Website and coding updates:

For user and data security, SSL (Secure Sockets Layer) has now been implemented on Plant Reactome. The entire site and all services are now available over https. The latest Plant Reactome pathway data has also 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 82 projected species currently hosted by Plant Reactome.

Curation of reference rice pathways: 

In Gramene Release 61, we have added 4 newly curated pathways, 2 updated pathways, and 1 "container" pathway, resulting in a total of 298 reference rice pathways.

• • New Pathways:

- Root hair development

         - Phytic Acid biosynthesis (lipid-independent)

         - Response to aluminum stress 

         - Root-specific gene-network of NAC10_TF induced by drought, salinity, and ABA

• • Updated pathways:

-HSFA7-regulatory network induced by drought and ABA

-SNAC1 transcription network involved in drought and salinity tolerance

We have extended orthology-based pathway projections for three new species: Actinidia chinensis (kiwi fruit), Panicum hallii FIL2 ("Hall's panicgrass"), and Panicum hallii var. hallii HAL2. Plant Reactome now hosts pathway projections for 82 species ranging from unicellular autotrophs to higher 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.