Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
Names
More detailed information about this field from each metasource.
Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
Gramene database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
gramene
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
Names
More detailed information about this field from each metasource.
Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
Gramene database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
gramene
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
Other names: Gramene, Gramene database, gramene
Names
More detailed information about this field from each metasource.
Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
Gramene database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
gramene
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.
Description
More detailed information about this field from each metasource.
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses. Both automatic and manual curation are performed to combine and interrelate information on genomic and EST sequences, genetic, physical, and sequence-based maps, proteins, molecular markers, mutant phenotypes and QTL, and publications. There are currently nine main search modules within Gramene: Genome Browser, BLAST, CMap, Marker, Protein, Ontology, Mutant, QTL, and Literature. The Genome Browser (http://www.gramene.org/japonica/mapview?chr=1) allows users to view the sequenced rice genome with sequenced features from multiple grass species aligned to it. BLAST (http://www.gramene.org/db/searches/blast) is a local alignment tool that allows users to find the best match to a sequence of interest. CMap (http://www.gramene.org/cmap/), a comparative mapping tool, allows users to view maps from different grass species and to construct comparisons between them. The Marker database (http://www.gramene.org/markers/) allows users to search for markers used for mapping in multiple grass species. The Protein database (http://www.gramene.org/protein/) allows users to find known rice proteins, learn about their functions, and find orthologs from other grasses. The Ontology database (http://www.gramene.org/plant_ontology/) allows users to search the standardized (controlled) vocabularies to find associated genes, proteins and phenotypes. The Mutant database (http://www.gramene.org/rice_mutant/) allows users to find rice genes with known phenotypes. The QTL database (http://www.gramene.org/qtl/) allows users to find quantitative trait loci for multiple grass species such as rice, maize, oat, barley, pearl and foxtail millets and wild rice. The Literature database (http://www.gramene.org/literature/) allows users to search Gramene's collection of curated citations. Future Plans:Future plans for Gramene include completing the migration to MySQL, the addition of a Diversity module, the addition of new maps and markers for millet in CMap, integration of the Plant Structure (anatomy) ontology from the Plant Ontology Consortium, the addition of phenotypes (QTL and mutants) and proteins from other grass species, updating of the existing data types, the addition of advanced search interfaces, off-site curation tools, and the furthering of outreach activities which will include the development of species specific educational pages and the organization of Research Coordination Network workshops. The Gramene project is a collaborative effort between Cold Spring Harbor Laboratory (http://www.cshl.edu/), the Department of Plant Breeding and Genetics at Cornell University (http://plbrgen.cals.cornell.edu/), and various national and international projects dedicated to cereal genomics and genetics research (see http://www.gramene.org/collaborators/). The database and the datasets are freely available for local use and installation. Quarterly releases provide researchers with current information and tools. For information about the most recent release, view the release notes at http://www.gramene.org/documentation/release_notes/ , and the database statistics at ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/statistics/. Gramene hosts the sequenced genome assembly of rice (Rice-japonica) and Arabidopsis provided by TIGR, in addition to the clone-based map of maize provided by AGI (http://www.genome.arizona.edu/fpc/maize/). Users may browse and search genes, markers, ESTs, cDNAs, clones, etc. on these genomes, as well as sequenced features from, sorghum, Triticeae (wheat, oat and barley), other grasses mapped on rice and maize genomes. See http://www.gramene.org/genome_browser/. The CMap Viewer can be used to search over 160 map sets (each with multiple maps of linkage groups or chromosomes) from 22 species, see http://www.gramene.org/cmap/. Over 4.5 million markers from more than 180 species can be searched to find a marker and get its detailed information on species, source and mapped locations, see http://www.gramene.org/markers/. The database contains over 68,000 protein entries detailing their biochemical characteristics and expression in association with the Gene (GO) and Plant (PO) Ontologies, sequence and cited literature, see http://www.gramene.org/protein/. The database contains about 1,400 genes from rice which have been characterized by phenotype. Among them, 425 genes have been fully annotated with phenotypic descriptions, associations to trait (TO), plant (PO) and gene ontologies (GO), map positions, alleles, phenotypic studies, germplasms, sequences, gene products, and related public references, see http://www.gramene.org/rice_mutant/. Over 9,800 QTL (http://www.gramene.org/qtl/) have been identified for numerous agronomic traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet and wild rice. The Ontologies link (http://www.gramene.org/plant_ontology/) can be used to find keywords for plant structure, growth stages, traits, function, process, cellular component, environment and taxonomy. The Literature link (http://www.gramene.org/literature/) allows searching for articles about genes, proteins, QTL, markers, or ontologies. Sequence similarity matches can be done using the BLAST link (http://www.gramene.org/Multi/blastview). GrameneMart (http://www.gramene.org/Multi/martview) is a search tool that allows complex searches to filter out large amounts of superfluous data.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Gramene is a platform for comparative genomic analysis of agriculturally important grasses, including maize, rice, sorghum, wheat and barley. Relationships between cereals are queried and displayed using controlled vocabularies (Gene, Plant, Trait, Environment, and Gramene Taxonomy) and web-based displays, including the Genes and Quantitative Trait Loci (QTL) modules.
metasource: re3data.orgversion: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
This database is a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. The database has an Ensembl genome browser and host a wide array of data sets including quantitative trait loci, metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
Webpage:
http://www.gramene.orgWebpage
More detailed information about this field from each metasource.
http://www.gramene.org
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
http://www.gramene.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
Licence:
Name: Gramene Copyright StatementLicence name
More detailed information about this field from each metasource.
Gramene Copyright Statement
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Public Domain
metasource: re3data.orgversion: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
http://www.gramene.org/node/225
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
Publications:
(15)
Publications
More detailed information about this field from each metasource.
Ensembl Genomes 2020-enabling non-vertebrate genomic research
PMID: 31598706
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Expression Atlas: gene and protein expression across multiple studies and organisms
PMID: 29165655
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene database in 2010: updates and extensions
PMID: 21076153
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
Gramene 2018: unifying comparative genomics and pathway resources for plant research
PMID: 29165610
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene: a growing plant comparative genomics resource
PMID: 17984077
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene 2016: comparative plant genomics and pathway resources
PMID: 26553803
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Plant Reactome: a resource for plant pathways and comparative analysis
PMID: 27799469
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
PMID: 30239679
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene Database: Navigating Plant Comparative Genomics Resources
PMID: 28713666
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
PMID: 33170273
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Plant Reactome: a knowledgebase and resource for comparative pathway analysis
PMID: 31680153
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Involving community in genes and pathway curation
PMID: 30649295
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Variant Effect Prediction Analysis Using Resources Available at Gramene Database
PMID: 27987178
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study
PMID: 27987175
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkt1110
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Ensembl Genomes 2020-enabling non-vertebrate genomic research
PMID: 31598706
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Expression Atlas: gene and protein expression across multiple studies and organisms
PMID: 29165655
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene database in 2010: updates and extensions
PMID: 21076153
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
Gramene 2018: unifying comparative genomics and pathway resources for plant research
PMID: 29165610
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene: a growing plant comparative genomics resource
PMID: 17984077
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene 2016: comparative plant genomics and pathway resources
PMID: 26553803
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Plant Reactome: a resource for plant pathways and comparative analysis
PMID: 27799469
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
PMID: 30239679
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene Database: Navigating Plant Comparative Genomics Resources
PMID: 28713666
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
PMID: 33170273
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Plant Reactome: a knowledgebase and resource for comparative pathway analysis
PMID: 31680153
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Involving community in genes and pathway curation
PMID: 30649295
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Variant Effect Prediction Analysis Using Resources Available at Gramene Database
PMID: 27987178
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study
PMID: 27987175
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkt1110
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
-
Ensembl Genomes 2020-enabling non-vertebrate genomic research
PubMed citations: 167.
