A method for gene regulatory network estimation based on high-throughput sequencer data

• Project/Area Number: 24700294
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: Osaka University
• Principal Investigator: Seno Shigeto 大阪大学, 情報科学研究科, 助教 (30432462)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2013: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2012: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: バイオインフォマティクス / 遺伝子発現解析 / 褐色脂肪細胞

Outline of Final Research Achievements

We developed a method for the estimation of gene regulatory networks based on the gene expression data obtained by using both microarray technology and high throughput sequencer technology. Our method was applied to the data observing the effects of cold exposure against adipocytes, we successfully detected some candidate genes concerning browning mechanism.

Research Products

• [Journal Article] Proinflammatory cytokine interleukin-1β suppresses cold-induced thermogenesis in adipocytes (2016)
  • Author(s): Tsuyoshi Goto, Supaporn Naknukool, Rieko Yoshitake, Yuki Hanafusa, Soshi Tokiwa, Yongjia Li, Tomoya Sakamoto, Takahiro Nitta, Minji Kim, Nobuyuki Takahashi, Rina Yu, Hiromi Daiyasu, Shigeto Seno, Hideo Matsuda, Teruo Kawada
  • Journal Title: Cytokine Volume: 77 Pages: 107-114
  • DOI: 10.1016/j.cyto.2015.11.001
  • Peer Reviewed
• [Journal Article] Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution (2016)
  • Author(s): Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
  • Journal Title: J. Bioinformatics and Computational Biology Volume: 13 Issue: 05 Pages: 1543002-1543020
  • DOI: 10.1142/s0219720015430027
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Metagenome fragment classification based on multiple motif-occurrence profiles (2014)
  • Author(s): Naoki Matsushita, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: PeerJ Volume: 2: e559 Pages: 1-13
  • DOI: 10.7717/peerj.559
  • Peer Reviewed / Open Access
• [Journal Article] 複数時系列遺伝子発現プロファイルを利用した遺伝子制御ネットワーク推定の精度向上手法 (2013)
  • Author(s): 渡邉之人, 瀬尾茂人, 竹中要一, 松田秀雄
  • Journal Title: 情報処理学会論文誌 数理モデル化と応用 Volume: 6 Pages: 151-162
  • NAID: 110009550160
  • Peer Reviewed
• [Journal Article] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles (2013)
  • Author(s): Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: Gene Volume: Vol.518 Issue: 1 Pages: 17-25
  • DOI: 10.1016/j.gene.2012.11.090
  • Peer Reviewed
• [Journal Article] A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping (2012)
  • Author(s): Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: IPSJ Transactions on Bioinformatics（TBIO） Volume: 5 Pages: 27-33
  • Peer Reviewed
• [Presentation] イメージングデータの定量化とトランスオミクス解析 (2015)
  • Author(s): 瀬尾茂人
  • Organizer: 生理学研究所研究会
  • Place of Presentation: 自然科学研究機構岡崎コンファレンスセンター（岡崎市）
  • Year and Date: 2015-09-14
  • Invited
• [Presentation] Detecting the shifts of gene regulatory networks during time-course experiments with a single time point temporal resolution (2015)
  • Author(s): Yoichi Takenaka, Shigeto Seno, Hideo Matsuda
  • Organizer: GIW/InCOB2015
  • Place of Presentation: 日本科学未来館（江東区）
  • Year and Date: 2015-09-09
  • Int'l Joint Research
• [Presentation] ダイナミックベイジアンネットワークを用いた遺伝子制御ネットワーク推定の部分問題化による近似解法 (2015)
  • Author(s): 上木怜, 瀬尾茂人, 竹中要一, 松田秀雄
  • Organizer: 第42回バイオ情報学研究会
  • Place of Presentation: 沖縄科学技術大学院大学（沖縄県）
  • Year and Date: 2015-06-23
• [Presentation] ベイジアンネットワークによる遺伝子制御ネットワーク推定結果の反復構築のための計算速度向上手法 (2014)
  • Author(s): 津田絢子,瀬尾茂人,竹中要一,松田秀雄
  • Organizer: 第98回MPS・第38回BIO合同研究発表会
  • Place of Presentation: 沖縄科学技術大学院大学
  • Year and Date: 2014-06-25 – 2014-06-27
• [Presentation] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles (2012)
  • Author(s): Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: GIW2012
  • Place of Presentation: Tainan, Taiwan
• [Presentation] Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data (2012)
  • Author(s): Tomoyoshi Nakayama, Yoshiyuki Kido, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: GIW2012
  • Place of Presentation: Tainan, Taiwan
• [Presentation] Bayes-based inference of gene regulatory network for multiple time series gene expression profile (2012)
  • Author(s): Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Joint Conference on Informatics is Biology, Medicine and Pharmacology 2012
  • Place of Presentation: Tokyo, Japan
• [Presentation] Transcript-Type Dependent Normalization of Expression Levels in RNA-Seq Data for Non-Coding RNA Analysis (2012)
  • Author(s): Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: Joint Conference on Informatics is Biology, Medicine and Pharmacology 2012
  • Place of Presentation: Tokyo, Japan
• [Presentation] Gene Set Enrichment Analysis for a Long Time Series Gene Expression Profile
  • Author(s): Yuta Okuma, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: BIOCOMP2013
  • Place of Presentation: Las Vegas, Nevada, USA
• [Presentation] A Method of Sequence Analysis for High-Throughput Sequencer Data Based on Shifted Short Read Clustering
  • Author(s): Kensuke Suzuki, Daisuke Ueta, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: BIOCOMP2013
  • Place of Presentation: Las Vegas, Nevada, USA
• [Presentation] Reconstruction of Dynamic Gene Regulatory Networks for Cell Differentiation by Separation of Time-course Data
  • Author(s): Tomoyoshi Nakayama, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: BIOCOMP2013
  • Place of Presentation: Las Vegas, Nevada, USA
• [Presentation] Integrative prediction of miRNA-mRNA interactions from high-throughput sequencing data
  • Author(s): Tomoshige Ohno, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: RECOMB DREAM 2013
  • Place of Presentation: Las Vegas, Nevada, USA