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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: April 16, 2021, 8:55 p.m.; Last accessed: Sep 25 2021 1:22 a.m.

Publication for citation  Gramene 2018: unifying comparative genomics and pathway resources for plant research. Tello-Ruiz MK,Naithani S,Stein JC et al.; Nucleic Acids Res ; 2018; 10.1093/nar/gkx1111;


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

Record updated: April 16, 2021, 8:48 p.m. by The FAIRsharing Team.

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Applies to: Data use

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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 et al.
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 et al.
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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Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.

Tello-Ruiz MK,Naithani S,Gupta P,Olson A,Wei S,Preece J,Jiao Y,Wang B,Chougule K,Garg P,Elser J,Kumari S,Kumar V, George N,Cook J,Bolser D,D'Eustachio P,Stein LD,Gupta A,Xu W, Papatheodorou I,Kersey PJ,Flicek P,Taylor C,Jaiswal P,Ware D
Nucleic Acids Res 2020

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Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

Naithani S,Gupta P,Preece J,D'Eustachio P,Elser JL,Garg P,Dikeman DA,Kiff J,Cook J,Olson A,Wei S,Tello-Ruiz MK,Mundo AF,Munoz-Pomer A,Mohammed S,Cheng T,Bolton E,Papatheodorou I,Stein L,Ware D,Jaiswal P
Nucleic Acids Res 2019

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Ensembl Genomes 2020-enabling non-vertebrate genomic research.

Howe KL, et al.
Nucleic Acids Res 2019

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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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Expression Atlas: gene and protein expression across multiple studies and organisms.

Papatheodorou I,Fonseca NA,Keays M,Tang YA,Barrera E,Bazant W,Burke M,Fullgrabe A,Fuentes AM,George N,Huerta L,Koskinen S,Mohammed S,Geniza M,Preece J,Jaiswal P,Jarnuczak AF,Huber W,Stegle O,Vizcaino JA,Brazma A,Petryszak R
Nucleic Acids Res 2017

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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,Wei S,Preece J,Geniza MJ,Jiao Y,Lee YK,Wang B,Mulvaney J,Chougule K,Elser J,Al-Bader N,Kumari S,Bolser DM,Naamati G,Huerta L,Keays M,D'Eustachio P,Stein LD,Papatheodorou I,Taylor C,Jaiswal P,Ware D
Nucleic Acids Res 2017

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AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.

AgBioData consortium
Database (Oxford) 2018

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Variant Effect Prediction Analysis Using Resources Available at Gramene Database.

Naithani S,Geniza M,Jaiswal P
Methods Mol Biol 2016

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Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.

Naithani S,Jaiswal P
Methods Mol Biol 2016

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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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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 2016

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This record is not implemented by any policy.


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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))