Literature DB >> 28713666

Gramene Database: Navigating Plant Comparative Genomics Resources.

Parul Gupta1, Sushma Naithani1, Marcela Karey Tello-Ruiz2, Kapeel Chougule2, Peter D'Eustachio3, Antonio Fabregat4, Yinping Jiao2, Maria Keays4, Young Koung Lee2, Sunita Kumari2, Joseph Mulvaney2, Andrew Olson2, Justin Preece1, Joshua Stein2, Sharon Wei2, Joel Weiser5, Laura Huerta4, Robert Petryszak4, Paul Kersey4, Lincoln D Stein5, Doreen Ware2,6, Pankaj Jaiswal1.   

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.

Entities:  

Year:  2016        PMID： 28713666      PMCID： PMC5509230          DOI： 10.1016/j.cpb.2016.12.005

Source DB:  PubMed          Journal:  Curr Plant Biol        ISSN： 2214-6628


  11 in total

1.  Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.

Authors:  Marcela Karey Tello-Ruiz; Joshua Stein; Sharon Wei; Ken Youens-Clark; Pankaj Jaiswal; Doreen Ware
Journal:  Methods Mol Biol       Date:  2016

2.  EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.

Authors:  Albert J Vilella; Jessica Severin; Abel Ureta-Vidal; Li Heng; Richard Durbin; Ewan Birney
Journal:  Genome Res       Date:  2008-11-24       Impact factor: 9.043

3.  Reactome: a database of reactions, pathways and biological processes.

Authors:  David Croft; Gavin O'Kelly; Guanming Wu; Robin Haw; Marc Gillespie; Lisa Matthews; Michael Caudy; Phani Garapati; Gopal Gopinath; Bijay Jassal; Steven Jupe; Irina Kalatskaya; Shahana Mahajan; Bruce May; Nelson Ndegwa; Esther Schmidt; Veronica Shamovsky; Christina Yung; Ewan Birney; Henning Hermjakob; Peter D'Eustachio; Lincoln Stein
Journal:  Nucleic Acids Res       Date:  2010-11-09       Impact factor: 16.971

4.  Gramene database in 2010: updates and extensions.

Authors:  Ken Youens-Clark; Ed Buckler; Terry Casstevens; Charles Chen; Genevieve Declerck; Paul Derwent; Palitha Dharmawardhana; Pankaj Jaiswal; Paul Kersey; A S Karthikeyan; Jerry Lu; Susan R McCouch; Liya Ren; William Spooner; Joshua C Stein; Jim Thomason; Sharon Wei; Doreen Ware
Journal:  Nucleic Acids Res       Date:  2010-11-13       Impact factor: 16.971

5.  GrameneMart: the BioMart data portal for the Gramene project.

Authors:  William Spooner; Ken Youens-Clark; Daniel Staines; Doreen Ware
Journal:  Database (Oxford)       Date:  2012-02-28       Impact factor: 3.451

6.  Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Authors:  Robert Petryszak; Maria Keays; Y Amy Tang; Nuno A Fonseca; Elisabet Barrera; Tony Burdett; Anja Füllgrabe; Alfonso Muñoz-Pomer Fuentes; Simon Jupp; Satu Koskinen; Oliver Mannion; Laura Huerta; Karine Megy; Catherine Snow; Eleanor Williams; Mitra Barzine; Emma Hastings; Hendrik Weisser; James Wright; Pankaj Jaiswal; Wolfgang Huber; Jyoti Choudhary; Helen E Parkinson; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2015-10-19       Impact factor: 16.971

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

Authors:  Sushma Naithani; Justin Preece; Peter D'Eustachio; Parul Gupta; Vindhya Amarasinghe; Palitha D Dharmawardhana; Guanming Wu; Antonio Fabregat; Justin L Elser; Joel Weiser; Maria Keays; Alfonso Munoz-Pomer Fuentes; Robert Petryszak; Lincoln D Stein; Doreen Ware; Pankaj Jaiswal
Journal:  Nucleic Acids Res       Date:  2016-10-30       Impact factor: 16.971

8.  Gramene 2013: comparative plant genomics resources.

Authors:  Marcela K Monaco; Joshua Stein; Sushma Naithani; Sharon Wei; Palitha Dharmawardhana; Sunita Kumari; Vindhya Amarasinghe; Ken Youens-Clark; James Thomason; Justin Preece; Shiran Pasternak; Andrew Olson; Yinping Jiao; Zhenyuan Lu; Dan Bolser; Arnaud Kerhornou; Dan Staines; Brandon Walts; Guanming Wu; Peter D'Eustachio; Robin Haw; David Croft; Paul J Kersey; Lincoln Stein; Pankaj Jaiswal; Doreen Ware
Journal:  Nucleic Acids Res       Date:  2013-11-11       Impact factor: 16.971