167 articles citing: Ensembl Genomes 2020-enabling non-vertebrate genomic research
Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. PMID:35909764
Contrasting Water Withholding Responses of Young Maize Plants Reveal Link Between Lipid Peroxidation and Osmotic Regulation Corroborated by Genetic Analysis. PMID:35873985
Seed DNA damage responses promote germination and growth in Arabidopsis thaliana. PMID:35858436
First Plant Cell Atlas symposium report. PMID:35774620
Transcription factor retention through multiple polyploidization steps in wheat. PMID:35748743
Intron-derived small RNAs for silencing viral RNAs in mosquito cells. PMID:35737714
Functional Divergence of the bag-of-marbles Gene in the Drosophila melanogaster Species Group. PMID:35714266
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
Intron losses and gains in the nematodes. PMID:35659725
A comparative meta-proteomic pipeline for the identification of plasmodesmata proteins and regulatory conditions in diverse plant species. PMID:35655273
Cost-Effective Transcriptome-Wide Profiling of Circular RNAs by the Improved-tdMDA-NGS Method. PMID:35647023
Genome Replication Is Associated With Release of Immunogenic DNA Waste. PMID:35634291
GrainGenes: a data-rich repository for small grains genetics and genomics. PMID:35616118
TCMPG: an integrative database for traditional Chinese medicine plant genomes. PMID:35591924
The Triticum ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1. PMID:35583655
Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding. PMID:35474897
A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans. PMID:35463453
An interolog-based barley interactome as an integration framework for immune signaling. PMID:35435213
Comparative Transcriptome Analysis between Two Potato Cultivars in Tuber Induction to Reveal Associated Genes with Anthocyanin Accumulation. PMID:35409041
Molecular Characterization, Evolutionary Analysis, and Expression Profiling of BOR Genes in Important Cereals. PMID:35406892
Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines. PMID:35401589
Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response. PMID:35399062
JaponicusDB: rapid deployment of a model organism database for an emerging model species. PMID:35380656
Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62. PMID:35338132
Role of Wheat Phosphorus Starvation Tolerance 1 Genes in Phosphorus Acquisition and Root Architecture. PMID:35328041
BmPMFBP1 regulates the development of eupyrene sperm in the silkworm, Bombyx mori. PMID:35312700
The Identity of the Constriction Region of the Ribosomal Exit Tunnel Is Important to Maintain Gene Expression in Escherichia coli. PMID:35311583
Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat. PMID:35300015
Phylogenetic analysis of forkhead transcription factors in the Panarthropoda. PMID:35230523
High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat. PMID:35217965
Reactive Oxygen Species Differentially Modulate the Metabolic and Transcriptomic Response of Endothelial Cells. PMID:35204316
The MoPah1 phosphatidate phosphatase is involved in lipid metabolism, development, and pathogenesis in Magnaporthe oryzae. PMID:35191164
RicENN: Prediction of Rice Enhancers with Neural Network Based on DNA Sequences. PMID:35190950
Developmental alterations in DNA methylation during gametogenesis from primordial germ cells to sperm. PMID:35146397
Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. PMID:35100403
Florigen and its homologs of FT/CETS/PEBP/RKIP/YbhB family may be the enzymes of small molecule metabolism: review of the evidence. PMID:35086479
Rubiscosome gene expression is balanced across the hexaploid wheat genome. PMID:35083631
Genome-wide survey of the dehydrin genes in bread wheat (Triticum aestivum L.) and its relatives: identification, evolution and expression profiling under various abiotic stresses. PMID:35065618
how_are_we_stranded_here: quick determination of RNA-Seq strandedness. PMID:35065593
CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource. PMID:35037203
Scripting Analyses of Genomes in Ensembl Plants. PMID:35037199
SorghumBase: a web-based portal for sorghum genetic information and community advancement. PMID:35015132
Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study. PMID:35011598
A single nucleotide deletion in the third exon of FT-D1 increases the spikelet number and delays heading date in wheat (Triticum aestivum L.). PMID:34978137
Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses. PMID:34961135
Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences. PMID:34960726
Brassinazole Resistant 1 Activity Is Organ-Specific and Genotype-Dependent in Barley Seedlings. PMID:34948366
Geographical Origin Does Not Modulate Pathogenicity or Response to Climatic Variables of Fusarium oxysporum Associated with Vascular Wilt on Asparagus. PMID:34947038
Common Features in lncRNA Annotation and Classification: A Survey. PMID:34940758
GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells. PMID:34928370
A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride. PMID:34900134
Trend, population structure, and trait mapping from 15 years of national varietal trials of UK winter wheat. PMID:34897454
No one tool to rule them all: Prokaryotic gene prediction tool annotations are highly dependent on the organism of study. PMID:34875010
VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. PMID:34864248
Single-nucleus transcriptomes reveal evolutionary and functional properties of cell types in the Drosophila accessory gland. PMID:34849871
Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes. PMID:34830231
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. PMID:34791415
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. PMID:34751401
Temporal and spatial transcriptomic dynamics across brain development in Xenopus laevis tadpoles. PMID:34751375
MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species. PMID:34718719
Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development. PMID:34681022
Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems. PMID:34673769
Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning. PMID:34645826
The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. PMID:34634797
Evolutionary Implications of the RNA N6-Methyladenosine Methylome in Plants. PMID:34633447
A systems approach using Diversity Outbred mice distinguishes the cardiovascular effects and genetics of circulating GDF11 from those of its homolog, myostatin. PMID:34510201
Accuracy of GEBV of sires based on pooled allele frequency of their progeny. PMID:34510188
A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling. PMID:34506483
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Adverse Maternal Environment and Postweaning Western Diet Alter Hepatic CD36 Expression and Methylation Concurrently with Nonalcoholic Fatty Liver Disease in Mouse Offspring. PMID:34486661
Predicting host dependency factors of pathogens in Drosophila melanogaster using machine learning. PMID:34471501
Will Plant Genome Editing Play a Decisive Role in "Quantum-Leap" Improvements in Crop Yield to Feed an Increasing Global Human Population? PMID:34451712
Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides. PMID:34436291
Comprehensive in silico Characterization of Universal Stress Proteins in Rice (Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. PMID:34394169
'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life. PMID:34357062
mRNA Inventory of Extracellular Vesicles from Ustilago maydis. PMID:34356940
Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. PMID:34354718
Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum. PMID:34354159
Transcriptome Response to Cadmium Exposure in Barley (Hordeum vulgare L.). PMID:34335638
Web tools to perform long non-coding RNAs analysis in oncology research. PMID:34296748
Non-coding RNAs in the interaction between rice and Meloidogyne graminicola. PMID:34284724
