New Plant Reactome pathway projections

Plant Reactome now provides projections for eighteen plant species (nine monocots and nine dicots).

Using curated rice pathways as a reference, Plant Reactome predicts pathways in other plant species on the basis of Compara orthology projections.

We isolated gene identifiers and their Uniprot counterparts in our curated rice pathways and downloaded Ensembl Plants rel.40 orthology predictions for several plant species, using O. sativa as the reference. Using Compara's reciprocal identity data, we limited the orthology predictions to those meeting a threshold of 30% reciprocal identity for dicots and 40% reciprocal identity for monocots. Both high and low confidence Compara data were utilized.

We then ran Reactome projection inference scripts on our curated rice pathway data to generate predicted pathways, reactions, orthologous gene products, and other required data instances. We accepted defined sets and complexes with a minimum of one orthologous member. Finally, we generated separate pathway diagrams for these projected pathways and deployed the results on this web site.