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ready Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants

Abbreviation:Gramene

General Information
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.




How to cite this record FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: March 3, 2020, 1:49 p.m.; Last accessed: Jun 02 2020 6:41 p.m.

Publication for citation  Gramene 2018: unifying comparative genomics and pathway resources for plant research. Tello-Ruiz MK,Naithani S,Stein JC,Gupta P,Campbell M,Olson A,Wei S,Preece J,Geniza MJ,Jiao Y,Lee YK,Wang B,Mulvaney J,Chougule K,Elser J,Al-Bader N,Kumari S,Thomason J,Kumar V,Bolser DM,Naamati G,Tapanari E,Fonseca N,Huerta L,Iqbal H,Keays M,Munoz-Pomer Fuentes A,Tang A,Fabregat A,D'Eustachio P,Weiser J,Stein LD,Petryszak R,Papatheodorou I,Kersey PJ,Lockhart P,Taylor C,Jaiswal P,Ware D; Nucleic Acids Res ; 2018; 10.1093/nar/gkx1111;


This record is maintained by Gramene  (gramene)  and jaiswalp  ORCID

Record updated: March 3, 2020, 1:47 p.m. by The FAIRsharing Team.

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Publications

Gramene database in 2010: updates and extensions.

Youens-Clark K., Buckler E., Casstevens T., Chen C., Declerck G., Derwent P., Dharmawardhana P., Jaiswal P., Kersey P., Karthikeyan AS., Lu J., McCouch SR., Ren L., Spooner W., Stein JC., Thomason J., Wei S., Ware D.,
Nucleic Acids Res. 2011

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Gramene: a growing plant comparative genomics resource.

Liang C., Jaiswal P., Hebbard C., Avraham S., Buckler ES., Casstevens T., Hurwitz B., McCouch S., Ni J., Pujar A., Ravenscroft D., Ren L., Spooner W., Tecle I., Thomason J., Tung CW., Wei X., Yap I., Youens-Clark K., Ware D., Stein L.,
Nucleic Acids Res. 2008

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

Tello-Ruiz MK,Naithani S,Stein JC,Gupta P,Campbell M,Olson A,Wei S,Preece J,Geniza MJ,Jiao Y,Lee YK,Wang B,Mulvaney J,Chougule K,Elser J,Al-Bader N,Kumari S,Thomason J,Kumar V,Bolser DM,Naamati G,Tapanari E,Fonseca N,Huerta L,Iqbal H,Keays M,Munoz-Pomer Fuentes A,Tang A,Fabregat A,D'Eustachio P,Weiser J,Stein LD,Petryszak R,Papatheodorou I,Kersey PJ,Lockhart P,Taylor C,Jaiswal P,Ware D
Nucleic Acids Res 2018

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Gramene Database: Navigating Plant Comparative Genomics Resources.

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
Curr Plant Biol 2017

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Gramene 2016: comparative plant genomics and pathway resources.

Tello-Ruiz MK,Stein J,Wei S,Preece J,Olson A,Naithani S,Amarasinghe V,Dharmawardhana P,Jiao Y,Mulvaney J,Kumari S,Chougule K,Elser J,Wang B,Thomason J,Bolser DM,Kerhornou A,Walts B,Fonseca NA,Huerta L,Keays M,Tang YA,Parkinson H,Fabregat A,McKay S,Weiser J,D'Eustachio P,Stein L,Petryszak R,Kersey PJ,Jaiswal P,Ware D
Nucleic Acids Res 2015

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Plant Reactome: a resource for plant pathways and comparative analysis.

Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P.
Nucleic Acids Res. 2017

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Variant Effect Prediction Analysis Using Resources Available at Gramene Database.

Naithani S, Geniza M, Jaiswal P
Methods Mol Biol 2017

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Involving community in genes and pathway curation.

Naithani S,Gupta P,Preece J,Garg P,Fraser V,Padgitt-Cobb LK,Martin M,Vining K,Jaiswal P
Database (Oxford) 2019

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Grant Number(s)

  • 00-52100-9622 (United States Department of Agriculture, Agricultural Research Service (USDA-ARS))

  • 0321685 (National Science Foundation (NSF), USA)

  • 0703908 (National Science Foundation (NSF), USA)

  • 0851652 (National Science Foundation (NSF), USA)

  • 1127112 (National Science Foundation (NSF), USA)

  • 58-1907-0-041 (United States Department of Agriculture, Agricultural Research Service (USDA-ARS))

  • 58-1907-0-041 (United States Department of Agriculture, Agricultural Research Service (USDA-ARS))