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Gramene 2016: comparative plant genomics and pathway resources Public Deposited

https://ir.library.oregonstate.edu/concern/articles/z890rv95z

Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US. The published article can be found at:  http://nar.oxfordjournals.org/content/44/D1/D1133

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Abstract
  • Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials.
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  • Tello-Ruiz, M. K., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., ... & Ware, D. (2016). Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Research, 44(D1), D1133-D1140. doi:10.1093/nar/gkv1179
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  • National Science Foundation [IOS-0703908 and IOS-1127112]; United States Department of Agriculture - Agricultural Research Service [58-1907-4-030 and 1907-21000-030-00D to D.W.]; European Community's 7th Framework Programme (FP7/2007-2013; Infrastructures) [contract # 283496 to P.K.]; United Kingdom Biotechnology and Biosciences Research Council [BB/J000328X/1, I008071/1 and H531519/1 to P.K.]. The in-kind infrastructure and intellectual support for the development and running the Plant Reactome is supported by the Reactome database project via a grant from the US National Institutes of Health [P41 HG003751 to L.S.]; EU grant [LSHG-CT-2005-518254]; 'ENFIN', Ontario Research Fund; EBI Industry Programme. The funders had no role in the study design, data analysis or preparation of the manuscript. Funding for open access charge: "Gramene - Exploring Function through Comparative Genomics and Network Analysis" [NSF award #1127112].
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  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2016-03-30T15:27:37Z (GMT) No. of bitstreams: 2 Tello-RuizGramene2016Comparative.pdf: 4487478 bytes, checksum: 6ee3fd618bd6159e686351c44dcf833c (MD5) Tello-RuizGramene2016ComparativeSupplementaryTablesS1-S6.pdf: 479596 bytes, checksum: 0cc2727cc9ae11fdc3f598c6546ba50d (MD5)
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