Isolation and Characterization of Barley (Hordeum vulgare) Extracellular Vesicles to Assess Their Role in RNA Spray-Based Crop Protection. PMID:34281265
Structural and biophysical aspects of l-asparaginases: a growing family with amazing diversity. PMID:34258001
Genome-Wide Identification of Powdery Mildew Resistance in Common Bean (Phaseolus vulgaris L.). PMID:34239540
Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis). PMID:34177145
Wheat ATIs: Characteristics and Role in Human Disease. PMID:34124122
Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. PMID:34045362
Extracellular DNA of slow growers of mycobacteria and its contribution to biofilm formation and drug tolerance. PMID:34040029
Diversified amino acid-mediated allosteric regulation of phosphoglycerate dehydrogenase for serine biosynthesis in land plants. PMID:34032263
Proline codon pair selection determines ribosome pausing strength and translation efficiency in bacteria. PMID:34002016
De novo transcriptome analysis for examination of the nutrition metabolic system related to the evolutionary process through which stick insects gain the ability of flight (Phasmatodea). PMID:33985569
Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat. PMID:33968112
Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish. PMID:33958755
Annotation and Molecular Characterisation of the TaIRO3 and TaHRZ Iron Homeostasis Genes in Bread Wheat (Triticum aestivum L.). PMID:33925484
Arthropod Ectoparasites Have Potential to Bind SARS-CoV-2 via ACE. PMID:33921873
Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron. PMID:33921675
Unfolded Protein Response and Scaffold Independent Pheromone MAP Kinase Signaling Control Verticillium dahliae Growth, Development, and Plant Pathogenesis. PMID:33921172
Developmental Transcriptomics Reveals a Gene Network Driving Mimetic Color Variation in a Bumble Bee. PMID:33881508
Developmental Transcriptomics Reveals a Gene Network Driving Mimetic Color Variation in a Bumble Bee. PMID:33881508
Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias. PMID:33871580
Using precision phenotyping to inform de novo domestication. PMID:33848336
Magnesium and calcium overaccumulate in the leaves of a schengen3 mutant of Brassica rapa. PMID:33831190
MolluscDB: a genome and transcriptome database for molluscs. PMID:33813885
Genome-Wide Association of Stem Carbohydrate Accumulation and Remobilization during Grain Growth in Bread Wheat (Triticum aestivum L.) in Mediterranean Environments. PMID:33809230
Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor. PMID:33798202
Mediation of a GDSL Esterase/Lipase in Carotenoid Esterification in Tritordeum Suggests a Common Mechanism of Carotenoid Esterification in Triticeae Species. PMID:33746990
Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example. PMID:33744946
RNA-seq analysis and gene expression dynamics in the salivary glands of the argasid tick Ornithodoros erraticus along the trophogonic cycle. PMID:33743776
Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference. PMID:33726665
Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A. PMID:33712876
The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. PMID:33620121
Shared aspects of mRNA expression associated with oocyte maturation failure in humans and rhesus monkeys indicating compromised oocyte quality. PMID:33554756
Sialotranscriptomics of the argasid tick Ornithodoros moubata along the trophogonic cycle. PMID:33544727
BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence. PMID:33532841
Identification of the Genetic Basis of Response to De-Acclimation in Winter Barley. PMID:33494371
RNAi gene knockdown in the poultry red mite, Dermanyssus gallinae (De Geer 1778), a tool for functional genomics. PMID:33461614
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. PMID:33420081
Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function. PMID:33383823
UniBioDicts: Unified access to biological dictionaries. PMID:33367853
Multi-omics data integration considerations and study design for biological systems and disease. PMID:33347526
Genome-wide identification and evolution of HECT genes in wheat. PMID:33344088
CRISPR/Cas9-mediated knock-in of alligator cathelicidin gene in a non-coding region of channel catfish genome. PMID:33335280
Microbial single-cell RNA sequencing by split-pool barcoding. PMID:33335020
Helixer: Cross-species gene annotation of large eukaryotic genomes using deep learning. PMID:33325516
A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor. PMID:33274716
Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. PMID:33234025
Rfam 14: expanded coverage of metagenomic, viral and microRNA families. PMID:33211869
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. PMID:33196801
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.). PMID:33167859
Study of the TEAD-binding domain of the YAP protein from animal species. PMID:33146905
Genetic variant affecting the myosin light chain 2 related to familial hypertrophic cardiomyopathy. PMID:33139982
Ensembl 2021. PMID:33137190
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. PMID:33106848
In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues. PMID:33092180
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
Divergence and Remarkable Diversity of the Y Chromosome in Guppies. PMID:33022040
Regulatory gene function handoff allows essential gene loss in mosquitoes. PMID:32999445
A Reference Genome Sequence for Giant Sequoia. PMID:32948606
Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes. PMID:32938380
Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney. PMID:32908900
Towards an understanding of the role of intrinsic protein disorder on plant adaptation to environmental challenges. PMID:32902806
Histone chaperone FACT represses retrotransposon MERVL and MERVL-derived cryptic promoters. PMID:32894293
TB1: from domestication gene to tool for many trades. PMID:32761247
Defects in the Ferroxidase That Participates in the Reductive Iron Assimilation System Results in Hypervirulence in Botrytis Cinerea. PMID:32753496
A conserved coccidian gene is involved in Toxoplasma sensitivity to the anti-apicomplexan compound, tartrolon E. PMID:32738587
Cas13b-dependent and Cas13b-independent RNA knockdown of viral sequences in mosquito cells following guide RNA expression. PMID:32737398
A single QTL on chromosome 6DS derived from a winter wheat cultivar 'OW104' confers resistance to Wheat yellow mosaic virus. PMID:32714060
A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean. PMID:32707968
Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity. PMID:32647371
Direct evidence for a new mode of plant defense against insects via a novel polygalacturonase-inhibiting protein expression strategy. PMID:32611768
Evolutionary Aspects of TRPMLs and TPCs. PMID:32545371
Applying genomic resources to accelerate wheat biofortification. PMID:32528079
Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning. PMID:32516876
Analysis of FGF20-regulated genes in organ of Corti progenitors by translating ribosome affinity purification. PMID:32492250
Comparative (Within Species) Genomics of the Vitis vinifera L. Terpene Synthase Family to Explore the Impact of Genotypic Variation Using Phased Diploid Genomes. PMID:32431727
Intron and gene size expansion during nervous system evolution. PMID:32410625
Long-term outcomes and response to treatment in diacylglycerol kinase epsilon nephropathy. PMID:32386968
A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. PMID:32208137
Selected neuropeptide genes show genetic differentiation between Africans and non-Africans. PMID:32171244
Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections. PMID:32155892
Wheat PP2C-a10 regulates seed germination and drought tolerance in transgenic Arabidopsis. PMID:32065246
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604
PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets. PMID:31866958 -
Expression Atlas: gene and protein expression across multiple studies and organisms
PubMed citations: 167.
167 articles citing: Expression Atlas: gene and protein expression across multiple studies and organisms
Insight into the Roles of Proline-Rich Extensin-like Receptor Protein Kinases of Bread Wheat (Triticum aestivum L.). PMID:35888032
The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. PMID:35832065
Epithelial to mesenchymal transition influences fibroblast phenotype in colorectal cancer by altering miR-200 levels in extracellular vesicles. PMID:35595718
DUSP4 protects BRAF- and NRAS-mutant melanoma from oncogene overdose through modulation of MITF. PMID:35580987
Differential expression analysis of genes and long non-coding RNAs associated with KRAS mutation in colorectal cancer cells. PMID:35562390
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
Exploring synergies between plant metabolic modelling and machine learning. PMID:35521559
A Cancer Associated Fibroblasts-Related Six-Gene Panel for Anti-PD-1 Therapy in Melanoma Driven by Weighted Correlation Network Analysis and Supervised Machine Learning. PMID:35479936
Molecular Characterization, Evolutionary Analysis, and Expression Profiling of BOR Genes in Important Cereals. PMID:35406892
Investigation of Roles of TaTALE Genes during Development and Stress Response in Bread Wheat. PMID:35270056
Integration of Transcriptome and Exome Genotyping Identifies Significant Variants with Autism Spectrum Disorder. PMID:35215271
RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells. PMID:35143476
An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection. PMID:35102208
Molecular Characterization Revealed the Role of Thaumatin-Like Proteins of Bread Wheat in Stress Response. PMID:35087559
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes. PMID:35010832
TF-Marker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human. PMID:34986601
Intellectual disability genomics: current state, pitfalls and future challenges. PMID:34930158
Progesterone Receptor Membrane Component (PGRMC)1 and PGRMC2 and Their Roles in Ovarian and Endometrial Cancer. PMID:34885064
High endogenous CCL2 expression promotes the aggressive phenotype of human inflammatory breast cancer. PMID:34824220
Overexpressing IFITM family genes predict poor prognosis in kidney renal clear cell carcinoma. PMID:34804826
ProteomicsDB: toward a FAIR open-source resource for life-science research. PMID:34791421
BioSamples database: FAIRer samples metadata to accelerate research data management. PMID:34747489
ScaffComb: A Phenotype-Based Framework for Drug Combination Virtual Screening in Large-Scale Chemical Datasets. PMID:34723439
New Prognostic Biomarkers and Drug Targets for Skin Cutaneous Melanoma via Comprehensive Bioinformatic Analysis and Validation. PMID:34722301
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans. PMID:34680971
No Expression Divergence despite Transcriptional Interference between Nested Protein-Coding Genes in Mammals. PMID:34573363
Influence of the rs6736 Polymorphism on Ischemic Stroke Susceptibility in Han Chinese Individuals via the Disruption of miR-7-1 Binding to the C14orf119 Gene. PMID:34510374
The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases. PMID:34465729
Comprehensive Omics Analysis of a Novel Small-Molecule Inhibitor of Chemoresistant Oncogenic Signatures in Colorectal Cancer Cell with Antitumor Effects. PMID:34440739
Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. PMID:34354718
CDH12 as a Candidate Gene for Kidney Injury in Posterior Urethral Valve Cases: A Genome-wide Association Study Among Patients with Obstructive Uropathies. PMID:34337522
A Personalized Therapeutics Approach Using an In Silico Drosophila Patient Model Reveals Optimal Chemo- and Targeted Therapy Combinations for Colorectal Cancer. PMID:34336681
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. PMID:34288907
Big Data in Nephrology. PMID:34194006
The Role of GIP Receptor in the CNS for the Pathogenesis of Obesity. PMID:34176784
Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions. PMID:34076249
Cancer-Associated circRNA-miRNA-mRNA Regulatory Networks: A Meta-Analysis. PMID:34055888
Exploration of glutathione reductase for abiotic stress response in bread wheat (Triticum aestivum L.). PMID:34032897
ZebraShare: a new venue for rapid dissemination of zebrafish mutant data. PMID:33954026
Genome-wide characterization and expression and co-expression analysis suggested diverse functions of WOX genes in bread wheat. PMID:33937537
Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Data Mining Approach. PMID:33924631
An integrated landscape of protein expression in human cancer. PMID:33893311
Lysosomal Calcium Channels in Autophagy and Cancer. PMID:33803964
Selective Inhibition of 2-Oxoglutarate and 2-Oxoadipate Dehydrogenases by the Phosphonate Analogs of Their 2-Oxo Acid Substrates. PMID:33511099
AIM2 in regulatory T cells restrains autoimmune diseases. PMID:33505023
Expression and prognostic analyses of SCAMPs in pancreatic adenocarcinoma. PMID:33493138
Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. PMID:33491336
Detection of aberrant gene expression events in RNA sequencing data. PMID:33462443
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Endolysosomal TRPMLs in Cancer. PMID:33419007
Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function. PMID:33383823
Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods. PMID:33354424
Increased NFATC4 Correlates With Poor Prognosis of AML Through Recruiting Regulatory T Cells. PMID:33329712
Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale. PMID:33302607
Prospects for Using Expression Patterns of Paramyxovirus Receptors as Biomarkers for Oncolytic Virotherapy. PMID:33291506
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PMID:33206638
An Integrating Immune-Related Signature to Improve Prognosis of Hepatocellular Carcinoma. PMID:33204302
Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites. PMID:33188057
The mouse Gene Expression Database (GXD): 2021 update. PMID:33104772
Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin. PMID:33075080
[Application of RNA sequencing in clinical diagnosis of Mendelian disease]. PMID:33059815
LncExpDB: an expression database of human long non-coding RNAs. PMID:33045751
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
Evaluation of the potential role of long non-coding RNA LINC00961 in luminal breast cancer: a case-control and systems biology study. PMID:33024416
Genome-wide characterization and expression analysis suggested diverse functions of the mechanosensitive channel of small conductance-like (MSL) genes in cereal crops. PMID:33024170
Structural and functional modelling of SARS-CoV-2 entry in animal models. PMID:32985513
Protein-Coding Genes in Euarchontoglires with Pseudogene Homologs in Humans. PMID:32927891
The HMGB1-2 Ovarian Cancer Interactome. The Role of HMGB Proteins and Their Interacting Partners MIEN1 and NOP53 in Ovary Cancer and Drug-Response. PMID:32867128
Novel tumour suppressor roles for GZMA and RASGRP1 in Theileria annulata-transformed macrophages and human B lymphoma cells. PMID:32830401
Collagen Type III Alpha 1 chain regulated by GATA-Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade glioma. PMID:32757451
Mutations in MYLPF Cause a Novel Segmental Amyoplasia that Manifests as Distal Arthrogryposis. PMID:32707087
KF-1607, a Novel Pan Src Kinase Inhibitor, Attenuates Obstruction-Induced Tubulointerstitial Fibrosis in Mice. PMID:32690822
Tumors induce de novo steroid biosynthesis in T cells to evade immunity. PMID:32680985
Structural insights into the activity and regulation of human Josephin-2. PMID:32647816
Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies. PMID:32630753
How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets. PMID:32508872
Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis. PMID:32457808
In silico identification of MAPK14-related lncRNAs and assessment of their expression in breast cancer samples. PMID:32433496
The Birth of Bio-data Science: Trends, Expectations, and Applications. PMID:32428604
Intron and gene size expansion during nervous system evolution. PMID:32410625
Tryptophan catabolism reflects disease activity in human tuberculosis. PMID:32369456
Bioinformatic analysis and identification of single-stranded RNA sequences recognized by TLR7/8 in the SARS-CoV-2, SARS-CoV, and MERS-CoV genomes. PMID:32361001
Testis-specific serine kinase protein family in male fertility and as targets for non-hormonal male contraception†. PMID:32337545
Identification of Potential Biomarkers for Anti-PD-1 Therapy in Melanoma by Weighted Correlation Network Analysis. PMID:32316408
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Genome-wide analysis of glycerol-3-phosphate O-acyltransferase gene family and functional characterization of two cutin group GPATs in Brassica napus. PMID:32246349
A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. PMID:32191846
Drosophila SLC22 Orthologs Related to OATs, OCTs, and OCTNs Regulate Development and Responsiveness to Oxidative Stress. PMID:32183456
UBB pseudogene 4 encodes functional ubiquitin variants. PMID:32161257
Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs. PMID:32150922
BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L. PMID:32133024
A Direct Comparison of Thyroid Hormone Receptor Protein Levels in Mice Provides Unexpected Insights into Thyroid Hormone Action. PMID:32122258
epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis. PMID:32117461
Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas. PMID:32117413
Variability in estimated gene expression among commonly used RNA-seq pipelines. PMID:32066774
Loss of phosphatase activity in PTEN (phosphatase and tensin homolog deleted on chromosome ten) results in endometrial carcinoma in humans: An in-silico study. PMID:32042934
Pan-cancer analysis of whole genomes. PMID:32025007
Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. PMID:32024885
miR-TV: an interactive microRNA Target Viewer for microRNA and target gene expression interrogation for human cancer studies. PMID:31950188
Sex Determination Using RNA-Sequencing Analyses in Early Prenatal Pig Development. PMID:31817322
BEST: a web server for brain expression Spatio-temporal pattern analysis. PMID:31805847
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. PMID:31799603
Multivariable regulation of gene expression plasticity in metazoans. PMID:31795914
The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data. PMID:31784565
miR-590-3p and Its Downstream Target Genes in HCC Cell Lines. PMID:31781476
An omics perspective on drug target discovery platforms. PMID:31774113
The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases. PMID:31744855
Screening for mouse genes lost in mammals with long lifespans. PMID:31728160
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. PMID:31686107
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
Expression Atlas update: from tissues to single cells. PMID:31665515
Differential Treatments Based on Drug-induced Gene Expression Signatures and Longitudinal Systemic Lupus Erythematosus Stratification. PMID:31664045
How is the acyl chain composition of phosphoinositides created and does it matter? PMID:31657437
Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development. PMID:31608120
Ensembl Genomes 2020-enabling non-vertebrate genomic research. PMID:31598706
QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes. PMID:31598699
Estrogen-related receptor β activation and isoform shifting by cdc2-like kinase inhibition restricts migration and intracranial tumor growth in glioblastoma. PMID:31570001
Paralog dependency indirectly affects the robustness of human cells. PMID:31556487
miRDB: an online database for prediction of functional microRNA targets. PMID:31504780
Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. PMID:31481099
