TY - JOUR
T1 - Gramene 2018
T2 - Unifying comparative genomics and pathway resources for plant research
AU - Tello-Ruiz, Marcela K.
AU - Naithani, Sushma
AU - Stein, Joshua C.
AU - Gupta, Parul
AU - Campbell, Michael
AU - Olson, Andrew
AU - Wei, Sharon
AU - Preece, Justin
AU - Geniza, Matthew J.
AU - Jiao, Yinping
AU - Lee, Young Koung
AU - Wang, Bo
AU - Mulvaney, Joseph
AU - Chougule, Kapeel
AU - Elser, Justin
AU - Al-Bader, Noor
AU - Kumari, Sunita
AU - Thomason, James
AU - Kumar, Vivek
AU - Bolser, Daniel M.
AU - Naamati, Guy
AU - Tapanari, Electra
AU - Fonseca, Nuno
AU - Huerta, Laura
AU - Iqbal, Haider
AU - Keays, Maria
AU - Munoz-Pomer Fuentes, Alfonso
AU - Tang, Amy
AU - Fabregat, Antonio
AU - D'Eustachio, Peter
AU - Weiser, Joel
AU - Stein, Lincoln D.
AU - Petryszak, Robert
AU - Papatheodorou, Irene
AU - Kersey, Paul J.
AU - Lockhart, Patti
AU - Taylor, Crispin
AU - Jaiswal, Pankaj
AU - Ware, Doreen
N1 - Publisher Copyright:
© Published by Oxford University Press on behalf of Nucleic Acids Research 2017.
PY - 2018/1/1
Y1 - 2018/1/1
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.
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.
UR - http://www.scopus.com/inward/record.url?scp=85040926094&partnerID=8YFLogxK
U2 - 10.1093/nar/gkx1111
DO - 10.1093/nar/gkx1111
M3 - Article
C2 - 29165610
AN - SCOPUS:85040926094
SN - 0305-1048
VL - 46
SP - D1181-D1189
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -