Figure 6

Interactive analysis of metabolomics and transcriptomics data using PMR. A. Volcano plot (p-value vs. fold change) comparison of metabolites in 25 DAF versus 50 DAF seeds in PMR http://metnetdb.org/PMR/. Clicking or mousing-over a metabolite brings up its annotation information. The data indicate that almost every amino acid is more abundant in 25 DAF seeds than 50 DAF seeds, while almost all sterols are more abundant in 50 DAF seeds than in 25 DAF seeds. B. Transcript Glyma05g07420.1 has a high correlation with asparagine accumulation during seed development (Pearson Correlation>0.86; p-value = 0.06). There are six genes in the soybean genome annotated as having sequence similarity to known asparaginase; of these, only Glyma05g07420.1 has an expression pattern similar to that of asparagine. These data indicate that Glyma05g07420.1 is a likely candidate for encoding the asparaginase activity associated with protein synthesis during seed fill. C. Other over-represented pathways in the set of genes that have a high correlation with asparagine accumulation. D. Asparaginase reaction in soybean visualized in PMR via Cytoscape [62].