TY - JOUR
AU - Marcela Tello-Ruiz
AU - Sushma Naithani
AU - Joshua Stein
AU - Parul Gupta
AU - Michael Campbell
AU - Andrew Olson
AU - Sharon Wei
AU - Justin Preece
AU - Matthew Geniza
AU - Yinping Jiao
AU - Young Lee
AU - Bo Wang
AU - Joseph Mulvaney
AU - Kapeel Chougule
AU - Justin Elser
AU - Noor Al-Bader
AU - Sunita Kumari
AU - James Thomason
AU - Vivek Kumar
AU - Daniel Bolser
AU - Guy Naamati
AU - Electra Tapanari
AU - Nuno Fonseca
AU - Laura Huerta
AU - Haider Iqbal
AU - Maria Keays
AU - Alfonso Fuentes
AU - Amy Tang
AU - Antonio Fabregat
AU - Peter D'Eustachio
AU - Joel Weiser
AU - Lincoln Stein
AU - Robert Petryszak
AU - Irene Papatheodorou
AU - Paul Kersey
AU - Patti Lockhart
AU - Crispin Taylor
AU - Pankaj Jaiswal
AU - Doreen Ware
AB - Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.
BT - Nucleic acids research
C1 - http://www.ncbi.nlm.nih.gov/pubmed/29165610?dopt=Abstract
DA - 2018 Jan 04
DO - 10.1093/nar/gkx1111
IS - D1
J2 - Nucleic Acids Res.
LA - eng
N2 - Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.
PY - 2018
SP - D1181
EP - D1189
T2 - Nucleic acids research
TI - Gramene 2018: unifying comparative genomics and pathway resources for plant research.
VL - 46
SN - 1362-4962
ER -