Website and coding updates:

The latest Plant Reactome pathway data has been re-indexed and made available via Gramene search.

Analytical Tools:

Currently, Plant Reactome supports researchers with the following analytical tools:

• - Search for gene/protein, metabolites, pathways
  - Upload and analyze gene-expression data on plant pathways
  - Upload and analyze gene-gene interaction data on plant pathways
  - Compare reference rice pathways with pathways from any of 79 projected species currently hosted by Plant Reactome.

Curation of reference rice pathways: 

In Gramene Release 60, we have added 10 newly curated pathways and 3 "container" pathways, and updated 2 other existing pathways, resulting in a total of 293 reference rice pathways.

    New Pathways:

•          - Regulation of embryo development
•          - Maternal tissue PCD
           - Cell cycle regulation
           - Aleurone layer formation
           - Regulatory network of nutrient accumulation
           - Regulation of seed size
           - Regulation of leaf development
           - HSFA7/ HSFA6B-regulatory network-induced by drought and ABA.
           - SNAC1 transcription network involved in drought and salinity tolerance
           - Arsenic uptake and detoxification

Pathway Projection Statistics:

We have extended orthology-based pathway projections for 1 new species: Arabidopsis halleri. Plant Reactome now hosts pathway projections for 79 species ranging from unicellular autotrophs to higher plants. In addition, we have revised pathways for Solanum lycopersicum (tomato) and Glycine max (soybean), based on their recent genome updates (source: Ensembl Plants).

*data from sequenced transcriptomes
^ projections currently exclude cell-cycle pathways and annotations
Planteome Inparanoid data was kindly provided by the Planteome project
When available the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources

NOTE: The pathway counts for both reference and projected species include a few organizational “container” names, such as “Hormone biosyntheses” and “Metabolism”. Additionally, the bulk of the projected pathways occur in the areas of metabolic and regulatory function, whereas the rice reference data set has additional pathways related to cell cycle functions. We are not currently using these additional pathways as a source for orthology projection.

The Plant Reactome increasingly includes curated regulatory and developmental pathways, which require more reference DNA and RNA sequence elements, in addition to the traditional protein-coding elements. These sequence elements are not included in Reactome orthoinference at this time, although we are actively working to enhance the projection process to include these elements on projected pathways in future releases.