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


ABSTRACT: 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.

SUBMITTER: Tello-Ruiz MK 

PROVIDER: S-EPMC5753211 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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

Tello-Ruiz Marcela K MK   Naithani Sushma S   Stein Joshua C JC   Gupta Parul P   Campbell Michael M   Olson Andrew A   Wei Sharon S   Preece Justin J   Geniza Matthew J MJ   Jiao Yinping Y   Lee Young Koung YK   Wang Bo B   Mulvaney Joseph J   Chougule Kapeel K   Elser Justin J   Al-Bader Noor N   Kumari Sunita S   Thomason James J   Kumar Vivek V   Bolser Daniel M DM   Naamati Guy G   Tapanari Electra E   Fonseca Nuno N   Huerta Laura L   Iqbal Haider H   Keays Maria M   Munoz-Pomer Fuentes Alfonso A   Tang Amy A   Fabregat Antonio A   D'Eustachio Peter P   Weiser Joel J   Stein Lincoln D LD   Petryszak Robert R   Papatheodorou Irene I   Kersey Paul J PJ   Lockhart Patti P   Taylor Crispin C   Jaiswal Pankaj P   Ware Doreen D  

Nucleic acids research 20180101 D1


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 path  ...[more]

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