Stimulated upregulation of HO-1 is associated with inadequate response of gastric and ovarian cancer cell lines to hyperthermia and cisplatin treatment. PMID:31423266
Transcriptional Profiling of Stem Cells: Moving from Descriptive to Predictive Paradigms. PMID:31412285
Human APOBEC3G Prevents Emergence of Infectious Endogenous Retrovirus in Mice. PMID:31341050
Functional DNA variations associated with Saudi female with low VO2max: a pilot microarray study. PMID:31312377
NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets. PMID:31307154
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
Tau tubulin kinase is required for spermatogenesis and development of motile cilia in planarian flatworms. PMID:31141462
Exome-wide search and functional annotation of genes associated in patients with severe tick-borne encephalitis in a Russian population. PMID:31122248
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. PMID:31110304
A novel conserved family of Macro-like domains-putative new players in ADP-ribosylation signaling. PMID:31106069
Computational analysis of data from a genome-wide screening identifies new PARP1 functional interactors as potential therapeutic targets. PMID:31105872
Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues. PMID:31095599
HumCFS: a database of fragile sites in human chromosomes. PMID:30999860
GPR34 in spinal microglia exacerbates neuropathic pain in mice. PMID:30975169
Sclerostin inhibition alleviates breast cancer-induced bone metastases and muscle weakness. PMID:30965315
Digital expression explorer 2: a repository of uniformly processed RNA sequencing data. PMID:30942868
A novel assay for detection and quantification of C-mannosyl tryptophan in normal or diabetic mice. PMID:30886328
The long non-coding RNA LINC00460 predicts the prognosis and promotes the proliferation and migration of cells in bladder urothelial carcinoma. PMID:30881506
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Recent advances in gene function prediction using context-specific coexpression networks in plants. PMID:30800290
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_. PMID:30691411
Genome-Wide Characterization and Identification of Trihelix Transcription Factor and Expression Profiling in Response to Abiotic Stresses in Rice (Oryza sativa L.). PMID:30634597
Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome. PMID:30611210
Calmodulinopathy: A Novel, Life-Threatening Clinical Entity Affecting the Young. PMID:30574507
Diagnosing rare diseases after the exome. PMID:30559314
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. PMID:30481257
Open Targets Platform: new developments and updates two years on. PMID:30462303
Stemformatics: visualize and download curated stem cell data. PMID:30407577
Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication. PMID:30398650
The protein interaction networks of mucolipins and two-pore channels. PMID:30395881
The PRIDE database and related tools and resources in 2019: improving support for quantification data. PMID:30395289
SAGD: a comprehensive sex-associated gene database from transcriptomes. PMID:30380119
A call for public archives for biological image data. PMID:30377375
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
ArrayExpress update - from bulk to single-cell expression data. PMID:30357387
PopHumanScan: the online catalog of human genome adaptation. PMID:30335169
POSTAR2: deciphering the post-transcriptional regulatory logics. PMID:30239819
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes. PMID:30205473
Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. PMID:30127393
A tissue-based draft map of the murine MHC class I immunopeptidome. PMID:30084848
Community-driven roadmap for integrated disease maps. PMID:29688273
A family of long intergenic non-coding RNA genes in human chromosomal region 22q11.2 carry a DNA translocation breakpoint/AT-rich sequence. PMID:29668722
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510 -
Gramene database in 2010: updates and extensions
PubMed citations: 91.
91 articles citing: Gramene database in 2010: updates and extensions
Rice functional genomics: decades' efforts and roads ahead. PMID:34881420
Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44. PMID:34073512
Using precision phenotyping to inform de novo domestication. PMID:33848336
Identification of superior parental lines for biparental crossing via genomic prediction. PMID:33270706
Comparative study on cytogenetics and transcriptome between diploid and autotetraploid rice hybrids harboring double neutral genes. PMID:32986735
Production Assessment and Genome Comparison Revealed High Yield Potential and Novel Specific Alleles Associated with Fertility and Yield in Neo-Tetraploid Rice. PMID:32494867
Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles. PMID:32085735
Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots. PMID:32024696
Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor). PMID:32005168
Quantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains. PMID:31396264
Carbohydrate metabolism and fertility related genes high expression levels promote heterosis in autotetraploid rice harboring double neutral genes. PMID:31076936
A Portion of the Apomixis Locus of Paspalum Simplex is Microsyntenic with an Unstable Chromosome Segment Highly Conserved Among Poaceae. PMID:30824748
Pathways and Network Based Analysis of Candidate Genes to Reveal Cross-Talk and Specificity in the Sorghum (Sorghum bicolor (L.) Moench) Responses to Drought and It's Co-occurring Stresses. PMID:30515190
Discovery of Anthocyanin Acyltransferase1 (AAT1) in Maize Using Genotyping-by-Sequencing (GBS). PMID:30257861
High Performance of Photosynthesis and Osmotic Adjustment Are Associated With Salt Tolerance Ability in Rice Carrying Drought Tolerance QTL: Physiological and Co-expression Network Analysis. PMID:30127798
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
Gramene 2018: unifying comparative genomics and pathway resources for plant research. PMID:29165610
Similarities between plant traits based on their connection to underlying gene functions. PMID:28797052
Gramene Database: Navigating Plant Comparative Genomics Resources. PMID:28713666
Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice. PMID:28611791
Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach. PMID:28181537
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
Genetic control of flowering time in rice: integration of Mendelian genetics and genomics. PMID:27695876
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
OGRO: The Overview of functionally characterized Genes in Rice online database. PMID:27234245
Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication. PMID:27118394
LEAFDATA: a literature-curated database for Arabidopsis leaf development. PMID:26884807
Gramene 2016: comparative plant genomics and pathway resources. PMID:26553803
Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica. PMID:26443104
Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross. PMID:26366113
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
Genetic architecture of variation in heading date among Asian rice accessions. PMID:25953146
Genome-wide association of carbon and nitrogen metabolism in the maize nested association mapping population. PMID:25918116
Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement. PMID:25874133
Genetic basis and detection of unintended effects in genetically modified crop plants. PMID:25716164
plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. PMID:25566282
Finding our way through phenotypes. PMID:25562316
Low genetic diversity and high differentiation among relict populations of the neotropical gymnosperm Podocarpus sellowii (Klotz.) in the Atlantic Forest. PMID:25532751
Metabolic trade-offs between biomass synthesis and photosynthate export at different light intensities in a genome-scale metabolic model of rice. PMID:25506349
Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. PMID:25492368
Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes. PMID:25393533
Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. PMID:25384563
Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. PMID:25129133
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. PMID:24927599
The genome of Eucalyptus grandis. PMID:24919147
From plant genomes to protein families: computational tools. PMID:24688740
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
Comparative transcriptional profiling of three super-hybrid rice combinations. PMID:24595241
QTL map meets population genomics: an application to rice. PMID:24376738
Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. PMID:24363285
A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. PMID:24280345
WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. PMID:24280312
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
Gramene 2013: comparative plant genomics resources. PMID:24217918
Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture. PMID:24170127
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. PMID:24147765
Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PMID:24040164
GnpIS: an information system to integrate genetic and genomic data from plants and fungi. PMID:23959375
Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. PMID:23860794
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
Responses to light intensity in a genome-scale model of rice metabolism. PMID:23640755
Subcellular compartmentation of sugar signaling: links among carbon cellular status, route of sucrolysis, sink-source allocation, and metabolic partitioning. PMID:23346090
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PMID:23299411
PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. PMID:23292601
UniProtKB amid the turmoil of plant proteomics research. PMID:23230445
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
TropGeneDB, the multi-tropical crop information system updated and extended. PMID:23161680
PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PMID:23144785
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. PMID:23110892
CerealsDB 2.0: an integrated resource for plant breeders and scientists. PMID:22943283
Molecular characterization and comparative sequence analysis of defense-related gene, Oryza rufipogon receptor-like protein kinase 1. PMID:22942769
Determinants of exon-level evolutionary rates in Arabidopsis species. PMID:22844194
Mining plant genome browsers as a means for efficient connection of physical, genetic and cytogenetic mapping: An example using soybean. PMID:22802719
Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. PMID:22793791
Taking the next step: building an Arabidopsis information portal. PMID:22751211
A beginner's guide to eukaryotic genome annotation. PMID:22510764
GrameneMart: the BioMart data portal for the Gramene project. PMID:22374386
Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits. PMID:22319070
POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data. PMID:22253616
Computational identification of protein-protein interactions in rice based on the predicted rice interactome network. PMID:22196356
Advances in omics and bioinformatics tools for systems analyses of plant functions. PMID:22156726
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. PMID:22120662
PLEXdb: gene expression resources for plants and plant pathogens. PMID:22084198
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. PMID:22067447
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. PMID:22008187
QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. PMID:21965557
Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. PMID:21915109
The integrated web service and genome database for agricultural plants with biotechnology information. PMID:21887015
PRIN: a predicted rice interactome network. PMID:21575196 -
Gramene 2018: unifying comparative genomics and pathway resources for plant research
PubMed citations: 71.