9.  The Ensembl Variant Effect Predictor.

Authors:  William McLaren; Laurent Gil; Sarah E Hunt; Harpreet Singh Riat; Graham R S Ritchie; Anja Thormann; Paul Flicek; Fiona Cunningham
Journal:  Genome Biol       Date:  2016-06-06       Impact factor: 13.583

10.  Gramene 2016: comparative plant genomics and pathway resources.

Authors:  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
Journal:  Nucleic Acids Res       Date:  2015-11-08       Impact factor: 16.971
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  19 in total

Review 1.  Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.

Authors:  Parul Gupta; Sushma Naithani; Justin Preece; Sunghwan Kim; Tiejun Cheng; Peter D'Eustachio; Justin Elser; Evan E Bolton; Pankaj Jaiswal
Journal:  Methods Mol Biol       Date:  2022

2.  CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource.

Authors:  Mark Winfield; Paul Wilkinson; Amanda Burridge; Alexandra Allen; Jane Coghill; Christy Waterfall; Keith Edwards; Gary Barker
Journal:  Methods Mol Biol       Date:  2022

Review 3.  Omics: a tool for resilient rice genetic improvement strategies.

Authors:  Muhammad Naeem; Zeeshan Ali; Anzal Khan; Hassan Javed Chaudhary; Javeria Ashraf; Faheem Shahzad Baloch
Journal:  Mol Biol Rep       Date:  2022-03-17       Impact factor: 2.742

4.  Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum.

Authors:  Nicolas M Doll; Jeremy Just; Véronique Brunaud; José Caïus; Aurélie Grimault; Nathalie Depège-Fargeix; Eddi Esteban; Asher Pasha; Nicholas J Provart; Gwyneth C Ingram; Peter M Rogowsky; Thomas Widiez
Journal:  Plant Cell       Date:  2020-02-21       Impact factor: 11.277

5.  Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants.

Authors:  Cornelia M Hooper; Ian R Castleden; Sandra K Tanz; Sally V Grasso; A Harvey Millar
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

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

Authors:  Marcela K Tello-Ruiz; Sushma Naithani; Joshua C Stein; Parul Gupta; Michael Campbell; Andrew Olson; Sharon Wei; Justin Preece; Matthew J Geniza; Yinping Jiao; Young Koung Lee; Bo Wang; Joseph Mulvaney; Kapeel Chougule; Justin Elser; Noor Al-Bader; Sunita Kumari; James Thomason; Vivek Kumar; Daniel M Bolser; Guy Naamati; Electra Tapanari; Nuno Fonseca; Laura Huerta; Haider Iqbal; Maria Keays; Alfonso Munoz-Pomer Fuentes; Amy Tang; Antonio Fabregat; Peter D'Eustachio; Joel Weiser; Lincoln D Stein; Robert Petryszak; Irene Papatheodorou; Paul J Kersey; Patti Lockhart; Crispin Taylor; Pankaj Jaiswal; Doreen Ware
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

Review 7.  Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.

Authors:  Luca Ambrosino; Chiara Colantuono; Gianfranco Diretto; Alessia Fiore; Maria Luisa Chiusano
Journal:  Plants (Basel)       Date:  2020-05-06

8.  Functionally redundant LNG3 and LNG4 genes regulate turgor-driven polar cell elongation through activation of XTH17 and XTH24.

Authors:  Young Koung Lee; Ji Ye Rhee; Seong Hee Lee; Gap Chae Chung; Soon Ju Park; Shoji Segami; Masayohi Maeshima; Giltsu Choi
Journal:  Plant Mol Biol       Date:  2018-04-03       Impact factor: 4.076

9.  PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics.

Authors:  Michiel Van Bel; Tim Diels; Emmelien Vancaester; Lukasz Kreft; Alexander Botzki; Yves Van de Peer; Frederik Coppens; Klaas Vandepoele
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

10.  Fine mapping a self-fertility locus in perennial ryegrass.

Authors:  Javier Do Canto; Bruno Studer; Ursula Frei; Thomas Lübberstedt
Journal:  Theor Appl Genet       Date:  2017-12-15       Impact factor: 5.699
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