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An integrated network of Arabidopsis growth regulators and its use for gene prioritization

Ehsan Sabaghian (UGent) , Zuzanna Drebert (UGent) , Dirk Inzé (UGent) and Yvan Saeys (UGent)
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Organization
Project
Biotechnology for a sustainable economy (Bio-Economy)
Abstract
Elucidating the molecular mechanisms that govern plant growth has been an important topic in plant research, and current advances in large-scale data generation call for computational tools that efficiently combine these different data sources to generate novel hypotheses. In this work, we present a novel, integrated network that combines multiple large-scale data sources to characterize growth regulatory genes in Arabidopsis, one of the main plant model organisms. The contributions of this work are twofold: first, we characterized a set of carefully selected growth regulators with respect to their connectivity patterns in the integrated network, and, subsequently, we explored to which extent these connectivity patterns can be used to suggest new growth regulators. Using a large-scale comparative study, we designed new supervised machine learning methods to prioritize growth regulators. Our results show that these methods significantly improve current state-of-the-art prioritization techniques, and are able to suggest meaningful new growth regulators. In addition, the integrated network is made available to the scientific community, providing a rich data source that will be useful for many biological processes, not necessarily restricted to plant growth.
Keywords
PREDICTION, ASSOCIATION, PLANTS, THALIANA, SIZE, ORGAN GROWTH, DISEASE-GENES, CANDIDATE GENES, PROTEIN-PROTEIN INTERACTIONS, TRANSCRIPTION FACTORS

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Chicago
Sabaghian, Ehsan, Zuzanna Drebert, Dirk Inzé, and Yvan Saeys. 2015. “An Integrated Network of Arabidopsis Growth Regulators and Its Use for Gene Prioritization.” Scientific Reports 5.
APA
Sabaghian, E., Drebert, Z., Inzé, D., & Saeys, Y. (2015). An integrated network of Arabidopsis growth regulators and its use for gene prioritization. SCIENTIFIC REPORTS, 5.
Vancouver
1.
Sabaghian E, Drebert Z, Inzé D, Saeys Y. An integrated network of Arabidopsis growth regulators and its use for gene prioritization. SCIENTIFIC REPORTS. 2015;5.
MLA
Sabaghian, Ehsan, Zuzanna Drebert, Dirk Inzé, et al. “An Integrated Network of Arabidopsis Growth Regulators and Its Use for Gene Prioritization.” SCIENTIFIC REPORTS 5 (2015): n. pag. Print.
@article{7035302,
  abstract     = {Elucidating the molecular mechanisms that govern plant growth has been an important topic in plant research, and current advances in large-scale data generation call for computational tools that efficiently combine these different data sources to generate novel hypotheses. In this work, we present a novel, integrated network that combines multiple large-scale data sources to characterize growth regulatory genes in Arabidopsis, one of the main plant model organisms. The contributions of this work are twofold: first, we characterized a set of carefully selected growth regulators with respect to their connectivity patterns in the integrated network, and, subsequently, we explored to which extent these connectivity patterns can be used to suggest new growth regulators. Using a large-scale comparative study, we designed new supervised machine learning methods to prioritize growth regulators. Our results show that these methods significantly improve current state-of-the-art prioritization techniques, and are able to suggest meaningful new growth regulators. In addition, the integrated network is made available to the scientific community, providing a rich data source that will be useful for many biological processes, not necessarily restricted to plant growth.},
  articleno    = {17617},
  author       = {Sabaghian, Ehsan and Drebert, Zuzanna and Inz{\'e}, Dirk and Saeys, Yvan},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keyword      = {PREDICTION,ASSOCIATION,PLANTS,THALIANA,SIZE,ORGAN GROWTH,DISEASE-GENES,CANDIDATE GENES,PROTEIN-PROTEIN INTERACTIONS,TRANSCRIPTION FACTORS},
  language     = {eng},
  pages        = {13},
  title        = {An integrated network of Arabidopsis growth regulators and its use for gene prioritization},
  url          = {http://dx.doi.org/10.1038/srep17617},
  volume       = {5},
  year         = {2015},
}

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