71 articles citing: Gramene 2018: unifying comparative genomics and pathway resources for plant research
Predicting Tissue-Specific mRNA and Protein Abundance in Maize: A Machine Learning Approach. PMID:35719692
Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants. PMID:35426911
PlantGF: an analysis and annotation platform for plant gene families. PMID:35134149
Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. PMID:35113396
CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource. PMID:35037203
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. PMID:35037202
Scripting Analyses of Genomes in Ensembl Plants. PMID:35037199
A cascade of bHLH-regulated pathways programs maize anther development. PMID:35018475
CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. PMID:34782688
Evaluation of gene flow and genetic diversity in rice accessions across Kurdistan region-iraq using SSR markers. PMID:34746989
Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy. PMID:34644381
LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes. PMID:34643715
Fine Mapping of a New Major QTL-qGLS8 for Gray Leaf Spot Resistance in Maize. PMID:34603363
QTL mapping for bioenergy traits in sweet sorghum recombinant inbred lines. PMID:34519766
Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation. PMID:34416918
Gene Ontology Meta Annotator for Plants (GOMAP). PMID:34034755
Underpinning the molecular programming attributing heat stress associated thermotolerance in tea (Camellia sinensis (L.) O. Kuntze). PMID:33931616
FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. PMID:33879057
Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts. PMID:33863807
Using precision phenotyping to inform de novo domestication. PMID:33848336
Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily. PMID:33777532
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB. PMID:33602974
Characterization of CHARK, an unusual cytokinin receptor of rice. PMID:33462253
Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. PMID:33384856
Comparative Transcriptome Analysis of Iron and Zinc Deficiency in Maize (Zea mays L.). PMID:33371388
Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. PMID:33266228
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
TaDrAp1 and TaDrAp2, Partner Genes of a Transcription Repressor, Coordinate Plant Development and Drought Tolerance in Spelt and Bread Wheat. PMID:33167455
PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome. PMID:32895427
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development. PMID:32646368
Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae). PMID:32625218
Barley's Second Spring as A Model Organism for Chloroplast Research. PMID:32604986
Resistance and susceptibility QTL identified in a rice MAGIC population by screening with a minor-effect virulence factor from Xanthomonas oryzae pv. oryzae. PMID:32594636
MaizeCUBIC: a comprehensive variation database for a maize synthetic population. PMID:32548639
Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize. PMID:32518237
Using multiple reference genomes to identify and resolve annotation inconsistencies. PMID:32264824
TeaMiD: a comprehensive database of simple sequence repeat markers of tea. PMID:32159215
Variant phasing and haplotypic expression from long-read sequencing in maize. PMID:32071408
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits. PMID:31744902
A Bioinformatics Guide to Plant Microbiome Analysis. PMID:31708944
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
Expression Atlas update: from tissues to single cells. PMID:31665515
Double triage to identify poorly annotated genes in maize: The missing link in community curation. PMID:31658277
A Sequence-Indexed Mutator Insertional Library for Maize Functional Genomics Study. PMID:31636104
MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. PMID:31624841
The explant developmental stage profoundly impacts small RNA-mediated regulation at the dedifferentiation step of maize somatic embryogenesis. PMID:31601893
Ensembl Genomes 2020-enabling non-vertebrate genomic research. PMID:31598706
Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module. PMID:31597271
RiceRelativesGD: a genomic database of rice relatives for rice research. PMID:31560050
Is reliance on an inaccurate genome sequence sabotaging your experiments? PMID:31513692
Ionic selectivity and coordinated transport of Na+ and K+ in flag leaves render differential salt tolerance in rice at the reproductive stage. PMID:31399792
Transcription factors involved in abiotic stress responses in Maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era. PMID:31328030
Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum. PMID:31195966
Modern technologies and algorithms for scaffolding assembled genomes. PMID:31166948
Analysis of the autophagy gene expression profile of pancreatic cancer based on autophagy-related protein microtubule-associated protein 1A/1B-light chain 3. PMID:31114135
Rice Galaxy: an open resource for plant science. PMID:31107941
Technological advances in maize breeding: past, present and future. PMID:30798332
Rice Genomics: over the Past Two Decades and into the Future. PMID:30771506
Lectin Sequence Distribution in QTLs from Rice (Oryza sativa) Suggest A Role in Morphological Traits and Stress Responses. PMID:30669545
Involving community in genes and pathway curation. PMID:30649295
Ensembl variation resources. PMID:30576484
The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA Methylation Changes at a Linked Transposon. PMID:30563848
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. PMID:30353370
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize. PMID:30194092
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:29316735 -
Gramene: a growing plant comparative genomics resource
PubMed citations: 70.
