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Araport is a collaborative effort built with critical contributions by the following Arabidopsis research labs. Araport welcomes new contributors; please contact us.

BAR: the Bio-Analytic Resource for Plant Biology

  • Website: BAR
  • People: Nick Provart, Provart Lab, Jamie Waese, Asher Pasha
  • Institution: Center for the Analysis of Genome Evolution and Function (CAGEF) at University of Toronto.
  • Recent publication: de Lucas M, Provart NJ, Brady SM (2014) Bioinformatic tools in Arabidopsis research. Methods Mol Biol [pubmed 24057362]
  • Contributions to Araport:
    • Web services: efp_by_locus, expressologs_by_locus
    • BAR Expression Viewer, a science app for comparative transcriptomics [pubmed 17684564]
    • BAR Interactions Viewer, a science app to visualize protein-protein interaction networks [pubmed 17675552]
    • BAR Gene Slider, a science app for analysis of conserved regulatory elements
    • 50 Years of Arabidopsis Research, a science app to accompany a literature review [pubmed 26465351]

EPIC-CoGe: the Comparative Genomics Platform extended for Epigenetics

FLOR-ID: the Flowering Interactive Database

  • Website: FLOR-ID
  • People: Frédéric Bouché, Guillaume Lobet, Pierre Tocquin, Claire Périlleux
  • Institution: Plant Physiology laboratory of the Université de Liège
  • Recent publication: Frédéric Bouché, Guillaume Lobet, Pierre Tocquin, and Claire Périlleux (2016) FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. NAR [pubmed 26476447]
  • Contributions to Araport:
    • Web services: florid_adapter

HRGRN: a Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks

  • Website: HRGRN
  • People: Patrick Zhao, Xinbin Dai
  • Institution: The Samuel Roberts Noble Foundation
  • Recent publication: Dai X, Li J, Liu T, Zhao PX (2016) HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. Plant Cell Physiol [pubmied 26657893]
  • Contributions to Araport:
    • Web services: hrgrn_list_network, hrgrn_node_details_by_locus, hrgrn_node_info_by_locus, hrgrn_search_path_by_locus, hrgrn_subnetwork_by_locus
    • HRGRN App, a science app for visualizing a subnetwork

PhosPhAt: the Arabidopsis Protein Phosphorylation Site Database

  • Website: PhosPhAt
  • People: Waltraud Schulze
  • Institution: The Max Planck Institute for Molecular Plant Physiology [English]
  • Recent publication: Pawel Durek, Robert Schmidt, Joshua L. Heazlewood, Alexandra Jones, Daniel MacLean, Axel Nagel, Birgit Kersten, and Waltraud X. Schulze (2010) PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. NAR [pubmed 19880383]
  • Contributions to Araport:
    • Web services: phosphorylated_experimental, phosphorylated_predicted
    • PhosPhAt App, a science app for listing predicted and observed protein phosphorylation sites

PMR: the Plant, Eukaryotic and Microbial Systems Resource

  • Website: PMR
  • People: Eve Syrkin Wurtele, Manhoi Hur.
  • Institution: Department of Genetics, Development, and Cell Biology at Iowa State University.
  • Recent publication: Hur M, Campbell AA, Almeida-de-Macedo M, Li L, Ransom N, Jose A, Crispin M, Nikolau BJ, Wurtele ES (2013) A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Nat Prod Rep [pubmed 23447050]
  • Contributions to Araport:
    • Web services: pmr_boxplot_api, pmr_experiments_api, pmr_metabolite_api, pmr_platform_api
    • PMR Plotter, a science app for comparative metabolomics

SUBA: the Arabidopsis Subcellular Database

  • Website: SUBA
  • People: Cornelia Hooper, Ian Castleden
  • Institution: Plant Energy Biology at the University of Western Australia.
  • Recent publication: Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA (2013) SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. NAR [pubmed 23180787]
  • Contributions to Araport:
    • Web services: location_by_locus