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Gupta P, Naithani S, Tello-Ruiz MK, et al. Gramene Database: Navigating Plant Comparative Genomics Resources. Curr Plant Biol. 2016;7:10-15doi: 10.1016/j.cpb.2016.12.005.
Gupta, P., Naithani, S., Tello-Ruiz, M. K., Chougule, K., D'Eustachio, P., Fabregat, A., Jiao, Y., Keays, M., Lee, Y. K., Kumari, S., Mulvaney, J., Olson, A., Preece, J., Stein, J., Wei, S., Weiser, J., Huerta, L., Petryszak, R., Kersey, P., Stein, L. D., Ware, D., & Jaiswal, P. (2016). Gramene Database: Navigating Plant Comparative Genomics Resources. Current plant biology, 710-15. https://doi.org/10.1016/j.cpb.2016.12.005
Gupta, Parul, et al. "Gramene Database: Navigating Plant Comparative Genomics Resources." Current plant biology vol. 7 (2016): 10-15. doi: https://doi.org/10.1016/j.cpb.2016.12.005
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P. Gramene Database: Navigating Plant Comparative Genomics Resources. Curr Plant Biol. 2016 Nov;7:10-15. doi: 10.1016/j.cpb.2016.12.005. PMID: 28713666; PMCID: PMC5509230.
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Curr Plant Biol. 2016 Nov;7:10-15. doi: 10.1016/j.cpb.2016.12.005.

Gramene Database: Navigating Plant Comparative Genomics Resources.

Current plant biology

Parul Gupta, Sushma Naithani, Marcela Karey Tello-Ruiz, Kapeel Chougule, Peter D'Eustachio, Antonio Fabregat, Yinping Jiao, Maria Keays, Young Koung Lee, Sunita Kumari, Joseph Mulvaney, Andrew Olson, Justin Preece, Joshua Stein, Sharon Wei, Joel Weiser, Laura Huerta, Robert Petryszak, Paul Kersey, Lincoln D Stein, Doreen Ware, Pankaj Jaiswal

Affiliations

  1. Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA.
  2. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
  3. NYU School of Medicine, New York, NY, USA.
  4. European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK.
  5. Ontario Institute for Cancer Research, Toronto, ON, Canada.
  6. USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY, USA.

PMID: 28713666 PMCID: PMC5509230 DOI: 10.1016/j.cpb.2016.12.005

Abstract

Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.

References

  1. Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7 - PubMed
  2. Nucleic Acids Res. 2017 Jan 4;45(D1):D1029-D1039 - PubMed
  3. Nucleic Acids Res. 2016 Jan 4;44(D1):D746-52 - PubMed
  4. Genome Biol. 2016 Jun 06;17 (1):122 - PubMed
  5. Genome Res. 2009 Feb;19(2):327-35 - PubMed
  6. Nucleic Acids Res. 2011 Jan;39(Database issue):D1085-94 - PubMed
  7. Methods Mol Biol. 2016;1374:141-63 - PubMed
  8. Nucleic Acids Res. 2016 Jan 4;44(D1):D1133-40 - PubMed
  9. Nucleic Acids Res. 2014 Jan;42(Database issue):D1193-9 - PubMed
  10. Database (Oxford). 2012 Feb 28;2012:bar056 - PubMed
  11. Plant J. 2015 Apr;82(1):174-82 - PubMed

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Grant support