70 articles citing: Gramene: a growing plant comparative genomics resource
Serial-Omics and Molecular Function Study Provide Novel Insight into Cucumber Variety Improvement. PMID:35736760
Genome-wide identification of superoxide dismutase gene families and their expression patterns under low-temperature, salt and osmotic stresses in watermelon and melon. PMID:33927985
A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae. PMID:29873704
Genome sequence of the progenitor of wheat A subgenome Triticum urartu. PMID:29743678
Identification of MicroRNA Targets of Capsicum spp. Using MiRTrans-a Trans-Omics Approach. PMID:28443105
Determining Phenological Patterns Associated with the Onset of Senescence in a Wheat MAGIC Mapping Population. PMID:27822218
MGFD: the maize gene families database. PMID:26896848
Genome-Wide Identification and Analysis of the VQ Motif-Containing Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis). PMID:26633387
Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. PMID:26628745
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid. PMID:25116687
Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. PMID:24249833
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. PMID:24225315
Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. PMID:23958387
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. PMID:23879659
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993
The potential of C4 grasses for cellulosic biofuel production. PMID:23653628
PlantGSEA: a gene set enrichment analysis toolkit for plant community. PMID:23632162
Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases. PMID:23586394
Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. PMID:23377560
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. PMID:22992304
AlliumMap-A comparative genomics resource for cultivated Allium vegetables. PMID:22559261
Current challenges in de novo plant genome sequencing and assembly. PMID:22546054
The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species. PMID:22250003
Phytozome: a comparative platform for green plant genomics. PMID:22110026
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. PMID:22102576
Alteration of gene expression profile in maize infected with a double-stranded RNA fijivirus associated with symptom development. PMID:21955602
A survey of metabolic databases emphasizing the MetaCyc family. PMID:21523460
Rice-Map: a new-generation rice genome browser. PMID:21450055
Exploration of plant genomes in the FLAGdb++ environment. PMID:21447150
SyMAP v3.4: a turnkey synteny system with application to plant genomes. PMID:21398631
Rice TOGO Browser: A platform to retrieve integrated information on rice functional and applied genomics. PMID:21216747
OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. PMID:21186175
Gramene database in 2010: updates and extensions. PMID:21076153
miSolRNA: A tomato micro RNA relational database. PMID:21059227
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. PMID:20964836
Flapjack--graphical genotype visualization. PMID:20956241
Sustainable digital infrastructure. Although databases and other online resources have become a central tool for biological research, their long-term support and maintenance is far from secure. PMID:20847740
Digital gene expression signatures for maize development. PMID:20833728
Choosing a genome browser for a Model Organism Database: surveying the maize community. PMID:20627860
Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration. PMID:20525377
SOBA: sequence ontology bioinformatics analysis. PMID:20494974
A database and API for variation, dense genotyping and resequencing data. PMID:20459810
A genetic model for the female sterility barrier between Asian and African cultivated rice species. PMID:20457876
The case for cloud computing in genome informatics. PMID:20441614
agriGO: a GO analysis toolkit for the agricultural community. PMID:20435677
Genomics and bioinformatics resources for crop improvement. PMID:20208064
Gramene QTL database: development, content and applications. PMID:20157478
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. PMID:20040540
Genetic control of photoperiod sensitivity in maize revealed by joint multiple population analysis. PMID:20008571
Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. PMID:19936069
NBRP databases: databases of biological resources in Japan. PMID:19934255
Toward a quantitative theory of intrinsically disordered proteins and their function. PMID:19903882
Ensembl Genomes: extending Ensembl across the taxonomic space. PMID:19884133
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. PMID:19850718
CMap 1.01: a comparative mapping application for the Internet. PMID:19648141
The ankyrin repeat gene family in rice: genome-wide identification, classification and expression profiling. PMID:19609685
Evidence-based gene predictions in plant genomes. PMID:19541913
Semantic Web-based integration of cancer pathways and allele frequency data. PMID:19458791
TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. PMID:19448038
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
Genomic and genetic database resources for the grasses. PMID:19126704
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. PMID:19084081
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes. PMID:19043069
RICD: a rice indica cDNA database resource for rice functional genomics. PMID:19036133
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. PMID:18820292
TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae. PMID:18590523
A community-based annotation framework for linking solanaceae genomes with phenomes. PMID:18539779
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. PMID:18467421 -
Gramene 2016: comparative plant genomics and pathway resources
PubMed citations: 57.
57 articles citing: Gramene 2016: comparative plant genomics and pathway resources
Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice. PMID:35154193
Reference Gene Selection for RT-qPCR Analysis in Maize Kernels Inoculated with Aspergillus flavus. PMID:34071223
Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. PMID:33623026
Engineering 6-phosphogluconate dehydrogenase improves grain yield in heat-stressed maize. PMID:33323483
Transit Peptides From Photosynthesis-Related Proteins Mediate Import of a Marker Protein Into Different Plastid Types and Within Different Species. PMID:33101328
Current status of genomic resources on wild relatives of rice. PMID:32523396
Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). PMID:31245718
Variations in the Structure and Evolution of Rice WRKY Genes in Indica and Japonica Genotypes and their Co-expression Network in Mediating Disease Resistance. PMID:31236008
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
The potentiality of rice microsatellite markers in assessment of cross-species transferability and genetic diversity of rice and its wild relatives. PMID:31114741
The Road to Resistance in Forest Trees. PMID:31001287
Involving community in genes and pathway curation. PMID:30649295
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. PMID:30497367
SSRome: an integrated database and pipelines for exploring microsatellites in all organisms. PMID:30365025
Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus). PMID:30285631
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution. PMID:30239708
Plant data visualisation using network graphs. PMID:30186704
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. PMID:30115101
Interpretation of differential gene expression results of RNA-seq data: review and integration. PMID:30099484
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
Molecular Profiling of Pierce's Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection. PMID:29937771
Transcriptome profiling of short-term response to chilling stress in tolerant and sensitive Oryza sativa ssp. Japonica seedlings. PMID:29876699
Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics. PMID:29799487
A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. PMID:29712755
The Sequenced Angiosperm Genomes and Genome Databases. PMID:29706973
Functionally redundant LNG3 and LNG4 genes regulate turgor-driven polar cell elongation through activation of XTH17 and XTH24. PMID:29616436
Efficient Identification of Causal Mutations through Sequencing of Bulked F 2 from Two Allelic Bloomless Mutants of Sorghum bicolor. PMID:29379518
Expression Atlas: gene and protein expression across multiple studies and organisms. PMID:29165655
Gramene 2018: unifying comparative genomics and pathway resources for plant research. PMID:29165610
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. PMID:29092050
Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. PMID:28900432
The gymnastics of epigenomics in rice. PMID:28866772
Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. PMID:28821707
The cereal pathogen Fusarium pseudograminearum produces a new class of active cytokinins during infection. PMID:28802024
Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. PMID:28732548
Gramene Database: Navigating Plant Comparative Genomics Resources. PMID:28713666
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species. PMID:28605774
Genome Wide Identification of Orthologous ZIP Genes Associated with Zinc and Iron Translocation in Setaria italica. PMID:28555148
Global Transcriptome Analysis of Combined Abiotic Stress Signaling Genes Unravels Key Players in Oryza sativa L.: An In silico Approach. PMID:28555143
Evolutionary forces affecting synonymous variations in plant genomes. PMID:28531201
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. PMID:28520864
Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace. PMID:28507554
The PhytoClust tool for metabolic gene clusters discovery in plant genomes. PMID:28486689
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. PMID:28472432
Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat. PMID:28302069
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. PMID:28043950
PlaMoM: a comprehensive database compiles plant mobile macromolecules. PMID:27924044
Towards an open grapevine information system. PMID:27917288
Rice SNP-seek database update: new SNPs, indels, and queries. PMID:27899667
Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor. PMID:27826302
PMDBase: a database for studying microsatellite DNA and marker development in plants. PMID:27733507
Gene Overexpression Resources in Cereals for Functional Genomics and Discovery of Useful Genes. PMID:27708649
Dynein axonemal heavy chain 8 promotes androgen receptor activity and associates with prostate cancer progression. PMID:27363033
FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca. PMID:26973684 -
Plant Reactome: a resource for plant pathways and comparative analysis
PubMed citations: 27.
27 articles citing: Plant Reactome: a resource for plant pathways and comparative analysis
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes. PMID:34716373
Analysis of the chromosomal clustering of Fusarium-responsive wheat genes uncovers new players in the defence against head blight disease. PMID:33811222
Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. PMID:33384856
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
Proteomics in Non-model Organisms: A New Analytical Frontier. PMID:32786681
Phaeophyceaean (Brown Algal) Extracts Activate Plant Defense Systems in Arabidopsis thaliana Challenged With Phytophthora cinnamomi. PMID:32765538
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L. PMID:32133024
Analysis of the Barley Malt Rootlet Proteome. PMID:31887991
A Bioinformatics Guide to Plant Microbiome Analysis. PMID:31708944
Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties. PMID:31687375
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
Ensembl Genomes 2020-enabling non-vertebrate genomic research. PMID:31598706
Improved gene co-expression network quality through expression dataset down-sampling and network aggregation. PMID:31594989
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Recent advances in gene function prediction using context-specific coexpression networks in plants. PMID:30800290
Involving community in genes and pathway curation. PMID:30649295
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
From Plant Compounds to Botanicals and Back: A Current Snapshot. PMID:30042375
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
Expression Atlas: gene and protein expression across multiple studies and organisms. PMID:29165655
Gramene 2018: unifying comparative genomics and pathway resources for plant research. PMID:29165610
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. PMID:29092050
Gramene Database: Navigating Plant Comparative Genomics Resources. PMID:28713666 -
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
PubMed citations: 23.
