1. Example outputs from the updated Arabidopsis Interactions Viewer.
Example outputs from the updated Arabidopsis Interactions Viewer. A, “Stacked” layout from outside the cell (“extracellular”) to nucleus. Circular nodes represent proteins, and the numbers in each node represent MapMan terms, while colored “doughnuts” around the nodes represent subcellular localizations (predicted localizations have been turned off in this example) from SUBA. Clicking on the square chromosomal containers (chromosome 5 in this example) calls up the protein-DNA interactions (PDIs) associated with that chromosome (here 234 PDIs are associated with At1g19040). Dashed red line shows connection from a Pseudomonas syringae effector, AvrC, through yellow highlighted proteins to a transcription factor, At1g B, Clicking on interaction edges between proteins that have been predicted as part of our S-PPI study (mouse pointer in A) calls a page where the docking frequency for 500 runs of the HEX docking algorithm with the other protein is mapped onto the surface of that protein as a heatmap (red, high frequency of docking at that location), and vice versa (the view for At4g16760 and At5g53160, ranked #8519 of 9065 S-PPIs presented in this paper, is shown here).
Shaowei Dong et al. Plant Physiol. 2019;179:
©2019 by American Society of Plant Biologists