A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis

Frontiers in Plant Science
Ying NiLenwood S Heath


Gene regulatory networks (GRNs) provide a representation of relationships between regulators and their target genes. Several methods for GRN inference, both unsupervised and supervised, have been developed to date. Because regulatory relationships consistently reprogram in diverse tissues or under different conditions, GRNs inferred without specific biological contexts are of limited applicability. In this report, a machine learning approach is presented to predict GRNs specific to developing Arabidopsis thaliana embryos. We developed the Beacon GRN inference tool to predict GRNs occurring during seed development in Arabidopsis based on a support vector machine (SVM) model. We developed both global and local inference models and compared their performance, demonstrating that local models are generally superior for our application. Using both the expression levels of the genes expressed in developing embryos and prior known regulatory relationships, GRNs were predicted for specific embryonic developmental stages. The targets that are strongly positively correlated with their regulators are mostly expressed at the beginning of seed development. Potential direct targets were identified based on a match between the promoter regions...Continue Reading


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Mar 25, 2020·Current Protocols in Plant Biology·Zahra Razaghi-Moghadam, Zoran Nikoloski
Apr 25, 2020·Nucleic Acids Research·Qi SongSong Li
Oct 17, 2017·Frontiers in Plant Science·David C HaakSong Li
Jul 2, 2020·NPJ Systems Biology and Applications·Zahra Razaghi-Moghadam, Zoran Nikoloski
Oct 27, 2020·Nucleic Acids Research·Adam B Zaborowski, Dirk Walther


Jun 18, 2005·Bioinformatics·Asa Ben-Hur, William Stafford Noble
Feb 24, 2006·Proceedings of the National Academy of Sciences of the United States of America·Siobhan A BraybrookJohn J Harada
Aug 12, 2008·Bioinformatics·Fantine Mordelet, Jean-Philippe Vert
Nov 1, 2008·PLoS Computational Biology·Asa Ben-HurGunnar Rätsch
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Feb 4, 2009·Bioinformatics·Brian C Haynes, Michael R Brent
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam Stafford Noble
Aug 12, 2009·Nature Biotechnology·Nicolas Le NovèreHiroaki Kitano
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Apr 20, 2010·Trends in Plant Science·Astrid JunkerHelmut Bäumlein
May 7, 2010·BMC Bioinformatics·Luigi CeruloMichele Ceccarelli
Feb 19, 2011·Bioinformatics·Charles E GrantWilliam Stafford Noble
May 20, 2011·Proceedings of the National Academy of Sciences of the United States of America·George W BasselNicholas J Provart
Jan 1, 2008·The Arabidopsis Book·Sébastien BaudLoïc Lepiniec
Jun 26, 2012·Nucleic Acids Research·Gudrun MönkeLothar Altschmied
Jul 17, 2012·Nature Methods·Daniel MarbachGustavo Stolovitzky
Nov 24, 2012·BMC Systems Biology·Anne-Claire HauryJean-Philippe Vert
Dec 12, 2012·Interface Focus·Christopher A Penfold, David L Wild
Jan 15, 2013·Plant Physiology·Fangfang Wang, Sharyn E Perry
Mar 5, 2013·Annual Review of Plant Biology·Nese Sreenivasulu, Ulrich Wobus
Mar 29, 2013·Plant Cell Reports·Kazuo Nakashima, Kazuko Yamaguchi-Shinozaki
May 24, 2013·Briefings in Bioinformatics·Stefan R MaetschkeMark A Ragan
Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth
Feb 11, 2014·Current Opinion in Plant Biology·Clément Lafon-Placette, Claudia Köhler
Jun 7, 2014·Wiley Interdisciplinary Reviews. Developmental Biology·Haiyan JiaDonald R McCarty
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Jul 24, 2015·Genesis : the Journal of Genetics and Development·Tanya Z BerardiniEva Huala
Nov 14, 2015·Journal of Biosciences·Nihir Patel, Jason Tl Wang
Dec 19, 2015·The Plant Journal : for Cell and Molecular Biology·Andrew SchneiderEva Collakova
Feb 13, 2016·Scientific Reports·Nooshin OmranianZoran Nikoloski
Apr 16, 2016·BMC Plant Biology·Vivek VermaPrakash P Kumar
Apr 20, 2016·Frontiers in Plant Science·Elise A R SerinWilco Ligterink
Aug 24, 2016·Proceedings of the National Academy of Sciences of the United States of America·Sandra Isabel González-MoralesLuis Herrera-Estrella

Related Concepts

Seed Development
Gene Expression
Cellular Reprogramming
Genetic Vectors
Grn protein, mouse

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