Gramene 2016: Comparative plant genomics and pathway resources

Marcela K. Tello-Ruiz; Joshua Stein; Sharon Wei; Justin Preece; Andrew Olson; Sushma Naithani; Vindhya Amarasinghe; Palitha Dharmawardhana; Yinping Jiao; Joseph Mulvaney; Sunita Kumari; Kapeel Chougule; Justin Elser; Bo Wang; James Thomason; Daniel M. Bolser; Arnaud Kerhornou; Brandon Walts; Nuno A. Fonseca; Laura Huerta; Maria Keays; Y. Amy Tang; Helen Parkinson; Antonio Fabregat; Sheldon McKay; Joel Weiser; Peter D'Eustachio; Lincoln Stein; Robert Petryszak; Paul J. Kersey; Pankaj Jaiswal; Doreen Ware

doi:10.1093/nar/gkv1179

Gramene 2016: Comparative plant genomics and pathway resources

Marcela K. Tello-Ruiz, Joshua Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca, Laura HuertaMaria Keays, Y. Amy Tang, Helen Parkinson, Antonio Fabregat, Sheldon McKay, Joel Weiser, Peter D'Eustachio, Lincoln Stein, Robert Petryszak, Paul J. Kersey, Pankaj Jaiswal, Doreen Ware

Plant & Soil Science

Research output: Contribution to journal › Article › peer-review

92 Scopus citations

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 ontologybased 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.

Original language	English
Pages (from-to)	D1133-D1140
Journal	Nucleic Acids Research
Volume	44
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkv1179
State	Published - 2016

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Tello-Ruiz, M. K., 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, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., ... Ware, D. (2016). Gramene 2016: Comparative plant genomics and pathway resources. Nucleic Acids Research, 44(D1), D1133-D1140. https://doi.org/10.1093/nar/gkv1179

@article{bf208560c5a647c086193b84ae3db7cc,

title = "Gramene 2016: Comparative plant genomics and pathway resources",

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 ontologybased 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.",

author = "Tello-Ruiz, {Marcela K.} and Joshua Stein and Sharon Wei and Justin Preece and Andrew Olson and Sushma Naithani and Vindhya Amarasinghe and Palitha Dharmawardhana and Yinping Jiao and Joseph Mulvaney and Sunita Kumari and Kapeel Chougule and Justin Elser and Bo Wang and James Thomason and Bolser, {Daniel M.} and Arnaud Kerhornou and Brandon Walts and Fonseca, {Nuno A.} and Laura Huerta and Maria Keays and Tang, {Y. Amy} and Helen Parkinson and Antonio Fabregat and Sheldon McKay and Joel Weiser and Peter D'Eustachio and Lincoln Stein and Robert Petryszak and Kersey, {Paul J.} and Pankaj Jaiswal and Doreen Ware",

note = "Funding Information: 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].",

year = "2016",

doi = "10.1093/nar/gkv1179",

language = "English",

volume = "44",

pages = "D1133--D1140",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press (OUP)",

number = "D1",

}

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 2016, 'Gramene 2016: Comparative plant genomics and pathway resources', Nucleic Acids Research, vol. 44, no. D1, pp. D1133-D1140. https://doi.org/10.1093/nar/gkv1179

TY - JOUR

T1 - Gramene 2016

T2 - Comparative plant genomics and pathway resources

AU - Tello-Ruiz, Marcela K.

AU - Stein, Joshua

AU - Wei, Sharon

AU - Preece, Justin

AU - Olson, Andrew

AU - Naithani, Sushma

AU - Amarasinghe, Vindhya

AU - Dharmawardhana, Palitha

AU - Jiao, Yinping

AU - Mulvaney, Joseph

AU - Kumari, Sunita

AU - Chougule, Kapeel

AU - Elser, Justin

AU - Wang, Bo

AU - Thomason, James

AU - Bolser, Daniel M.

AU - Kerhornou, Arnaud

AU - Walts, Brandon

AU - Fonseca, Nuno A.

AU - Huerta, Laura

AU - Keays, Maria

AU - Tang, Y. Amy

AU - Parkinson, Helen

AU - Fabregat, Antonio

AU - McKay, Sheldon

AU - Weiser, Joel

AU - D'Eustachio, Peter

AU - Stein, Lincoln

AU - Petryszak, Robert

AU - Kersey, Paul J.

AU - Jaiswal, Pankaj

AU - Ware, Doreen

N1 - Funding Information: 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].

PY - 2016

Y1 - 2016

N2 - 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 ontologybased 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.

AB - 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 ontologybased 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.

UR - http://www.scopus.com/inward/record.url?scp=84979255809&partnerID=8YFLogxK

U2 - 10.1093/nar/gkv1179

DO - 10.1093/nar/gkv1179

M3 - Article

C2 - 26553803

AN - SCOPUS:84979255809

SN - 0305-1048

VL - 44

SP - D1133-D1140

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

Gramene 2016: Comparative plant genomics and pathway resources

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