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Nucleic Acids Res. 2018 Jan 04;46:D1181-D1189. doi: 10.1093/nar/gkx1111.

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M Bolser, Guy Naamati, Electra Tapanari, Nuno Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Munoz-Pomer Fuentes, Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D Stein, Robert Petryszak, Irene Papatheodorou, Paul J Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware

Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  2. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
  3. Division of Biological Sciences and Institute for Basic Science, Wonkwang University, Iksan 54538, Korea.
  4. EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.
  5. Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
  6. Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada.
  7. Adaptive Oncology Program, Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.
  8. American Society of Plant Biologists, 15501 Monona Drive, Rockville, MD 20855-2768, USA.
  9. USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA.

PMID: 29165610 PMCID: PMC5753211 DOI: 10.1093/nar/gkx1111

Abstract

Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.

Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

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