23 articles citing: AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
Plant Genotype to Phenotype Prediction Using Machine Learning. PMID:35664329
GrainGenes: a data-rich repository for small grains genetics and genomics. PMID:35616118
The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities. PMID:34980221
CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PMID:34961276
Integrating Genomic and Phenomic Approaches to Support Plant Genetic Resources Conservation and Use. PMID:34834625
Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database. PMID:34354820
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. PMID:34251419
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies. PMID:33991093
Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS). PMID:33763204
Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS. PMID:33313522
Machine learning in agriculture: from silos to marketplaces. PMID:33289294
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
WTO, an ontology for wheat traits and phenotypes in scientific publications. PMID:32634868
Pulse Crop Genetics for a Sustainable Future: Where We Are Now and Where We Should Be Heading. PMID:32431724
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. PMID:31624841
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. PMID:31328773
GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. PMID:31210272
Involving community in genes and pathway curation. PMID:30649295
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
MaizeGDB 2018: the maize multi-genome genetics and genomics database. PMID:30407532
15 years of GDR: New data and functionality in the Genome Database for Rosaceae. PMID:30357347 -
Gramene Database: Navigating Plant Comparative Genomics Resources
PubMed citations: 22.
22 articles citing: Gramene Database: Navigating Plant Comparative Genomics Resources
LSAP: A Machine Learning Method for Leaf-Senescence-Associated Genes Prediction. PMID:35888183
Exploring synergies between plant metabolic modelling and machine learning. PMID:35521559
Omics: a tool for resilient rice genetic improvement strategies. PMID:35298758
Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. PMID:35113396
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource. PMID:35037203
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). PMID:34911434
PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes. PMID:34716373
Super determinant1A, a RAWULdomain-containing protein, modulates axillary meristem formation and compound leaf development in tomato. PMID:34009392
GreenPhylDB v5: a comparative pangenomic database for plant genomes. PMID:33237299
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
Current status of genomic resources on wild relatives of rice. PMID:32523396
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L. PMID:32133024
Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. PMID:32086366
Prospects of genomic resources available at the global databases for the flora of United Arab Emirates. PMID:31475085
OryzaGP: rice gene and protein dataset for named-entity recognition. PMID:31307132
Conserved and differential transcriptional responses of peroxisome associated pathways to drought, dehydration and ABA. PMID:30032264
Functionally redundant LNG3 and LNG4 genes regulate turgor-driven polar cell elongation through activation of XTH17 and XTH24. PMID:29616436
Fine mapping a self-fertility locus in perennial ryegrass. PMID:29247258
Gramene 2018: unifying comparative genomics and pathway resources for plant research. PMID:29165610
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. PMID:29069403 -
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
PubMed citations: 22.
22 articles citing: Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
First Plant Cell Atlas symposium report. PMID:35774620
GrainGenes: a data-rich repository for small grains genetics and genomics. PMID:35616118
Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis. PMID:35440059
Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants. PMID:35426911
Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62. PMID:35338132
The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement. PMID:35111182
Green plant genomes: What we know in an era of rapidly expanding opportunities. PMID:35042803
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
SorghumBase: a web-based portal for sorghum genetic information and community advancement. PMID:35015132
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. PMID:34791415
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
Leveraging histone modifications to improve genome annotations. PMID:34568920
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Will Plant Genome Editing Play a Decisive Role in "Quantum-Leap" Improvements in Crop Yield to Feed an Increasing Global Human Population? PMID:34451712
Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome. PMID:34440376
Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. PMID:34354718
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. PMID:34353948
SorGSD: updating and expanding the sorghum genome science database with new contents and tools. PMID:34344425
Ranked Choice Voting for Representative Transcripts with TRaCE. PMID:34297055
Gene Ontology Meta Annotator for Plants (GOMAP). PMID:34034755
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:33396976 -
Plant Reactome: a knowledgebase and resource for comparative pathway analysis
PubMed citations: 20.
20 articles citing: Plant Reactome: a knowledgebase and resource for comparative pathway analysis
Rice transcriptome upon infection with Xanthomonas oryzae pv. oryzae relative to its avirulent T3SS-defective strain exposed modulation of many stress responsive genes. PMID:35607392
Exploring synergies between plant metabolic modelling and machine learning. PMID:35521559
Transcriptome Analyses of Near Isogenic Lines Reveal Putative Drought Tolerance Controlling Genes in Wheat. PMID:35422827
GXP: Analyze and Plot Plant Omics Data in Web Browsers. PMID:35336631
Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. PMID:35288949
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data. PMID:35227770
Student biocuration projects as a learning environment. PMID:35211294
Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice. PMID:35163531
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. PMID:35037202
Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources. PMID:35037201
Scripting Analyses of Genomes in Ensembl Plants. PMID:35037199
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals. PMID:33868343
Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily. PMID:33777532
Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. PMID:33384856
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
PubChem in 2021: new data content and improved web interfaces. PMID:33151290
Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture. PMID:32796695 -
Involving community in genes and pathway curation
PubMed citations: 6.
6 articles citing: Involving community in genes and pathway curation
Student biocuration projects as a learning environment. PMID:35211294
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily. PMID:33777532
Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. PMID:33384856
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153 -
Variant Effect Prediction Analysis Using Resources Available at Gramene Database
PubMed citations: 2.
2 articles citing: Variant Effect Prediction Analysis Using Resources Available at Gramene Database
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
Elevated mutation and selection in wild emmer wheat in response to 28 years of global warming. PMID:31527251 -
Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study
PubMed citations: 0.
0 articles citing: Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study
- http://dx.doi.org/10.1093/nar/gkt1110
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chloroplast sequence
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
coding sequence
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
differential gene expression analysis
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene feature
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene model annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene name
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene prediction
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene report
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genetic interaction
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genetic map
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genetic marker
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genomic assembly
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
mitochondrial sequence
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleic acid sequence
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleic acid sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
plastid sequence
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein sequence identification
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequence
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence feature
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence variant
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
region
metasource: Fairsharing.org
version: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
general plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
genomics
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
grain
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
physiology, comparative
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
plant genomes
metasource: re3data.org
version: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
plant biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
endocrinology and metabolism
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.178249
Tags
More detailed information about this field from each metasource.
chloroplast sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
coding sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
differential gene expression analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene ontology enrichment
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene feature
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene functional annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene model annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene name
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene prediction
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene report
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genetic interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genetic map
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genetic marker
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genomic assembly
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
mitochondrial sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
multiple sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleic acid sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
nucleic acid sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
pathway model
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
plastid sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein sequence identification
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence feature
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence variant
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
region
metasource: Fairsharing.orgversion: FAIRsharing.org: Gramene; Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants; DOI: https://doi.org/10.25504/FAIRsharing.zjdfxz; Last edited: April 16, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
plant databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
general plant databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
genomics
metasource: re3data.orgversion: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
grain
metasource: re3data.orgversion: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
physiology, comparative
metasource: re3data.orgversion: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
plant genomes
metasource: re3data.orgversion: re3data.org: Gramene; editing status 2021-05-31; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3GG7M last accessed: 2022-11-04
mapping
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
plant biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
endocrinology and metabolism
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.178249
chloroplast sequence coding sequence computational predictions dna sequences differential gene expression analysis gene gene ontology enrichment gene expression gene expression gene feature gene functional annotation gene model annotation gene name gene prediction gene report genetic interaction genetic map genetic marker genome genomic assembly mitochondrial sequence multiple sequence alignment nucleic acid sequence nucleic acid sequence alignment pathway model plastid sequence protein sequence identification rna sequence sequence alignment sequence annotation sequence feature sequence variant polypeptide region region plant plant genomics grain physiology, comparative plant genomes mapping plant biology molecular interactions, pathways and networks endocrinology and metabolism
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