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Methods for the bottom-up reconstruction of gene-regulatory networks

Research Project

Project/Area Number 23710235
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionOsaka University

Principal Investigator

DIEGO Miranda-saavedra  大阪大学, 免疫学フロンティア研究センター, 特任准教授 (20572366)

Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2012: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2011: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
KeywordsEnhancer identification / Transcriptional regulatory network / Epigenetics / Computational genomics / Genetic algorithm / Support vector machine / Transcriptional regulatory module / エンハンサー同定 / 転写制御ネットワーク / エピジェネティクス / 計算ゲノミクス / 遺伝的アルゴリズム / サポートベクターマシン / 転写制御モジュール / エンハンサーの特定 / 転写調節ネットワーク / コンピュテーショナル・ゲノミクス
Research Abstract

Development of the best computational method for enhancer detection, capable of identifying enhancers from ChIP-chip and ChIP-seq libraries with a better comparative performance than other published methods for enhancer prediction (Fernandez and Miranda-Saavedra, 2012).
Development of a novel method for the reconstruction of Transcriptional Regulatory Modules (TRMs) (Hutchins et al, 2013).
The above methods have provided new and fundamental insights into the STAT3 controlled anti-inflammatory response network (Hutchins et al, Blood, 2012; Hutchins et al, JAK-STAT, 2013).

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Research-status Report
  • Research Products

    (11 results)

All 2013 2012 2011 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results) Presentation (5 results) (of which Invited: 1 results)

  • [Journal Article] Genomic and computational approaches to dissect the mechanisms of STAT3's universal and cell type-specific functions.2013

    • Author(s)
      Hutchins AP, Diez D, Miranda-Saavedra D.*
    • Journal Title

      JAK-STAT. Peer-reviewed

      Volume: (in press)

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions2013

    • Author(s)
      Andrew Paul Hutchins, Diego Diez, Yoshiko Takahashi, Shandar Ahmad, Ralf Jauch, Michel Lucien Tremblay, Diego Miranda-Saavedra
    • Journal Title

      Nucleic Acids Research

      Volume: 41 Issue: 4 Pages: 2155-2170

    • DOI

      10.1093/nar/gks1300

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.2012

    • Author(s)
      Miranda-Saavedra D*
    • Journal Title

      Genomics.

      Volume: 100(5) Issue: 5 Pages: 303-13

    • DOI

      10.1016/j.ygeno.2012.07.014

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines.2012

    • Author(s)
      Miranda-Saavedra D*.
    • Journal Title

      Nucleic Acids Research

      Volume: 40(10):e77. Issue: 10 Pages: e77-e77

    • DOI

      10.1093/nar/gks149

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages.2012

    • Author(s)
      Hutchins AP, Poulain S, Miranda-SaavedraD.*
    • Journal Title

      Blood. Peer-reviewed.

      Volume: 119(13) Issue: 13 Pages: e110-e119

    • DOI

      10.1182/blood-2011-09-381483

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines.2012

    • Author(s)
      Fernandez, M. and D. Miranda-Saavedra
    • Journal Title

      Nucleic Acids Research

      Volume: -

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Presentation] Control of the anti-inflammatory response by STAT3.2012

    • Author(s)
      Diego Miranda-Saavedra
    • Organizer
      European Congress of Immunology 2012 (Glasgow)
    • Place of Presentation
      UK
    • Year and Date
      2012-06-09
    • Related Report
      2012 Final Research Report
  • [Presentation] Prediction of the effectors of the anti-inflammatory response by ChIP-seq and RNA-seq analysis.2012

    • Author(s)
      Diego Miranda-Saavedra.
    • Organizer
      Information Processing in Cells and Tissues (IPCAT) Conference 2012.
    • Place of Presentation
      Trinity College, Cambridge.UK.
    • Year and Date
      2012-01-04
    • Related Report
      2012 Final Research Report
  • [Presentation] Genome-wide Enhancer Predictions from Chromatin Methylation Marks using Genetic Algorithm-Optimised Support Vector Machines.2011

    • Author(s)
      Diego Miranda-Saavedra
    • Organizer
      2^<nd> Next Generation Sequencing Asia Congress
    • Place of Presentation
      Singapore
    • Year and Date
      2011-10-04
    • Related Report
      2012 Final Research Report
  • [Presentation] “Control of the anti-inflammatory response by STAT3”

    • Author(s)
      Diego Miranda-saavedra
    • Organizer
      European Congress of Immunology 2012
    • Place of Presentation
      Scottish Exhibition & Conference Centre (SECC) Glasgow England
    • Related Report
      2012 Annual Research Report
  • [Presentation] “Prediction of the effectors of the anti-inflammatory response by ChIP-seq and RNA-seq analysis”

    • Author(s)
      Diego Miranda-Saavedra
    • Organizer
      Information Processing in Cells and Tissues (IPCAT) Conference 2012
    • Place of Presentation
      Trinity College, Cambridge England
    • Related Report
      2012 Annual Research Report
    • Invited

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

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