Integrate gene abundances with a plant primary metabolic network
The PlantSEED pipeline was implemented within KBase to enable users to reconstruct genome-scale metabolic networks of plant primary metabolism. The documentation of the PlantSEED pipeline can be viewed here.
The resulting metabolic reconstruction contains a set of gene-reaction links that can be used to integrate several kinds of large datasets such as transcriptomes or metabolomes. This app was written to integrate the results generated by the KBase RNA-Seq pipeline, which results in a ExpressionMatrix, containing a set of gene abundances derived from different experimental conditions.
The result of the integration is a Reaction Matrix, containing a set of computed reaction expression scores, for each of the same experimental conditions. The app generally applies the "best" gene abundance to a reaction, where there are multiple genes, and where there are genes encoding protein complexes. The underlying concept is that a reaction is only as "active" in its catalysis as allowed by the formation of the enzymes that catalyze the reaction. In turn, the results here can be used as a proxy for the activity of different primary metabolic pathways, and how they may respond to different experimental conditions.Data
- The plant metabolic subsystems are curated as part of the PlantSEED project. The curation can be explored here
- The biochemistry comes from the ModelSEED Biochemistry Database. The database can be explored here
-  Seaver SMD, Bradbury LM, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. Front Plant Sci. 2015;6: 142. doi: 10.3389/fpls.2015.00142 , https://www.ncbi.nlm.nih.gov/pubmed/25806041
Module Commit: a8031aa0f4320c7cd96f78170d7644f696614f8d