The Gramene Database build 53 is out!

The Gramene Team is pleased to announce its release #53 with 1,759,450 genes and 44 reference plant genomes.

Website features

• Gramene has a new front page
• New integrated pathway visualization in Gramene's search interface

Genomes

• Updated genomes
  • New genome and genebuild for Sorghum bicolor (sorghum V2)
• New data
  • New variation data for Triticum aestivum (wheat) consisting of over 7.4 million EMS-induced point mutations
  • New Oryza sativa Japonica (rice) QTL data from the Q-TARO database
• Updated data
  • Updated genebuild for Zea mays (maize RefGen_V4)
  • Reincorporated Japonica rice SSR/RFLP and QTLs from Gramene's archives remapped to IRGSPv1
  • Updated protein features from InterPro
  • Updated peptide comparative genomics with updated barley, sorghum, corn and wheat gene builds
  • Updated split gene predictions (potential annotation artifacts)
  • Updated gene and variation BioMarts
• Updated software
  • Updated software, genome browser, database schema, Mart and API to Ensembl 88 software

Pathways:  The Plant Reactome underwent a major software, user interface and functionality upgrade: 

• Upgraded to the Reactome v3.3 platform, which includes a new Neo4j graph database and a new Fireworks hierarchical graph display of pathways
• Improved visualization of uploaded Omics data, capabilities to import gene-gene interaction data from external resources for overlaying on pathway diagram and including them in analysis, and comparative pathway analysis between the reference and projected species.
• Supports display of gene expression profiles in the context of pathways accessed remotely from the EMBL-EBI gene expression ATLAS.
• Added ContentService and AnalysisService data APIs that allow direct RESTful access to Plant Reactome data.
• Implemented DiagramJs and FireworksJs graphical widget APIs for users to embed interactive pathway navigation in their web sites.
• Implemented a revised Solr Search data index and search results layout.
• All data objects carry stable IDs for cross-referencing.
• Plant Reactome data and diagrams are now integrated with Gramene’s new search interface mentioned above.

A complete description of the contents of this new release is available in our release notes.  The genome databases were built in direct collaboration with Ensembl Plants and the Plant Reactome database was built in collaboration with the Human Reactome project.

Please let us know if you have questions or suggestions.

The Gramene Team