Area Number: 23700355
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: HUKUSHIMA Atsushi 独立行政法人理化学研究所, メタボローム情報チーム, 研究員 (80415281)
• Project Period (FY): 2011 – 2012
• Keywords: バイオインフォマティクス / トランスクリプトミクス / 遺伝子共発現 / データ統合 / データ正規化 / differential correlation / マイクロアレイ

Research Abstract

We have investigated an integrated data mining that facilitates functional analysis to improve limits in gene coexpression approach for function prediction. We have developed the DiffCorr package, a simple method for identifying pattern changes between 2 experimental conditions in correlation networks, which builds on a commonly used association measure. Our method is suitable for the first step towards inferring causal relationships and detecting biomarker candidates.

Research Products

• [Journal Article] Recent progress in the development of metabolome databases for plant systems biology (2013)
  • Author(s): Atsushi Fukushima, Miyako Kusano
  • Journal Title: Front. Plant Sci Volume: 4 Pages: 73
  • Peer Reviewed
• [Journal Article] DiffCorr: an R package to analyze and visualize differential correlations in biological networks (2013)
  • Author(s): Atsushi Fukushima
  • Journal Title: Gene Volume: 518 Pages: 209-214
  • Peer Reviewed
• [Journal Article] Transcriptome data modeling : an approach toward target identification for plant metabolic engineering (2013)
  • Author(s): Keiko Yonekura-Sakakibara, Atsushi Fukushima, Kazuki Saito
  • Journal Title: Curr. Opin. Biotechnol Volume: 24 Pages: 285-290
  • Peer Reviewed
• [Journal Article] Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches (2012)
  • Author(s): Atsushi Fukushima, Tomoko Nishizawa, Mariko Hayakumo, Shoko Hikosaka, Kazuki Saito, Eiji Goto, Miyako Kusano
  • Journal Title: Plant Physiol Volume: 158 Pages: 1487-1502
  • Peer Reviewed
• [Journal Article] Deciphering starch quality of rice kernels using metabolite profiling and pedigree network analysis (2012)
  • Author(s): Miyako Kusano, Atsushi Fukushima, Naoko Fujita, Yozo Okazaki, Makoto Kobayashi, Naoko Fujita Oitome, Kaworu Ebana, Kazuki Saito
  • Journal Title: Mol. Plant Volume: 5 Pages: 442-451
  • Peer Reviewed
• [Journal Article] Transcriptional and metabolic programs following exposure of plants to UV-B irradiation (2011)
  • Author(s): Takayuki Tohge, Miyako Kusano, Atsushi Fukushima, Kazuki Saito, Alisdair R. Fernie
  • Journal Title: Plant Signal. Behav Volume: 6 Pages: 1987-1992
  • Peer Reviewed
• [Journal Article] Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to ultraviolet-B light (2011)
  • Author(s): Miyako Kusano, Takayuki Tohge, Atsushi Fukushima, Makoto Kobayashi, Naomi Hayashi, Hitomi Otsuki, Youichi Kondou, Hiroto Goto, Mika Kawashima, Fumio Matsuda, Rie Niida, Minami Matsui, Kazuki Saito, Alisdair R. Fernie
  • Journal Title: Plant J Volume: 67 Pages: 354-369
  • Peer Reviewed
• [Journal Article] Current challenges and future potential of tomato breeding using omics approaches
  • Author(s): Miyako Kusano, Atsushi Fukushima
  • Journal Title: Breed. Sci Volume: (in press)
  • Peer Reviewed
• [Presentation] DiffCorr: an R package to analyze and visualize differential correlations in biological networks (2012)
  • Author(s): Atsushi Fukushima
  • Organizer: PRIB 2012
  • Place of Presentation: Tokyo Japan
  • Year and Date: 20121108-10
• [Presentation] DiffCorr: an R package to analyze and visualize differential correlations in biological networks (2012)
  • Author(s): 福島 敦史
  • Organizer: 生命医薬情報学連合大会(2012 年日本バイオインフォマティクス学会年会情報計算化学生物学会(CBI 学会)年次大会オミックス医療研究会年会)
  • Place of Presentation: 東京, 日本
  • Year and Date: 20121028-31
• [Presentation] Transcriptome Independent Component Analysis Lead to the Identification of Two Glycosyltransferases Involved in Anthocyanin Modification in Arabidopsis thaliana (2012)
  • Author(s): Keiko Sakakibara, Atsushi Fukushima, Ryo Nakabayashi, Kousuke Hanada, Fumio Matsuda, Satoko Sugawara, Eri Inoue, Takashi Kuromori, Takuya Ito, Kazuo Shinozaki, Bunyapa Wangwattana, Mami Yamazaki, Kazuki Saito
  • Organizer: 26th International Conference on Polyphenols (ICP2012)
  • Place of Presentation: Florence, Italy
  • Year and Date: 20120722-26
• [Presentation] Characterizing coexpression modules using graph clustering and differential coexpression approaches in Solanum lycopersicum (2012)
  • Author(s): 福島 敦史, 西澤 具子, 早雲 まり子, 彦坂 晶子, 斉藤 和季, 後藤 英司, 草野 都
  • Organizer: 第53回日本植物生理学会年会
  • Place of Presentation: 京都, 日本
  • Year and Date: 20120316-18
• [Presentation] 独立成分分析によるアントシアニン修飾関連配糖化酵素遺伝子の機能同定 (2012)
  • Author(s): 榊原 圭子, 福島 敦史, 中林 亮, 花田 耕介, 松田 史生, 菅原 聡子, 井上 恵理, 黒森 崇, 伊藤 卓也, 篠崎 一雄, Wangwattana Bunyapa, 山崎 真巳, 斉藤 和季
  • Organizer: 第53回日本植物生理学会年会
  • Place of Presentation: 京都, 日本
  • Year and Date: 20120316-18
• [Presentation] Characterizing coexpression modules using graph clustering and differential coexpression approaches in Solanum lycopersicum (2011)
  • Author(s): Atsushi Fukushima, Tomoko Nishizawa, Mariko Hayakumo, Shoko Hikosaka, Kazuki Saito, Eiji Goto, Miyako Kusano
  • Organizer: 8th Solanaceae and 2nd Cucurbitaceae Genome Joint Conference (SOL&ICuGI2011)
  • Place of Presentation: Kobe, Japan
  • Year and Date: 20111128-1202
• [Presentation] Exploring tomato gene functions based on coexpression modules using graph clustering approaches (2011)
  • Author(s): Atsushi Fukushima, Tomoko Nishizawa, Mariko Hayakumo, Shoko Hikosaka, Kazuki Saito, Eiji Goto, Miyako Kusano
  • Organizer: The 2011 Annual Conference of the Japanese Society for Bioinformatic
  • Place of Presentation: Kobe, Japan
  • Year and Date: 20111108-10
• [Presentation] Two Glycosyltransferases Involved in Anthocyanin Modification Delimited by Transcriptome Independent Component Analysis in Arabidopsis thaliana (2011)
  • Author(s): Keiko Sakakibara, Atsushi Fukushima, Ryo Nakabayashi, Kousuke Hanada, Fumio Matsuda, Satoko Sugawara, Eri Inoue, Takashi Kuromori, Takuya Ito, Kazuo Shinozaki, Bunyapa Wangwattana, Mami Yamazaki, Kazuki Saito
  • Organizer: Gordon Research Conference on Plant Metabolic Engineering, Waterville
  • Place of Presentation: Valley, USA
  • Year and Date: 20110724-29
• [Remarks] DiffCorr package
  • URL: http://diffcorr.sourceforge.net/