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Research ArticleLARGE-SCALE BIOLOGY ARTICLE
Open Access

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

Jamie Waese, Jim Fan, Asher Pasha, Hans Yu, Geoffrey Fucile, Ruian Shi, Matthew Cumming, Lawrence A. Kelley, Michael J. Sternberg, Vivek Krishnakumar, Erik Ferlanti, Jason Miller, Chris Town, Wolfgang Stuerzlinger, Nicholas J. Provart
Jamie Waese
Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Jim Fan
Department of Computer Science, University of Waterloo, Ontario N2L 3G1, Canada
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Asher Pasha
Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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  • ORCID record for Asher Pasha
Hans Yu
Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Geoffrey Fucile
SIB Swiss Institute of Bioinformatics, sciCORE Computing Center, University of Basel, CH-4056 Basel, Switzerland
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Ruian Shi
Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Matthew Cumming
Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Lawrence A. Kelley
Imperial College London, London SW7 2AZ, United Kingdom
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  • ORCID record for Lawrence A. Kelley
Michael J. Sternberg
Imperial College London, London SW7 2AZ, United Kingdom
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Vivek Krishnakumar
Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
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  • ORCID record for Vivek Krishnakumar
Erik Ferlanti
Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
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  • ORCID record for Erik Ferlanti
Jason Miller
Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
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Chris Town
Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
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Wolfgang Stuerzlinger
School of Interactive Arts and Technology, Simon Fraser University, British Columbia V3T 0A3, Canada
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Nicholas J. Provart
Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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  • For correspondence: nicholas.provart@utoronto.ca

Published August 2017. DOI: https://doi.org/10.1105/tpc.17.00073

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  • Figure 1.
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    Figure 1.

    Connections between Biological Entities at Different Levels of Analysis.

  • Figure 2.
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    Figure 2.

    ePlant’s Module Viewers (Each Displaying Data for ABI3), Illustrating ePlant’s Hierarchy of Scale.

    To see detail, view the online version. World eFP Viewer (A), Plant eFP Viewer (B), Tissue and Experiment eFP Viewer (C), Subcellular eFP Viewer (D), Chromosome Viewer (E), Interaction Viewer (F), Molecule Viewer (G), and Sequence Viewer (H). High-resolution vector graphics are available for most views (see example in Supplemental File 1). ePlant outputs are freely usable via an “open” license.

  • Figure 3.
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    Figure 3.

    ePlant System Design and User Interface.

    (A) ePlant system architecture.

    (B) ePlant user interface showing the expression pattern of ABI3 with the Plant eFP Viewer. See detail in online version of figure.

  • Figure 4.
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    Figure 4.

    ePlant Views Providing Information from Araport.

    (A) ePlant Gene Information Viewer.

    (B) ePlant Publications Viewer.

  • Figure 5.
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    Figure 5.

    The Heat Map Viewer Showing 350+ Expression Level Samples for 25 Genes Identified with the Expression Angler for Having Similar Expression Patterns to ABI3 (At3g24650).

    The “global” color gradient is selected, making it easy to see the variability in the expression levels of the various genes.

  • Figure 6.
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    Figure 6.

    Six of More Than 20 Views from the Tissue and Experiment eFP Viewer.

    Each view displays expression levels for ABI3 with the “custom” color gradient setting, with red = 100 expression units: root (A), guard and mesophyll cells (B), microgametogenesis (C), biotic stress: Pseudomonas syringae (D), abiotic stress (E), and pollen germination (F). Some views are truncated for display here; see online version of the figure to be able to see detail. ePlant outputs for all views may be downloaded as high-resolution vector graphic files and are freely available for use by any researcher under an “open” license.

  • Figure 7.
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    Figure 7.

    The Subcellular Localization eFP Viewer.

    (A) ABI3 is mostly localized in the nucleus.

    (B) An inset of a high-resolution version of the same image.

  • Figure 8.
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    Figure 8.

    ePlant Interaction and Molecule Viewers.

    (A) Protein and DNA Interaction Viewer showing interactions for At1g54330.

    (B) Molecule Viewer showing the transcription factor ABI3’s Phyre2-predicted partial 3D structure with its DNA binding site highlighted in blue and two nonsynonymous changes (from a web service provided by the 1001 Proteomes site) highlighted in green. Changes of higher frequency are denoted by larger, redder pins above the sequence below.

Tables

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    Table 1. Experimental and Tissue eFP Views and Data Sources
    ViewData Source
    Abiotic stressKilian et al. (2007)
    Biotic stress: Botrytis cinereaAtGenExpress initiative
    Biotic stress: ElicitorsAtGenExpress initiative
    Biotic stress: Erysiphe orontiiAtGenExpress initiative
    Biotic stress: Hyaloperonospora arabidopsidisWang et al. (2011)
    Biotic stress: Myzus persicaereCouldridge et al. (2007)
    Biotic stress: Phytophthora infestansAtGenExpress initiative
    Biotic stress: Pseudomonas syringaeAtGenExpress initiative
    ChemicalGoda et al. (2008)
    Guard cell: meristemoidsPillitteri et al. (2011)
    Guard cell: mutant and wild-type guard cell ABA responsePandey et al. (2010)
    Guard cell: suspension cell ABA response with ROS scavengerBöhmer and Schroeder (2011)
    Tissue specific: embryo developmentCasson et al. (2005)
    Tissue specific: guard and mesophyll cellsYang et al. (2008)
    Tissue specific: microgametogenesisHonys and Twell (2004)
    Tissue specific: pollen germinationQin et al. (2009)
    Tissue specific: rootBirnbaum et al. (2003); 
Nawy et al. (2005)
    Tissue specific: shoot apical meristemYadav et al. (2009)
    Tissue specific: stem epidermisSuh et al. (2005)
    Tissue specific: stigma and ovariesSwanson et al. (2005)
    Tissue specific: trichomesGilding and Marks (2010); Marks et al. (2009)
    Tissue specific: xylem and corkNASCArrays experiment #92

Additional Files

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    • Supplemental File 1
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ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology
Jamie Waese, Jim Fan, Asher Pasha, Hans Yu, Geoffrey Fucile, Ruian Shi, Matthew Cumming, Lawrence A. Kelley, Michael J. Sternberg, Vivek Krishnakumar, Erik Ferlanti, Jason Miller, Chris Town, Wolfgang Stuerzlinger, Nicholas J. Provart
The Plant Cell Aug 2017, 29 (8) 1806-1821; DOI: 10.1105/tpc.17.00073

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ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology
Jamie Waese, Jim Fan, Asher Pasha, Hans Yu, Geoffrey Fucile, Ruian Shi, Matthew Cumming, Lawrence A. Kelley, Michael J. Sternberg, Vivek Krishnakumar, Erik Ferlanti, Jason Miller, Chris Town, Wolfgang Stuerzlinger, Nicholas J. Provart
The Plant Cell Aug 2017, 29 (8) 1806-1821; DOI: 10.1105/tpc.17.00073
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The Plant Cell: 29 (8)
The Plant Cell
Vol. 29, Issue 8
Aug 2017
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  • Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover
  • Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice
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